Dynamic Graphics in Excel for Teaching Statistics: Understanding the Probability Density Function

ERIC Educational Resources Information Center

Coll-Serrano, Vicente; Blasco-Blasco, Olga; Alvarez-Jareno, Jose A.

2011-01-01

In this article, we show a dynamic graphic in Excel that is used to introduce an important concept in our subject, Statistics I: the probability density function. This interactive graphic seeks to facilitate conceptual understanding of the main aspects analysed by the learners.

An ab-initio study of mechanical, dynamical and electronic properties of MgEu intermetallic

NASA Astrophysics Data System (ADS)

Kumar, S. Ramesh; Jaiganesh, G.; Jayalakshmi, V.

2018-04-01

The theoretical investigation on the mechanical, dynamical and electronic properties of MgEu in CsCl-type structure has been carried out through the ab-initio calculations within the framework of the density functional theory and the density functional perturbation theory. For the purpose, Vienna Ab initio Simulation Package and Phonopy packages were used. Our calculated ground-state properties of MgEu are in good agreement with other available results. Our computed elastic constants and phonon spectrum results suggest that MgEu is mechanically and dynamically stable up to 5 GPa. The thermodynamic quantities as a function of temperatures are also reported and discussed. The band structure, density of states and charge density also calculated to understand the electronic properties of MgEu.

Transitioning NWChem to the Next Generation of Manycore Machines

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

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

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

Nonadiabatic Dynamics in Single-Electron Tunneling Devices with Time-Dependent Density-Functional Theory

NASA Astrophysics Data System (ADS)

Dittmann, Niklas; Splettstoesser, Janine; Helbig, Nicole

2018-04-01

We simulate the dynamics of a single-electron source, modeled as a quantum dot with on-site Coulomb interaction and tunnel coupling to an adjacent lead in time-dependent density-functional theory. Based on this system, we develop a time-nonlocal exchange-correlation potential by exploiting analogies with quantum-transport theory. The time nonlocality manifests itself in a dynamical potential step. We explicitly link the time evolution of the dynamical step to physical relaxation timescales of the electron dynamics. Finally, we discuss prospects for simulations of larger mesoscopic systems.

Nonadiabatic Dynamics in Single-Electron Tunneling Devices with Time-Dependent Density-Functional Theory.

PubMed

Dittmann, Niklas; Splettstoesser, Janine; Helbig, Nicole

2018-04-13

We simulate the dynamics of a single-electron source, modeled as a quantum dot with on-site Coulomb interaction and tunnel coupling to an adjacent lead in time-dependent density-functional theory. Based on this system, we develop a time-nonlocal exchange-correlation potential by exploiting analogies with quantum-transport theory. The time nonlocality manifests itself in a dynamical potential step. We explicitly link the time evolution of the dynamical step to physical relaxation timescales of the electron dynamics. Finally, we discuss prospects for simulations of larger mesoscopic systems.

Analysis of Different Cost Functions in the Geosect Airspace Partitioning Tool

NASA Technical Reports Server (NTRS)

Wong, Gregory L.

2010-01-01

A new cost function representing air traffic controller workload is implemented in the Geosect airspace partitioning tool. Geosect currently uses a combination of aircraft count and dwell time to select optimal airspace partitions that balance controller workload. This is referred to as the aircraft count/dwell time hybrid cost function. The new cost function is based on Simplified Dynamic Density, a measure of different aspects of air traffic controller workload. Three sectorizations are compared. These are the current sectorization, Geosect's sectorization based on the aircraft count/dwell time hybrid cost function, and Geosect s sectorization based on the Simplified Dynamic Density cost function. Each sectorization is evaluated for maximum and average workload along with workload balance using the Simplified Dynamic Density as the workload measure. In addition, the Airspace Concept Evaluation System, a nationwide air traffic simulator, is used to determine the capacity and delay incurred by each sectorization. The sectorization resulting from the Simplified Dynamic Density cost function had a lower maximum workload measure than the other sectorizations, and the sectorization based on the combination of aircraft count and dwell time did a better job of balancing workload and balancing capacity. However, the current sectorization had the lowest average workload, highest sector capacity, and the least system delay.

A cumulant functional for static and dynamic correlation

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

Hollett, Joshua W., E-mail: j.hollett@uwinnipeg.ca; Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2; Hosseini, Hessam

A functional for the cumulant energy is introduced. The functional is composed of a pair-correction and static and dynamic correlation energy components. The pair-correction and static correlation energies are functionals of the natural orbitals and the occupancy transferred between near-degenerate orbital pairs, rather than the orbital occupancies themselves. The dynamic correlation energy is a functional of the statically correlated on-top two-electron density. The on-top density functional used in this study is the well-known Colle-Salvetti functional. Using the cc-pVTZ basis set, the functional effectively models the bond dissociation of H{sub 2}, LiH, and N{sub 2} with equilibrium bond lengths and dissociationmore » energies comparable to those provided by multireference second-order perturbation theory. The performance of the cumulant functional is less impressive for HF and F{sub 2}, mainly due to an underestimation of the dynamic correlation energy by the Colle-Salvetti functional.« less

Bypassing the Kohn-Sham equations with machine learning.

PubMed

Brockherde, Felix; Vogt, Leslie; Li, Li; Tuckerman, Mark E; Burke, Kieron; Müller, Klaus-Robert

2017-10-11

Last year, at least 30,000 scientific papers used the Kohn-Sham scheme of density functional theory to solve electronic structure problems in a wide variety of scientific fields. Machine learning holds the promise of learning the energy functional via examples, bypassing the need to solve the Kohn-Sham equations. This should yield substantial savings in computer time, allowing larger systems and/or longer time-scales to be tackled, but attempts to machine-learn this functional have been limited by the need to find its derivative. The present work overcomes this difficulty by directly learning the density-potential and energy-density maps for test systems and various molecules. We perform the first molecular dynamics simulation with a machine-learned density functional on malonaldehyde and are able to capture the intramolecular proton transfer process. Learning density models now allows the construction of accurate density functionals for realistic molecular systems.Machine learning allows electronic structure calculations to access larger system sizes and, in dynamical simulations, longer time scales. Here, the authors perform such a simulation using a machine-learned density functional that avoids direct solution of the Kohn-Sham equations.

Transitioning NWChem to the Next Generation of Manycore Machines

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

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

The NorthWest chemistry (NWChem) modeling software is a popular molecular chemistry simulation software that was designed from the start to work on massively parallel processing supercomputers [1-3]. It contains an umbrella of modules that today includes self-consistent eld (SCF), second order Møller-Plesset perturbation theory (MP2), coupled cluster (CC), multiconguration self-consistent eld (MCSCF), selected conguration interaction (CI), tensor contraction engine (TCE) many body methods, density functional theory (DFT), time-dependent density functional theory (TDDFT), real-time time-dependent density functional theory, pseudopotential plane-wave density functional theory (PSPW), band structure (BAND), ab initio molecular dynamics (AIMD), Car-Parrinello molecular dynamics (MD), classical MD, hybrid quantum mechanicsmore » molecular mechanics (QM/MM), hybrid ab initio molecular dynamics molecular mechanics (AIMD/MM), gauge independent atomic orbital nuclear magnetic resonance (GIAO NMR), conductor like screening solvation model (COSMO), conductor-like screening solvation model based on density (COSMO-SMD), and reference interaction site model (RISM) solvation models, free energy simulations, reaction path optimization, parallel in time, among other capabilities [4]. Moreover, new capabilities continue to be added with each new release.« less

Angle-dependent strong-field molecular ionization rates with tuned range-separated time-dependent density functional theory.

PubMed

Sissay, Adonay; Abanador, Paul; Mauger, François; Gaarde, Mette; Schafer, Kenneth J; Lopata, Kenneth

2016-09-07

Strong-field ionization and the resulting electronic dynamics are important for a range of processes such as high harmonic generation, photodamage, charge resonance enhanced ionization, and ionization-triggered charge migration. Modeling ionization dynamics in molecular systems from first-principles can be challenging due to the large spatial extent of the wavefunction which stresses the accuracy of basis sets, and the intense fields which require non-perturbative time-dependent electronic structure methods. In this paper, we develop a time-dependent density functional theory approach which uses a Gaussian-type orbital (GTO) basis set to capture strong-field ionization rates and dynamics in atoms and small molecules. This involves propagating the electronic density matrix in time with a time-dependent laser potential and a spatial non-Hermitian complex absorbing potential which is projected onto an atom-centered basis set to remove ionized charge from the simulation. For the density functional theory (DFT) functional we use a tuned range-separated functional LC-PBE*, which has the correct asymptotic 1/r form of the potential and a reduced delocalization error compared to traditional DFT functionals. Ionization rates are computed for hydrogen, molecular nitrogen, and iodoacetylene under various field frequencies, intensities, and polarizations (angle-dependent ionization), and the results are shown to quantitatively agree with time-dependent Schrödinger equation and strong-field approximation calculations. This tuned DFT with GTO method opens the door to predictive all-electron time-dependent density functional theory simulations of ionization and ionization-triggered dynamics in molecular systems using tuned range-separated hybrid functionals.

Angle-dependent strong-field molecular ionization rates with tuned range-separated time-dependent density functional theory

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

Sissay, Adonay; Abanador, Paul; Mauger, François

2016-09-07

Strong-field ionization and the resulting electronic dynamics are important for a range of processes such as high harmonic generation, photodamage, charge resonance enhanced ionization, and ionization-triggered charge migration. Modeling ionization dynamics in molecular systems from first-principles can be challenging due to the large spatial extent of the wavefunction which stresses the accuracy of basis sets, and the intense fields which require non-perturbative time-dependent electronic structure methods. In this paper, we develop a time-dependent density functional theory approach which uses a Gaussian-type orbital (GTO) basis set to capture strong-field ionization rates and dynamics in atoms and small molecules. This involves propagatingmore » the electronic density matrix in time with a time-dependent laser potential and a spatial non-Hermitian complex absorbing potential which is projected onto an atom-centered basis set to remove ionized charge from the simulation. For the density functional theory (DFT) functional we use a tuned range-separated functional LC-PBE*, which has the correct asymptotic 1/r form of the potential and a reduced delocalization error compared to traditional DFT functionals. Ionization rates are computed for hydrogen, molecular nitrogen, and iodoacetylene under various field frequencies, intensities, and polarizations (angle-dependent ionization), and the results are shown to quantitatively agree with time-dependent Schrödinger equation and strong-field approximation calculations. This tuned DFT with GTO method opens the door to predictive all-electron time-dependent density functional theory simulations of ionization and ionization-triggered dynamics in molecular systems using tuned range-separated hybrid functionals.« less

Structural, Electronic and Dynamical Properties of Curium Monopnictides: Density Functional Calculations

NASA Astrophysics Data System (ADS)

Roondhe, Basant; Upadhyay, Deepak; Som, Narayan; Pillai, Sharad B.; Shinde, Satyam; Jha, Prafulla K.

2017-03-01

The structural, electronic, dynamical and thermodynamical properties of CmX (X = N, P, As, Sb, and Bi) compounds are studied using first principles calculations within density functional theory. The Perdew-Burke-Ernzerhof spin polarized generalized gradient approximation and Perdew-Wang (PW) spin polarized local density approximation as the exchange correlational functionals are used in these calculations. There is a good agreement between the present and previously reported data. The calculated electronic density of states suggests that the curium monopnictides are metallic in nature, which is consistent with earlier studies. The significant values of magnetic moment suggest their magnetic nature. The phonon dispersion curves and phonon density of states are also calculated, which depict the dynamical stability of these compounds. There is a significant separation between the optical and acoustical phonon branches. The temperature dependence of the thermodynamical functions are also calculated and discussed. Internal energy and vibrational contribution to the Helmholtz free energy increases and decreases, respectively, with temperature. The entropy increases with temperature. The specific heat at constant volume and Debye temperature obey Debye theory. The temperature variation of the considered thermodynamical functions is in line with those of other crystalline solids.

Density matrix renormalization group with efficient dynamical electron correlation through range separation

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

Hedegård, Erik Donovan, E-mail: erik.hedegard@phys.chem.ethz.ch; Knecht, Stefan; Reiher, Markus, E-mail: markus.reiher@phys.chem.ethz.ch

2015-06-14

We present a new hybrid multiconfigurational method based on the concept of range-separation that combines the density matrix renormalization group approach with density functional theory. This new method is designed for the simultaneous description of dynamical and static electron-correlation effects in multiconfigurational electronic structure problems.

Bulk dynamics of Brownian hard disks: Dynamical density functional theory versus experiments on two-dimensional colloidal hard spheres

NASA Astrophysics Data System (ADS)

Stopper, Daniel; Thorneywork, Alice L.; Dullens, Roel P. A.; Roth, Roland

2018-03-01

Using dynamical density functional theory (DDFT), we theoretically study Brownian self-diffusion and structural relaxation of hard disks and compare to experimental results on quasi two-dimensional colloidal hard spheres. To this end, we calculate the self-van Hove correlation function and distinct van Hove correlation function by extending a recently proposed DDFT-approach for three-dimensional systems to two dimensions. We find that the theoretical results for both self-part and distinct part of the van Hove function are in very good quantitative agreement with the experiments up to relatively high fluid packing fractions of roughly 0.60. However, at even higher densities, deviations between the experiment and the theoretical approach become clearly visible. Upon increasing packing fraction, in experiments, the short-time self-diffusive behavior is strongly affected by hydrodynamic effects and leads to a significant decrease in the respective mean-squared displacement. By contrast, and in accordance with previous simulation studies, the present DDFT, which neglects hydrodynamic effects, shows no dependence on the particle density for this quantity.

Density functional theory calculation of refractive indices of liquid-forming silicon oil compounds

NASA Astrophysics Data System (ADS)

Lee, Sanghun; Park, Sung Soo; Hagelberg, Frank

2012-02-01

A combination of quantum chemical calculation and molecular dynamics simulation is applied to compute refractive indices of liquid-forming silicon oils. The densities of these species are obtained from molecular dynamics simulations based on the NPT ensemble while the molecular polarizabilities are evaluated by density functional theory. This procedure is shown to yield results well compatible with available experimental data, suggesting that it represents a robust and economic route for determining the refractive indices of liquid-forming organic complexes containing silicon.

General framework for fluctuating dynamic density functional theory

NASA Astrophysics Data System (ADS)

Durán-Olivencia, Miguel A.; Yatsyshin, Peter; Goddard, Benjamin D.; Kalliadasis, Serafim

2017-12-01

We introduce a versatile bottom-up derivation of a formal theoretical framework to describe (passive) soft-matter systems out of equilibrium subject to fluctuations. We provide a unique connection between the constituent-particle dynamics of real systems and the time evolution equation of their measurable (coarse-grained) quantities, such as local density and velocity. The starting point is the full Hamiltonian description of a system of colloidal particles immersed in a fluid of identical bath particles. Then, we average out the bath via Zwanzig’s projection-operator techniques and obtain the stochastic Langevin equations governing the colloidal-particle dynamics. Introducing the appropriate definition of the local number and momentum density fields yields a generalisation of the Dean-Kawasaki (DK) model, which resembles the stochastic Navier-Stokes description of a fluid. Nevertheless, the DK equation still contains all the microscopic information and, for that reason, does not represent the dynamical law of observable quantities. We address this controversial feature of the DK description by carrying out a nonequilibrium ensemble average. Adopting a natural decomposition into local-equilibrium and nonequilibrium contribution, where the former is related to a generalised version of the canonical distribution, we finally obtain the fluctuating-hydrodynamic equation governing the time-evolution of the mesoscopic density and momentum fields. Along the way, we outline the connection between the ad hoc energy functional introduced in previous DK derivations and the free-energy functional from classical density-functional theory. The resultant equation has the structure of a dynamical density-functional theory (DDFT) with an additional fluctuating force coming from the random interactions with the bath. We show that our fluctuating DDFT formalism corresponds to a particular version of the fluctuating Navier-Stokes equations, originally derived by Landau and Lifshitz. Our framework thus provides the formal apparatus for ab initio derivations of fluctuating DDFT equations capable of describing the dynamics of soft-matter systems in and out of equilibrium.

Dynamic density functional theory with hydrodynamic interactions: theoretical development and application in the study of phase separation in gas-liquid systems.

PubMed

Kikkinides, E S; Monson, P A

2015-03-07

Building on recent developments in dynamic density functional theory, we have developed a version of the theory that includes hydrodynamic interactions. This is achieved by combining the continuity and momentum equations eliminating velocity fields, so the resulting model equation contains only terms related to the fluid density and its time and spatial derivatives. The new model satisfies simultaneously continuity and momentum equations under the assumptions of constant dynamic or kinematic viscosity and small velocities and/or density gradients. We present applications of the theory to spinodal decomposition of subcritical temperatures for one-dimensional and three-dimensional density perturbations for both a van der Waals fluid and for a lattice gas model in mean field theory. In the latter case, the theory provides a hydrodynamic extension to the recently studied dynamic mean field theory. We find that the theory correctly describes the transition from diffusive phase separation at short times to hydrodynamic behaviour at long times.

Dynamic density functional theory with hydrodynamic interactions: Theoretical development and application in the study of phase separation in gas-liquid systems

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

Kikkinides, E. S.; Monson, P. A.

Building on recent developments in dynamic density functional theory, we have developed a version of the theory that includes hydrodynamic interactions. This is achieved by combining the continuity and momentum equations eliminating velocity fields, so the resulting model equation contains only terms related to the fluid density and its time and spatial derivatives. The new model satisfies simultaneously continuity and momentum equations under the assumptions of constant dynamic or kinematic viscosity and small velocities and/or density gradients. We present applications of the theory to spinodal decomposition of subcritical temperatures for one-dimensional and three-dimensional density perturbations for both a van dermore » Waals fluid and for a lattice gas model in mean field theory. In the latter case, the theory provides a hydrodynamic extension to the recently studied dynamic mean field theory. We find that the theory correctly describes the transition from diffusive phase separation at short times to hydrodynamic behaviour at long times.« less

Charge transport calculations by a wave-packet dynamical approach using maximally localized Wannier functions based on density functional theory: Application to high-mobility organic semiconductors

NASA Astrophysics Data System (ADS)

Ishii, Hiroyuki; Kobayashi, Nobuhiko; Hirose, Kenji

2017-01-01

We present a wave-packet dynamical approach to charge transport using maximally localized Wannier functions based on density functional theory including van der Waals interactions. We apply it to the transport properties of pentacene and rubrene single crystals and show the temperature-dependent natures from bandlike to thermally activated behaviors as a function of the magnitude of external static disorder. We compare the results with those obtained by the conventional band and hopping models and experiments.

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

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

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

2001-10-01

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

Dynamics and density distributions in a capillary-discharge waveguide with an embedded supersonic jet

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

Matlis, N. H., E-mail: nmatlis@gmail.com; Gonsalves, A. J.; Steinke, S.

We present an analysis of the gas dynamics and density distributions within a capillary-discharge waveguide with an embedded supersonic jet. This device provides a target for a laser plasma accelerator which uses longitudinal structuring of the gas-density profile to enable control of electron trapping and acceleration. The functionality of the device depends sensitively on the details of the density profile, which are determined by the interaction between the pulsed gas in the jet and the continuously-flowing gas in the capillary. These dynamics are captured by spatially resolving recombination light from several emission lines of the plasma as a function ofmore » the delay between the jet and the discharge. We provide a phenomenological description of the gas dynamics as well as a quantitative evaluation of the density evolution. In particular, we show that the pressure difference between the jet and the capillary defines three regimes of operation with qualitatively different longitudinal density profiles and show that jet timing provides a sensitive method for tuning between these regimes.« less

Coarse-grained forms for equations describing the microscopic motion of particles in a fluid.

PubMed

Das, Shankar P; Yoshimori, Akira

2013-10-01

Exact equations of motion for the microscopically defined collective density ρ(x,t) and the momentum density ĝ(x,t) of a fluid have been obtained in the past starting from the corresponding Langevin equations representing the dynamics of the fluid particles. In the present work we average these exact equations of microscopic dynamics over the local equilibrium distribution to obtain stochastic partial differential equations for the coarse-grained densities with smooth spatial and temporal dependence. In particular, we consider Dean's exact balance equation for the microscopic density of a system of interacting Brownian particles to obtain the basic equation of the dynamic density functional theory with noise. Our analysis demonstrates that on thermal averaging the dependence of the exact equations on the bare interaction potential is converted to dependence on the corresponding thermodynamic direct correlation functions in the coarse-grained equations.

Melting slope of MgO from molecular dynamics and density functional theory

NASA Astrophysics Data System (ADS)

Tangney, Paul; Scandolo, Sandro

2009-09-01

We combine density functional theory (DFT) with molecular dynamics simulations based on an accurate atomistic force field to calculate the pressure derivative of the melting temperature of magnesium oxide at ambient pressure—a quantity for which a serious disagreement between theory and experiment has existed for almost 15 years. We find reasonable agreement with previous DFT results and with a very recent experimental determination of the slope. We pay particular attention to areas of possible weakness in theoretical calculations and conclude that the long-standing discrepancy with experiment could only be explained by a dramatic failure of existing density functionals or by flaws in the original experiment.

Dynamics of a spin-boson model with structured spectral density

NASA Astrophysics Data System (ADS)

Kurt, Arzu; Eryigit, Resul

2018-05-01

We report the results of a study of the dynamics of a two-state system coupled to an environment with peaked spectral density. An exact analytical expression for the bath correlation function is obtained. Validity range of various approximations to the correlation function for calculating the population difference of the system is discussed as function of tunneling splitting, oscillator frequency, coupling constant, damping rate and the temperature of the bath. An exact expression for the population difference, for a limited range of parameters, is derived.

Molecular dynamics simulations of dense plasmas

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

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

1993-12-31

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

Gentlest ascent dynamics for calculating first excited state and exploring energy landscape of Kohn-Sham density functionals.

PubMed

Li, Chen; Lu, Jianfeng; Yang, Weitao

2015-12-14

We develop the gentlest ascent dynamics for Kohn-Sham density functional theory to search for the index-1 saddle points on the energy landscape of the Kohn-Sham density functionals. These stationary solutions correspond to excited states in the ground state functionals. As shown by various examples, the first excited states of many chemical systems are given by these index-1 saddle points. Our novel approach provides an alternative, more robust way to obtain these excited states, compared with the widely used ΔSCF approach. The method can be easily generalized to target higher index saddle points. Our results also reveal the physical interest and relevance of studying the Kohn-Sham energy landscape.

BRIEF COMMUNICATION: A note on the Coulomb collision operator in curvilinear coordinates

NASA Astrophysics Data System (ADS)

Goncharov, P. R.

2010-10-01

The dynamic friction force, diffusion tensor, flux density in velocity space and Coulomb collision term are expressed in curvilinear coordinates via Trubnikov potential functions corresponding to each species of a background plasma. For comparison, explicit formulae are given for the dynamic friction force, diffusion tensor and collisional flux density in velocity space in curvilinear coordinates via Rosenbluth potential functions summed over all species of the background plasma.

Dynamics of two-phase interfaces and surface tensions: A density-functional theory perspective

NASA Astrophysics Data System (ADS)

Yatsyshin, Petr; Sibley, David N.; Duran-Olivencia, Miguel A.; Kalliadasis, Serafim

2016-11-01

Classical density functional theory (DFT) is a statistical mechanical framework for the description of fluids at the nanoscale, where the inhomogeneity of the fluid structure needs to be carefully accounted for. By expressing the grand free-energy of the fluid as a functional of the one-body density, DFT offers a theoretically consistent and computationally accessible way to obtain two-phase interfaces and respective interfacial tensions in a ternary solid-liquid-gas system. The dynamic version of DFT (DDFT) can be rigorously derived from the Smoluchowsky picture of the dynamics of colloidal particles in a solvent. It is generally agreed that DDFT can capture the diffusion-driven evolution of many soft-matter systems. In this context, we use DDFT to investigate the dynamic behaviour of two-phase interfaces in both equilibrium and dynamic wetting and discuss the possibility of defining a time-dependent surface tension, which still remains in debate. We acknowledge financial support from the European Research Council via Advanced Grant No. 247031 and from the Engineering and Physical Sciences Research Council of the UK via Grants No. EP/L027186 and EP/L020564.

Tuning of electronic properties and dynamical stability of graphene oxide with different functional groups

NASA Astrophysics Data System (ADS)

Dabhi, Shweta D.; Jha, Prafulla K.

2017-09-01

The structural, electronic and vibrational properties of graphene oxide (GO) with varying proportion of epoxy and hydroxyl functional groups have been studied using density functional theory. The functional groups and oxygen density have an obvious influence on the electronic and vibrational properties. The dependence of band gap on associated functional groups and oxygen density shows a possibility of tuning the band gap of graphene by varying the functional groups as well as oxidation level. The absorption of high oxygen content in graphene leads to the gap opening and resulting in a transition from semimetal to semiconductor. Phonon dispersion curves show no imaginary frequency or no softening of any phonon mode throughout the Brillouin zone which confirms the dynamical stability of all considered GO models. Different groups and different oxygen density result into the varying characteristics of phonon modes. The computed results show good agreement with the experimental observations. Our results present interesting possibilities for engineering the electronic properties of graphene and GO and impact the fabrication of new electronics.

Finite-temperature dynamics of the Mott insulating Hubbard chain

NASA Astrophysics Data System (ADS)

Nocera, Alberto; Essler, Fabian H. L.; Feiguin, Adrian E.

2018-01-01

We study the dynamical response of the half-filled one-dimensional Hubbard model for a range of interaction strengths U and temperatures T by a combination of numerical and analytical techniques. Using time-dependent density matrix renormalization group computations we find that the single-particle spectral function undergoes a crossover to a spin-incoherent Luttinger liquid regime at temperatures T ˜J =4 t2/U for sufficiently large U >4 t . At smaller values of U and elevated temperatures the spectral function is found to exhibit two thermally broadened bands of excitations, reminiscent of what is found in the Hubbard-I approximation. The dynamical density-density response function is shown to exhibit a finite-temperature resonance at low frequencies inside the Mott gap, with a physical origin similar to the Villain mode in gapped quantum spin chains. We complement our numerical computations by developing an analytic strong-coupling approach to the low-temperature dynamics in the spin-incoherent regime.

Sedimentation of a two-dimensional colloidal mixture exhibiting liquid-liquid and gas-liquid phase separation: a dynamical density functional theory study.

PubMed

Malijevský, Alexandr; Archer, Andrew J

2013-10-14

We present dynamical density functional theory results for the time evolution of the density distribution of a sedimenting model two-dimensional binary mixture of colloids. The interplay between the bulk phase behaviour of the mixture, its interfacial properties at the confining walls, and the gravitational field gives rise to a rich variety of equilibrium and non-equilibrium morphologies. In the fluid state, the system exhibits both liquid-liquid and gas-liquid phase separation. As the system sediments, the phase separation significantly affects the dynamics and we explore situations where the final state is a coexistence of up to three different phases. Solving the dynamical equations in two-dimensions, we find that in certain situations the final density profiles of the two species have a symmetry that is different from that of the external potentials, which is perhaps surprising, given the statistical mechanics origin of the theory. The paper concludes with a discussion on this.

Role of density modulation in the spatially resolved dynamics of strongly confined liquids

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

Saw, Shibu, E-mail: shibu.saw@sydney.edu.au; Dasgupta, Chandan, E-mail: cdgupta@physics.iisc.ernet.in

Confinement by walls usually produces a strong modulation in the density of dense liquids near the walls. Using molecular dynamics simulations, we examine the effects of the density modulation on the spatially resolved dynamics of a liquid confined between two parallel walls, using a resolution of a fraction of the interparticle distance in the liquid. The local dynamics is quantified by the relaxation time associated with the temporal autocorrelation function of the local density. We find that this local relaxation time varies in phase with the density modulation. The amplitude of the spatial modulation of the relaxation time can bemore » quite large, depending on the characteristics of the wall and thermodynamic parameters of the liquid. To disentangle the effects of confinement and density modulation on the spatially resolved dynamics, we compare the dynamics of a confined liquid with that of an unconfined one in which a similar density modulation is induced by an external potential. We find several differences indicating that density modulation alone cannot account for all the features seen in the spatially resolved dynamics of confined liquids. We also examine how the dynamics near a wall depends on the separation between the two walls and show that the features seen in our simulations persist in the limit of large wall separation.« less

Dynamic kinetic energy potential for orbital-free density functional theory.

PubMed

Neuhauser, Daniel; Pistinner, Shlomo; Coomar, Arunima; Zhang, Xu; Lu, Gang

2011-04-14

A dynamic kinetic energy potential (DKEP) is developed for time-dependent orbital-free (TDOF) density function theory applications. This potential is constructed to affect only the dynamical (ω ≠ 0) response of an orbital-free electronic system. It aims at making the orbital-free simulation respond in the same way as that of a noninteracting homogenous electron gas (HEG), as required by a correct kinetic energy, therefore enabling extension of the success of orbital-free density functional theory in the static case (e.g., for embedding and description of processes in bulk materials) to dynamic processes. The potential is constructed by expansions of terms, each of which necessitates only simple time evolution (concurrent with the TDOF evolution) and a spatial convolution at each time-step. With 14 such terms a good fit is obtained to the response of the HEG at a large range of frequencies, wavevectors, and densities. The method is demonstrated for simple jellium spheres, approximating Na(9)(+) and Na(65)(+) clusters. It is applicable both to small and large (even ultralarge) excitations and the results converge (i.e., do not blow up) as a function of time. An extension to iterative frequency-resolved extraction is briefly outlined, as well as possibly numerically simpler expansions. The approach could also be extended to fit, instead of the HEG susceptibility, either an experimental susceptibility or a theoretically derived one for a non-HEG system. The DKEP potential should be a powerful tool for embedding a dynamical system described by a more accurate method (such as time-dependent density functional theory, TDDFT) in a large background described by TDOF with a DKEP potential. The type of expansions used and envisioned should be useful for other approaches, such as memory functionals in TDDFT. Finally, an appendix details the formal connection between TDOF and TDDFT.

Handling times and saturating transmission functions in a snail-worm symbiosis.

PubMed

Hopkins, Skylar R; McGregor, Cari M; Belden, Lisa K; Wojdak, Jeremy M

2018-06-16

All dynamic species interaction models contain an assumption that describes how contact rates scale with population density. Choosing an appropriate contact-density function is important, because different functions have different implications for population dynamics and stability. However, this choice can be challenging, because there are many possible functions, and most are phenomenological and thus difficult to relate to underlying ecological processes. Using one such phenomenological function, we described a nonlinear relationship between field transmission rates and host density in a common snail-oligochaete symbiosis. We then used a well-known contact function from predator-prey models, the Holling Type II functional response, to describe and predict host snail contact rates in the laboratory. The Holling Type II functional response accurately described both the nonlinear contact-density relationship and the average contact duration that we observed. Therefore, we suggest that contact rates saturate with host density in this system because each snail contact requires a non-instantaneous handling time, and additional possible contacts do not occur during that handling time. Handling times and nonlinear contact rates might also explain the nonlinear relationship between symbiont transmission and snail density that we observed in the field, which could be confirmed by future work that controls for other potential sources of seasonal variation in transmission rates. Because most animal contacts are not instantaneous, the Holling Type II functional response might be broadly relevant to diverse host-symbiont systems.

Layered interfaces between immiscible liquids studied by density-functional theory and molecular-dynamics simulations.

PubMed

Geysermans, P; Elyeznasni, N; Russier, V

2005-11-22

We present a study of the structure in the interface between two immiscible liquids by density-functional theory and molecular-dynamics calculations. The liquids are modeled by Lennard-Jones potentials, which achieve immiscibility by suppressing the attractive interaction between unlike particles. The density profiles of the liquids display oscillations only in a limited part of the simple liquid-phase diagram (rho,T). When approaching the liquid-vapor coexistence, a significant depletion appears while the layering behavior of the density profile vanishes. By analogy with the liquid-vapor interface and the analysis of the adsorption this behavior is suggested to be strongly related to the drying transition.

Observations of non-linear plasmon damping in dense plasmas

NASA Astrophysics Data System (ADS)

Witte, B. B. L.; Sperling, P.; French, M.; Recoules, V.; Glenzer, S. H.; Redmer, R.

2018-05-01

We present simulations using finite-temperature density-functional-theory molecular-dynamics to calculate dynamic dielectric properties in warm dense aluminum. The comparison between exchange-correlation functionals in the Perdew, Burke, Ernzerhof approximation, Strongly Constrained and Appropriately Normed Semilocal Density Functional, and Heyd, Scuseria, Ernzerhof (HSE) approximation indicates evident differences in the electron transition energies, dc conductivity, and Lorenz number. The HSE calculations show excellent agreement with x-ray scattering data [Witte et al., Phys. Rev. Lett. 118, 225001 (2017)] as well as dc conductivity and absorption measurements. These findings demonstrate non-Drude behavior of the dynamic conductivity above the Cooper minimum that needs to be taken into account to determine optical properties in the warm dense matter regime.

First-passage problems: A probabilistic dynamic analysis for degraded structures

NASA Technical Reports Server (NTRS)

Shiao, Michael C.; Chamis, Christos C.

1990-01-01

Structures subjected to random excitations with uncertain system parameters degraded by surrounding environments (a random time history) are studied. Methods are developed to determine the statistics of dynamic responses, such as the time-varying mean, the standard deviation, the autocorrelation functions, and the joint probability density function of any response and its derivative. Moreover, the first-passage problems with deterministic and stationary/evolutionary random barriers are evaluated. The time-varying (joint) mean crossing rate and the probability density function of the first-passage time for various random barriers are derived.

How to formulate and solve "optimal stand density over time" problems for even-aged stands using dynamic programming.

Treesearch

Chung M. Chen; Dietmar W. Rose; Rolfe A. Leary

1980-01-01

Describes how dynamic programming can be used to solve optimal stand density problems when yields are given by prior simulation or by a new stand growth equation that is a function of the decision variable. Formulations of the latter type allow use of a calculus-based search procedure; they determine exact optimal residual density at each stage.

Lattice dynamics of Ru2FeX (X = Si, Ge) Full Heusler alloys

NASA Astrophysics Data System (ADS)

Rizwan, M.; Afaq, A.; Aneeza, A.

2018-05-01

In present work, the lattice dynamics of Ru2FeX (X = Si, Ge) full Heusler alloys are investigated using density functional theory (DFT) within generalized gradient approximation (GGA) in a plane wave basis, with norm-conserving pseudopotentials. Phonon dispersion curves and phonon density of states are obtained using first-principles linear response approach of density functional perturbation theory (DFPT) as implemented in Quantum ESPRESSO code. Phonon dispersion curves indicates for both Heusler alloys that there is no imaginary phonon in whole Brillouin zone, confirming dynamical stability of these alloys in L21 type structure. There is a considerable overlapping between acoustic and optical phonon modes predicting no phonon band gap exists in dispersion curves of alloys. The same result is shown by phonon density of states curves for both Heusler alloys. Reststrahlen band for Ru2FeSi is found smaller than Ru2FeGe.

An open-source framework for analyzing N-electron dynamics. II. Hybrid density functional theory/configuration interaction methodology.

PubMed

Hermann, Gunter; Pohl, Vincent; Tremblay, Jean Christophe

2017-10-30

In this contribution, we extend our framework for analyzing and visualizing correlated many-electron dynamics to non-variational, highly scalable electronic structure method. Specifically, an explicitly time-dependent electronic wave packet is written as a linear combination of N-electron wave functions at the configuration interaction singles (CIS) level, which are obtained from a reference time-dependent density functional theory (TDDFT) calculation. The procedure is implemented in the open-source Python program detCI@ORBKIT, which extends the capabilities of our recently published post-processing toolbox (Hermann et al., J. Comput. Chem. 2016, 37, 1511). From the output of standard quantum chemistry packages using atom-centered Gaussian-type basis functions, the framework exploits the multideterminental structure of the hybrid TDDFT/CIS wave packet to compute fundamental one-electron quantities such as difference electronic densities, transient electronic flux densities, and transition dipole moments. The hybrid scheme is benchmarked against wave function data for the laser-driven state selective excitation in LiH. It is shown that all features of the electron dynamics are in good quantitative agreement with the higher-level method provided a judicious choice of functional is made. Broadband excitation of a medium-sized organic chromophore further demonstrates the scalability of the method. In addition, the time-dependent flux densities unravel the mechanistic details of the simulated charge migration process at a glance. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Comparing ab initio density-functional and wave function theories: the impact of correlation on the electronic density and the role of the correlation potential.

PubMed

Grabowski, Ireneusz; Teale, Andrew M; Śmiga, Szymon; Bartlett, Rodney J

2011-09-21

The framework of ab initio density-functional theory (DFT) has been introduced as a way to provide a seamless connection between the Kohn-Sham (KS) formulation of DFT and wave-function based ab initio approaches [R. J. Bartlett, I. Grabowski, S. Hirata, and S. Ivanov, J. Chem. Phys. 122, 034104 (2005)]. Recently, an analysis of the impact of dynamical correlation effects on the density of the neon atom was presented [K. Jankowski, K. Nowakowski, I. Grabowski, and J. Wasilewski, J. Chem. Phys. 130, 164102 (2009)], contrasting the behaviour for a variety of standard density functionals with that of ab initio approaches based on second-order Møller-Plesset (MP2) and coupled cluster theories at the singles-doubles (CCSD) and singles-doubles perturbative triples [CCSD(T)] levels. In the present work, we consider ab initio density functionals based on second-order many-body perturbation theory and coupled cluster perturbation theory in a similar manner, for a range of small atomic and molecular systems. For comparison, we also consider results obtained from MP2, CCSD, and CCSD(T) calculations. In addition to this density based analysis, we determine the KS correlation potentials corresponding to these densities and compare them with those obtained for a range of ab initio density functionals via the optimized effective potential method. The correlation energies, densities, and potentials calculated using ab initio DFT display a similar systematic behaviour to those derived from electronic densities calculated using ab initio wave function theories. In contrast, typical explicit density functionals for the correlation energy, such as VWN5 and LYP, do not show behaviour consistent with this picture of dynamical correlation, although they may provide some degree of correction for already erroneous explicitly density-dependent exchange-only functionals. The results presented here using orbital dependent ab initio density functionals show that they provide a treatment of exchange and correlation contributions within the KS framework that is more consistent with traditional ab initio wave function based methods.

Self-Consistent Determination of Atomic Charges of Ionic Liquid through a Combination of Molecular Dynamics Simulation and Density Functional Theory.

PubMed

Ishizuka, Ryosuke; Matubayasi, Nobuyuki

2016-02-09

A self-consistent scheme is developed to determine the atomic partial charges of ionic liquid. Molecular dynamics (MD) simulation was conducted to sample a set of ion configurations, and these configurations were subject to density functional theory (DFT) calculations to determine the partial charges. The charges were then averaged and used as inputs for the subsequent MD simulation, and MD and DFT calculations were repeated until the MD results are not altered any more. We applied this scheme to 1,3-dimethylimidazolium bis(trifluoromethylsulfonyl) imide ([C1mim][NTf2]) and investigated its structure and dynamics as a function of temperature. At convergence, the average ionic charges were ±0.84 e at 350 K due to charge transfer among ions, where e is the elementary charge, while the reduced ionic charges do not affect strongly the density of [C1mim][NTf2] and radial distribution function. Instead, major effects are found on the energetics and dynamics, with improvements of the overestimated heat of vaporization and the too slow motions of ions observed in MD simulations using commonly used force fields.

On-top density functionals for the short-range dynamic correlation between electrons of opposite and parallel spin

NASA Astrophysics Data System (ADS)

Hollett, Joshua W.; Pegoretti, Nicholas

2018-04-01

Separate, one-parameter, on-top density functionals are derived for the short-range dynamic correlation between opposite and parallel-spin electrons, in which the electron-electron cusp is represented by an exponential function. The combination of both functionals is referred to as the Opposite-spin exponential-cusp and Fermi-hole correction (OF) functional. The two parameters of the OF functional are set by fitting the ionization energies and electron affinities, of the atoms He to Ar, predicted by ROHF in combination with the OF functional to the experimental values. For ionization energies, the overall performance of ROHF-OF is better than completely renormalized coupled-cluster [CR-CC(2,3)] and better than, or as good as, conventional density functional methods. For electron affinities, the overall performance of ROHF-OF is less impressive. However, for both ionization energies and electron affinities of third row atoms, the mean absolute error of ROHF-OF is only 3 kJ mol-1.

Frequency dispersion of sound propagation in Rouse polymer melts via generalized dynamic random phase approximation.

PubMed

Erukhimovich, I Ya; Kudryavtsev, Ya V

2003-08-01

An extended generalization of the dynamic random phase approximation (DRPA) for L-component polymer systems is presented. Unlike the original version of the DRPA, which relates the (LxL) matrices of the collective density-density time correlation functions and the corresponding susceptibilities of concentrated polymer systems to those of the tracer macromolecules and so-called broken-links system (BLS), our generalized DRPA solves this problem for the (5xL) x (5xL) matrices of the coupled susceptibilities and time correlation functions of the component number, kinetic energy and flux densities. The presented technique is used to study propagation of sound and dynamic form-factor in disentangled (Rouse) monodisperse homopolymer melt. The calculated ultrasonic velocity and absorption coefficient reveal substantial frequency dispersion. The relaxation time tau is proportional to the degree of polymerization N, which is N times less than the Rouse time and evidences strong dynamic screening because of interchain interaction. We discuss also some peculiarities of the Brillouin scattering in polymer melts. Besides, a new convenient expression for the dynamic structure function of the single Rouse chain in (q,p) representation is found.

Density, structure, and dynamics of water: The effect of van der Waals interactions

NASA Astrophysics Data System (ADS)

Wang, Jue; Román-Pérez, G.; Soler, Jose M.; Artacho, Emilio; Fernández-Serra, M.-V.

2011-01-01

It is known that ab initio molecular dynamics (AIMD) simulations of liquid water at ambient conditions, based on the generalized gradient approximation (GGA) to density functional theory (DFT), with commonly used functionals fail to produce structural and diffusive properties in reasonable agreement with experiment. This is true for canonical, constant temperature simulations where the density of the liquid is fixed to the experimental density. The equilibrium density, at ambient conditions, of DFT water has recently been shown by Schmidt et al. [J. Phys. Chem. B, 113, 11959 (2009)] to be underestimated by different GGA functionals for exchange and correlation, and corrected by the addition of interatomic pair potentials to describe van der Waals (vdW) interactions. In this contribution we present a DFT-AIMD study of liquid water using several GGA functionals as well as the van der Waals density functional (vdW-DF) of Dion et al. [Phys. Rev. Lett. 92, 246401 (2004)]. As expected, we find that the density of water is grossly underestimated by GGA functionals. When a vdW-DF is used, the density improves drastically and the experimental diffusivity is reproduced without the need of thermal corrections. We analyze the origin of the density differences between all the functionals. We show that the vdW-DF increases the population of non-H-bonded interstitial sites, at distances between the first and second coordination shells. However, it excessively weakens the H-bond network, collapsing the second coordination shell. This structural problem is partially associated to the choice of GGA exchange in the vdW-DF. We show that a different choice for the exchange functional is enough to achieve an overall improvement both in structure and diffusivity.

Experimental Investigation of Ultrafast Hydration Structure and Dynamics at Sub-Angstrom Lengthscales

ERIC Educational Resources Information Center

Coridan, Robert Henry

2009-01-01

This thesis outlines how meV-resolution inelastic x-ray scattering and causality-enforcing mathematics can be used to measure the dynamical density-density linear response function for liquid water with Angstrom spatial resolution and 50fs temporal resolution. The results are compared to high-resolution spectroscopic and scattering experiments and…

Brownian systems with spatially inhomogeneous activity

NASA Astrophysics Data System (ADS)

Sharma, A.; Brader, J. M.

2017-09-01

We generalize the Green-Kubo approach, previously applied to bulk systems of spherically symmetric active particles [J. Chem. Phys. 145, 161101 (2016), 10.1063/1.4966153], to include spatially inhomogeneous activity. The method is applied to predict the spatial dependence of the average orientation per particle and the density. The average orientation is given by an integral over the self part of the Van Hove function and a simple Gaussian approximation to this quantity yields an accurate analytical expression. Taking this analytical result as input to a dynamic density functional theory approximates the spatial dependence of the density in good agreement with simulation data. All theoretical predictions are validated using Brownian dynamics simulations.

Dynamical density functional theory analysis of the laning instability in sheared soft matter.

PubMed

Scacchi, A; Archer, A J; Brader, J M

2017-12-01

Using dynamical density functional theory (DDFT) methods we investigate the laning instability of a sheared colloidal suspension. The nonequilibrium ordering at the laning transition is driven by nonaffine particle motion arising from interparticle interactions. Starting from a DDFT which incorporates the nonaffine motion, we perform a linear stability analysis that enables identification of the regions of parameter space where lanes form. We illustrate our general approach by applying it to a simple one-component fluid of soft penetrable particles.

Ab initio molecular dynamics with nuclear quantum effects at classical cost: Ring polymer contraction for density functional theory.

PubMed

Marsalek, Ondrej; Markland, Thomas E

2016-02-07

Path integral molecular dynamics simulations, combined with an ab initio evaluation of interactions using electronic structure theory, incorporate the quantum mechanical nature of both the electrons and nuclei, which are essential to accurately describe systems containing light nuclei. However, path integral simulations have traditionally required a computational cost around two orders of magnitude greater than treating the nuclei classically, making them prohibitively costly for most applications. Here we show that the cost of path integral simulations can be dramatically reduced by extending our ring polymer contraction approach to ab initio molecular dynamics simulations. By using density functional tight binding as a reference system, we show that our ring polymer contraction scheme gives rapid and systematic convergence to the full path integral density functional theory result. We demonstrate the efficiency of this approach in ab initio simulations of liquid water and the reactive protonated and deprotonated water dimer systems. We find that the vast majority of the nuclear quantum effects are accurately captured using contraction to just the ring polymer centroid, which requires the same number of density functional theory calculations as a classical simulation. Combined with a multiple time step scheme using the same reference system, which allows the time step to be increased, this approach is as fast as a typical classical ab initio molecular dynamics simulation and 35× faster than a full path integral calculation, while still exactly including the quantum sampling of nuclei. This development thus offers a route to routinely include nuclear quantum effects in ab initio molecular dynamics simulations at negligible computational cost.

Electron-Ion Dynamics with Time-Dependent Density Functional Theory: Towards Predictive Solar Cell Modeling: Final Technical Report

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

Maitra, Neepa

2016-07-14

This project investigates the accuracy of currently-used functionals in time-dependent density functional theory, which is today routinely used to predict and design materials and computationally model processes in solar energy conversion. The rigorously-based electron-ion dynamics method developed here sheds light on traditional methods and overcomes challenges those methods have. The fundamental research undertaken here is important for building reliable and practical methods for materials discovery. The ultimate goal is to use these tools for the computational design of new materials for solar cell devices of high efficiency.

Velocity Gradient Power Functional for Brownian Dynamics.

PubMed

de Las Heras, Daniel; Schmidt, Matthias

2018-01-12

We present an explicit and simple approximation for the superadiabatic excess (over ideal gas) free power functional, admitting the study of the nonequilibrium dynamics of overdamped Brownian many-body systems. The functional depends on the local velocity gradient and is systematically obtained from treating the microscopic stress distribution as a conjugate field. The resulting superadiabatic forces are beyond dynamical density functional theory and are of a viscous nature. Their high accuracy is demonstrated by comparison to simulation results.

Velocity Gradient Power Functional for Brownian Dynamics

NASA Astrophysics Data System (ADS)

de las Heras, Daniel; Schmidt, Matthias

2018-01-01

We present an explicit and simple approximation for the superadiabatic excess (over ideal gas) free power functional, admitting the study of the nonequilibrium dynamics of overdamped Brownian many-body systems. The functional depends on the local velocity gradient and is systematically obtained from treating the microscopic stress distribution as a conjugate field. The resulting superadiabatic forces are beyond dynamical density functional theory and are of a viscous nature. Their high accuracy is demonstrated by comparison to simulation results.

Warm Dense Matter Demonstrating Non-Drude Conductivity from Observations of Nonlinear Plasmon Damping

NASA Astrophysics Data System (ADS)

Witte, B. B. L.; Fletcher, L. B.; Galtier, E.; Gamboa, E.; Lee, H. J.; Zastrau, U.; Redmer, R.; Glenzer, S. H.; Sperling, P.

2017-06-01

We present simulations using finite-temperature density-functional-theory molecular dynamics to calculate the dynamic electrical conductivity in warm dense aluminum. The comparison between exchange-correlation functionals in the Perdew-Burke-Enzerhof and Heyd-Scuseria-Enzerhof (HSE) approximation indicates evident differences in the density of states and the dc conductivity. The HSE calculations show excellent agreement with experimental Linac Coherent Light Source x-ray plasmon scattering spectra revealing plasmon damping below the widely used random phase approximation. These findings demonstrate non-Drude-like behavior of the dynamic conductivity that needs to be taken into account to determine the optical properties of warm dense matter.

A density matrix-based method for the linear-scaling calculation of dynamic second- and third-order properties at the Hartree-Fock and Kohn-Sham density functional theory levels.

PubMed

Kussmann, Jörg; Ochsenfeld, Christian

2007-11-28

A density matrix-based time-dependent self-consistent field (D-TDSCF) method for the calculation of dynamic polarizabilities and first hyperpolarizabilities using the Hartree-Fock and Kohn-Sham density functional theory approaches is presented. The D-TDSCF method allows us to reduce the asymptotic scaling behavior of the computational effort from cubic to linear for systems with a nonvanishing band gap. The linear scaling is achieved by combining a density matrix-based reformulation of the TDSCF equations with linear-scaling schemes for the formation of Fock- or Kohn-Sham-type matrices. In our reformulation only potentially linear-scaling matrices enter the formulation and efficient sparse algebra routines can be employed. Furthermore, the corresponding formulas for the first hyperpolarizabilities are given in terms of zeroth- and first-order one-particle reduced density matrices according to Wigner's (2n+1) rule. The scaling behavior of our method is illustrated for first exemplary calculations with systems of up to 1011 atoms and 8899 basis functions.

Active Space Dependence in Multiconfiguration Pair-Density Functional Theory.

PubMed

Sharma, Prachi; Truhlar, Donald G; Gagliardi, Laura

2018-02-13

In multiconfiguration pair-density functional theory (MC-PDFT), multiconfiguration self-consistent-field calculations and on-top density functionals are combined to describe both static and dynamic correlation. Here, we investigate how the MC-PDFT total energy and its components depend on the active space choice in the case of the H 2 and N 2 molecules. The active space dependence of the on-top pair density, the total density, the ratio of on-top pair density to half the square of the electron density, and the satisfaction of the virial theorem are also explored. We find that the density and on-top pair density do not change significantly with changes in the active space. However, the on-top ratio does change significantly with respect to active space change, and this affects the on-top energy. This study provides a foundation for designing on-top density functionals and automatizing the active space choice in MC-PDFT.

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.

Structural relaxation of polydisperse hard spheres: comparison of the mode-coupling theory to a Langevin dynamics simulation.

PubMed

Weysser, F; Puertas, A M; Fuchs, M; Voigtmann, Th

2010-07-01

We analyze the slow glassy structural relaxation as measured through collective and tagged-particle density correlation functions obtained from Brownian dynamics simulations for a polydisperse system of quasi-hard spheres in the framework of the mode-coupling theory (MCT) of the glass transition. Asymptotic analyses show good agreement for the collective dynamics when polydispersity effects are taken into account in a multicomponent calculation, but qualitative disagreement at small q when the system is treated as effectively monodisperse. The origin of the different small-q behavior is attributed to the interplay between interdiffusion processes and structural relaxation. Numerical solutions of the MCT equations are obtained taking properly binned partial static structure factors from the simulations as input. Accounting for a shift in the critical density, the collective density correlation functions are well described by the theory at all densities investigated in the simulations, with quantitative agreement best around the maxima of the static structure factor and worst around its minima. A parameter-free comparison of the tagged-particle dynamics however reveals large quantitative errors for small wave numbers that are connected to the well-known decoupling of self-diffusion from structural relaxation and to dynamical heterogeneities. While deviations from MCT behavior are clearly seen in the tagged-particle quantities for densities close to and on the liquid side of the MCT glass transition, no such deviations are seen in the collective dynamics.

Density Functional Methods for Shock Physics and High Energy Density Science

NASA Astrophysics Data System (ADS)

Desjarlais, Michael

2017-06-01

Molecular dynamics with density functional theory has emerged over the last two decades as a powerful and accurate framework for calculating thermodynamic and transport properties with broad application to dynamic compression, high energy density science, and warm dense matter. These calculations have been extensively validated against shock and ramp wave experiments, are a principal component of high-fidelity equation of state generation, and are having wide-ranging impacts on inertial confinement fusion, planetary science, and shock physics research. In addition to thermodynamic properties, phase boundaries, and the equation of state, one also has access to electrical conductivity, thermal conductivity, and lower energy optical properties. Importantly, all these properties are obtained within the same theoretical framework and are manifestly consistent. In this talk I will give a brief history and overview of molecular dynamics with density functional theory and its use in calculating a wide variety of thermodynamic and transport properties for materials ranging from ambient to extreme conditions and with comparisons to experimental data. I will also discuss some of the limitations and difficulties, as well as active research areas. Sandia is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

Time-dependent density functional theory for open systems with a positivity-preserving decomposition scheme for environment spectral functions

NASA Astrophysics Data System (ADS)

Wang, RuLin; Zheng, Xiao; Kwok, YanHo; Xie, Hang; Chen, GuanHua; Yam, ChiYung

2015-04-01

Understanding electronic dynamics on material surfaces is fundamentally important for applications including nanoelectronics, inhomogeneous catalysis, and photovoltaics. Practical approaches based on time-dependent density functional theory for open systems have been developed to characterize the dissipative dynamics of electrons in bulk materials. The accuracy and reliability of such approaches depend critically on how the electronic structure and memory effects of surrounding material environment are accounted for. In this work, we develop a novel squared-Lorentzian decomposition scheme, which preserves the positive semi-definiteness of the environment spectral matrix. The resulting electronic dynamics is guaranteed to be both accurate and convergent even in the long-time limit. The long-time stability of electronic dynamics simulation is thus greatly improved within the current decomposition scheme. The validity and usefulness of our new approach are exemplified via two prototypical model systems: quasi-one-dimensional atomic chains and two-dimensional bilayer graphene.

Coupling of ab initio density functional theory and molecular dynamics for the multiscale modeling of carbon nanotubes

NASA Astrophysics Data System (ADS)

Ng, T. Y.; Yeak, S. H.; Liew, K. M.

2008-02-01

A multiscale technique is developed that couples empirical molecular dynamics (MD) and ab initio density functional theory (DFT). An overlap handshaking region between the empirical MD and ab initio DFT regions is formulated and the interaction forces between the carbon atoms are calculated based on the second-generation reactive empirical bond order potential, the long-range Lennard-Jones potential as well as the quantum-mechanical DFT derived forces. A density of point algorithm is also developed to track all interatomic distances in the system, and to activate and establish the DFT and handshaking regions. Through parallel computing, this multiscale method is used here to study the dynamic behavior of single-walled carbon nanotubes (SWCNTs) under asymmetrical axial compression. The detection of sideways buckling due to the asymmetrical axial compression is reported and discussed. It is noted from this study on SWCNTs that the MD results may be stiffer compared to those with electron density considerations, i.e. first-principle ab initio methods.

Fluids density functional theory and initializing molecular dynamics simulations of block copolymers

NASA Astrophysics Data System (ADS)

Brown, Jonathan R.; Seo, Youngmi; Maula, Tiara Ann D.; Hall, Lisa M.

2016-03-01

Classical, fluids density functional theory (fDFT), which can predict the equilibrium density profiles of polymeric systems, and coarse-grained molecular dynamics (MD) simulations, which are often used to show both structure and dynamics of soft materials, can be implemented using very similar bead-based polymer models. We aim to use fDFT and MD in tandem to examine the same system from these two points of view and take advantage of the different features of each methodology. Additionally, the density profiles resulting from fDFT calculations can be used to initialize the MD simulations in a close to equilibrated structure, speeding up the simulations. Here, we show how this method can be applied to study microphase separated states of both typical diblock and tapered diblock copolymers in which there is a region with a gradient in composition placed between the pure blocks. Both methods, applied at constant pressure, predict a decrease in total density as segregation strength or the length of the tapered region is increased. The predictions for the density profiles from fDFT and MD are similar across materials with a wide range of interfacial widths.

Spectral densities for Frenkel exciton dynamics in molecular crystals: A TD-DFTB approach

NASA Astrophysics Data System (ADS)

Plötz, Per-Arno; Megow, Jörg; Niehaus, Thomas; Kühn, Oliver

2017-02-01

Effects of thermal fluctuations on the electronic excitation energies and intermonomeric Coulomb couplings are investigated for a perylene-tetracarboxylic-diimide crystal. To this end, time dependent density functional theory based tight binding (TD-DFTB) in the linear response formulation is used in combination with electronic ground state classical molecular dynamics. As a result, a parametrized Frenkel exciton Hamiltonian is obtained, with the effect of exciton-vibrational coupling being described by spectral densities. Employing dynamically defined normal modes, these spectral densities are analyzed in great detail, thus providing insight into the effect of specific intramolecular motions on excitation energies and Coulomb couplings. This distinguishes the present method from approaches using fixed transition densities. The efficiency by which intramolecular contributions to the spectral density can be calculated is a clear advantage of this method as compared with standard TD-DFT.

When can a single-species, density-dependent model capture the dynamics of a consumer-resource system?

PubMed

Reynolds, Sara A; Brassil, Chad E

2013-12-21

Single-species population models often include density-dependence phenomenologically in order to approximate higher order mechanisms. Here we consider the common scenario in which density-dependence acts via depletion of a renewed resource. When the response of the resource is very quick relative to that of the consumer, the consumer dynamics can be captured by a single-species, density-dependent model. Time scale separation is used to show analytically how the shape of the density-dependent relationship depends on the type of resource and the form of the functional response. Resource types of abiotic, biotic, and biotic with migration are considered, in combination with linear and saturating functional responses. In some cases, we derive familiar forms of single-species models, adding to the justification for their use. In other scenarios novel forms of density-dependence are derived, for example an abiotic resource and a saturating functional response can result in a nonlinear density-dependent relationship in the associated single-species model of the consumer. In this case, the per capita relationship has both concave-up and concave-down sections. © 2013 Published by Elsevier Ltd. All rights reserved.

Identification of Stochastically Perturbed Autonomous Systems from Temporal Sequences of Probability Density Functions

NASA Astrophysics Data System (ADS)

Nie, Xiaokai; Luo, Jingjing; Coca, Daniel; Birkin, Mark; Chen, Jing

2018-03-01

The paper introduces a method for reconstructing one-dimensional iterated maps that are driven by an external control input and subjected to an additive stochastic perturbation, from sequences of probability density functions that are generated by the stochastic dynamical systems and observed experimentally.

Correlation of Tumor Immunohistochemistry with Dynamic Contrast-Enhanced and DSC-MRI Parameters in Patients with Gliomas.

PubMed

Nguyen, T B; Cron, G O; Bezzina, K; Perdrizet, K; Torres, C H; Chakraborty, S; Woulfe, J; Jansen, G H; Thornhill, R E; Zanette, B; Cameron, I G

2016-12-01

Tumor CBV is a prognostic and predictive marker for patients with gliomas. Tumor CBV can be measured noninvasively with different MR imaging techniques; however, it is not clear which of these techniques most closely reflects histologically-measured tumor CBV. Our aim was to investigate the correlations between dynamic contrast-enhanced and DSC-MR imaging parameters and immunohistochemistry in patients with gliomas. Forty-three patients with a new diagnosis of glioma underwent a preoperative MR imaging examination with dynamic contrast-enhanced and DSC sequences. Unnormalized and normalized cerebral blood volume was obtained from DSC MR imaging. Two sets of plasma volume and volume transfer constant maps were obtained from dynamic contrast-enhanced MR imaging. Plasma volume obtained from the phase-derived vascular input function and bookend T1 mapping (Vp_Φ) and volume transfer constant obtained from phase-derived vascular input function and bookend T1 mapping (K trans _Φ) were determined. Plasma volume obtained from magnitude-derived vascular input function (Vp_SI) and volume transfer constant obtained from magnitude-derived vascular input function (K trans _SI) were acquired, without T1 mapping. Using CD34 staining, we measured microvessel density and microvessel area within 3 representative areas of the resected tumor specimen. The Mann-Whitney U test was used to test for differences according to grade and degree of enhancement. The Spearman correlation was performed to determine the relationship between dynamic contrast-enhanced and DSC parameters and histopathologic measurements. Microvessel area, microvessel density, dynamic contrast-enhanced, and DSC-MR imaging parameters varied according to the grade and degree of enhancement (P < .05). A strong correlation was found between microvessel area and Vp_Φ and between microvessel area and unnormalized blood volume (r s ≥ 0.61). A moderate correlation was found between microvessel area and normalized blood volume, microvessel area and Vp_SI, microvessel area and K trans _Φ, microvessel area and K trans _SI, microvessel density and Vp_Φ, microvessel density and unnormalized blood volume, and microvessel density and normalized blood volume (0.44 ≤ r s ≤ 0.57). A weaker correlation was found between microvessel density and K trans _Φ and between microvessel density and K trans _SI (r s ≤ 0.41). With dynamic contrast-enhanced MR imaging, use of a phase-derived vascular input function and bookend T1 mapping improves the correlation between immunohistochemistry and plasma volume, but not between immunohistochemistry and the volume transfer constant. With DSC-MR imaging, normalization of tumor CBV could decrease the correlation with microvessel area. © 2016 by American Journal of Neuroradiology.

The force distribution probability function for simple fluids by density functional theory.

PubMed

Rickayzen, G; Heyes, D M

2013-02-28

Classical density functional theory (DFT) is used to derive a formula for the probability density distribution function, P(F), and probability distribution function, W(F), for simple fluids, where F is the net force on a particle. The final formula for P(F) ∝ exp(-AF(2)), where A depends on the fluid density, the temperature, and the Fourier transform of the pair potential. The form of the DFT theory used is only applicable to bounded potential fluids. When combined with the hypernetted chain closure of the Ornstein-Zernike equation, the DFT theory for W(F) agrees with molecular dynamics computer simulations for the Gaussian and bounded soft sphere at high density. The Gaussian form for P(F) is still accurate at lower densities (but not too low density) for the two potentials, but with a smaller value for the constant, A, than that predicted by the DFT theory.

Dynamics of a Two-Dimensional System of Quantum Dipoles

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

Mazzanti, F.; Astrakharchik, G. E.; Boronat, J.

2009-03-20

A detailed microscopic analysis of the dynamic structure function S(k,{omega}) of a two-dimensional Bose system of dipoles polarized along the direction perpendicular to the plane is presented and discussed. Starting from ground-state quantities obtained using a quantum diffusion Monte Carlo algorithm, the density-density response is evaluated in the context of the correlated basis functions (CBF) theory. CBF predicts a sharp peak and a multiexcitation component at higher energies produced by the decay of excitations. We discuss the structure of the phonon-roton peak and show that the Feynman and Bogoliubov predictions depart from the CBF result already at low densities. Wemore » finally discuss the emergence of a roton in the spectrum, but find the roton energy not low enough to make the system unstable under density fluctuations up to the highest density considered that is close to the freezing point.« less

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

PubMed

Thummuru, Dhileep Nagi Reddy; Mallik, Bhabani S

2017-10-26

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

Ab initio molecular dynamics with nuclear quantum effects at classical cost: Ring polymer contraction for density functional theory

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

Marsalek, Ondrej; Markland, Thomas E., E-mail: tmarkland@stanford.edu

Path integral molecular dynamics simulations, combined with an ab initio evaluation of interactions using electronic structure theory, incorporate the quantum mechanical nature of both the electrons and nuclei, which are essential to accurately describe systems containing light nuclei. However, path integral simulations have traditionally required a computational cost around two orders of magnitude greater than treating the nuclei classically, making them prohibitively costly for most applications. Here we show that the cost of path integral simulations can be dramatically reduced by extending our ring polymer contraction approach to ab initio molecular dynamics simulations. By using density functional tight binding asmore » a reference system, we show that our ring polymer contraction scheme gives rapid and systematic convergence to the full path integral density functional theory result. We demonstrate the efficiency of this approach in ab initio simulations of liquid water and the reactive protonated and deprotonated water dimer systems. We find that the vast majority of the nuclear quantum effects are accurately captured using contraction to just the ring polymer centroid, which requires the same number of density functional theory calculations as a classical simulation. Combined with a multiple time step scheme using the same reference system, which allows the time step to be increased, this approach is as fast as a typical classical ab initio molecular dynamics simulation and 35× faster than a full path integral calculation, while still exactly including the quantum sampling of nuclei. This development thus offers a route to routinely include nuclear quantum effects in ab initio molecular dynamics simulations at negligible computational cost.« less

Population Density Modulates Drug Inhibition and Gives Rise to Potential Bistability of Treatment Outcomes for Bacterial Infections.

PubMed

Karslake, Jason; Maltas, Jeff; Brumm, Peter; Wood, Kevin B

2016-10-01

The inoculum effect (IE) is an increase in the minimum inhibitory concentration (MIC) of an antibiotic as a function of the initial size of a microbial population. The IE has been observed in a wide range of bacteria, implying that antibiotic efficacy may depend on population density. Such density dependence could have dramatic effects on bacterial population dynamics and potential treatment strategies, but explicit measures of per capita growth as a function of density are generally not available. Instead, the IE measures MIC as a function of initial population size, and population density changes by many orders of magnitude on the timescale of the experiment. Therefore, the functional relationship between population density and antibiotic inhibition is generally not known, leaving many questions about the impact of the IE on different treatment strategies unanswered. To address these questions, here we directly measured real-time per capita growth of Enterococcus faecalis populations exposed to antibiotic at fixed population densities using multiplexed computer-automated culture devices. We show that density-dependent growth inhibition is pervasive for commonly used antibiotics, with some drugs showing increased inhibition and others decreased inhibition at high densities. For several drugs, the density dependence is mediated by changes in extracellular pH, a community-level phenomenon not previously linked with the IE. Using a simple mathematical model, we demonstrate how this density dependence can modulate population dynamics in constant drug environments. Then, we illustrate how time-dependent dosing strategies can mitigate the negative effects of density-dependence. Finally, we show that these density effects lead to bistable treatment outcomes for a wide range of antibiotic concentrations in a pharmacological model of antibiotic treatment. As a result, infections exceeding a critical density often survive otherwise effective treatments.

Population Density Modulates Drug Inhibition and Gives Rise to Potential Bistability of Treatment Outcomes for Bacterial Infections

PubMed Central

Maltas, Jeff; Brumm, Peter; Wood, Kevin B.

2016-01-01

The inoculum effect (IE) is an increase in the minimum inhibitory concentration (MIC) of an antibiotic as a function of the initial size of a microbial population. The IE has been observed in a wide range of bacteria, implying that antibiotic efficacy may depend on population density. Such density dependence could have dramatic effects on bacterial population dynamics and potential treatment strategies, but explicit measures of per capita growth as a function of density are generally not available. Instead, the IE measures MIC as a function of initial population size, and population density changes by many orders of magnitude on the timescale of the experiment. Therefore, the functional relationship between population density and antibiotic inhibition is generally not known, leaving many questions about the impact of the IE on different treatment strategies unanswered. To address these questions, here we directly measured real-time per capita growth of Enterococcus faecalis populations exposed to antibiotic at fixed population densities using multiplexed computer-automated culture devices. We show that density-dependent growth inhibition is pervasive for commonly used antibiotics, with some drugs showing increased inhibition and others decreased inhibition at high densities. For several drugs, the density dependence is mediated by changes in extracellular pH, a community-level phenomenon not previously linked with the IE. Using a simple mathematical model, we demonstrate how this density dependence can modulate population dynamics in constant drug environments. Then, we illustrate how time-dependent dosing strategies can mitigate the negative effects of density-dependence. Finally, we show that these density effects lead to bistable treatment outcomes for a wide range of antibiotic concentrations in a pharmacological model of antibiotic treatment. As a result, infections exceeding a critical density often survive otherwise effective treatments. PMID:27764095

Thermodynamics of technetium: Reconciling theory and experiment using density functional perturbation analysis

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

Weck, Philippe F.; Kim, Eunja

The structure, lattice dynamics and thermodynamic properties of bulk technetium were investigated within the framework of density functional theory. The phonon density of states spectrum computed with density functional perturbation theory closely matches inelastic coherent neutron scattering measurements. The thermal properties of technetium were derived from phonon frequencies calculated within the quasi-harmonic approximation (QHA), which introduces a volume dependence of phonon frequencies as a part of the anharmonic effect. As a result, the predicted thermal expansion and isobaric heat capacity of technetium are in excellent agreement with available experimental data for temperatures up to ~1600 K.

Thermodynamics of technetium: Reconciling theory and experiment using density functional perturbation analysis

DOE PAGES

Weck, Philippe F.; Kim, Eunja

2015-06-11

The structure, lattice dynamics and thermodynamic properties of bulk technetium were investigated within the framework of density functional theory. The phonon density of states spectrum computed with density functional perturbation theory closely matches inelastic coherent neutron scattering measurements. The thermal properties of technetium were derived from phonon frequencies calculated within the quasi-harmonic approximation (QHA), which introduces a volume dependence of phonon frequencies as a part of the anharmonic effect. As a result, the predicted thermal expansion and isobaric heat capacity of technetium are in excellent agreement with available experimental data for temperatures up to ~1600 K.

Structural, elastic, electronic and dynamical properties of OsB and ReB: Density functional calculations

NASA Astrophysics Data System (ADS)

Li, Yanling; Zeng, Zhi; Lin, Haiqing

2010-06-01

The structural, elastic, electronic and dynamical properties of ReB and OsB are investigated by first-principles calculations based on density functional theory. It turns out that ReB and OsB are metallic ultra-incompressible solids with small elastic anisotropy and high hardness. The change of c/ a ratio in OsB indicates that there is a structural phase transition at about 31 GPa. Phonon spectra calculations show that both OsB and ReB are stable dynamically and there are abnormal phonon dispersions along special directions in Brillouin zone. OsB and ReB do not show superconductivity due to very weak electron-phonon interactions in them.

Canonical-ensemble extended Lagrangian Born-Oppenheimer molecular dynamics for the linear scaling density functional theory.

PubMed

Hirakawa, Teruo; Suzuki, Teppei; Bowler, David R; Miyazaki, Tsuyoshi

2017-10-11

We discuss the development and implementation of a constant temperature (NVT) molecular dynamics scheme that combines the Nosé-Hoover chain thermostat with the extended Lagrangian Born-Oppenheimer molecular dynamics (BOMD) scheme, using a linear scaling density functional theory (DFT) approach. An integration scheme for this canonical-ensemble extended Lagrangian BOMD is developed and discussed in the context of the Liouville operator formulation. Linear scaling DFT canonical-ensemble extended Lagrangian BOMD simulations are tested on bulk silicon and silicon carbide systems to evaluate our integration scheme. The results show that the conserved quantity remains stable with no systematic drift even in the presence of the thermostat.

Collision dynamics of H+ + N2 at low energies based on time-dependent density-functional theory

NASA Astrophysics Data System (ADS)

Yu, W.; Zhang, Y.; Zhang, F. S.; Hutton, R.; Zou, Y.; Gao, C.-Z.; Wei, B.

2018-02-01

Using time-dependent density-functional theory at the level of local density approximation augmented by a self-interaction correction and coupled non-adiabatically to molecular dynamics, we study, from a theoretical perspective, scattering dynamics of the proton in collisions with the N2 molecule at 30 eV. Nine different collision configurations are employed to analyze the proton energy loss spectra, electron depletion, scattering angles and self-interaction effects. Our results agree qualitatively with the experimental data and previous theoretical calculations. The discrepancies are ascribed to the limitation of the theoretical models in use. We find that self-interaction effects can significantly influence the electron capture and the excited diatomic vibrational motion, which is in consistent with other calculations. In addition, it is found that the molecular structure can be readily retrieved from the proton energy loss spectra due to a significant momentum transfer in head-on collisions.

Total-energy Assisted Tight-binding Method Based on Local Density Approximation of Density Functional Theory

NASA Astrophysics Data System (ADS)

Fujiwara, Takeo; Nishino, Shinya; Yamamoto, Susumu; Suzuki, Takashi; Ikeda, Minoru; Ohtani, Yasuaki

2018-06-01

A novel tight-binding method is developed, based on the extended Hückel approximation and charge self-consistency, with referring the band structure and the total energy of the local density approximation of the density functional theory. The parameters are so adjusted by computer that the result reproduces the band structure and the total energy, and the algorithm for determining parameters is established. The set of determined parameters is applicable to a variety of crystalline compounds and change of lattice constants, and, in other words, it is transferable. Examples are demonstrated for Si crystals of several crystalline structures varying lattice constants. Since the set of parameters is transferable, the present tight-binding method may be applicable also to molecular dynamics simulations of large-scale systems and long-time dynamical processes.

Local Descriptors of Dynamic and Nondynamic Correlation.

PubMed

Ramos-Cordoba, Eloy; Matito, Eduard

2017-06-13

Quantitatively accurate electronic structure calculations rely on the proper description of electron correlation. A judicious choice of the approximate quantum chemistry method depends upon the importance of dynamic and nondynamic correlation, which is usually assesed by scalar measures. Existing measures of electron correlation do not consider separately the regions of the Cartesian space where dynamic or nondynamic correlation are most important. We introduce real-space descriptors of dynamic and nondynamic electron correlation that admit orbital decomposition. Integration of the local descriptors yields global numbers that can be used to quantify dynamic and nondynamic correlation. Illustrative examples over different chemical systems with varying electron correlation regimes are used to demonstrate the capabilities of the local descriptors. Since the expressions only require orbitals and occupation numbers, they can be readily applied in the context of local correlation methods, hybrid methods, density matrix functional theory, and fractional-occupancy density functional theory.

Towards time-dependent current-density-functional theory in the non-linear regime

NASA Astrophysics Data System (ADS)

Escartín, J. M.; Vincendon, M.; Romaniello, P.; Dinh, P. M.; Reinhard, P.-G.; Suraud, E.

2015-02-01

Time-Dependent Density-Functional Theory (TDDFT) is a well-established theoretical approach to describe and understand irradiation processes in clusters and molecules. However, within the so-called adiabatic local density approximation (ALDA) to the exchange-correlation (xc) potential, TDDFT can show insufficiencies, particularly in violently dynamical processes. This is because within ALDA the xc potential is instantaneous and is a local functional of the density, which means that this approximation neglects memory effects and long-range effects. A way to go beyond ALDA is to use Time-Dependent Current-Density-Functional Theory (TDCDFT), in which the basic quantity is the current density rather than the density as in TDDFT. This has been shown to offer an adequate account of dissipation in the linear domain when the Vignale-Kohn (VK) functional is used. Here, we go beyond the linear regime and we explore this formulation in the time domain. In this case, the equations become very involved making the computation out of reach; we hence propose an approximation to the VK functional which allows us to calculate the dynamics in real time and at the same time to keep most of the physics described by the VK functional. We apply this formulation to the calculation of the time-dependent dipole moment of Ca, Mg and Na2. Our results show trends similar to what was previously observed in model systems or within linear response. In the non-linear domain, our results show that relaxation times do not decrease with increasing deposited excitation energy, which sets some limitations to the practical use of TDCDFT in such a domain of excitations.

Towards time-dependent current-density-functional theory in the non-linear regime.

PubMed

Escartín, J M; Vincendon, M; Romaniello, P; Dinh, P M; Reinhard, P-G; Suraud, E

2015-02-28

Time-Dependent Density-Functional Theory (TDDFT) is a well-established theoretical approach to describe and understand irradiation processes in clusters and molecules. However, within the so-called adiabatic local density approximation (ALDA) to the exchange-correlation (xc) potential, TDDFT can show insufficiencies, particularly in violently dynamical processes. This is because within ALDA the xc potential is instantaneous and is a local functional of the density, which means that this approximation neglects memory effects and long-range effects. A way to go beyond ALDA is to use Time-Dependent Current-Density-Functional Theory (TDCDFT), in which the basic quantity is the current density rather than the density as in TDDFT. This has been shown to offer an adequate account of dissipation in the linear domain when the Vignale-Kohn (VK) functional is used. Here, we go beyond the linear regime and we explore this formulation in the time domain. In this case, the equations become very involved making the computation out of reach; we hence propose an approximation to the VK functional which allows us to calculate the dynamics in real time and at the same time to keep most of the physics described by the VK functional. We apply this formulation to the calculation of the time-dependent dipole moment of Ca, Mg and Na2. Our results show trends similar to what was previously observed in model systems or within linear response. In the non-linear domain, our results show that relaxation times do not decrease with increasing deposited excitation energy, which sets some limitations to the practical use of TDCDFT in such a domain of excitations.

Rich Global Dynamics in a Prey-Predator Model with Allee Effect and Density Dependent Death Rate of Predator

NASA Astrophysics Data System (ADS)

Sen, Moitri; Banerjee, Malay

In this work we have considered a prey-predator model with strong Allee effect in the prey growth function, Holling type-II functional response and density dependent death rate for predators. It presents a comprehensive study of the complete global dynamics for the considered system. Especially to see the effect of the density dependent death rate of predator on the system behavior, we have presented the two parametric bifurcation diagrams taking it as one of the bifurcation parameters. In course of that we have explored all possible local and global bifurcations that the system could undergo, namely the existence of transcritical bifurcation, saddle node bifurcation, cusp bifurcation, Hopf-bifurcation, Bogdanov-Takens bifurcation and Bautin bifurcation respectively.

Ultra-stiff metallic glasses through bond energy density design.

PubMed

Schnabel, Volker; Köhler, Mathias; Music, Denis; Bednarcik, Jozef; Clegg, William J; Raabe, Dierk; Schneider, Jochen M

2017-07-05

The elastic properties of crystalline metals scale with their valence electron density. Similar observations have been made for metallic glasses. However, for metallic glasses where covalent bonding predominates, such as metalloid metallic glasses, this relationship appears to break down. At present, the reasons for this are not understood. Using high energy x-ray diffraction analysis of melt spun and thin film metallic glasses combined with density functional theory based molecular dynamics simulations, we show that the physical origin of the ultrahigh stiffness in both metalloid and non-metalloid metallic glasses is best understood in terms of the bond energy density. Using the bond energy density as novel materials design criterion for ultra-stiff metallic glasses, we are able to predict a Co 33.0 Ta 3.5 B 63.5 short range ordered material by density functional theory based molecular dynamics simulations with a high bond energy density of 0.94 eV Å -3 and a bulk modulus of 263 GPa, which is 17% greater than the stiffest Co-B based metallic glasses reported in literature.

Experimental investigation of alternative transmission functions: Quantitative evidence for the importance of nonlinear transmission dynamics in host-parasite systems.

PubMed

Orlofske, Sarah A; Flaxman, Samuel M; Joseph, Maxwell B; Fenton, Andy; Melbourne, Brett A; Johnson, Pieter T J

2018-05-01

Understanding pathogen transmission is crucial for predicting and managing disease. Nonetheless, experimental comparisons of alternative functional forms of transmission remain rare, and those experiments that are conducted are often not designed to test the full range of possible forms. To differentiate among 10 candidate transmission functions, we used a novel experimental design in which we independently varied four factors-duration of exposure, numbers of parasites, numbers of hosts and parasite density-in laboratory infection experiments. We used interactions between amphibian hosts and trematode parasites as a model system and all candidate models incorporated parasite depletion. An additional manipulation involving anaesthesia addressed the effects of host behaviour on transmission form. Across all experiments, nonlinear transmission forms involving either a power law or a negative binomial function were the best-fitting models and consistently outperformed the linear density-dependent and density-independent functions. By testing previously published data for two other host-macroparasite systems, we also found support for the same nonlinear transmission forms. Although manipulations of parasite density are common in transmission studies, the comprehensive set of variables tested in our experiments revealed that variation in density alone was least likely to differentiate among competing transmission functions. Across host-pathogen systems, nonlinear functions may often more accurately represent transmission dynamics and thus provide more realistic predictions for infection. © 2017 The Authors. Journal of Animal Ecology published by John Wiley & Sons Ltd on behalf of British Ecological Society.

A Navier-Stokes phase-field crystal model for colloidal suspensions

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

Praetorius, Simon, E-mail: simon.praetorius@tu-dresden.de; Voigt, Axel, E-mail: axel.voigt@tu-dresden.de

2015-04-21

We develop a fully continuous model for colloidal suspensions with hydrodynamic interactions. The Navier-Stokes Phase-Field Crystal model combines ideas of dynamic density functional theory with particulate flow approaches and is derived in detail and related to other dynamic density functional theory approaches with hydrodynamic interactions. The derived system is numerically solved using adaptive finite elements and is used to analyze colloidal crystallization in flowing environments demonstrating a strong coupling in both directions between the crystal shape and the flow field. We further validate the model against other computational approaches for particulate flow systems for various colloidal sedimentation problems.

Interaction potential for indium phosphide: a molecular dynamics and first-principles study of the elastic constants, generalized stacking fault and surface energies.

PubMed

Branicio, Paulo Sergio; Rino, José Pedro; Gan, Chee Kwan; Tsuzuki, Hélio

2009-03-04

Indium phosphide is investigated using molecular dynamics (MD) simulations and density-functional theory calculations. MD simulations use a proposed effective interaction potential for InP fitted to a selected experimental dataset of properties. The potential consists of two- and three-body terms that represent atomic-size effects, charge-charge, charge-dipole and dipole-dipole interactions as well as covalent bond bending and stretching. Predictions are made for the elastic constants as a function of density and temperature, the generalized stacking fault energy and the low-index surface energies.

A Navier-Stokes phase-field crystal model for colloidal suspensions.

PubMed

Praetorius, Simon; Voigt, Axel

2015-04-21

We develop a fully continuous model for colloidal suspensions with hydrodynamic interactions. The Navier-Stokes Phase-Field Crystal model combines ideas of dynamic density functional theory with particulate flow approaches and is derived in detail and related to other dynamic density functional theory approaches with hydrodynamic interactions. The derived system is numerically solved using adaptive finite elements and is used to analyze colloidal crystallization in flowing environments demonstrating a strong coupling in both directions between the crystal shape and the flow field. We further validate the model against other computational approaches for particulate flow systems for various colloidal sedimentation problems.

Nonstationary Dynamics Data Analysis with Wavelet-SVD Filtering

NASA Technical Reports Server (NTRS)

Brenner, Marty; Groutage, Dale; Bessette, Denis (Technical Monitor)

2001-01-01

Nonstationary time-frequency analysis is used for identification and classification of aeroelastic and aeroservoelastic dynamics. Time-frequency multiscale wavelet processing generates discrete energy density distributions. The distributions are processed using the singular value decomposition (SVD). Discrete density functions derived from the SVD generate moments that detect the principal features in the data. The SVD standard basis vectors are applied and then compared with a transformed-SVD, or TSVD, which reduces the number of features into more compact energy density concentrations. Finally, from the feature extraction, wavelet-based modal parameter estimation is applied.

Multigrid based First-Principles Molecular Dynamics

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

Fattebert, Jean-Luc; Osei-Kuffuor, Daniel; Dunn, Ian

2017-06-01

MGmol ls a First-Principles Molecular Dynamics code. It relies on the Born-Oppenheimer approximation and models the electronic structure using Density Functional Theory, either LDA or PBE. Norm-conserving pseudopotentials are used to model atomic cores.

Learning the dynamics of objects by optimal functional interpolation.

PubMed

Ahn, Jong-Hoon; Kim, In Young

2012-09-01

Many areas of science and engineering rely on functional data and their numerical analysis. The need to analyze time-varying functional data raises the general problem of interpolation, that is, how to learn a smooth time evolution from a finite number of observations. Here, we introduce optimal functional interpolation (OFI), a numerical algorithm that interpolates functional data over time. Unlike the usual interpolation or learning algorithms, the OFI algorithm obeys the continuity equation, which describes the transport of some types of conserved quantities, and its implementation shows smooth, continuous flows of quantities. Without the need to take into account equations of motion such as the Navier-Stokes equation or the diffusion equation, OFI is capable of learning the dynamics of objects such as those represented by mass, image intensity, particle concentration, heat, spectral density, and probability density.

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

Escartín, J. M.; CNRS, UMR5152, F-31062 Toulouse Cedex; Theory of Condensed Matter Group, Cavendish Laboratory, University of Cambridge, J.J. Thomson Avenue, Cambridge CB3 0HE

Time-Dependent Density-Functional Theory (TDDFT) is a well-established theoretical approach to describe and understand irradiation processes in clusters and molecules. However, within the so-called adiabatic local density approximation (ALDA) to the exchange-correlation (xc) potential, TDDFT can show insufficiencies, particularly in violently dynamical processes. This is because within ALDA the xc potential is instantaneous and is a local functional of the density, which means that this approximation neglects memory effects and long-range effects. A way to go beyond ALDA is to use Time-Dependent Current-Density-Functional Theory (TDCDFT), in which the basic quantity is the current density rather than the density as in TDDFT.more » This has been shown to offer an adequate account of dissipation in the linear domain when the Vignale-Kohn (VK) functional is used. Here, we go beyond the linear regime and we explore this formulation in the time domain. In this case, the equations become very involved making the computation out of reach; we hence propose an approximation to the VK functional which allows us to calculate the dynamics in real time and at the same time to keep most of the physics described by the VK functional. We apply this formulation to the calculation of the time-dependent dipole moment of Ca, Mg and Na{sub 2}. Our results show trends similar to what was previously observed in model systems or within linear response. In the non-linear domain, our results show that relaxation times do not decrease with increasing deposited excitation energy, which sets some limitations to the practical use of TDCDFT in such a domain of excitations.« less

Dielectric properties of organic solvents from non-polarizable molecular dynamics simulation with electronic continuum model and density functional theory.

PubMed

Lee, Sanghun; Park, Sung Soo

2011-11-03

Dielectric constants of electrolytic organic solvents are calculated employing nonpolarizable Molecular Dynamics simulation with Electronic Continuum (MDEC) model and Density Functional Theory. The molecular polarizabilities are obtained by the B3LYP/6-311++G(d,p) level of theory to estimate high-frequency refractive indices while the densities and dipole moment fluctuations are computed using nonpolarizable MD simulations. The dielectric constants reproduced from these procedures are evaluated to provide a reliable approach for estimating the experimental data. An additional feature, two representative solvents which have similar molecular weights but are different dielectric properties, i.e., ethyl methyl carbonate and propylene carbonate, are compared using MD simulations and the distinctly different dielectric behaviors are observed at short times as well as at long times.

Fast and accurate quantum molecular dynamics of dense plasmas across temperature regimes

DOE PAGES

Sjostrom, Travis; Daligault, Jerome

2014-10-10

Here, we develop and implement a new quantum molecular dynamics approximation that allows fast and accurate simulations of dense plasmas from cold to hot conditions. The method is based on a carefully designed orbital-free implementation of density functional theory. The results for hydrogen and aluminum are in very good agreement with Kohn-Sham (orbital-based) density functional theory and path integral Monte Carlo calculations for microscopic features such as the electron density as well as the equation of state. The present approach does not scale with temperature and hence extends to higher temperatures than is accessible in the Kohn-Sham method and lowermore » temperatures than is accessible by path integral Monte Carlo calculations, while being significantly less computationally expensive than either of those two methods.« less

Phase diagram of two-dimensional hard rods from fundamental mixed measure density functional theory

NASA Astrophysics Data System (ADS)

Wittmann, René; Sitta, Christoph E.; Smallenburg, Frank; Löwen, Hartmut

2017-10-01

A density functional theory for the bulk phase diagram of two-dimensional orientable hard rods is proposed and tested against Monte Carlo computer simulation data. In detail, an explicit density functional is derived from fundamental mixed measure theory and freely minimized numerically for hard discorectangles. The phase diagram, which involves stable isotropic, nematic, smectic, and crystalline phases, is obtained and shows good agreement with the simulation data. Our functional is valid for a multicomponent mixture of hard particles with arbitrary convex shapes and provides a reliable starting point to explore various inhomogeneous situations of two-dimensional hard rods and their Brownian dynamics.

Assessing Density Functionals Using Many Body Theory for Hybrid Perovskites

NASA Astrophysics Data System (ADS)

Bokdam, Menno; Lahnsteiner, Jonathan; Ramberger, Benjamin; Schäfer, Tobias; Kresse, Georg

2017-10-01

Which density functional is the "best" for structure simulations of a particular material? A concise, first principles, approach to answer this question is presented. The random phase approximation (RPA)—an accurate many body theory—is used to evaluate various density functionals. To demonstrate and verify the method, we apply it to the hybrid perovskite MAPbI3 , a promising new solar cell material. The evaluation is done by first creating finite temperature ensembles for small supercells using RPA molecular dynamics, and then evaluating the variance between the RPA and various approximate density functionals for these ensembles. We find that, contrary to recent suggestions, van der Waals functionals do not improve the description of the material, whereas hybrid functionals and the strongly constrained appropriately normed (SCAN) density functional yield very good agreement with the RPA. Finally, our study shows that in the room temperature tetragonal phase of MAPbI3 , the molecules are preferentially parallel to the shorter lattice vectors but reorientation on ps time scales is still possible.

Influence of surface oxidation on ion dynamics and capacitance in porous and nonporous carbon electrodes

DOE PAGES

Dyatkin, Boris; Zhang, Yu; Mamontov, Eugene; ...

2016-04-07

Here, we investigate the influence of surface chemistry and ion confinement on capacitance and electrosorption dynamics of room-temperature ionic liquids (RTILs) in supercapacitors. Using air oxidation and vacuum annealing, we produced defunctionalized and oxygen-rich surfaces of carbide-derived carbons (CDCs) and graphene nanoplatelets (GNPs). While oxidized surfaces of porous CDCs improve capacitance and rate handling abilities of ions, defunctionalized nonporous GNPs improve charge storage densities on planar electrodes. Quasi-elastic neutron scattering (QENS) and inelastic neutron scattering (INS) probed the structure, dynamics, and orientation of RTIL ions confined in divergently functionalized pores. Oxidized, ionophilic surfaces draw ions closer to pore surfaces andmore » enhance potential-driven ion transport during electrosorption. Molecular dynamics (MD) simulations corroborated experimental data and demonstrated the significance of surface functional groups on ion orientations, accumulation densities, and capacitance.« less

Many-Body Theory of Pyrochlore Iridates and Related Materials

NASA Astrophysics Data System (ADS)

Wang, Runzhi

In this thesis we focus on two problems. First we propose a numerical method for generating optimized Wannier functions with desired properties. Second we perform the state of the art density functional plus dynamical mean-field calculations in pyrochlore iridates, to investigate the physics induced by the cooperation of spin-orbit coupling and electron correlation. We begin with the introduction for maximally localized Wannier functions and other related extensions. Then we describe the current research in the field of spin-orbit coupling and its interplay with correlation effects, followed by a brief introduction of the `hot' materials of iridates. Before the end of the introduction, we discuss the numerical methods employed in our work, including the density functional theory; dynamical mean-field theory and its combination with the exact diagonalization impurity solver. Then we propose our approach for constructing an optimized set of Wannier functions, which is a generalization of the functionality of the classic maximal localization method put forward by Marzari and Vanderbilt. Our work is motivated by the requirement of the effective description of the local subspace of the Hamiltonian by the beyond density functional theory methods. In extensions of density functional theory such as dynamical mean-field theory, one may want highly accurate description of particular local orbitals, including correct centers and symmetries; while the basis for the remaining degrees of freedom is unimportant. Therefore, we develop the selectively localized Wannier function approach which allows for a greater localization in the selected subset of Wannier functions and at the same time allows us to fix the centers and ensure the point symmetries. Applications in real materials are presented to demonstrate the power of our approach. Next we move to the investigation of pyrochlore iridates, focussing on the metal-insulator transition and material dependence in these compounds. We perform combined density functional plus dynamical mean-field calculations in Lu2Ir2O7, Y2Ir2O 7, Eu2Ir2O7, with spin-orbit coupling included and both single-site and cluster approximations appiled. A broad range of Weyl metal is predicted as the intervening phase in the metal-insulator transition. By comparing to experiments, we find that the single-site approximation fails to predict the gap values and substantial difference between the Y and Eu-compound, demonstrating the inadequacy of this approximation and indicating the key role played by the intersite effects. Finally, we provide a more accurate description of the vicinity of the metal-insulator and topological transitions implied by density functional plus cluster dynamical mean-field calculations of pyrochlore iridates. We find definitive evidence of the Weyl semimetal phase, the electronic structure of which can be approximately described as ``Weyl rings" with an extremely flat dispersion of one of the Weyl bands. This Weyl semimetal phase is further investigated by the k • p analysis fitting to the numerical results. We find that this unusual structure leads to interesting behavior in the optical conductivity including a Hall effect in the interband component, and to an enhanced susceptibility.

Role of the Pair Correlation Function in the Dynamical Transition Predicted by Mode Coupling Theory

NASA Astrophysics Data System (ADS)

Nandi, Manoj Kumar; Banerjee, Atreyee; Dasgupta, Chandan; Bhattacharyya, Sarika Maitra

2017-12-01

In a recent study, we have found that for a large number of systems the configurational entropy at the pair level Sc 2, which is primarily determined by the pair correlation function, vanishes at the dynamical transition temperature Tc. Thus, it appears that the information of the transition temperature is embedded in the structure of the liquid. In order to investigate this, we describe the dynamics of the system at the mean field level and, using the concepts of the dynamical density functional theory, show that the dynamical transition temperature depends only on the pair correlation function. Thus, this theory is similar in spirit to the microscopic mode coupling theory (MCT). However, unlike microscopic MCT, which predicts a very high transition temperature, the present theory predicts a transition temperature that is similar to Tc. This implies that the information of the dynamical transition temperature is embedded in the pair correlation function.

Lattice model for calcium dynamics

NASA Astrophysics Data System (ADS)

Guisoni, Nara; de Oliveira, Mario José

2005-06-01

We present a simplified lattice model to study calcium dynamics in the endoplasmic reticulum membrane. Calcium channels and calcium ions are placed in two interpenetrating square lattices which are connected in two ways: (i) via calcium release and (ii) because transitions between channel states are calcium dependent. The opening or closing of a channel is a stochastic process controlled by two functions which depend on the calcium density on the channel neighborhood. The model is studied through mean field calculations and simulations. We show that the critical behavior of the model changes drastically depending on the opening/closing functions. For certain choices of these functions, all channels are closed at very low and high calcium densities and the model presents one absorbing state.

Self-consistent Green's function embedding for advanced electronic structure methods based on a dynamical mean-field concept

NASA Astrophysics Data System (ADS)

Chibani, Wael; Ren, Xinguo; Scheffler, Matthias; Rinke, Patrick

2016-04-01

We present an embedding scheme for periodic systems that facilitates the treatment of the physically important part (here a unit cell or a supercell) with advanced electronic structure methods, that are computationally too expensive for periodic systems. The rest of the periodic system is treated with computationally less demanding approaches, e.g., Kohn-Sham density-functional theory, in a self-consistent manner. Our scheme is based on the concept of dynamical mean-field theory formulated in terms of Green's functions. Our real-space dynamical mean-field embedding scheme features two nested Dyson equations, one for the embedded cluster and another for the periodic surrounding. The total energy is computed from the resulting Green's functions. The performance of our scheme is demonstrated by treating the embedded region with hybrid functionals and many-body perturbation theory in the GW approach for simple bulk systems. The total energy and the density of states converge rapidly with respect to the computational parameters and approach their bulk limit with increasing cluster (i.e., computational supercell) size.

On an aggregation in birth-and-death stochastic dynamics

NASA Astrophysics Data System (ADS)

Finkelshtein, Dmitri; Kondratiev, Yuri; Kutoviy, Oleksandr; Zhizhina, Elena

2014-06-01

We consider birth-and-death stochastic dynamics of particle systems with attractive interaction. The heuristic generator of the dynamics has a constant birth rate and density-dependent decreasing death rate. The corresponding statistical dynamics is constructed. Using the Vlasov-type scaling we derive the limiting mesoscopic evolution and prove that this evolution propagates chaos. We study a nonlinear non-local kinetic equation for the first correlation function (density of population). The existence of uniformly bounded solutions as well as solutions growing inside of a bounded domain and expanding in the space are shown. These solutions describe two regimes in the mesoscopic system: regulation and aggregation.

Observation of dynamic atom-atom correlation in liquid helium in real space

DOE PAGES

Dmowski, W.; Diallo, S. O.; Lokshin, K.; ...

2017-05-04

Liquid 4He becomes superfluid and flows without resistance below temperature 2.17 K. Superfluidity has been a subject of intense studies and notable advances were made in elucidating the phenomenon by experiment and theory. Nevertheless, details of the microscopic state, including dynamic atom–atom correlations in the superfluid state, are not fully understood. Here using a technique of neutron dynamic pair-density function (DPDF) analysis we show that 4He atoms in the Bose–Einstein condensate have environment significantly different from uncondensed atoms, with the interatomic distance larger than the average by about 10%, whereas the average structure changes little through the superfluid transition. DPDFmore » peak not seen in the snap-shot pair-density function is found at 2.3 Å, and is interpreted in terms of atomic tunnelling. The real space picture of dynamic atom–atom correlations presented here reveal characteristics of atomic dynamics not recognized so far, compelling yet another look at the phenomenon.« less

Observation of dynamic atom-atom correlation in liquid helium in real space

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

Dmowski, W.; Diallo, S. O.; Lokshin, K.

Liquid 4He becomes superfluid and flows without resistance below temperature 2.17 K. Superfluidity has been a subject of intense studies and notable advances were made in elucidating the phenomenon by experiment and theory. Nevertheless, details of the microscopic state, including dynamic atom–atom correlations in the superfluid state, are not fully understood. Here using a technique of neutron dynamic pair-density function (DPDF) analysis we show that 4He atoms in the Bose–Einstein condensate have environment significantly different from uncondensed atoms, with the interatomic distance larger than the average by about 10%, whereas the average structure changes little through the superfluid transition. DPDFmore » peak not seen in the snap-shot pair-density function is found at 2.3 Å, and is interpreted in terms of atomic tunnelling. The real space picture of dynamic atom–atom correlations presented here reveal characteristics of atomic dynamics not recognized so far, compelling yet another look at the phenomenon.« less

Observation of dynamic atom-atom correlation in liquid helium in real space.

PubMed

Dmowski, W; Diallo, S O; Lokshin, K; Ehlers, G; Ferré, G; Boronat, J; Egami, T

2017-05-04

Liquid 4 He becomes superfluid and flows without resistance below temperature 2.17 K. Superfluidity has been a subject of intense studies and notable advances were made in elucidating the phenomenon by experiment and theory. Nevertheless, details of the microscopic state, including dynamic atom-atom correlations in the superfluid state, are not fully understood. Here using a technique of neutron dynamic pair-density function (DPDF) analysis we show that 4 He atoms in the Bose-Einstein condensate have environment significantly different from uncondensed atoms, with the interatomic distance larger than the average by about 10%, whereas the average structure changes little through the superfluid transition. DPDF peak not seen in the snap-shot pair-density function is found at 2.3 Å, and is interpreted in terms of atomic tunnelling. The real space picture of dynamic atom-atom correlations presented here reveal characteristics of atomic dynamics not recognized so far, compelling yet another look at the phenomenon.

Short-range density functional correlation within the restricted active space CI method

NASA Astrophysics Data System (ADS)

Casanova, David

2018-03-01

In the present work, I introduce a hybrid wave function-density functional theory electronic structure method based on the range separation of the electron-electron Coulomb operator in order to recover dynamic electron correlations missed in the restricted active space configuration interaction (RASCI) methodology. The working equations and the computational algorithm for the implementation of the new approach, i.e., RAS-srDFT, are presented, and the method is tested in the calculation of excitation energies of organic molecules. The good performance of the RASCI wave function in combination with different short-range exchange-correlation functionals in the computation of relative energies represents a quantitative improvement with respect to the RASCI results and paves the path for the development of RAS-srDFT as a promising scheme in the computation of the ground and excited states where nondynamic and dynamic electron correlations are important.

Density of states and dynamical crossover in a dense fluid revealed by exponential mode analysis of the velocity autocorrelation function

NASA Astrophysics Data System (ADS)

Bellissima, S.; Neumann, M.; Guarini, E.; Bafile, U.; Barocchi, F.

2017-01-01

Extending a preceding study of the velocity autocorrelation function (VAF) in a simulated Lennard-Jones fluid [Phys. Rev. E 92, 042166 (2015), 10.1103/PhysRevE.92.042166] to cover higher-density and lower-temperature states, we show that the recently demonstrated multiexponential expansion method allows for a full account and understanding of the basic dynamical processes encompassed by a fundamental quantity as the VAF. In particular, besides obtaining evidence of a persisting long-time tail, we assign specific and unambiguous physical meanings to groups of exponential modes related to the longitudinal and transverse collective dynamics, respectively. We have made this possible by consistently introducing the interpretation of the VAF frequency spectrum as a global density of states in fluids, generalizing a solid-state concept, and by giving to specific spectral components, obtained through the VAF exponential expansion, the corresponding meaning of partial densities of states relative to specific dynamical processes. The clear identification of a high-frequency oscillation of the VAF with the near-top excitation frequency in the dispersion curve of acoustic waves is a neat example of the power of the method. As for the transverse mode contribution, its analysis turns out to be particularly important, because the multiexponential expansion reveals a transition marking the onset of propagating excitations when the density is increased beyond a threshold value. While this finding agrees with the recent literature debating the issue of dynamical crossover boundaries, such as the one identified with the Frenkel line, we can add detailed information on the modes involved in this specific process in the domains of both time and frequency. This will help obtain a still missing full account of transverse dynamics, in both its nonpropagating and propagating aspects which are linked through dynamical transitions depending on both the thermodynamic states and the excitation wave vectors.

Functionally graded biomimetic energy absorption concept development for transportation systems.

DOT National Transportation Integrated Search

2014-02-01

Mechanics of a functionally graded cylinder subject to static or dynamic axial loading is considered, including a potential application as energy absorber. The mass density and stiffness are power functions of the radial coordinate as may be the case...

Surveillance system and method having an adaptive sequential probability fault detection test

NASA Technical Reports Server (NTRS)

Herzog, James P. (Inventor); Bickford, Randall L. (Inventor)

2005-01-01

System and method providing surveillance of an asset such as a process and/or apparatus by providing training and surveillance procedures that numerically fit a probability density function to an observed residual error signal distribution that is correlative to normal asset operation and then utilizes the fitted probability density function in a dynamic statistical hypothesis test for providing improved asset surveillance.

Surveillance system and method having an adaptive sequential probability fault detection test

NASA Technical Reports Server (NTRS)

Bickford, Randall L. (Inventor); Herzog, James P. (Inventor)

2006-01-01

System and method providing surveillance of an asset such as a process and/or apparatus by providing training and surveillance procedures that numerically fit a probability density function to an observed residual error signal distribution that is correlative to normal asset operation and then utilizes the fitted probability density function in a dynamic statistical hypothesis test for providing improved asset surveillance.

Surveillance System and Method having an Adaptive Sequential Probability Fault Detection Test

NASA Technical Reports Server (NTRS)

Bickford, Randall L. (Inventor); Herzog, James P. (Inventor)

2008-01-01

System and method providing surveillance of an asset such as a process and/or apparatus by providing training and surveillance procedures that numerically fit a probability density function to an observed residual error signal distribution that is correlative to normal asset operation and then utilizes the fitted probability density function in a dynamic statistical hypothesis test for providing improved asset surveillance.

Pressure effects on collective density fluctuations in water and protein solutions

PubMed Central

Russo, Daniela; Laloni, Alessio; Filabozzi, Alessandra; Heyden, Matthias

2017-01-01

Neutron Brillouin scattering and molecular dynamics simulations have been used to investigate protein hydration water density fluctuations as a function of pressure. Our results show significant differences between the pressure and density dependence of collective dynamics in bulk water and in concentrated protein solutions. Pressure-induced changes in the tetrahedral order of the water HB network have direct consequences for the high-frequency sound velocity and damping coefficients, which we find to be a sensitive probe for changes in the HB network structure as well as the wetting of biomolecular surfaces. PMID:29073065

Multiconfiguration Pair-Density Functional Theory.

PubMed

Li Manni, Giovanni; Carlson, Rebecca K; Luo, Sijie; Ma, Dongxia; Olsen, Jeppe; Truhlar, Donald G; Gagliardi, Laura

2014-09-09

We present a new theoretical framework, called Multiconfiguration Pair-Density Functional Theory (MC-PDFT), which combines multiconfigurational wave functions with a generalization of density functional theory (DFT). A multiconfigurational self-consistent-field (MCSCF) wave function with correct spin and space symmetry is used to compute the total electronic density, its gradient, the on-top pair density, and the kinetic and Coulomb contributions to the total electronic energy. We then use a functional of the total density, its gradient, and the on-top pair density to calculate the remaining part of the energy, which we call the on-top-density-functional energy in contrast to the exchange-correlation energy of Kohn-Sham DFT. Because the on-top pair density is an element of the two-particle density matrix, this goes beyond the Hohenberg-Kohn theorem that refers only to the one-particle density. To illustrate the theory, we obtain first approximations to the required new type of density functionals by translating conventional density functionals of the spin densities using a simple prescription, and we perform post-SCF density functional calculations using the total density, density gradient, and on-top pair density from the MCSCF calculations. Double counting of dynamic correlation or exchange does not occur because the MCSCF energy is not used. The theory is illustrated by applications to the bond energies and potential energy curves of H2, N2, F2, CaO, Cr2, and NiCl and the electronic excitation energies of Be, C, N, N(+), O, O(+), Sc(+), Mn, Co, Mo, Ru, N2, HCHO, C4H6, c-C5H6, and pyrazine. The method presented has a computational cost and scaling similar to MCSCF, but a quantitative accuracy, even with the present first approximations to the new types of density functionals, that is comparable to much more expensive multireference perturbation theory methods.

Light-front representation of chiral dynamics in peripheral transverse densities

DOE PAGES

Granados, Carlos G.; Weiss, Christian

2015-07-31

The nucleon's electromagnetic form factors are expressed in terms of the transverse densities of charge and magnetization at fixed light-front time. At peripheral transverse distances b = O(M_pi^{-1}) the densities are governed by chiral dynamics and can be calculated model-independently using chiral effective field theory (EFT). We represent the leading-order chiral EFT results for the peripheral transverse densities as overlap integrals of chiral light-front wave functions, describing the transition of the initial nucleon to soft pion-nucleon intermediate states and back. The new representation (a) explains the parametric order of the peripheral transverse densities; (b) establishes an inequality between the spin-independentmore » and -dependent densities; (c) exposes the role of pion orbital angular momentum in chiral dynamics; (d) reveals a large left-right asymmetry of the current in a transversely polarized nucleon and suggests a simple interpretation. The light-front representation enables a first-quantized, quantum-mechanical view of chiral dynamics that is fully relativistic and exactly equivalent to the second-quantized, field-theoretical formulation. It relates the charge and magnetization densities measured in low-energy elastic scattering to the generalized parton distributions probed in peripheral high-energy scattering processes. The method can be applied to nucleon form factors of other operators, e.g. the energy-momentum tensor.« less

Electron correlation by polarization of interacting densities

NASA Astrophysics Data System (ADS)

Whitten, Jerry L.

2017-02-01

Coulomb interactions that occur in electronic structure calculations are correlated by allowing basis function components of the interacting densities to polarize dynamically, thereby reducing the magnitude of the interaction. Exchange integrals of molecular orbitals are not correlated. The modified Coulomb interactions are used in single-determinant or configuration interaction calculations. The objective is to account for dynamical correlation effects without explicitly introducing higher spherical harmonic functions into the molecular orbital basis. Molecular orbital densities are decomposed into a distribution of spherical components that conserve the charge and each of the interacting components is considered as a two-electron wavefunction embedded in the system acted on by an average field Hamiltonian plus r12-1. A method of avoiding redundancy is described. Applications to atoms, negative ions, and molecules representing different types of bonding and spin states are discussed.

Phonon and magnetic structure in δ-plutonium from density-functional theory

DOE PAGES

Söderlind, Per; Zhou, F.; Landa, A.; ...

2015-10-30

We present phonon properties of plutonium metal obtained from a combination of density-functional-theory (DFT) electronic structure and the recently developed compressive sensing lattice dynamics (CSLD). The CSLD model is here trained on DFT total energies of several hundreds of quasi-random atomic configurations for best possible accuracy of the phonon properties. The calculated phonon dispersions compare better with experiment than earlier results obtained from dynamical mean-field theory. The density-functional model of the electronic structure consists of disordered magnetic moments with all relativistic effects and explicit orbital-orbital correlations. The magnetic disorder is approximated in two ways: (i) a special quasi-random structure andmore » (ii) the disordered-local-moment (DLM) method within the coherent potential approximation. Magnetism in plutonium has been debated intensely, However, the present magnetic approach for plutonium is validated by the close agreement between the predicted magnetic form factor and that of recent neutron-scattering experiments.« less

Formulation of state projected centroid molecular dynamics: Microcanonical ensemble and connection to the Wigner distribution.

PubMed

Orr, Lindsay; Hernández de la Peña, Lisandro; Roy, Pierre-Nicholas

2017-06-07

A derivation of quantum statistical mechanics based on the concept of a Feynman path centroid is presented for the case of generalized density operators using the projected density operator formalism of Blinov and Roy [J. Chem. Phys. 115, 7822-7831 (2001)]. The resulting centroid densities, centroid symbols, and centroid correlation functions are formulated and analyzed in the context of the canonical equilibrium picture of Jang and Voth [J. Chem. Phys. 111, 2357-2370 (1999)]. The case where the density operator projects onto a particular energy eigenstate of the system is discussed, and it is shown that one can extract microcanonical dynamical information from double Kubo transformed correlation functions. It is also shown that the proposed projection operator approach can be used to formally connect the centroid and Wigner phase-space distributions in the zero reciprocal temperature β limit. A Centroid Molecular Dynamics (CMD) approximation to the state-projected exact quantum dynamics is proposed and proven to be exact in the harmonic limit. The state projected CMD method is also tested numerically for a quartic oscillator and a double-well potential and found to be more accurate than canonical CMD. In the case of a ground state projection, this method can resolve tunnelling splittings of the double well problem in the higher barrier regime where canonical CMD fails. Finally, the state-projected CMD framework is cast in a path integral form.

Formulation of state projected centroid molecular dynamics: Microcanonical ensemble and connection to the Wigner distribution

NASA Astrophysics Data System (ADS)

Orr, Lindsay; Hernández de la Peña, Lisandro; Roy, Pierre-Nicholas

2017-06-01

A derivation of quantum statistical mechanics based on the concept of a Feynman path centroid is presented for the case of generalized density operators using the projected density operator formalism of Blinov and Roy [J. Chem. Phys. 115, 7822-7831 (2001)]. The resulting centroid densities, centroid symbols, and centroid correlation functions are formulated and analyzed in the context of the canonical equilibrium picture of Jang and Voth [J. Chem. Phys. 111, 2357-2370 (1999)]. The case where the density operator projects onto a particular energy eigenstate of the system is discussed, and it is shown that one can extract microcanonical dynamical information from double Kubo transformed correlation functions. It is also shown that the proposed projection operator approach can be used to formally connect the centroid and Wigner phase-space distributions in the zero reciprocal temperature β limit. A Centroid Molecular Dynamics (CMD) approximation to the state-projected exact quantum dynamics is proposed and proven to be exact in the harmonic limit. The state projected CMD method is also tested numerically for a quartic oscillator and a double-well potential and found to be more accurate than canonical CMD. In the case of a ground state projection, this method can resolve tunnelling splittings of the double well problem in the higher barrier regime where canonical CMD fails. Finally, the state-projected CMD framework is cast in a path integral form.

Nanoscale hydrodynamics near solids

NASA Astrophysics Data System (ADS)

Camargo, Diego; de la Torre, J. A.; Duque-Zumajo, D.; Español, Pep; Delgado-Buscalioni, Rafael; Chejne, Farid

2018-02-01

Density Functional Theory (DFT) is a successful and well-established theory for the study of the structure of simple and complex fluids at equilibrium. The theory has been generalized to dynamical situations when the underlying dynamics is diffusive as in, for example, colloidal systems. However, there is no such a clear foundation for Dynamic DFT (DDFT) for the case of simple fluids in contact with solid walls. In this work, we derive DDFT for simple fluids by including not only the mass density field but also the momentum density field of the fluid. The standard projection operator method based on the Kawasaki-Gunton operator is used for deriving the equations for the average value of these fields. The solid is described as featureless under the assumption that all the internal degrees of freedom of the solid relax much faster than those of the fluid (solid elasticity is irrelevant). The fluid moves according to a set of non-local hydrodynamic equations that include explicitly the forces due to the solid. These forces are of two types, reversible forces emerging from the free energy density functional, and accounting for impenetrability of the solid, and irreversible forces that involve the velocity of both the fluid and the solid. These forces are localized in the vicinity of the solid surface. The resulting hydrodynamic equations should allow one to study dynamical regimes of simple fluids in contact with solid objects in isothermal situations.

Modeling ultrafast solvated electronic dynamics using time-dependent density functional theory and polarizable continuum model.

PubMed

Liang, Wenkel; Chapman, Craig T; Ding, Feizhi; Li, Xiaosong

2012-03-01

A first-principles solvated electronic dynamics method is introduced. Solvent electronic degrees of freedom are coupled to the time-dependent electronic density of a solute molecule by means of the implicit reaction field method, and the entire electronic system is propagated in time. This real-time time-dependent approach, incorporating the polarizable continuum solvation model, is shown to be very effective in describing the dynamical solvation effect in the charge transfer process and yields a consistent absorption spectrum in comparison to the conventional linear response results in solution. © 2012 American Chemical Society

Assessment of Real-Time Time-Dependent Density Functional Theory (RT-TDDFT) in Radiation Chemistry: Ionized Water Dimer.

PubMed

Chalabala, Jan; Uhlig, Frank; Slavíček, Petr

2018-03-29

Ionization in the condensed phase and molecular clusters leads to a complicated chain of processes with coupled electron-nuclear dynamics. It is difficult to describe such dynamics with conventional nonadiabatic molecular dynamics schemes since the number of states swiftly increases as the molecular system grows. It is therefore attractive to use a direct electron and nuclear propagation such as the real-time time-dependent density functional theory (RT-TDDFT). Here we report a RT-TDDFT benchmark study on simulations of singly and doubly ionized states of a water monomer and dimer as a prototype for more complex processes in a condensed phase. We employed the RT-TDDFT based Ehrenfest molecular dynamics with a generalized gradient approximate (GGA) functional and compared it with wave-function-based surface hopping (SH) simulations. We found that the initial dynamics of a singly HOMO ionized water dimer is similar for both the RT-TDDFT/GGA and the SH simulations but leads to completely different reaction channels on a longer time scale. This failure is attributed to the self-interaction error in the GGA functionals and it can be avoided by using hybrid functionals with large fraction of exact exchange (represented here by the BHandHLYP functional). The simulations of doubly ionized states are reasonably described already at the GGA level. This suggests that the RT-TDDFT/GGA method could describe processes following the autoionization processes such as Auger emission, while its applicability to more complex processes such as intermolecular Coulombic decay remains limited.

Spherical harmonics analysis of surface density fluctuations of spherical ionic SDS and nonionic C12E8 micelles: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Yoshii, Noriyuki; Nimura, Yuki; Fujimoto, Kazushi; Okazaki, Susumu

2017-07-01

The surface structure and its fluctuation of spherical micelles were investigated using a series of density correlation functions newly defined by spherical harmonics and Legendre polynomials based on the molecular dynamics calculations. To investigate the influence of head-group charges on the micelle surface structure, ionic sodium dodecyl sulfate and nonionic octaethyleneglycol monododecylether (C12E8) micelles were investigated as model systems. Large-scale density fluctuations were observed for both micelles in the calculated surface static structure factor. The area compressibility of the micelle surface evaluated by the surface static structure factor was tens-of-times larger than a typical value of a lipid membrane surface. The structural relaxation time, which was evaluated from the surface intermediate scattering function, indicates that the relaxation mechanism of the long-range surface structure can be well described by the hydrostatic approximation. The density fluctuation on the two-dimensional micelle surface has similar characteristics to that of three-dimensional fluids near the critical point.

Spherical harmonics analysis of surface density fluctuations of spherical ionic SDS and nonionic C12E8 micelles: A molecular dynamics study.

PubMed

Yoshii, Noriyuki; Nimura, Yuki; Fujimoto, Kazushi; Okazaki, Susumu

2017-07-21

The surface structure and its fluctuation of spherical micelles were investigated using a series of density correlation functions newly defined by spherical harmonics and Legendre polynomials based on the molecular dynamics calculations. To investigate the influence of head-group charges on the micelle surface structure, ionic sodium dodecyl sulfate and nonionic octaethyleneglycol monododecylether (C 12 E 8 ) micelles were investigated as model systems. Large-scale density fluctuations were observed for both micelles in the calculated surface static structure factor. The area compressibility of the micelle surface evaluated by the surface static structure factor was tens-of-times larger than a typical value of a lipid membrane surface. The structural relaxation time, which was evaluated from the surface intermediate scattering function, indicates that the relaxation mechanism of the long-range surface structure can be well described by the hydrostatic approximation. The density fluctuation on the two-dimensional micelle surface has similar characteristics to that of three-dimensional fluids near the critical point.

Simplicity of condensed matter at its core: generic definition of a Roskilde-simple system.

PubMed

Schrøder, Thomas B; Dyre, Jeppe C

2014-11-28

The isomorph theory is reformulated by defining Roskilde-simple systems by the property that the order of the potential energies of configurations at one density is maintained when these are scaled uniformly to a different density. If the potential energy as a function of all particle coordinates is denoted by U(R), this requirement translates into U(Ra) < U(Rb) ⇒ U(λRa) < U(λRb). Isomorphs remain curves in the thermodynamic phase diagram along which structure, dynamics, and excess entropy are invariant, implying that the phase diagram is effectively one-dimensional with respect to many reduced-unit properties. In contrast to the original formulation of the isomorph theory, however, the density-scaling exponent is not exclusively a function of density and the isochoric heat capacity is not an exact isomorph invariant. A prediction is given for the latter quantity's variation along the isomorphs. Molecular dynamics simulations of the Lennard-Jones and Lennard-Jones Gaussian systems validate the new approach.

The effect of cross linking density on the mechanical properties and structure of the epoxy polymers: molecular dynamics simulation.

PubMed

Shokuhfar, Ali; Arab, Behrouz

2013-09-01

Recently, great attention has been focused on using epoxy polymers in different fields such as aerospace, automotive, biotechnology, and electronics, owing to their superior properties. In this study, the classical molecular dynamics (MD) was used to simulate the cross linking of diglycidyl ether of bisphenol-A (DGEBA) with diethylenetriamine (DETA) curing agent, and to study the behavior of resulted epoxy polymer with different conversion rates. The constant-strain (static) approach was then applied to calculate the mechanical properties (Bulk, shear and Young's moduli, elastic stiffness constants, and Poisson's ratio) of the uncured and cross-linked systems. Estimated material properties were found to be in good agreement with experimental observations. Moreover, the dependency of mechanical properties on the cross linking density was investigated and revealed improvements in the mechanical properties with increasing the cross linking density. The radial distribution function (RDF) was also used to study the evolution of local structures of the simulated systems as a function of cross linking density.

Molecular dynamics simulation of polyacrylamides in potassium montmorillonite clay hydrates

NASA Astrophysics Data System (ADS)

Zhang, Junfang; Rivero, Mayela; Choi, S. K.

2007-02-01

We present molecular dynamics simulation results for polyacrylamide in potassium montmorillonite clay-aqueous systems. Interlayer molecular structure and dynamics properties are investigated. The number density profile, radial distribution function, root-mean-square deviation (RMSD), mean-square displacement (MSD) and diffusion coefficient are reported. The calculations are conducted in constant NVT ensembles, at T = 300 K and with layer spacing of 40 Å. Our simulation results showed that polyacrylamides had little impact on the structure of interlayer water. Density profiles and radial distribution function indicated that hydration shells were formed. In the presence of polyacrylamides more potassium counterions move close to the clay surface while water molecules move away, indicating that potassium counterions are hydrated to a lesser extent than the system in which no polyacrylamides were added. The diffusion coefficients for potassium and water decreased when polyacrylamides were added.

Encircling the dark: constraining dark energy via cosmic density in spheres

NASA Astrophysics Data System (ADS)

Codis, S.; Pichon, C.; Bernardeau, F.; Uhlemann, C.; Prunet, S.

2016-08-01

The recently published analytic probability density function for the mildly non-linear cosmic density field within spherical cells is used to build a simple but accurate maximum likelihood estimate for the redshift evolution of the variance of the density, which, as expected, is shown to have smaller relative error than the sample variance. This estimator provides a competitive probe for the equation of state of dark energy, reaching a few per cent accuracy on wp and wa for a Euclid-like survey. The corresponding likelihood function can take into account the configuration of the cells via their relative separations. A code to compute one-cell-density probability density functions for arbitrary initial power spectrum, top-hat smoothing and various spherical-collapse dynamics is made available online, so as to provide straightforward means of testing the effect of alternative dark energy models and initial power spectra on the low-redshift matter distribution.

An Optimization Principle for Deriving Nonequilibrium Statistical Models of Hamiltonian Dynamics

NASA Astrophysics Data System (ADS)

Turkington, Bruce

2013-08-01

A general method for deriving closed reduced models of Hamiltonian dynamical systems is developed using techniques from optimization and statistical estimation. Given a vector of resolved variables, selected to describe the macroscopic state of the system, a family of quasi-equilibrium probability densities on phase space corresponding to the resolved variables is employed as a statistical model, and the evolution of the mean resolved vector is estimated by optimizing over paths of these densities. Specifically, a cost function is constructed to quantify the lack-of-fit to the microscopic dynamics of any feasible path of densities from the statistical model; it is an ensemble-averaged, weighted, squared-norm of the residual that results from submitting the path of densities to the Liouville equation. The path that minimizes the time integral of the cost function determines the best-fit evolution of the mean resolved vector. The closed reduced equations satisfied by the optimal path are derived by Hamilton-Jacobi theory. When expressed in terms of the macroscopic variables, these equations have the generic structure of governing equations for nonequilibrium thermodynamics. In particular, the value function for the optimization principle coincides with the dissipation potential that defines the relation between thermodynamic forces and fluxes. The adjustable closure parameters in the best-fit reduced equations depend explicitly on the arbitrary weights that enter into the lack-of-fit cost function. Two particular model reductions are outlined to illustrate the general method. In each example the set of weights in the optimization principle contracts into a single effective closure parameter.

Three pillars for achieving quantum mechanical molecular dynamics simulations of huge systems: Divide-and-conquer, density-functional tight-binding, and massively parallel computation.

PubMed

Nishizawa, Hiroaki; Nishimura, Yoshifumi; Kobayashi, Masato; Irle, Stephan; Nakai, Hiromi

2016-08-05

The linear-scaling divide-and-conquer (DC) quantum chemical methodology is applied to the density-functional tight-binding (DFTB) theory to develop a massively parallel program that achieves on-the-fly molecular reaction dynamics simulations of huge systems from scratch. The functions to perform large scale geometry optimization and molecular dynamics with DC-DFTB potential energy surface are implemented to the program called DC-DFTB-K. A novel interpolation-based algorithm is developed for parallelizing the determination of the Fermi level in the DC method. The performance of the DC-DFTB-K program is assessed using a laboratory computer and the K computer. Numerical tests show the high efficiency of the DC-DFTB-K program, a single-point energy gradient calculation of a one-million-atom system is completed within 60 s using 7290 nodes of the K computer. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Scaling within the spectral function approach

NASA Astrophysics Data System (ADS)

Sobczyk, J. E.; Rocco, N.; Lovato, A.; Nieves, J.

2018-03-01

Scaling features of the nuclear electromagnetic response functions unveil aspects of nuclear dynamics that are crucial for interpreting neutrino- and electron-scattering data. In the large momentum-transfer regime, the nucleon-density response function defines a universal scaling function, which is independent of the nature of the probe. In this work, we analyze the nucleon-density response function of 12C, neglecting collective excitations. We employ particle and hole spectral functions obtained within two distinct many-body methods, both widely used to describe electroweak reactions in nuclei. We show that the two approaches provide compatible nucleon-density scaling functions that for large momentum transfers satisfy first-kind scaling. Both methods yield scaling functions characterized by an asymmetric shape, although less pronounced than that of experimental scaling functions. This asymmetry, only mildly affected by final state interactions, is mostly due to nucleon-nucleon correlations, encoded in the continuum component of the hole spectral function.

Tunable non-interacting free-energy functionals: development and applications to low-density aluminum

NASA Astrophysics Data System (ADS)

Trickey, Samuel; Karasiev, Valentin

We introduce the concept of tunable orbital-free non-interacting free-energy density functionals and present a generalized gradient approximation (GGA) with a subset of parameters defined from constraints and a few free parameters. Those free parameters are tuned to reproduce reference Kohn-Sham (KS) static-lattice pressures for Al at T=8 kK for bulk densities between 0.6 and 2 g/cm3. The tuned functional then is used in OF molecular dynamics (MD) simulations for Al with densities between 0.1 and 2 g/cm3 and T between 6 and 50 kK to calculate the equation of state and generate configurations for electrical conductivity calculations. The tunable functional produces accurate results. Computationally it is very effective especially at elevated temperature. Kohn-Shiam calculations for such low densities are affordable only up to T=10 kK, while other OF approximations, including two-point functionals, fail badly in that regime. Work supported by US DoE Grant DE-SC0002139.

Large-Scale Hybrid Density Functional Theory Calculations in the Condensed-Phase: Ab Initio Molecular Dynamics in the Isobaric-Isothermal Ensemble

NASA Astrophysics Data System (ADS)

Ko, Hsin-Yu; Santra, Biswajit; Distasio, Robert A., Jr.; Wu, Xifan; Car, Roberto

Hybrid functionals are known to alleviate the self-interaction error in density functional theory (DFT) and provide a more accurate description of the electronic structure of molecules and materials. However, hybrid DFT in the condensed-phase has a prohibitively high associated computational cost which limits their applicability to large systems of interest. In this work, we present a general-purpose order(N) implementation of hybrid DFT in the condensed-phase using Maximally localized Wannier function; this implementation is optimized for massively parallel computing architectures. This algorithm is used to perform large-scale ab initio molecular dynamics simulations of liquid water, ice, and aqueous ionic solutions. We have performed simulations in the isothermal-isobaric ensemble to quantify the effects of exact exchange on the equilibrium density properties of water at different thermodynamic conditions. We find that the anomalous density difference between ice I h and liquid water at ambient conditions as well as the enthalpy differences between ice I h, II, and III phases at the experimental triple point (238 K and 20 Kbar) are significantly improved using hybrid DFT over previous estimates using the lower rungs of DFT This work has been supported by the Department of Energy under Grants No. DE-FG02-05ER46201 and DE-SC0008626.

Diffusive dynamics during the high-to-low density transition in amorphous ice

DOE PAGES

Perakis, Fivos; Amann-Winkel, Katrin; Lehmkuhler, Felix; ...

2017-06-26

Water exists in high- and low-density amorphous ice forms (HDA and LDA), which could correspond to the glassy states of high- (HDL) and low-density liquid (LDL) in the metastable part of the phase diagram. However, the nature of both the glass transition and the high-to-low-density transition are debated and new experimental evidence is needed. Here we combine wide-angle X-ray scattering (WAXS) with X-ray photon-correlation spectroscopy (XPCS) in the small-angle X-ray scattering (SAXS) geometry to probe both the structural and dynamical properties during the high-to-low-density transition in amorphous ice at 1 bar. By analyzing the structure factor and the radial distributionmore » function, the coexistence of two structurally distinct domains is observed at T = 125 K. XPCS probes the dynamics in momentum space, which in the SAXS geometry reflects structural relaxation on the nanometer length scale. The dynamics of HDA are characterized by a slow component with a large time constant, arising from viscoelastic relaxation and stress release from nanometer-sized heterogeneities. Above 110 K a faster, strongly temperature-dependent component appears, with momentum transfer dependence pointing toward nanoscale diffusion. This dynamical component slows down after transition into the low-density form at 130 K, but remains diffusive. In conclusion, the diffusive character of both the high- and low-density forms is discussed among different interpretations and the results are most consistent with the hypothesis of a liquid–liquid transition in the ultraviscous regime.« less

Diffusive dynamics during the high-to-low density transition in amorphous ice

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

Perakis, Fivos; Amann-Winkel, Katrin; Lehmkuhler, Felix

Water exists in high- and low-density amorphous ice forms (HDA and LDA), which could correspond to the glassy states of high- (HDL) and low-density liquid (LDL) in the metastable part of the phase diagram. However, the nature of both the glass transition and the high-to-low-density transition are debated and new experimental evidence is needed. Here we combine wide-angle X-ray scattering (WAXS) with X-ray photon-correlation spectroscopy (XPCS) in the small-angle X-ray scattering (SAXS) geometry to probe both the structural and dynamical properties during the high-to-low-density transition in amorphous ice at 1 bar. By analyzing the structure factor and the radial distributionmore » function, the coexistence of two structurally distinct domains is observed at T = 125 K. XPCS probes the dynamics in momentum space, which in the SAXS geometry reflects structural relaxation on the nanometer length scale. The dynamics of HDA are characterized by a slow component with a large time constant, arising from viscoelastic relaxation and stress release from nanometer-sized heterogeneities. Above 110 K a faster, strongly temperature-dependent component appears, with momentum transfer dependence pointing toward nanoscale diffusion. This dynamical component slows down after transition into the low-density form at 130 K, but remains diffusive. In conclusion, the diffusive character of both the high- and low-density forms is discussed among different interpretations and the results are most consistent with the hypothesis of a liquid–liquid transition in the ultraviscous regime.« less

Diffusive dynamics during the high-to-low density transition in amorphous ice

NASA Astrophysics Data System (ADS)

Perakis, Fivos; Amann-Winkel, Katrin; Lehmkühler, Felix; Sprung, Michael; Mariedahl, Daniel; Sellberg, Jonas A.; Pathak, Harshad; Späh, Alexander; Cavalca, Filippo; Schlesinger, Daniel; Ricci, Alessandro; Jain, Avni; Massani, Bernhard; Aubree, Flora; Benmore, Chris J.; Loerting, Thomas; Grübel, Gerhard; Pettersson, Lars G. M.; Nilsson, Anders

2017-08-01

Water exists in high- and low-density amorphous ice forms (HDA and LDA), which could correspond to the glassy states of high- (HDL) and low-density liquid (LDL) in the metastable part of the phase diagram. However, the nature of both the glass transition and the high-to-low-density transition are debated and new experimental evidence is needed. Here we combine wide-angle X-ray scattering (WAXS) with X-ray photon-correlation spectroscopy (XPCS) in the small-angle X-ray scattering (SAXS) geometry to probe both the structural and dynamical properties during the high-to-low-density transition in amorphous ice at 1 bar. By analyzing the structure factor and the radial distribution function, the coexistence of two structurally distinct domains is observed at T = 125 K. XPCS probes the dynamics in momentum space, which in the SAXS geometry reflects structural relaxation on the nanometer length scale. The dynamics of HDA are characterized by a slow component with a large time constant, arising from viscoelastic relaxation and stress release from nanometer-sized heterogeneities. Above 110 K a faster, strongly temperature-dependent component appears, with momentum transfer dependence pointing toward nanoscale diffusion. This dynamical component slows down after transition into the low-density form at 130 K, but remains diffusive. The diffusive character of both the high- and low-density forms is discussed among different interpretations and the results are most consistent with the hypothesis of a liquid-liquid transition in the ultraviscous regime.

A consumer-resource approach to the density-dependent population dynamics of mutualism.

PubMed

Holland, J Nathaniel; DeAngelis, Donald L

2010-05-01

Like predation and competition, mutualism is now recognized as a consumer-resource (C-R) interaction, including, in particular, bi-directional (e.g., coral, plant-mycorrhizae) and uni-directional (e.g., ant-plant defense, plant-pollinator) C-R mutualisms. Here, we develop general theory for the density-dependent population dynamics of mutualism based on the C-R mechanism of interspecific interaction. To test the influence of C-R interactions on the dynamics and stability of bi- and uni-directional C-R mutualisms, we developed simple models that link consumer functional response of one mutualistic species with the resources supplied by another. Phase-plane analyses show that the ecological dynamics of C-R mutualisms are stable in general. Most transient behavior leads to an equilibrium of mutualistic coexistence, at which both species densities are greater than in the absence of interactions. However, due to the basic nature of C-R interactions, certain density-dependent conditions can lead to C-R dynamics characteristic of predator-prey interactions, in which one species overexploits and causes the other to go extinct. Consistent with empirical phenomena, these results suggest that the C-R interaction can provide a broad mechanism for understanding density-dependent population dynamics of mutualism. By unifying predation, competition, and mutualism under the common ecological framework of consumer-resource theory, we may also gain a better understanding of the universal features of interspecific interactions in general.

A consumer-resource approach to the density-dependent population dynamics of mutualism

USGS Publications Warehouse

Holland, J. Nathaniel; DeAngelis, Donald L.

2010-01-01

Like predation and competition, mutualism is now recognized as a consumer resource (C-R) interaction, including, in particular, bi-directional (e.g., coral, plant- mycorrhizae) and uni-directional (e.g., ant-plant defense, plant-pollinator) C-R mutualisms. Here, we develop general theory for the density-dependent population dynamics of mutualism based on the C-R mechanism of interspecific interaction. To test the influence of C-R interactions on the dynamics and stability of bi- and uni-directional C-R mutualisms, we developed simple models that link consumer functional response of one mutualistic species with the resources supplied by another. Phase-plane analyses show that the ecological dynamics of C-R mutualisms are stable in general. Most transient behavior leads to an equilibrium of mutualistic coexistence, at which both species densities are greater than in the absence of interactions. However, due to the basic nature of C-R interactions, certain density-dependent conditions can lead to C-R dynamics characteristic of predator-prey interactions, in which one species overexploits and causes the other to go extinct. Consistent with empirical phenomena, these results suggest that the C-R interaction can provide a broad mechanism for understanding density-dependent population dynamics of mutualism. By unifying predation, competition, and mutualism under the common ecological framework of consumer-resource theory, we may also gain a better understanding of the universal features of interspecific interactions in general.

Multiconfiguration pair-density functional theory: barrier heights and main group and transition metal energetics.

PubMed

Carlson, Rebecca K; Li Manni, Giovanni; Sonnenberger, Andrew L; Truhlar, Donald G; Gagliardi, Laura

2015-01-13

Kohn-Sham density functional theory, resting on the representation of the electronic density and kinetic energy by a single Slater determinant, has revolutionized chemistry, but for open-shell systems, the Kohn-Sham Slater determinant has the wrong symmetry properties as compared to an accurate wave function. We have recently proposed a theory, called multiconfiguration pair-density functional theory (MC-PDFT), in which the electronic kinetic energy and classical Coulomb energy are calculated from a multiconfiguration wave function with the correct symmetry properties, and the rest of the energy is calculated from a density functional, called the on-top density functional, that depends on the density and the on-top pair density calculated from this wave function. We also proposed a simple way to approximate the on-top density functional by translation of Kohn-Sham exchange-correlation functionals. The method is much less expensive than other post-SCF methods for calculating the dynamical correlation energy starting with a multiconfiguration self-consistent-field wave function as the reference wave function, and initial tests of the theory were quite encouraging. Here, we provide a broader test of the theory by applying it to bond energies of main-group molecules and transition metal complexes, barrier heights and reaction energies for diverse chemical reactions, proton affinities, and the water dimerization energy. Averaged over 56 data points, the mean unsigned error is 3.2 kcal/mol for MC-PDFT, as compared to 6.9 kcal/mol for Kohn-Sham theory with a comparable density functional. MC-PDFT is more accurate on average than complete active space second-order perturbation theory (CASPT2) for main-group small-molecule bond energies, alkyl bond dissociation energies, transition-metal-ligand bond energies, proton affinities, and the water dimerization energy.

AB INITIO Molecular Dynamics Simulations of Water Under Static and Shock Compressed Conditions

NASA Astrophysics Data System (ADS)

Goldman, Nir; Fried, Laurence E.; Mundy, Christopher J.; Kuo, I.-F. William; Curioni, Alessandro; Reed, Evan J.

2007-12-01

We report herein a series of ab initio simulations of water under both static and shocked conditions. We have calculated the coherent x-ray scattering intensity of several phases of water under high pressure, using ab initio Density Functional Theory (DFT). We provide new atomic scattering form factors for water at extreme conditions, which take into account frequently neglected changes in ionic charge and electron delocalization. We have also simulated liquid water undergoing shock loading of velocities from 5-11 km/s using the Multi-Scale Shock Technique (MSST). We show that Density Functional Theory (DFT) molecular dynamics results compare extremely well to experiments on the water shock Hugoniot.

Exciton recombination dynamics in CdSe nanowires: bimolecular to three-carrier Auger kinetics.

PubMed

Robel, István; Bunker, Bruce A; Kamat, Prashant V; Kuno, Masaru

2006-07-01

Ultrafast relaxation dynamics of charge carriers in CdSe quantum wires with diameters between 6 and 8 nm are studied as a function of carrier density. At high electron-hole pair densities above 10(19) cm(-3) the dominant process for carrier cooling is the "bimolecular" Auger recombination of one-dimensional (1D) excitons. However, below this excitation level an unexpected transition from a bimolecular (exciton-exciton) to a three-carrier Auger relaxation mechanism occurs. Thus, depending on excitation intensity, electron-hole pair relaxation dynamics in the nanowires exhibit either 1D or 0D (quantum dot) character. This dual nature of the recovery kinetics defines an optimal intensity for achieving optical gain in solution-grown nanowires given the different carrier-density-dependent scaling of relaxation rates in either regime.

Measurements of observables during detonator function

NASA Astrophysics Data System (ADS)

Smilowitz, Laura; Henson, Bryan; Remelius, Dennis

Thermal explosion and detonation are two phenomena which can both occur as the response of explosives to thermal or mechanical insults. Thermal explosion is typically considered in the safety envelope and detonation is considered in the performance regime of explosive behavior. However, the two regimes are tied together by a phenomenon called deflagration to detonation transition (DDT). In this talk, I will discuss experiments on commercial detonators aimed at understanding the mechanism for energy release during detonator function. Diagnostic development towards measuring temperature, pressure, and density during the extreme conditions and time scales of detonation will be discussed. Our current ability to perform table-top dynamic radiography on functioning detonators will be described. Dynamic measurements of temperature, pressure, and density will be shown and discussion of the function of a detonator will be given in terms of our current understanding of deflagration, detonation, and the transition between the two.

Quantum mechanical/molecular mechanical/continuum style solvation model: time-dependent density functional theory.

PubMed

Thellamurege, Nandun M; Cui, Fengchao; Li, Hui

2013-08-28

A combined quantum mechanical/molecular mechanical/continuum (QM/MMpol/C) style method is developed for time-dependent density functional theory (TDDFT, including long-range corrected TDDFT) method, induced dipole polarizable force field, and induced surface charge continuum model. Induced dipoles and induced charges are included in the TDDFT equations to solve for the transition energies, relaxed density, and transition density. Analytic gradient is derived and implemented for geometry optimization and molecular dynamics simulation. QM/MMpol/C style DFT and TDDFT methods are used to study the hydrogen bonding of the photoactive yellow protein chromopore in ground state and excited state.

Explicit densities of multidimensional ballistic Lévy walks.

PubMed

Magdziarz, Marcin; Zorawik, Tomasz

2016-08-01

Lévy walks have proved to be useful models of stochastic dynamics with a number of applications in the modeling of real-life phenomena. In this paper we derive explicit formulas for densities of the two- (2D) and three-dimensional (3D) ballistic Lévy walks, which are most important in applications. It turns out that in the 3D case the densities are given by elementary functions. The densities of the 2D Lévy walks are expressed in terms of hypergeometric functions and the right-side Riemann-Liouville fractional derivative, which allows us to efficiently evaluate them numerically. The theoretical results agree perfectly with Monte Carlo simulations.

Hybrid particle-continuum simulations coupling Brownian dynamics and local dynamic density functional theory.

PubMed

Qi, Shuanhu; Schmid, Friederike

2017-11-08

We present a multiscale hybrid particle-field scheme for the simulation of relaxation and diffusion behavior of soft condensed matter systems. It combines particle-based Brownian dynamics and field-based local dynamics in an adaptive sense such that particles can switch their level of resolution on the fly. The switching of resolution is controlled by a tuning function which can be chosen at will according to the geometry of the system. As an application, the hybrid scheme is used to study the kinetics of interfacial broadening of a polymer blend, and is validated by comparing the results to the predictions from pure Brownian dynamics and pure local dynamics calculations.

Density functional theory based molecular dynamics study of hydration and electronic properties of aqueous La(3+).

PubMed

Terrier, Cyril; Vitorge, Pierre; Gaigeot, Marie-Pierre; Spezia, Riccardo; Vuilleumier, Rodolphe

2010-07-28

Structural and electronic properties of La(3+) immersed in bulk water have been assessed by means of density functional theory (DFT)-based Car-Parrinello molecular dynamics (CPMD) simulations. Correct structural properties, i.e., La(III)-water distances and La(III) coordination number, can be obtained within the framework of Car-Parrinello simulations providing that both the La pseudopotential and conditions of the dynamics (fictitious mass and time step) are carefully set up. DFT-MD explicitly treats electronic densities and is shown here to provide a theoretical justification to the necessity of including polarization when studying highly charged cations such as lanthanoids(III) with classical MD. La(3+) was found to strongly polarize the water molecules located in the first shell, giving rise to dipole moments about 0.5 D larger than those of bulk water molecules. Finally, analyzing Kohn-Sham orbitals, we found La(3+) empty 4f orbitals extremely compact and to a great extent uncoupled from the water conduction band, while the 5d empty orbitals exhibit mixing with unoccupied states of water.

Molecular dynamics simulation of solute diffusion in Lennard-Jones fluids

NASA Astrophysics Data System (ADS)

Yamaguchi, T.; Kimura, Y.; Hirota, N.

We performed a molecular dynamics (MD) simulation for a system of 5 solute molecules in 495 solvent molecules interacting through the Lennard-Jones (LJ) 12-6 potential, in order to study solvent density effects on the diffusion coefficients in supercritical fluids. The effects of the size of the solute and the strength of the solute-solvent attractive interaction on the diffusion coefficient of the solute were examined. The diffusion coefficients of the solute molecules were calculated at T = 1.5 (in the LJ reduced unit), slightly above the critical temperature, from rho = 0.1 to rho = 0.95, where rho is the number density in the LJ reduced unit. The memory function in the generalized Langevin equation was calculated, in order to know the molecular origin of the friction on a solute. The memory function is separated into fast and slow components. The former arises from the solute-solvent repulsive interaction, and is interpreted as collisional Enskog-like friction. The interaction strength dependence of the collisional friction is larger in the low- and medium-density regions, which is consistent with the 'clustering' picture, i.e., the local density enhancement due to the solute-solvent attractive interaction. However, the slow component of the memory function suppresses the effect of the local density on the diffusion coefficients, and as a result the effect of the attractive interaction is smaller on the diffusion coefficients than on the local density. Nonetheless, the solvent density dependence of the effect of the attraction on the diffusion coefficient varies with the local density, and it is concluded that the local density is the principal factor that determines the interaction strength dependence of the diffusion coefficient in the low- and medium-density regions (p < 0.6).

Power-law tails and non-Markovian dynamics in open quantum systems: An exact solution from Keldysh field theory

NASA Astrophysics Data System (ADS)

Chakraborty, Ahana; Sensarma, Rajdeep

2018-03-01

The Born-Markov approximation is widely used to study the dynamics of open quantum systems coupled to external baths. Using Keldysh formalism, we show that the dynamics of a system of bosons (fermions) linearly coupled to a noninteracting bosonic (fermionic) bath falls outside this paradigm if the bath spectral function has nonanalyticities as a function of frequency. In this case, we show that the dissipative and noise kernels governing the dynamics have distinct power-law tails. The Green's functions show a short-time "quasi"-Markovian exponential decay before crossing over to a power-law tail governed by the nonanalyticity of the spectral function. We study a system of bosons (fermions) hopping on a one-dimensional lattice, where each site is coupled linearly to an independent bath of noninteracting bosons (fermions). We obtain exact expressions for the Green's functions of this system, which show power-law decay ˜|t - t'|-3 /2 . We use these to calculate the density and current profile, as well as unequal-time current-current correlators. While the density and current profiles show interesting quantitative deviations from Markovian results, the current-current correlators show qualitatively distinct long-time power-law tails |t - t'|-3 characteristic of non-Markovian dynamics. We show that the power-law decays survive in the presence of interparticle interaction in the system, but the crossover time scale is shifted to larger values with increasing interaction strength.

Role of the Pair Correlation Function in the Dynamical Transition Predicted by Mode Coupling Theory.

PubMed

Nandi, Manoj Kumar; Banerjee, Atreyee; Dasgupta, Chandan; Bhattacharyya, Sarika Maitra

2017-12-29

In a recent study, we have found that for a large number of systems the configurational entropy at the pair level S_{c2}, which is primarily determined by the pair correlation function, vanishes at the dynamical transition temperature T_{c}. Thus, it appears that the information of the transition temperature is embedded in the structure of the liquid. In order to investigate this, we describe the dynamics of the system at the mean field level and, using the concepts of the dynamical density functional theory, show that the dynamical transition temperature depends only on the pair correlation function. Thus, this theory is similar in spirit to the microscopic mode coupling theory (MCT). However, unlike microscopic MCT, which predicts a very high transition temperature, the present theory predicts a transition temperature that is similar to T_{c}. This implies that the information of the dynamical transition temperature is embedded in the pair correlation function.

Isobaric first-principles molecular dynamics of liquid water with nonlocal van der Waals interactions

NASA Astrophysics Data System (ADS)

Miceli, Giacomo; de Gironcoli, Stefano; Pasquarello, Alfredo

2015-01-01

We investigate the structural properties of liquid water at near ambient conditions using first-principles molecular dynamics simulations based on a semilocal density functional augmented with nonlocal van der Waals interactions. The adopted scheme offers the advantage of simulating liquid water at essentially the same computational cost of standard semilocal functionals. Applied to the water dimer and to ice Ih, we find that the hydrogen-bond energy is only slightly enhanced compared to a standard semilocal functional. We simulate liquid water through molecular dynamics in the NpH statistical ensemble allowing for fluctuations of the system density. The structure of the liquid departs from that found with a semilocal functional leading to more compact structural arrangements. This indicates that the directionality of the hydrogen-bond interaction has a diminished role as compared to the overall attractions, as expected when dispersion interactions are accounted for. This is substantiated through a detailed analysis comprising the study of the partial radial distribution functions, various local order indices, the hydrogen-bond network, and the selfdiffusion coefficient. The explicit treatment of the van der Waals interactions leads to an overall improved description of liquid water.

X-ray scattering measurements of dissociation-induced metallization of dynamically compressed deuterium

DOE PAGES

Davis, P.; Döppner, T.; Rygg, J. R.; ...

2016-04-18

Hydrogen, the simplest element in the universe, has a surprisingly complex phase diagram. Because of applications to planetary science, inertial confinement fusion and fundamental physics, its high-pressure properties have been the subject of intense study over the past two decades. While sophisticated static experiments have probed hydrogen’s structure at ever higher pressures, studies examining the higher-temperature regime using dynamic compression have mostly been limited to optical measurement techniques. Here we present spectrally resolved x-ray scattering measurements from plasmons in dynamically compressed deuterium. Combined with Compton scattering, and velocity interferometry to determine shock pressure and mass density, this allows us tomore » extract ionization state as a function of compression. Furthermore, the onset of ionization occurs close in pressure to where density functional theory-molecular dynamics (DFT-MD) simulations show molecular dissociation, suggesting hydrogen transitions from a molecular and insulating fluid to a conducting state without passing through an intermediate atomic phase.« less

Reduced quantum dynamics with arbitrary bath spectral densities: hierarchical equations of motion based on several different bath decomposition schemes.

PubMed

Liu, Hao; Zhu, Lili; Bai, Shuming; Shi, Qiang

2014-04-07

We investigated applications of the hierarchical equation of motion (HEOM) method to perform high order perturbation calculations of reduced quantum dynamics for a harmonic bath with arbitrary spectral densities. Three different schemes are used to decompose the bath spectral density into analytical forms that are suitable to the HEOM treatment: (1) The multiple Lorentzian mode model that can be obtained by numerically fitting the model spectral density. (2) The combined Debye and oscillatory Debye modes model that can be constructed by fitting the corresponding classical bath correlation function. (3) A new method that uses undamped harmonic oscillator modes explicitly in the HEOM formalism. Methods to extract system-bath correlations were investigated for the above bath decomposition schemes. We also show that HEOM in the undamped harmonic oscillator modes can give detailed information on the partial Wigner transform of the total density operator. Theoretical analysis and numerical simulations of the spin-Boson dynamics and the absorption line shape of molecular dimers show that the HEOM formalism for high order perturbations can serve as an important tool in studying the quantum dissipative dynamics in the intermediate coupling regime.

Reduced quantum dynamics with arbitrary bath spectral densities: Hierarchical equations of motion based on several different bath decomposition schemes

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

Liu, Hao; Zhu, Lili; Bai, Shuming

2014-04-07

We investigated applications of the hierarchical equation of motion (HEOM) method to perform high order perturbation calculations of reduced quantum dynamics for a harmonic bath with arbitrary spectral densities. Three different schemes are used to decompose the bath spectral density into analytical forms that are suitable to the HEOM treatment: (1) The multiple Lorentzian mode model that can be obtained by numerically fitting the model spectral density. (2) The combined Debye and oscillatory Debye modes model that can be constructed by fitting the corresponding classical bath correlation function. (3) A new method that uses undamped harmonic oscillator modes explicitly inmore » the HEOM formalism. Methods to extract system-bath correlations were investigated for the above bath decomposition schemes. We also show that HEOM in the undamped harmonic oscillator modes can give detailed information on the partial Wigner transform of the total density operator. Theoretical analysis and numerical simulations of the spin-Boson dynamics and the absorption line shape of molecular dimers show that the HEOM formalism for high order perturbations can serve as an important tool in studying the quantum dissipative dynamics in the intermediate coupling regime.« less

Spacecraft observations of a Maxwell Demon coating the separatrix of asymmetric magnetic reconnection with crescent-shaped electron distributions

NASA Astrophysics Data System (ADS)

Egedal, J.; Le, A.; Daughton, W.; Wetherton, B.; Cassak, Pa; Chen, Lj; Lavraud, B.; Dorell, J.; Avanov, L.; Gershman, D.

2016-10-01

During asymmetric magnetic reconnection in the dayside magnetopause in situ spacecraft mea- surements show that electrons from the high density inflow penetrate some distance into the low density inflow. Supported by a kinetic simulation, we present a general derivation of an exclusion energy parameter, which provides a lower kinetic energy bound for an electron to jump across the reconnection region from one inflow region to the other. As by a Maxwell Demon, only high energy electrons are permitted to cross the inner reconnection region, strongly impacting the form of the electron distribution function observed along the low density side separatrix. The dynamics produce two distinct flavors of crescent-shaped electron distributions in a thin boundary layer along the separatrix between the magnetospheric inflow and the reconnection exhaust. The analytical model presented relates these salient details of the distribution function to the electron dynamics in the inner reconnection region.

Dynamical and electronic properties of rare-earth aluminides

NASA Astrophysics Data System (ADS)

Sharma, Ramesh; Sharma, Yamini

2018-04-01

Rare-earth dialuminides belong to a large family of compounds that stabilize in cubic MgCu2 structure. A large number of these compounds are superconducting, amongst these YAl2, LaAl2 and LuAl2 have been chosen as reference materials for studying 4f-electron systems. In order to understand the role of the RE atoms, we have applied the FPLAPW and PAW methods within the density functional theory (DFT). Our results show that the contribution of RE atoms is dominant in both electronic structure and phonon dispersion. The anomalous behavior of superconducting LaAl2 is well explained from an analysis of the electron localization function (ELF), Bader charge analysis, density of electronic states as well as the dynamical phonon vibrational modes. The interaction of phonon modes contributed by low frequency vibrations of La atoms with the high density La 5d-states at EF in LaAl2 lead to strong electron-phonon coupling.

Matching-pursuit/split-operator-Fourier-transform computations of thermal correlation functions.

PubMed

Chen, Xin; Wu, Yinghua; Batista, Victor S

2005-02-08

A rigorous and practical methodology for evaluating thermal-equilibrium density matrices, finite-temperature time-dependent expectation values, and time-correlation functions is described. The method involves an extension of the matching-pursuit/split-operator-Fourier-transform method to the solution of the Bloch equation via imaginary-time propagation of the density matrix and the evaluation of Heisenberg time-evolution operators through real-time propagation in dynamically adaptive coherent-state representations.

Direct construction of mesoscopic models from microscopic simulations

NASA Astrophysics Data System (ADS)

Lei, Huan; Caswell, Bruce; Karniadakis, George Em

2010-02-01

Starting from microscopic molecular-dynamics (MD) simulations of constrained Lennard-Jones (LJ) clusters (with constant radius of gyration Rg ), we construct two mesoscopic models [Langevin dynamics and dissipative particle dynamics (DPD)] by coarse graining the LJ clusters into single particles. Both static and dynamic properties of the coarse-grained models are investigated and compared with the MD results. The effective mean force field is computed as a function of the intercluster distance, and the corresponding potential scales linearly with the number of particles per cluster and the temperature. We verify that the mean force field can reproduce the equation of state of the atomistic systems within a wide density range but the radial distribution function only within the dilute and the semidilute regime. The friction force coefficients for both models are computed directly from the time-correlation function of the random force field of the microscopic system. For high density or a large cluster size the friction force is overestimated and the diffusivity underestimated due to the omission of many-body effects as a result of the assumed pairwise form of the coarse-grained force field. When the many-body effect is not as pronounced (e.g., smaller Rg or semidilute system), the DPD model can reproduce the dynamic properties of the MD system.

Toward calculations of the 129Xe chemical shift in Xe@C60 at experimental conditions: relativity, correlation, and dynamics.

PubMed

Straka, Michal; Lantto, Perttu; Vaara, Juha

2008-03-27

We calculate the 129Xe chemical shift in endohedral Xe@C60 with systematic inclusion of the contributing physical effects to model the real experimental conditions. These are relativistic effects, electron correlation, the temperature-dependent dynamics, and solvent effects. The ultimate task is to obtain the right result for the right reason and to develop a physically justified methodological model for calculations and simulations of endohedral Xe fullerenes and other confined Xe systems. We use the smaller Xe...C6H6 model to calibrate density functional theory approaches against accurate correlated wave function methods. Relativistic effects as well as the coupling of relativity and electron correlation are evaluated using the leading-order Breit-Pauli perturbation theory. The dynamic effects are treated in two ways. In the first approximation, quantum dynamics of the Xe atom in a rigid cage takes advantage of the centrosymmetric potential for Xe within the thermally accessible distance range from the center of the cage. This reduces the problem of obtaining the solution of a diatomic rovibrational problem. In the second approach, first-principles classical molecular dynamics on the density functional potential energy hypersurface is used to produce the dynamical trajectory for the whole system, including the dynamic cage. Snapshots from the trajectory are used for calculations of the dynamic contribution to the absorption 129Xe chemical shift. The calculated nonrelativistic Xe shift is found to be highly sensitive to the optimized molecular structure and to the choice of the exchange-correlation functional. Relativistic and dynamic effects are significant and represent each about 10% of the nonrelativistic static shift at the minimum structure. While the role of the Xe dynamics inside of the rigid cage is negligible, the cage dynamics turns out to be responsible for most of the dynamical correction to the 129Xe shift. Solvent effects evaluated with a polarized continuum model are found to be very small.

Dynamic correlations in the highly dilute 2D electron liquid: Loss function, critical wave vector and analytic plasmon dispersion

NASA Astrophysics Data System (ADS)

Drachta, Jürgen T.; Kreil, Dominik; Hobbiger, Raphael; Böhm, Helga M.

2018-03-01

Correlations, highly important in low-dimensional systems, are known to decrease the plasmon dispersion of two-dimensional electron liquids. Here we calculate the plasmon properties, applying the 'Dynamic Many-Body Theory', accounting for correlated two-particle-two-hole fluctuations. These dynamic correlations are found to significantly lower the plasmon's energy. For the data obtained numerically, we provide an analytic expression that is valid across a wide range both of densities and of wave vectors. Finally, we demonstrate how this can be invoked in determining the actual electron densities from measurements on an AlGaAs quantum well.

Probabilistic density function method for nonlinear dynamical systems driven by colored noise

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

Barajas-Solano, David A.; Tartakovsky, Alexandre M.

2016-05-01

We present a probability density function (PDF) method for a system of nonlinear stochastic ordinary differential equations driven by colored noise. The method provides an integro-differential equation for the temporal evolution of the joint PDF of the system's state, which we close by means of a modified Large-Eddy-Diffusivity-type closure. Additionally, we introduce the generalized local linearization (LL) approximation for deriving a computable PDF equation in the form of the second-order partial differential equation (PDE). We demonstrate the proposed closure and localization accurately describe the dynamics of the PDF in phase space for systems driven by noise with arbitrary auto-correlation time.more » We apply the proposed PDF method to the analysis of a set of Kramers equations driven by exponentially auto-correlated Gaussian colored noise to study the dynamics and stability of a power grid.« less

Dynamic Optical Tuning of Interlayer Interactions in the Transition Metal Dichalcogenides

DOE PAGES

Mannebach, Ehren M.; Nyby, Clara; Ernst, Friederike; ...

2017-11-09

Modulation of weak interlayer interactions between quasi-two-dimensional atomic planes in the transition metal dichalcogenides (TMDCs) provides avenues for tuning their functional properties. Here we show that above-gap optical excitation in the TMDCs leads to an unexpected large-amplitude, ultrafast compressive force between the two-dimensional layers, as probed by in situ measurements of the atomic layer spacing at femtosecond time resolution. We show that this compressive response arises from a dynamic modulation of the interlayer van der Waals interaction and that this represents the dominant light-induced stress at low excitation densities. A simple analytic model predicts the magnitude and carrier density dependencemore » of the measured strains. Furthermore, this work establishes a new method for dynamic, nonequilibrium tuning of correlation-driven dispersive interactions and of the optomechanical functionality of TMDC quasi-two-dimensional materials.« less

Structural discrimination via density functional theory and lattice dynamics: Monoclinic Mg2NiH4

NASA Astrophysics Data System (ADS)

Herbst, J. F.; Hector, L. G., Jr.

2009-04-01

Two distinct crystal structures for the monoclinic, low-temperature phase of Mg2NiH4 , which we designate as LTI and LTII, are available in the published literature. We demonstrate that density functional theory and lattice dynamics can easily identify LTII as the preferable structure at two levels of inquiry. First, enthalpies of formation ΔH calculated using three different forms for the exchange-correlation energy functional are in better agreement with experiment for LTII. Second, the phonon spectrum calculated for LTII contains no anomalies while that for LTI exhibits a variety of soft modes. By analyzing the soft modes in LTI as well as those we find for the known CaMgNiH4 structure with Ca replaced by Mg we derive a crystal structure that closely approximates LTII.

Measurement Model Nonlinearity in Estimation of Dynamical Systems

NASA Astrophysics Data System (ADS)

Majji, Manoranjan; Junkins, J. L.; Turner, J. D.

2012-06-01

The role of nonlinearity of the measurement model and its interactions with the uncertainty of measurements and geometry of the problem is studied in this paper. An examination of the transformations of the probability density function in various coordinate systems is presented for several astrodynamics applications. Smooth and analytic nonlinear functions are considered for the studies on the exact transformation of uncertainty. Special emphasis is given to understanding the role of change of variables in the calculus of random variables. The transformation of probability density functions through mappings is shown to provide insight in to understanding the evolution of uncertainty in nonlinear systems. Examples are presented to highlight salient aspects of the discussion. A sequential orbit determination problem is analyzed, where the transformation formula provides useful insights for making the choice of coordinates for estimation of dynamic systems.

Course 4: Density Functional Theory, Methods, Techniques, and Applications

NASA Astrophysics Data System (ADS)

Chrétien, S.; Salahub, D. R.

Contents 1 Introduction 2 Density functional theory 2.1 Hohenberg and Kohn theorems 2.2 Levy's constrained search 2.3 Kohn-Sham method 3 Density matrices and pair correlation functions 4 Adiabatic connection or coupling strength integration 5 Comparing and constrasting KS-DFT and HF-CI 6 Preparing new functionals 7 Approximate exchange and correlation functionals 7.1 The Local Spin Density Approximation (LSDA) 7.2 Gradient Expansion Approximation (GEA) 7.3 Generalized Gradient Approximation (GGA) 7.4 meta-Generalized Gradient Approximation (meta-GGA) 7.5 Hybrid functionals 7.6 The Optimized Effective Potential method (OEP) 7.7 Comparison between various approximate functionals 8 LAP correlation functional 9 Solving the Kohn-Sham equations 9.1 The Kohn-Sham orbitals 9.2 Coulomb potential 9.3 Exchange-correlation potential 9.4 Core potential 9.5 Other choices and sources of error 9.6 Functionality 10 Applications 10.1 Ab initio molecular dynamics for an alanine dipeptide model 10.2 Transition metal clusters: The ecstasy, and the agony... 10.3 The conversion of acetylene to benzene on Fe clusters 11 Conclusions

Dynamical correlation effects in a weakly correlated material: Inelastic x-ray scattering and photoemission spectra of beryllium

NASA Astrophysics Data System (ADS)

Seidu, Azimatu; Marini, Andrea; Gatti, Matteo

2018-03-01

Beryllium is a weakly correlated simple metal. Still we find that dynamical correlation effects, beyond the independent-particle picture, are necessary to successfully interpret the electronic spectra measured by inelastic x-ray scattering (IXS) and photoemission spectroscopies (PES). By combining ab initio time-dependent density-functional theory (TDDFT) and many-body Green's function theory in the G W approximation (G W A ), we calculate the dynamic structure factor, the quasiparticle (QP) properties and PES spectra of bulk Be. We show that band-structure effects (i.e., due to interaction with the crystal potential) and QP lifetimes (LT) are both needed in order to explain the origin of the measured double-peak features in the IXS spectra. A quantitative agreement with experiment is obtained only when LT are supplemented to the adiabatic local-density approximation (ALDA) of TDDFT. Besides the valence band, PES spectra display a satellite, a signature of dynamical correlation due to the coupling of QPs and plasmons, which we are able to reproduce thanks to the combination of the G W A for the self-energy with the cumulant expansion of the Green's function.

Application of the Real-Time Time-Dependent Density Functional Theory to Excited-State Dynamics of Molecules and 2D Materials

NASA Astrophysics Data System (ADS)

Miyamoto, Yoshiyuki; Rubio, Angel

2018-04-01

We review our recent developments in the ab initio simulation of excited-state dynamics within the framework of time-dependent density functional theory (TDDFT). Our targets range from molecules to 2D materials, although the methods are general and can be applied to any other finite and periodic systems. We discuss examples of excited-state dynamics obtained by real-time TDDFT coupled with molecular dynamics (MD) and the Ehrenfest approximation, including photoisomerization in molecules, photoenhancement of the weak interatomic attraction of noble gas atoms, photoenhancement of the weak interlayer interaction of 2D materials, pulse-laser-induced local bond breaking of adsorbed atoms on 2D sheets, modulation of UV light intensity by graphene nanoribbons at terahertz frequencies, and collision of high-speed ions with the 2D material to simulate the images taken by He ion microscopy. We illustrate how the real-time TDDFT approach is useful for predicting and understanding non-equilibrium dynamics in condensed matter. We also discuss recent developments that address the excited-state dynamics of systems out of equilibrium and future challenges in this fascinating field of research.

A simple scaling law for the equation of state and the radial distribution functions calculated by density-functional theory molecular dynamics

NASA Astrophysics Data System (ADS)

Danel, J.-F.; Kazandjian, L.

2018-06-01

It is shown that the equation of state (EOS) and the radial distribution functions obtained by density-functional theory molecular dynamics (DFT-MD) obey a simple scaling law. At given temperature, the thermodynamic properties and the radial distribution functions given by a DFT-MD simulation remain unchanged if the mole fractions of nuclei of given charge and the average volume per atom remain unchanged. A practical interest of this scaling law is to obtain an EOS table for a fluid from that already obtained for another fluid if it has the right characteristics. Another practical interest of this result is that an asymmetric mixture made up of light and heavy atoms requiring very different time steps can be replaced by a mixture of atoms of equal mass, which facilitates the exploration of the configuration space in a DFT-MD simulation. The scaling law is illustrated by numerical results.

Liquid Aluminum: Atomic diffusion and viscosity from ab initio molecular dynamics

PubMed Central

Jakse, Noel; Pasturel, Alain

2013-01-01

We present a study of dynamic properties of liquid aluminum using density-functional theory within the local-density (LDA) and generalized gradient (GGA) approximations. We determine the temperature dependence of the self-diffusion coefficient as well the viscosity using direct methods. Comparisons with experimental data favor the LDA approximation to compute dynamic properties of liquid aluminum. We show that the GGA approximation induce more important backscattering effects due to an enhancement of the icosahedral short range order (ISRO) that impact directly dynamic properties like the self-diffusion coefficient. All these results are then used to test the Stokes-Einstein relation and the universal scaling law relating the diffusion coefficient and the excess entropy of a liquid. PMID:24190311

Structural arrest in an ideal gas.

PubMed

van Ketel, Willem; Das, Chinmay; Frenkel, Daan

2005-04-08

We report a molecular dynamics study of a simple model system that has the static properties of an ideal gas, yet exhibits nontrivial "glassy" dynamics behavior at high densities. The constituent molecules of this system are constructs of three infinitely thin hard rods of length L, rigidly joined at their midpoints. The crosses have random but fixed orientation. The static properties of this system are those of an ideal gas, and its collision frequency can be computed analytically. For number densities NL(3)/V>1, the single-particle diffusivity goes to zero. As the system is completely structureless, standard mode-coupling theory cannot describe the observed structural arrest. Nevertheless, the system exhibits many dynamical features that appear to be mode-coupling-like. All high-density incoherent intermediate scattering functions collapse onto master curves that depend only on the wave vector.

Pattern, growth, and aging in aggregation kinetics of a Vicsek-like active matter model

NASA Astrophysics Data System (ADS)

Das, Subir K.

2017-01-01

Via molecular dynamics simulations, we study kinetics in a Vicsek-like phase-separating active matter model. Quantitative results, for isotropic bicontinuous pattern, are presented on the structure, growth, and aging. These are obtained via the two-point equal-time density-density correlation function, the average domain length, and the two-time density autocorrelation function. Both the correlation functions exhibit basic scaling properties, implying self-similarity in the pattern dynamics, for which the average domain size exhibits a power-law growth in time. The equal-time correlation has a short distance behavior that provides reasonable agreement between the corresponding structure factor tail and the Porod law. The autocorrelation decay is a power-law in the average domain size. Apart from these basic similarities, the overall quantitative behavior of the above-mentioned observables is found to be vastly different from those of the corresponding passive limit of the model which also undergoes phase separation. The functional forms of these have been quantified. An exceptionally rapid growth in the active system occurs due to fast coherent motion of the particles, mean-squared-displacements of which exhibit multiple scaling regimes, including a long time ballistic one.

Actinide chemistry using singlet-paired coupled cluster and its combinations with density functionals

NASA Astrophysics Data System (ADS)

Garza, Alejandro J.; Sousa Alencar, Ana G.; Scuseria, Gustavo E.

2015-12-01

Singlet-paired coupled cluster doubles (CCD0) is a simplification of CCD that relinquishes a fraction of dynamic correlation in order to be able to describe static correlation. Combinations of CCD0 with density functionals that recover specifically the dynamic correlation missing in the former have also been developed recently. Here, we assess the accuracy of CCD0 and CCD0+DFT (and variants of these using Brueckner orbitals) as compared to well-established quantum chemical methods for describing ground-state properties of singlet actinide molecules. The f0 actinyl series (UO22+, NpO23+, PuO24+), the isoelectronic NUN, and thorium (ThO, ThO2+) and nobelium (NoO, NoO2) oxides are studied.

Continuous time random walk model with asymptotical probability density of waiting times via inverse Mittag-Leffler function

NASA Astrophysics Data System (ADS)

Liang, Yingjie; Chen, Wen

2018-04-01

The mean squared displacement (MSD) of the traditional ultraslow diffusion is a logarithmic function of time. Recently, the continuous time random walk model is employed to characterize this ultraslow diffusion dynamics by connecting the heavy-tailed logarithmic function and its variation as the asymptotical waiting time density. In this study we investigate the limiting waiting time density of a general ultraslow diffusion model via the inverse Mittag-Leffler function, whose special case includes the traditional logarithmic ultraslow diffusion model. The MSD of the general ultraslow diffusion model is analytically derived as an inverse Mittag-Leffler function, and is observed to increase even more slowly than that of the logarithmic function model. The occurrence of very long waiting time in the case of the inverse Mittag-Leffler function has the largest probability compared with the power law model and the logarithmic function model. The Monte Carlo simulations of one dimensional sample path of a single particle are also performed. The results show that the inverse Mittag-Leffler waiting time density is effective in depicting the general ultraslow random motion.

Abnormal rich club organization and functional brain dynamics in schizophrenia.

PubMed

van den Heuvel, Martijn P; Sporns, Olaf; Collin, Guusje; Scheewe, Thomas; Mandl, René C W; Cahn, Wiepke; Goñi, Joaquín; Hulshoff Pol, Hilleke E; Kahn, René S

2013-08-01

The human brain forms a large-scale structural network of regions and interregional pathways. Recent studies have reported the existence of a selective set of highly central and interconnected hub regions that may play a crucial role in the brain's integrative processes, together forming a central backbone for global brain communication. Abnormal brain connectivity may have a key role in the pathophysiology of schizophrenia. To examine the structure of the rich club in schizophrenia and its role in global functional brain dynamics. Structural diffusion tensor imaging and resting-state functional magnetic resonance imaging were performed in patients with schizophrenia and matched healthy controls. Department of Psychiatry, Rudolf Magnus Institute of Neuroscience, University Medical Center Utrecht, Utrecht, the Netherlands. Forty-eight patients and 45 healthy controls participated in the study. An independent replication data set of 41 patients and 51 healthy controls was included to replicate and validate significant findings. MAIN OUTCOME(S) AND MEASURES: Measures of rich club organization, connectivity density of rich club connections and connections linking peripheral regions to brain hubs, measures of global brain network efficiency, and measures of coupling between brain structure and functional dynamics. Rich club organization between high-degree hub nodes was significantly affected in patients, together with a reduced density of rich club connections predominantly comprising the white matter pathways that link the midline frontal, parietal, and insular hub regions. This reduction in rich club density was found to be associated with lower levels of global communication capacity, a relationship that was absent for other white matter pathways. In addition, patients had an increase in the strength of structural connectivity-functional connectivity coupling. Our findings provide novel biological evidence that schizophrenia is characterized by a selective disruption of brain connectivity among central hub regions of the brain, potentially leading to reduced communication capacity and altered functional brain dynamics.

Force Field Accelerated Density Functional Theory Molecular Dynamics for Simulation of Reactive Systems at Extreme Conditions

NASA Astrophysics Data System (ADS)

Lindsey, Rebecca; Goldman, Nir; Fried, Laurence

2017-06-01

Atomistic modeling of chemistry at extreme conditions remains a challenge, despite continuing advances in computing resources and simulation tools. While first principles methods provide a powerful predictive tool, the time and length scales associated with chemistry at extreme conditions (ns and μm, respectively) largely preclude extension of such models to molecular dynamics. In this work, we develop a simulation approach that retains the accuracy of density functional theory (DFT) while decreasing computational effort by several orders of magnitude. We generate n-body descriptions for atomic interactions by mapping forces arising from short density functional theory (DFT) trajectories on to simple Chebyshev polynomial series. We examine the importance of including greater than 2-body interactions, model transferability to different state points, and discuss approaches to ensure smooth and reasonable model shape outside of the distance domain sampled by the DFT training set. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

Force Field Accelerated Density Functional Theory Molecular Dynamics for Simulation of Reactive Systems at Extreme Conditions

NASA Astrophysics Data System (ADS)

Lindsey, Rebecca; Goldman, Nir; Fried, Laurence

Understanding chemistry at extreme conditions is crucial in fields including geochemistry, astrobiology, and alternative energy. First principles methods can provide valuable microscopic insights into such systems while circumventing the risks of physical experiments, however the time and length scales associated with chemistry at extreme conditions (ns and μm, respectively) largely preclude extension of such models to molecular dynamics. In this work, we develop a simulation approach that retains the accuracy of density functional theory (DFT) while decreasing computational effort by several orders of magnitude. We generate n-body descriptions for atomic interactions by mapping forces arising from short density functional theory (DFT) trajectories on to simple Chebyshev polynomial series. We examine the importance of including greater than 2-body interactions, model transferability to different state points, and discuss approaches to ensure smooth and reasonable model shape outside of the distance domain sampled by the DFT training set. This work performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

Random density matrices versus random evolution of open system

NASA Astrophysics Data System (ADS)

Pineda, Carlos; Seligman, Thomas H.

2015-10-01

We present and compare two families of ensembles of random density matrices. The first, static ensemble, is obtained foliating an unbiased ensemble of density matrices. As criterion we use fixed purity as the simplest example of a useful convex function. The second, dynamic ensemble, is inspired in random matrix models for decoherence where one evolves a separable pure state with a random Hamiltonian until a given value of purity in the central system is achieved. Several families of Hamiltonians, adequate for different physical situations, are studied. We focus on a two qubit central system, and obtain exact expressions for the static case. The ensemble displays a peak around Werner-like states, modulated by nodes on the degeneracies of the density matrices. For moderate and strong interactions good agreement between the static and the dynamic ensembles is found. Even in a model where one qubit does not interact with the environment excellent agreement is found, but only if there is maximal entanglement with the interacting one. The discussion is started recalling similar considerations for scattering theory. At the end, we comment on the reach of the results for other convex functions of the density matrix, and exemplify the situation with the von Neumann entropy.

Ab initio molecular dynamics in a finite homogeneous electric field.

PubMed

Umari, P; Pasquarello, Alfredo

2002-10-07

We treat homogeneous electric fields within density functional calculations with periodic boundary conditions. A nonlocal energy functional depending on the applied field is used within an ab initio molecular dynamics scheme. The reliability of the method is demonstrated in the case of bulk MgO for the Born effective charges, and the high- and low-frequency dielectric constants. We evaluate the static dielectric constant by performing a damped molecular dynamics in an electric field and avoiding the calculation of the dynamical matrix. Application of this method to vitreous silica shows good agreement with experiment and illustrates its potential for systems of large size.

Mode coupling theory for nonequilibrium glassy dynamics of thermal self-propelled particles.

PubMed

Feng, Mengkai; Hou, Zhonghuai

2017-06-28

We present a mode coupling theory study for the relaxation and glassy dynamics of a system of strongly interacting self-propelled particles, wherein the self-propulsion force is described by Ornstein-Uhlenbeck colored noise and thermal noises are included. Our starting point is an effective Smoluchowski equation governing the distribution function of particle positions, from which we derive a memory function equation for the time dependence of density fluctuations in nonequilibrium steady states. With the basic assumption of the absence of macroscopic currents and standard mode coupling approximation, we can obtain expressions for the irreducible memory function and other relevant dynamic terms, wherein the nonequilibrium character of the active system is manifested through an averaged diffusion coefficient D[combining macron] and a nontrivial structural function S 2 (q) with q being the magnitude of wave vector q. D[combining macron] and S 2 (q) enter the frequency term and the vertex term for the memory function, and thus influence both the short time and the long time dynamics of the system. With these equations obtained, we study the glassy dynamics of this thermal self-propelled particle system by investigating the Debye-Waller factor f q and relaxation time τ α as functions of the persistence time τ p of self-propulsion, the single particle effective temperature T eff as well as the number density ρ. Consequently, we find the critical density ρ c for given τ p shifts to larger values with increasing magnitude of propulsion force or effective temperature, in good accordance with previously reported simulation work. In addition, the theory facilitates us to study the critical effective temperature T for fixed ρ as well as its dependence on τ p . We find that T increases with τ p and in the limit τ p → 0, it approaches the value for a simple passive Brownian system as expected. Our theory also well recovers the results for passive systems and can be easily extended to more complex systems such as active-passive mixtures.

Characterizing water-metal interfaces and machine learning potential energy surfaces

NASA Astrophysics Data System (ADS)

Ryczko, Kevin

In this thesis, we first discuss the fundamentals of ab initio electronic structure theory and density functional theory (DFT). We also discuss statistics related to computing thermodynamic averages of molecular dynamics (MD). We then use this theory to analyze and compare the structural, dynamical, and electronic properties of liquid water next to prototypical metals including platinum, graphite, and graphene. Our results are built on Born-Oppenheimer molecular dynamics (BOMD) generated using density functional theory (DFT) which explicitly include van der Waals (vdW) interactions within a first principles approach. All calculations reported use large simulation cells, allowing for an accurate treatment of the water-electrode interfaces. We have included vdW interactions through the use of the optB86b-vdW exchange correlation functional. Comparisons with the Perdew-Burke-Ernzerhof (PBE) exchange correlation functional are also shown. We find an initial peak, due to chemisorption, in the density profile of the liquid water-Pt interface not seen in the liquid water-graphite interface, liquid watergraphene interface, nor interfaces studied previously. To further investigate this chemisorption peak, we also report differences in the electronic structure of single water molecules on both Pt and graphite surfaces. We find that a covalent bond forms between the single water molecule and the platinum surface, but not between the single water molecule and the graphite surface. We also discuss the effects that defects and dopants in the graphite and graphene surfaces have on the structure and dynamics of liquid water. Lastly, we introduce artificial neural networks (ANNs), and demonstrate how they can be used to machine learn electronic structure calculations. As a proof of principle, we show the success of an ANN potential energy surfaces for a dimer molecule with a Lennard-Jones potential.

Low-Dimensional Materials for Optoelectronic and Bioelectronic Applications

NASA Astrophysics Data System (ADS)

Hong, Tu

In this thesis, we first discuss the fundamentals of ab initio electronic structure theory and density functional theory (DFT). We also discuss statistics related to computing thermodynamic averages of molecular dynamics (MD). We then use this theory to analyze and compare the structural, dynamical, and electronic properties of liquid water next to prototypical metals including platinum, graphite, and graphene. Our results are built on Born-Oppenheimer molecular dynamics (BOMD) generated using density functional theory (DFT) which explicitly include van der Waals (vdW) interactions within a first principles approach. All calculations reported use large simulation cells, allowing for an accurate treatment of the water-electrode interfaces. We have included vdW interactions through the use of the optB86b-vdW exchange correlation functional. Comparisons with the Perdew-Burke-Ernzerhof (PBE) exchange correlation functional are also shown. We find an initial peak, due to chemisorption, in the density profile of the liquid water-Pt interface not seen in the liquid water-graphite interface, liquid watergraphene interface, nor interfaces studied previously. To further investigate this chemisorption peak, we also report differences in the electronic structure of single water molecules on both Pt and graphite surfaces. We find that a covalent bond forms between the single water molecule and the platinum surface, but not between the single water molecule and the graphite surface. We also discuss the effects that defects and dopants in the graphite and graphene surfaces have on the structure and dynamics of liquid water. Lastly, we introduce artificial neural networks (ANNs), and demonstrate how they can be used to machine learn electronic structure calculations. As a proof of principle, we show the success of an ANN potential energy surfaces for a dimer molecule with a Lennard-Jones potential.

Nonlocal and Nonadiabatic Effects in the Charge-Density Response of Solids: A Time-Dependent Density-Functional Approach

NASA Astrophysics Data System (ADS)

Panholzer, Martin; Gatti, Matteo; Reining, Lucia

2018-04-01

The charge-density response of extended materials is usually dominated by the collective oscillation of electrons, the plasmons. Beyond this feature, however, intriguing many-body effects are observed. They cannot be described by one of the most widely used approaches for the calculation of dielectric functions, which is time-dependent density functional theory (TDDFT) in the adiabatic local density approximation (ALDA). Here, we propose an approximation to the TDDFT exchange-correlation kernel which is nonadiabatic and nonlocal. It is extracted from correlated calculations in the homogeneous electron gas, where we have tabulated it for a wide range of wave vectors and frequencies. A simple mean density approximation allows one to use it in inhomogeneous materials where the density varies on a scale of 1.6 rs or faster. This kernel contains effects that are completely absent in the ALDA; in particular, it correctly describes the double plasmon in the dynamic structure factor of sodium, and it shows the characteristic low-energy peak that appears in systems with low electronic density. It also leads to an overall quantitative improvement of spectra.

Nonlocal and Nonadiabatic Effects in the Charge-Density Response of Solids: A Time-Dependent Density-Functional Approach.

PubMed

Panholzer, Martin; Gatti, Matteo; Reining, Lucia

2018-04-20

The charge-density response of extended materials is usually dominated by the collective oscillation of electrons, the plasmons. Beyond this feature, however, intriguing many-body effects are observed. They cannot be described by one of the most widely used approaches for the calculation of dielectric functions, which is time-dependent density functional theory (TDDFT) in the adiabatic local density approximation (ALDA). Here, we propose an approximation to the TDDFT exchange-correlation kernel which is nonadiabatic and nonlocal. It is extracted from correlated calculations in the homogeneous electron gas, where we have tabulated it for a wide range of wave vectors and frequencies. A simple mean density approximation allows one to use it in inhomogeneous materials where the density varies on a scale of 1.6 r_{s} or faster. This kernel contains effects that are completely absent in the ALDA; in particular, it correctly describes the double plasmon in the dynamic structure factor of sodium, and it shows the characteristic low-energy peak that appears in systems with low electronic density. It also leads to an overall quantitative improvement of spectra.

Resolution-of-identity stochastic time-dependent configuration interaction for dissipative electron dynamics in strong fields.

PubMed

Klinkusch, Stefan; Tremblay, Jean Christophe

2016-05-14

In this contribution, we introduce a method for simulating dissipative, ultrafast many-electron dynamics in intense laser fields. The method is based on the norm-conserving stochastic unraveling of the dissipative Liouville-von Neumann equation in its Lindblad form. The N-electron wave functions sampling the density matrix are represented in the basis of singly excited configuration state functions. The interaction with an external laser field is treated variationally and the response of the electronic density is included to all orders in this basis. The coupling to an external environment is included via relaxation operators inducing transition between the configuration state functions. Single electron ionization is represented by irreversible transition operators from the ionizing states to an auxiliary continuum state. The method finds its efficiency in the representation of the operators in the interaction picture, where the resolution-of-identity is used to reduce the size of the Hamiltonian eigenstate basis. The zeroth-order eigenstates can be obtained either at the configuration interaction singles level or from a time-dependent density functional theory reference calculation. The latter offers an alternative to explicitly time-dependent density functional theory which has the advantage of remaining strictly valid for strong field excitations while improving the description of the correlation as compared to configuration interaction singles. The method is tested on a well-characterized toy system, the excitation of the low-lying charge transfer state in LiCN.

Resolution-of-identity stochastic time-dependent configuration interaction for dissipative electron dynamics in strong fields

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

Klinkusch, Stefan; Tremblay, Jean Christophe

In this contribution, we introduce a method for simulating dissipative, ultrafast many-electron dynamics in intense laser fields. The method is based on the norm-conserving stochastic unraveling of the dissipative Liouville-von Neumann equation in its Lindblad form. The N-electron wave functions sampling the density matrix are represented in the basis of singly excited configuration state functions. The interaction with an external laser field is treated variationally and the response of the electronic density is included to all orders in this basis. The coupling to an external environment is included via relaxation operators inducing transition between the configuration state functions. Single electronmore » ionization is represented by irreversible transition operators from the ionizing states to an auxiliary continuum state. The method finds its efficiency in the representation of the operators in the interaction picture, where the resolution-of-identity is used to reduce the size of the Hamiltonian eigenstate basis. The zeroth-order eigenstates can be obtained either at the configuration interaction singles level or from a time-dependent density functional theory reference calculation. The latter offers an alternative to explicitly time-dependent density functional theory which has the advantage of remaining strictly valid for strong field excitations while improving the description of the correlation as compared to configuration interaction singles. The method is tested on a well-characterized toy system, the excitation of the low-lying charge transfer state in LiCN.« less

Generalized-active-space pair-density functional theory: an efficient method to study large, strongly correlated, conjugated systems.

PubMed

Ghosh, Soumen; Cramer, Christopher J; Truhlar, Donald G; Gagliardi, Laura

2017-04-01

Predicting ground- and excited-state properties of open-shell organic molecules by electronic structure theory can be challenging because an accurate treatment has to correctly describe both static and dynamic electron correlation. Strongly correlated systems, i.e. , systems with near-degeneracy correlation effects, are particularly troublesome. Multiconfigurational wave function methods based on an active space are adequate in principle, but it is impractical to capture most of the dynamic correlation in these methods for systems characterized by many active electrons. We recently developed a new method called multiconfiguration pair-density functional theory (MC-PDFT), that combines the advantages of wave function theory and density functional theory to provide a more practical treatment of strongly correlated systems. Here we present calculations of the singlet-triplet gaps in oligoacenes ranging from naphthalene to dodecacene. Calculations were performed for unprecedently large orbitally optimized active spaces of 50 electrons in 50 orbitals, and we test a range of active spaces and active space partitions, including four kinds of frontier orbital partitions. We show that MC-PDFT can predict the singlet-triplet splittings for oligoacenes consistent with the best available and much more expensive methods, and indeed MC-PDFT may constitute the benchmark against which those other models should be compared, given the absence of experimental data.

Efficient algorithm for multiconfiguration pair-density functional theory with application to the heterolytic dissociation energy of ferrocene

NASA Astrophysics Data System (ADS)

Sand, Andrew M.; Truhlar, Donald G.; Gagliardi, Laura

2017-01-01

The recently developed multiconfiguration pair-density functional theory (MC-PDFT) combines multiconfiguration wave function theory with a density functional that depends on the on-top pair density of an electronic system. In an MC-PDFT calculation, there are two steps: a conventional multiconfiguration self-consistent-field (MCSCF) calculation and a post-MCSCF evaluation of the energy with an on-top density functional. In this work, we present the details of the MC-PDFT algorithm that avoids steeply scaling steps that are present in other post-self-consistent-field multireference calculations of dynamic correlation energy. We demonstrate the favorable scaling by considering systems of H2 molecules with active spaces of several different sizes. We then apply the MC-PDFT method to calculate the heterolytic dissociation enthalpy of ferrocene. We find that MC-PDFT yields results that are at least as accurate as complete active space second-order perturbation theory and are more stable with respect to basis set, but at a fraction of the cost in both time and memory.

Efficient algorithm for multiconfiguration pair-density functional theory with application to the heterolytic dissociation energy of ferrocene.

PubMed

Sand, Andrew M; Truhlar, Donald G; Gagliardi, Laura

2017-01-21

The recently developed multiconfiguration pair-density functional theory (MC-PDFT) combines multiconfiguration wave function theory with a density functional that depends on the on-top pair density of an electronic system. In an MC-PDFT calculation, there are two steps: a conventional multiconfiguration self-consistent-field (MCSCF) calculation and a post-MCSCF evaluation of the energy with an on-top density functional. In this work, we present the details of the MC-PDFT algorithm that avoids steeply scaling steps that are present in other post-self-consistent-field multireference calculations of dynamic correlation energy. We demonstrate the favorable scaling by considering systems of H 2 molecules with active spaces of several different sizes. We then apply the MC-PDFT method to calculate the heterolytic dissociation enthalpy of ferrocene. We find that MC-PDFT yields results that are at least as accurate as complete active space second-order perturbation theory and are more stable with respect to basis set, but at a fraction of the cost in both time and memory.

Adaptive Dynamics, Control, and Extinction in Networked Populations

DTIC Science & Technology

2015-07-09

network geometries. From the pre-history of paths that go extinct, a density function is created from the prehistory of these paths, and a clear local...density plots of Fig. 3b. Using the IAMM to compute the most probable path and comparing it to the prehistory of extinction events on stochastic networks

Dynamic density functional theory with hydrodynamic interactions and fluctuations

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

Donev, Aleksandar, E-mail: donev@courant.nyu.edu; Vanden-Eijnden, Eric, E-mail: eve2@courant.nyu.edu

2014-06-21

We derive a closed equation for the empirical concentration of colloidal particles in the presence of both hydrodynamic and direct interactions. The ensemble average of our functional Langevin equation reproduces known deterministic Dynamic Density Functional Theory (DDFT) [M. Rex and H. Löwen, “Dynamical density functional theory with hydrodynamic interactions and colloids in unstable traps,” Phys. Rev. Lett. 101(14), 148302 (2008)], and, at the same time, it also describes the microscopic fluctuations around the mean behavior. We suggest separating the ideal (non-interacting) contribution from additional corrections due to pairwise interactions. We find that, for an incompressible fluid and in the absencemore » of direct interactions, the mean concentration follows Fick's law just as for uncorrelated walkers. At the same time, the nature of the stochastic terms in fluctuating DDFT is shown to be distinctly different for hydrodynamically-correlated and uncorrelated walkers. This leads to striking differences in the behavior of the fluctuations around Fick's law, even in the absence of pairwise interactions. We connect our own prior work [A. Donev, T. G. Fai, and E. Vanden-Eijnden, “A reversible mesoscopic model of diffusion in liquids: from giant fluctuations to Fick's law,” J. Stat. Mech.: Theory Exp. (2014) P04004] on fluctuating hydrodynamics of diffusion in liquids to the DDFT literature, and demonstrate that the fluid cannot easily be eliminated from consideration if one wants to describe the collective diffusion in colloidal suspensions.« less

A density-functional study on the electronic and vibrational properties of layered antimony telluride.

PubMed

Stoffel, Ralf P; Deringer, Volker L; Simon, Ronnie E; Hermann, Raphaël P; Dronskowski, Richard

2015-03-04

We present a comprehensive survey of electronic and lattice-dynamical properties of crystalline antimony telluride (Sb2Te3). In a first step, the electronic structure and chemical bonding have been investigated, followed by calculations of the atomic force constants, phonon dispersion relationships and densities of states. Then, (macroscopic) physical properties of Sb2Te3 have been computed, namely, the atomic thermal displacement parameters, the Grüneisen parameter γ, the volume expansion of the lattice, and finally the bulk modulus B. We compare theoretical results from three popular and economic density-functional theory (DFT) approaches: the local density approximation (LDA), the generalized gradient approximation (GGA), and a posteriori dispersion corrections to the latter. Despite its simplicity, the LDA shows excellent performance for all properties investigated-including the Grüneisen parameter, which only the LDA is able to recover with confidence. In the absence of computationally more demanding hybrid DFT methods, the LDA seems to be a good choice for further lattice dynamical studies of Sb2Te3 and related layered telluride materials.

The Equation of State of Triamino-Trinitrobenzene from Density Functional Theory Molecular Dynamics

NASA Astrophysics Data System (ADS)

Wixom, Ryan R.

2017-06-01

The US-uP shock Hugoniot has long been the fundamental relationship used to experimentally define the unreacted equations of state of explosives. These experiments are typically performed on porous or composite samples, providing data that is specific to the density of the samples being tested. However, If the crystalline Hugoniot is known, analytical or numerical methods can be used to transform the US-uP relationship to describe the shock response of the porous material. To obtain an accurate crystalline equation of state for TATB, density functional theory based molecular dynamics were used to map out points on the Hugoniot. Since this method provides the pressure, temperature, density, and internal energy at each point on the Hugoniot, a complete equation of state can be constructed. Isotropic, uniaxial, hydrostatic, and isothermal compression of the simulation cell were used to examine TATB under different thermodynamic conditions. A cusp is observed in the Hugoniot that correlates to loss of aromaticity of the molecule. Results of the calculations will be presented and compared to the available experimental data. Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque NM.

High accuracy satellite drag model (HASDM)

NASA Astrophysics Data System (ADS)

Storz, M.; Bowman, B.; Branson, J.

The dominant error source in the force models used to predict low perigee satellite trajectories is atmospheric drag. Errors in operational thermospheric density models cause significant errors in predicted satellite positions, since these models do not account for dynamic changes in atmospheric drag for orbit predictions. The Air Force Space Battlelab's High Accuracy Satellite Drag Model (HASDM) estimates and predicts (out three days) a dynamically varying high-resolution density field. HASDM includes the Dynamic Calibration Atmosphere (DCA) algorithm that solves for the phases and amplitudes of the diurnal, semidiurnal and terdiurnal variations of thermospheric density near real-time from the observed drag effects on a set of Low Earth Orbit (LEO) calibration satellites. The density correction is expressed as a function of latitude, local solar time and altitude. In HASDM, a time series prediction filter relates the extreme ultraviolet (EUV) energy index E10.7 and the geomagnetic storm index a p to the DCA density correction parameters. The E10.7 index is generated by the SOLAR2000 model, the first full spectrum model of solar irradiance. The estimated and predicted density fields will be used operationally to significantly improve the accuracy of predicted trajectories for all low perigee satellites.

High accuracy satellite drag model (HASDM)

NASA Astrophysics Data System (ADS)

Storz, Mark F.; Bowman, Bruce R.; Branson, Major James I.; Casali, Stephen J.; Tobiska, W. Kent

The dominant error source in force models used to predict low-perigee satellite trajectories is atmospheric drag. Errors in operational thermospheric density models cause significant errors in predicted satellite positions, since these models do not account for dynamic changes in atmospheric drag for orbit predictions. The Air Force Space Battlelab's High Accuracy Satellite Drag Model (HASDM) estimates and predicts (out three days) a dynamically varying global density field. HASDM includes the Dynamic Calibration Atmosphere (DCA) algorithm that solves for the phases and amplitudes of the diurnal and semidiurnal variations of thermospheric density near real-time from the observed drag effects on a set of Low Earth Orbit (LEO) calibration satellites. The density correction is expressed as a function of latitude, local solar time and altitude. In HASDM, a time series prediction filter relates the extreme ultraviolet (EUV) energy index E10.7 and the geomagnetic storm index ap, to the DCA density correction parameters. The E10.7 index is generated by the SOLAR2000 model, the first full spectrum model of solar irradiance. The estimated and predicted density fields will be used operationally to significantly improve the accuracy of predicted trajectories for all low-perigee satellites.

First-Principles Molecular Dynamics Simulations of NaCl in Water: Performance of Advanced Exchange-Correlation Approximations in Density Functional Theory

NASA Astrophysics Data System (ADS)

Yao, Yi; Kanai, Yosuke

Our ability to correctly model the association of oppositely charged ions in water is fundamental in physical chemistry and essential to various technological and biological applications of molecular dynamics (MD) simulations. MD simulations using classical force fields often show strong clustering of NaCl in the aqueous ionic solutions as a consequence of a deep contact pair minimum in the potential of mean force (PMF) curve. First-Principles Molecular Dynamics (FPMD) based on Density functional theory (DFT) with the popular PBE exchange-correlation approximation, on the other hand, show a different result with a shallow contact pair minimum in the PMF. We employed two of most promising exchange-correlation approximations, ωB97xv by Mardiorossian and Head-Gordon and SCAN by Sun, Ruzsinszky and Perdew, to examine the PMF using FPMD simulations. ωB97xv is highly empirically and optimized in the space of range-separated hybrid functional with a dispersion correction while SCAN is the most recent meta-GGA functional that is constructed by satisfying various known conditions in well-defined physical limits. We will discuss our findings for PMF, charge transfer, water dipoles, etc.

Theory of dynamic barriers, activated hopping, and the glass transition in polymer melts

NASA Astrophysics Data System (ADS)

Schweizer, Kenneth S.; Saltzman, Erica J.

2004-07-01

A statistical mechanical theory of collective dynamic barriers, slow segmental relaxation, and the glass transition of polymer melts is developed by combining, and in some aspects extending, methods of mode coupling, density functional, and activated hopping transport theories. A coarse-grained description of polymer chains is adopted and the melt is treated as a liquid of segments. The theory is built on the idea that collective density fluctuations on length scales considerably longer than the local cage scale are of primary importance in the deeply supercooled regime. The barrier hopping or segmental relaxation time is predicted to be a function primarily of a single parameter that is chemical structure, temperature, and pressure dependent. This parameter depends on the material-specific dimensionless amplitude of thermal density fluctuations (compressibility) and a reduced segmental density determined by the packing length and backbone characteristic ratio. Analytic results are derived for a crossover temperature Tc, collective barrier, and glass transition temperature Tg. The relation of these quantities to structural and thermodynamic properties of the polymer melt is established. A universal power-law scaling behavior of the relaxation time below Tc is predicted based on identification of a reduced temperature variable that quantifies the breadth of the supercooled regime. Connections between the ratio Tc/Tg, two measures of dynamic fragility, and the magnitude of the local relaxation time at Tg logically follow. Excellent agreement with experiment is found for these generic aspects, and the crucial importance of the experimentally observed near universality of the dynamic crossover time is established. Extensions of the theory to treat the full chain dynamics, heterogeneity, barrier fluctuations, and nonpolymeric thermal glass forming liquids are briefly discussed.

A new class of ensemble conserving algorithms for approximate quantum dynamics: Theoretical formulation and model problems.

PubMed

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

2015-06-28

We develop two classes of quasi-classical dynamics that are shown to conserve the initial quantum ensemble when used in combination with the Feynman-Kleinert approximation of the density operator. These dynamics are used to improve the Feynman-Kleinert implementation of the classical Wigner approximation for the evaluation of quantum time correlation functions known as Feynman-Kleinert linearized path-integral. As shown, both classes of dynamics are able to recover the exact classical and high temperature limits of the quantum time correlation function, while a subset is able to recover the exact harmonic limit. A comparison of the approximate quantum time correlation functions obtained from both classes of dynamics is made with the exact results for the challenging model problems of the quartic and double-well potentials. It is found that these dynamics provide a great improvement over the classical Wigner approximation, in which purely classical dynamics are used. In a special case, our first method becomes identical to centroid molecular dynamics.

Molecular mechanics and structure of the fluid-solid interface in simple fluids

NASA Astrophysics Data System (ADS)

Wang, Gerald J.; Hadjiconstantinou, Nicolas G.

2017-09-01

Near a fluid-solid interface, the fluid spatial density profile is highly nonuniform at the molecular scale. This nonuniformity can have profound effects on the dynamical behavior of the fluid and has been shown to play an especially important role when modeling a wide variety of nanoscale heat and momentum transfer phenomena. We use molecular-mechanics arguments and molecular-dynamics (MD) simulations to develop a better understanding of the structure of the first fluid layer directly adjacent to the solid in the layering regime, as delineated by a nondimensional number that compares the effects of wall-fluid interaction to thermal energy. Using asymptotic analysis of the Nernst-Planck equation, we show that features of the fluid density profile close to the wall, such as the areal density of the first layer ΣFL (defined as the number of atoms in this layer per unit of fluid-solid interfacial area), can be expressed as polynomial functions of the fluid average density ρave. This is found to be in agreement with MD simulations, which also show that the width of the first layer hFL is a linear function of the average density and only a weak function of the temperature T . These results can be combined to show that, for system average densities corresponding to a dense fluid (ρave≥0.7 ), the ratio C ≡ΣFLρavehFL, representing a density enhancement with respect to the bulk fluid, depends only weakly on temperature and is essentially independent of density. Further MD simulations suggest that the above results, nominally valid for large systems (solid in contact with semi-infinite fluid), also describe fluid-solid interfaces under considerable nanoconfinement, provided ρave is appropriately defined.

Binary collision approximations for the memory function for density fluctuations in equilibrium atomic liquids

NASA Astrophysics Data System (ADS)

Noah, Joyce E.

Time correlation functions of density fluctuations of liquids at equilibrium can be used to relate the microscopic dynamics of a liquid to its macroscopic transport properties. Time correlation functions are especially useful since they can be generated in a variety of ways, from scattering experiments to computer simulation to analytic theory. The kinetic theory of fluctuations in equilibrium liquids is an analytic theory for calculating correlation functions using memory functions. In this work, we use a diagrammatic formulation of the kinetic theory to develop a series of binary collision approximations for the collisional part of the memory function. We define binary collisions as collisions between two distinct density fluctuations whose identities are fixed during the duration of a collsion. R approximations are for the short time part of the memory function, and build upon the work of Ranganathan and Andersen. These approximations have purely repulsive interactions between the fluctuations. The second type of approximation, RA approximations, is for the longer time part of the memory function, where the density fluctuations now interact via repulsive and attractive forces. Although RA approximations are a natural extension of R approximations, they permit two density fluctuations to become trapped in the wells of the interaction potential, leading to long-lived oscillatory behavior, which is unphysical. Therefore we consider S approximations which describe binary particles which experience the random effect of the surroundings while interacting via repulsive or repulsive and attractive interactions. For each of these approximations for the memory function we numerically solve the kinetic equation to generate correlation functions. These results are compared to molecular dynamics results for the correlation functions. Comparing the successes and failures of the different approximations, we conclude that R approximations give more accurate intermediate and long time results while RA and S approximations do particularly well at predicting the short time behavior. Lastly, we also develop a series of non-graphically derived approximations and use an optimization procedure to determine the underlying memory function from the simulation data. These approaches provide valuable information about the memory function that will be used in the development of future kinetic theories.

Demographic models reveal the shape of density dependence for a specialist insect herbivore on variable host plants.

PubMed

Miller, Tom E X

2007-07-01

1. It is widely accepted that density-dependent processes play an important role in most natural populations. However, persistent challenges in our understanding of density-dependent population dynamics include evaluating the shape of the relationship between density and demographic rates (linear, concave, convex), and identifying extrinsic factors that can mediate this relationship. 2. I studied the population dynamics of the cactus bug Narnia pallidicornis on host plants (Opuntia imbricata) that varied naturally in relative reproductive effort (RRE, the proportion of meristems allocated to reproduction), an important plant quality trait. I manipulated per-plant cactus bug densities, quantified subsequent dynamics, and fit stage-structured models to the experimental data to ask if and how density influences demographic parameters. 3. In the field experiment, I found that populations with variable starting densities quickly converged upon similar growth trajectories. In the model-fitting analyses, the data strongly supported a model that defined the juvenile cactus bug retention parameter (joint probability of surviving and not dispersing) as a nonlinear decreasing function of density. The estimated shape of this relationship shifted from concave to convex with increasing host-plant RRE. 4. The results demonstrate that host-plant traits are critical sources of variation in the strength and shape of density dependence in insects, and highlight the utility of integrated experimental-theoretical approaches for identifying processes underlying patterns of change in natural populations.

Glass-like dynamics in confined and congested ant traffic.

PubMed

Gravish, Nick; Gold, Gregory; Zangwill, Andrew; Goodisman, Michael A D; Goldman, Daniel I

2015-09-07

The collective movement of animal groups often occurs in confined spaces. As animal groups are challenged to move at high density, their mobility dynamics may resemble the flow of densely packed non-living soft materials such as colloids, grains, or polymers. However, unlike inert soft-materials, self-propelled collective living systems often display social interactions whose influence on collective mobility are only now being explored. In this paper, we study the mobility of bi-directional traffic flow in a social insect (the fire ant Solenopsis invicta) as we vary the diameter of confining foraging tunnels. In all tunnel diameters, we observe the emergence of spatially heterogeneous regions of fast and slow traffic that are induced through two phenomena: physical obstruction, arising from the inability of individual ants to interpenetrate, and time-delay resulting from social interaction in which ants stop to briefly antennate. Density correlation functions reveal that the relaxation dynamics of high density traffic fluctuations scale linearly with fluctuation size and are sensitive to tunnel diameter. We separate the roles of physical obstruction and social interactions in traffic flow using cellular automata based simulation. Social interaction between ants is modeled as a dwell time (Tint) over which interacting ants remain stationary in the tunnel. Investigation over a range of densities and Tint reveals that the slowing dynamics of collective motion in social living systems are consistent with dynamics near a fragile glass transition in inert soft-matter systems. In particular, flow is relatively insensitive to density until a critical density is reached. As social interaction affinity is increased (increasing Tint) traffic dynamics change and resemble a strong glass transition. Thus, social interactions play an important role in the mobility of collective living systems at high density. Our experiments and model demonstrate that the concepts of soft-matter physics aid understanding of the mobility of collective living systems, and motivate further inquiry into the dynamics of densely confined social living systems.

The mass function and dynamical mass of young star clusters: why their initial crossing-time matters crucially

NASA Astrophysics Data System (ADS)

Parmentier, Geneviève; Baumgardt, Holger

2012-12-01

We highlight the impact of cluster-mass-dependent evolutionary rates upon the evolution of the cluster mass function during violent relaxation, that is, while clusters dynamically respond to the expulsion of their residual star-forming gas. Mass-dependent evolutionary rates arise when the mean volume density of cluster-forming regions is mass-dependent. In that case, even if the initial conditions are such that the cluster mass function at the end of violent relaxation has the same shape as the embedded-cluster mass function (i.e. infant weight-loss is mass-independent), the shape of the cluster mass function does change transiently during violent relaxation. In contrast, for cluster-forming regions of constant mean volume density, the cluster mass function shape is preserved all through violent relaxation since all clusters then evolve at the same mass-independent rate. On the scale of individual clusters, we model the evolution of the ratio of the dynamical mass to luminous mass of a cluster after gas expulsion. Specifically, we map the radial dependence of the time-scale for a star cluster to return to equilibrium. We stress that fields of view a few pc in size only, typical of compact clusters with rapid evolutionary rates, are likely to reveal cluster regions which have returned to equilibrium even if the cluster experienced a major gas expulsion episode a few Myr earlier. We provide models with the aperture and time expressed in units of the initial half-mass radius and initial crossing-time, respectively, so that our results can be applied to clusters with initial densities, sizes, and apertures different from ours.

Glass Formation of n-Butanol: Coarse-grained Molecular Dynamics Simulations Using Gay-Berne Potential Model

NASA Astrophysics Data System (ADS)

Xie, Gui-long; Zhang, Yong-hong; Huang, Shi-ping

2012-04-01

Using coarse-grained molecular dynamics simulations based on Gay-Berne potential model, we have simulated the cooling process of liquid n-butanol. A new set of GB parameters are obtained by fitting the results of density functional theory calculations. The simulations are carried out in the range of 290-50 K with temperature decrements of 10 K. The cooling characteristics are determined on the basis of the variations of the density, the potential energy and orientational order parameter with temperature, whose slopes all show discontinuity. Both the radial distribution function curves and the second-rank orientational correlation function curves exhibit splitting in the second peak. Using the discontinuous change of these thermodynamic and structure properties, we obtain the glass transition at an estimate of temperature Tg=120±10 K, which is in good agreement with experimental results 110±1 K.

The atomic scale structure of CXV carbon: wide-angle x-ray scattering and modeling studies.

PubMed

Hawelek, L; Brodka, A; Dore, J C; Honkimaki, V; Burian, A

2013-11-13

The disordered structure of commercially available CXV activated carbon produced from finely powdered wood-based carbon has been studied using the wide-angle x-ray scattering technique, molecular dynamics and density functional theory simulations. The x-ray scattering data has been converted to the real space representation in the form of the pair correlation function via the Fourier transform. Geometry optimizations using classical molecular dynamics based on the reactive empirical bond order potential and density functional theory at the B3LYP/6-31g* level have been performed to generate nanoscale models of CXV carbon consistent with the experimental data. The final model of the structure comprises four chain-like and buckled graphitic layers containing a small percentage of four-fold coordinated atoms (sp(3) defects) in each layer. The presence of non-hexagonal rings in the atomic arrangement has been also considered.

Structural, electronic, mechanical, and dynamical properties of graphene oxides: A first principles study

NASA Astrophysics Data System (ADS)

Dabhi, Shweta D.; Gupta, Sanjay D.; Jha, Prafulla K.

2014-05-01

We report the results of a theoretical study on the structural, electronic, mechanical, and vibrational properties of some graphene oxide models (GDO, a-GMO, z-GMO, ep-GMO and mix-GMO) at ambient pressure. The calculations are based on the ab-initio plane-wave pseudo potential density functional theory, within the generalized gradient approximations for the exchange and correlation functional. The calculated values of lattice parameters, bulk modulus, and its first order pressure derivative are in good agreement with other reports. A linear response approach to the density functional theory is used to derive the phonon frequencies. We discuss the contribution of the phonons in the dynamical stability of graphene oxides and detailed analysis of zone centre phonon modes in all the above mentioned models. Our study demonstrates a wide range of energy gap available in the considered models of graphene oxide and hence the possibility of their use in nanodevices.

Effect of total and pair configurational entropy in determining dynamics of supercooled liquids over a range of densities

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

Banerjee, Atreyee; Nandi, Manoj Kumar; Bhattacharyya, Sarika Maitra, E-mail: mb.sarika@ncl.res.in

2016-07-21

In this paper, we present a study of supercooled liquids interacting with the Lennard Jones potential and the corresponding purely repulsive (Weeks-Chandler-Andersen) potential, over a range of densities and temperatures, in order to understand the origin of their different dynamics in spite of their structures being similar. Using the configurational entropy as the thermodynamic marker via the Adam Gibbs relation, we show that the difference in the dynamics of these two systems at low temperatures can be explained from thermodynamics. At higher densities both the thermodynamical and dynamical difference between these model systems decrease, which is quantitatively demonstrated in thismore » paper by calculating different parameters. The study also reveals the origin of the difference in pair entropy despite the similarity in the structure. Although the maximum difference in structure is obtained in the partial radial distribution function of the B type of particles, the rdf of AA pairs and AB pairs gives rise to the differences in the entropy and dynamics. This work supports the observation made in an earlier study [A. Banerjee et al., Phys. Rev. Lett. 113, 225701 (2014)] and shows that they are generic in nature, independent of density.« less

Interfacial dynamic surface traps of lead sulfide (PbS) nanocrystals: test-platform for interfacial charge carrier traps at the organic/inorganic functional interface

NASA Astrophysics Data System (ADS)

Kim, Youngjun; Ko, Hyungduk; Park, Byoungnam

2018-04-01

Nanocrystal (NC) size and ligand dependent dynamic trap formation of lead sulfide (PbS) NCs in contact with an organic semiconductor were investigated using a pentacene/PbS field effect transistor (FET). We used a bilayer pentacene/PbS FET to extract information of the surface traps of PbS NCs at the pentacene/PbS interface through the field effect-induced charge carrier density measurement in the threshold and subthreshold regions. PbS size and ligand dependent trap properties were elucidated by the time domain and threshold voltage measurements in which threshold voltage shift occurs by carrier charging and discharging in the trap states of PbS NCs. The observed threshold voltage shift is interpreted in context of electron trapping through dynamic trap formation associated with PbS NCs. To the best of our knowledge, this is the first demonstration of the presence of interfacial dynamic trap density of PbS NC in contact with an organic semiconductor (pentacene). We found that the dynamic trap density of the PbS NC is size dependent and the carrier residence time in the specific trap sites is more sensitive to NC size variation than to NC ligand exchange. The probing method presented in the study offers a means to investigate the interfacial surface traps at the organic-inorganic hetero-junction, otherwise understanding of the buried surface traps at the functional interface would be elusive.

Avoiding fractional electrons in subsystem DFT based ab-initio molecular dynamics yields accurate models for liquid water and solvated OH radical

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

Genova, Alessandro, E-mail: alessandro.genova@rutgers.edu; Pavanello, Michele, E-mail: m.pavanello@rutgers.edu; Ceresoli, Davide, E-mail: davide.ceresoli@cnr.it

2016-06-21

In this work we achieve three milestones: (1) we present a subsystem DFT method capable of running ab-initio molecular dynamics simulations accurately and efficiently. (2) In order to rid the simulations of inter-molecular self-interaction error, we exploit the ability of semilocal frozen density embedding formulation of subsystem DFT to represent the total electron density as a sum of localized subsystem electron densities that are constrained to integrate to a preset, constant number of electrons; the success of the method relies on the fact that employed semilocal nonadditive kinetic energy functionals effectively cancel out errors in semilocal exchange–correlation potentials that aremore » linked to static correlation effects and self-interaction. (3) We demonstrate this concept by simulating liquid water and solvated OH{sup •} radical. While the bulk of our simulations have been performed on a periodic box containing 64 independent water molecules for 52 ps, we also simulated a box containing 256 water molecules for 22 ps. The results show that, provided one employs an accurate nonadditive kinetic energy functional, the dynamics of liquid water and OH{sup •} radical are in semiquantitative agreement with experimental results or higher-level electronic structure calculations. Our assessments are based upon comparisons of radial and angular distribution functions as well as the diffusion coefficient of the liquid.« less

Avoiding fractional electrons in subsystem DFT based ab-initio molecular dynamics yields accurate models for liquid water and solvated OH radical.

PubMed

Genova, Alessandro; Ceresoli, Davide; Pavanello, Michele

2016-06-21

In this work we achieve three milestones: (1) we present a subsystem DFT method capable of running ab-initio molecular dynamics simulations accurately and efficiently. (2) In order to rid the simulations of inter-molecular self-interaction error, we exploit the ability of semilocal frozen density embedding formulation of subsystem DFT to represent the total electron density as a sum of localized subsystem electron densities that are constrained to integrate to a preset, constant number of electrons; the success of the method relies on the fact that employed semilocal nonadditive kinetic energy functionals effectively cancel out errors in semilocal exchange-correlation potentials that are linked to static correlation effects and self-interaction. (3) We demonstrate this concept by simulating liquid water and solvated OH(•) radical. While the bulk of our simulations have been performed on a periodic box containing 64 independent water molecules for 52 ps, we also simulated a box containing 256 water molecules for 22 ps. The results show that, provided one employs an accurate nonadditive kinetic energy functional, the dynamics of liquid water and OH(•) radical are in semiquantitative agreement with experimental results or higher-level electronic structure calculations. Our assessments are based upon comparisons of radial and angular distribution functions as well as the diffusion coefficient of the liquid.

The Superstatistical Nature and Interoccurrence Time of Atmospheric Mercury Concentration Fluctuations

EPA Science Inventory

The probability density function (PDF) of the time intervals between subsequent extreme events in atmospheric Hg0 concentration data series from different latitudes has been investigated. The Hg0 dynamic possesses a long-term memory autocorrelation function. Above a fixed thresh...

Energetics and Dynamics of GaAs Epitaxial Growth via Quantum Wave Packet Studies

NASA Technical Reports Server (NTRS)

Dzegilenko, Fedor N.; Saini, Subhash (Technical Monitor)

1998-01-01

The dynamics of As(sub 2) molecule incorporation into the flat Ga-terminated GaAs(100) surface is studied computationally. The time-dependent Schrodinger equation is solved on a two-dimensional potential energy surface obtained using density functional theory calculations. The probabilities of trapping and subsequent dissociation of the molecular As(sub 2) bond are calculated as a function of beam translational energy and vibrational quantum number of As(sub 2).

Combination of Wavefunction and Density Functional Approximations for Describing Electronic Correlation

NASA Astrophysics Data System (ADS)

Garza, Alejandro J.

Perhaps the most important approximations to the electronic structure problem in quantum chemistry are those based on coupled cluster and density functional theories. Coupled cluster theory has been called the ``gold standard'' of quantum chemistry due to the high accuracy that it achieves for weakly correlated systems. Kohn-Sham density functionals based on semilocal approximations are, without a doubt, the most widely used methods in chemistry and material science because of their high accuracy/cost ratio. The root of the success of coupled cluster and density functionals is their ability to efficiently describe the dynamic part of the electron correlation. However, both traditional coupled cluster and density functional approximations may fail catastrophically when substantial static correlation is present. This severely limits the applicability of these methods to a plethora of important chemical and physical problems such as, e.g., the description of bond breaking, transition states, transition metal-, lanthanide- and actinide-containing compounds, and superconductivity. In an attempt to tackle this problem, nonstandard (single-reference) coupled cluster-based techniques that aim to describe static correlation have been recently developed: pair coupled cluster doubles (pCCD) and singlet-paired coupled cluster doubles (CCD0). The ability to describe static correlation in pCCD and CCD0 comes, however, at the expense of important amounts of dynamic correlation so that the high accuracy of standard coupled cluster becomes unattainable. Thus, the reliable and efficient description of static and dynamic correlation in a simultaneous manner remains an open problem for quantum chemistry and many-body theory in general. In this thesis, different ways to combine pCCD and CCD0 with density functionals in order to describe static and dynamic correlation simultaneously (and efficiently) are explored. The combination of wavefunction and density functional methods has a long history in quantum chemistry (practical implementations have appeared in the literature since the 1970s). However, this kind of techniques have not achieved widespread use due to problems such as double counting of correlation and the symmetry dilemma--the fact that wavefunction methods respect the symmetries of Hamiltonian, while modern functionals are designed to work with broken symmetry densities. Here, particular mathematical features of pCCD and CCD0 are exploited to avoid these problems in an efficient manner. The two resulting families of approximations, denoted as pCCD+DFT and CCD0+DFT, are shown to be able to describe static and dynamic correlation in standard benchmark calculations. Furthermore, it is also shown that CCD0+DFT lends itself to combination with correlation from the direct random phase approximation (dRPA). Inclusion of dRPA in the long-range via the technique of range-separation allows for the description of dispersion correlation, the remaining part of the correlation. Thus, when combined with the dRPA, CCD0+DFT can account for all three-types of electron correlation that are necessary to accurately describe molecular systems. Lastly, applications of CCD0+DFT to actinide chemistry are considered in this work. The accuracy of CCD0+DFT for predicting equilibrium geometries and vibrational frequencies of actinide molecules and ions is assessed and compared to that of well-established quantum chemical methods. For this purpose, the f0 actinyl series (UO2 2+, NpO 23+, PuO24+, the isoelectronic NUN, and Thorium (ThO, ThO2+) and Nobelium (NoO, NoO2) oxides are studied. It is shown that the CCD0+DFT description of these species agrees with available experimental data and is comparable with the results given by the highest-level calculations that are possible for such heavy compounds while being, at least, an order of magnitude lower in computational cost.

The role of nurse functional types in seedling recruitment dynamics of alternative states in rangelands

NASA Astrophysics Data System (ADS)

López, Dardo R.; Cavallero, Laura

2017-02-01

In arid ecosystems, recruitment dynamics are limited by harsh environmental conditions and greatly depend on the net outcome of the balance between facilitation and competition. This outcome can change as a consequence of degradation caused by livestock overgrazing. Also, distinct plant species may show a differential response to a common neighbour under the same environmental conditions. Therefore, ecosystem degradation could affect the net balance of plant-plant interactions, which can also depend on the functional traits of potential nurse species. The aim of this study is to assess the influence of alternative degradation states on (i) the density of seedlings of perennial species emerging in four microsite types, and on (ii) the relative interaction intensity (RII) between seedlings and potential nurses belonging to three functional types (deep- and shallow-rooted shrubs, and tussock grasses). During three years, we recorded seedling density of perennial species in four alternative degradation states in grass-shrubby steppes from northwestern Patagonia. The density of emerged seedlings of perennial species decreased sharply as degradation increased, showing non-linear responses in most microsites. Seedling density underneath deep-rooted shrubs was higher than underneath shallow-rooted shrubs and tussock grasses. Also, deep-rooted shrubs were the only functional type that recorded seedling emergence in highly degraded states. Deep-rooted shrubs had facilitative effects on the seedlings emerging and surviving underneath them, independently of ecosystem degradation. In contrast, RII between shallow-rooted shrubs and recently emerged seedlings, switched from positive effects in the less degraded states, to negative effects in the most degraded state. Tussock grasses recorded the weakest intensity of facilitative interactions with recently emerged seedlings, switching to competitive interactions as degradation increased. Our results suggest that species with key functional traits should be considered in management and restoration plans for rangelands with different degradation levels, since they have a strong influence in the net outcome of plant-plant interactions and in the recruitment dynamics of arid ecosystems.

Accurate van der Waals coefficients from density functional theory

PubMed Central

Tao, Jianmin; Perdew, John P.; Ruzsinszky, Adrienn

2012-01-01

The van der Waals interaction is a weak, long-range correlation, arising from quantum electronic charge fluctuations. This interaction affects many properties of materials. A simple and yet accurate estimate of this effect will facilitate computer simulation of complex molecular materials and drug design. Here we develop a fast approach for accurate evaluation of dynamic multipole polarizabilities and van der Waals (vdW) coefficients of all orders from the electron density and static multipole polarizabilities of each atom or other spherical object, without empirical fitting. Our dynamic polarizabilities (dipole, quadrupole, octupole, etc.) are exact in the zero- and high-frequency limits, and exact at all frequencies for a metallic sphere of uniform density. Our theory predicts dynamic multipole polarizabilities in excellent agreement with more expensive many-body methods, and yields therefrom vdW coefficients C6, C8, C10 for atom pairs with a mean absolute relative error of only 3%. PMID:22205765

Performance of extended Lagrangian schemes for molecular dynamics simulations with classical polarizable force fields and density functional theory

NASA Astrophysics Data System (ADS)

Vitale, Valerio; Dziedzic, Jacek; Albaugh, Alex; Niklasson, Anders M. N.; Head-Gordon, Teresa; Skylaris, Chris-Kriton

2017-03-01

Iterative energy minimization with the aim of achieving self-consistency is a common feature of Born-Oppenheimer molecular dynamics (BOMD) and classical molecular dynamics with polarizable force fields. In the former, the electronic degrees of freedom are optimized, while the latter often involves an iterative determination of induced point dipoles. The computational effort of the self-consistency procedure can be reduced by re-using converged solutions from previous time steps. However, this must be done carefully, as not to break time-reversal symmetry, which negatively impacts energy conservation. Self-consistent schemes based on the extended Lagrangian formalism, where the initial guesses for the optimized quantities are treated as auxiliary degrees of freedom, constitute one elegant solution. We report on the performance of two integration schemes with the same underlying extended Lagrangian structure, which we both employ in two radically distinct regimes—in classical molecular dynamics simulations with the AMOEBA polarizable force field and in BOMD simulations with the Onetep linear-scaling density functional theory (LS-DFT) approach. Both integration schemes are found to offer significant improvements over the standard (unpropagated) molecular dynamics formulation in both the classical and LS-DFT regimes.

A micromechanical approach for homogenization of elastic metamaterials with dynamic microstructure.

PubMed

Muhlestein, Michael B; Haberman, Michael R

2016-08-01

An approximate homogenization technique is presented for generally anisotropic elastic metamaterials consisting of an elastic host material containing randomly distributed heterogeneities displaying frequency-dependent material properties. The dynamic response may arise from relaxation processes such as viscoelasticity or from dynamic microstructure. A Green's function approach is used to model elastic inhomogeneities embedded within a uniform elastic matrix as force sources that are excited by a time-varying, spatially uniform displacement field. Assuming dynamic subwavelength inhomogeneities only interact through their volume-averaged fields implies the macroscopic stress and momentum density fields are functions of both the microscopic strain and velocity fields, and may be related to the macroscopic strain and velocity fields through localization tensors. The macroscopic and microscopic fields are combined to yield a homogenization scheme that predicts the local effective stiffness, density and coupling tensors for an effective Willis-type constitutive equation. It is shown that when internal degrees of freedom of the inhomogeneities are present, Willis-type coupling becomes necessary on the macroscale. To demonstrate the utility of the homogenization technique, the effective properties of an isotropic elastic matrix material containing isotropic and anisotropic spherical inhomogeneities, isotropic spheroidal inhomogeneities and isotropic dynamic spherical inhomogeneities are presented and discussed.

A micromechanical approach for homogenization of elastic metamaterials with dynamic microstructure

PubMed Central

Haberman, Michael R.

2016-01-01

An approximate homogenization technique is presented for generally anisotropic elastic metamaterials consisting of an elastic host material containing randomly distributed heterogeneities displaying frequency-dependent material properties. The dynamic response may arise from relaxation processes such as viscoelasticity or from dynamic microstructure. A Green's function approach is used to model elastic inhomogeneities embedded within a uniform elastic matrix as force sources that are excited by a time-varying, spatially uniform displacement field. Assuming dynamic subwavelength inhomogeneities only interact through their volume-averaged fields implies the macroscopic stress and momentum density fields are functions of both the microscopic strain and velocity fields, and may be related to the macroscopic strain and velocity fields through localization tensors. The macroscopic and microscopic fields are combined to yield a homogenization scheme that predicts the local effective stiffness, density and coupling tensors for an effective Willis-type constitutive equation. It is shown that when internal degrees of freedom of the inhomogeneities are present, Willis-type coupling becomes necessary on the macroscale. To demonstrate the utility of the homogenization technique, the effective properties of an isotropic elastic matrix material containing isotropic and anisotropic spherical inhomogeneities, isotropic spheroidal inhomogeneities and isotropic dynamic spherical inhomogeneities are presented and discussed. PMID:27616932

A micromechanical approach for homogenization of elastic metamaterials with dynamic microstructure

NASA Astrophysics Data System (ADS)

Muhlestein, Michael B.; Haberman, Michael R.

2016-08-01

An approximate homogenization technique is presented for generally anisotropic elastic metamaterials consisting of an elastic host material containing randomly distributed heterogeneities displaying frequency-dependent material properties. The dynamic response may arise from relaxation processes such as viscoelasticity or from dynamic microstructure. A Green's function approach is used to model elastic inhomogeneities embedded within a uniform elastic matrix as force sources that are excited by a time-varying, spatially uniform displacement field. Assuming dynamic subwavelength inhomogeneities only interact through their volume-averaged fields implies the macroscopic stress and momentum density fields are functions of both the microscopic strain and velocity fields, and may be related to the macroscopic strain and velocity fields through localization tensors. The macroscopic and microscopic fields are combined to yield a homogenization scheme that predicts the local effective stiffness, density and coupling tensors for an effective Willis-type constitutive equation. It is shown that when internal degrees of freedom of the inhomogeneities are present, Willis-type coupling becomes necessary on the macroscale. To demonstrate the utility of the homogenization technique, the effective properties of an isotropic elastic matrix material containing isotropic and anisotropic spherical inhomogeneities, isotropic spheroidal inhomogeneities and isotropic dynamic spherical inhomogeneities are presented and discussed.

Performance of extended Lagrangian schemes for molecular dynamics simulations with classical polarizable force fields and density functional theory.

PubMed

Vitale, Valerio; Dziedzic, Jacek; Albaugh, Alex; Niklasson, Anders M N; Head-Gordon, Teresa; Skylaris, Chris-Kriton

2017-03-28

Iterative energy minimization with the aim of achieving self-consistency is a common feature of Born-Oppenheimer molecular dynamics (BOMD) and classical molecular dynamics with polarizable force fields. In the former, the electronic degrees of freedom are optimized, while the latter often involves an iterative determination of induced point dipoles. The computational effort of the self-consistency procedure can be reduced by re-using converged solutions from previous time steps. However, this must be done carefully, as not to break time-reversal symmetry, which negatively impacts energy conservation. Self-consistent schemes based on the extended Lagrangian formalism, where the initial guesses for the optimized quantities are treated as auxiliary degrees of freedom, constitute one elegant solution. We report on the performance of two integration schemes with the same underlying extended Lagrangian structure, which we both employ in two radically distinct regimes-in classical molecular dynamics simulations with the AMOEBA polarizable force field and in BOMD simulations with the Onetep linear-scaling density functional theory (LS-DFT) approach. Both integration schemes are found to offer significant improvements over the standard (unpropagated) molecular dynamics formulation in both the classical and LS-DFT regimes.

Performance of extended Lagrangian schemes for molecular dynamics simulations with classical polarizable force fields and density functional theory

DOE PAGES

Vitale, Valerio; Dziedzic, Jacek; Albaugh, Alex; ...

2017-03-28

Iterative energy minimization with the aim of achieving self-consistency is a common feature of Born-Oppenheimer molecular dynamics (BOMD) and classical molecular dynamics with polarizable force fields. In the former, the electronic degrees of freedom are optimized, while the latter often involves an iterative determination of induced point dipoles. The computational effort of the self-consistency procedure can be reduced by re-using converged solutions from previous time steps. However, this must be done carefully, as not to break time-reversal symmetry, which negatively impacts energy conservation. Self-consistent schemes based on the extended Lagrangian formalism, where the initial guesses for the optimized quantities aremore » treated as auxiliary degrees of freedom, constitute one elegant solution. We report on the performance of two integration schemes with the same underlying extended Lagrangian structure, which we both employ in two radically distinct regimes—in classical molecular dynamics simulations with the AMOEBA polarizable force field and in BOMD simulations with the Onetep linear-scaling density functional theory (LS-DFT) approach. Furthermore, both integration schemes are found to offer significant improvements over the standard (unpropagated) molecular dynamics formulation in both the classical and LS-DFT regimes.« less

Performance of extended Lagrangian schemes for molecular dynamics simulations with classical polarizable force fields and density functional theory

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

Vitale, Valerio; Dziedzic, Jacek; Albaugh, Alex

Iterative energy minimization with the aim of achieving self-consistency is a common feature of Born-Oppenheimer molecular dynamics (BOMD) and classical molecular dynamics with polarizable force fields. In the former, the electronic degrees of freedom are optimized, while the latter often involves an iterative determination of induced point dipoles. The computational effort of the self-consistency procedure can be reduced by re-using converged solutions from previous time steps. However, this must be done carefully, as not to break time-reversal symmetry, which negatively impacts energy conservation. Self-consistent schemes based on the extended Lagrangian formalism, where the initial guesses for the optimized quantities aremore » treated as auxiliary degrees of freedom, constitute one elegant solution. We report on the performance of two integration schemes with the same underlying extended Lagrangian structure, which we both employ in two radically distinct regimes—in classical molecular dynamics simulations with the AMOEBA polarizable force field and in BOMD simulations with the Onetep linear-scaling density functional theory (LS-DFT) approach. Furthermore, both integration schemes are found to offer significant improvements over the standard (unpropagated) molecular dynamics formulation in both the classical and LS-DFT regimes.« less

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.

First-Principles Study of the Structural, Optical, Dynamical and Thermodynamic Properties of BaZnO2 Under Pressure

NASA Astrophysics Data System (ADS)

Wang, Yi-Xian; Hu, Cui-E.; Chen, Yang-Mei; Cheng, Yan; Ji, Guang-Fu

2016-11-01

The structural, optical, dynamical, and thermodynamic properties of BaZnO2 under pressure are studied based on the density functional theory. The calculated structural parameters are consistent with the available experimental data. In the ground state, the electronic band structure and density of states indicate that BaZnO2 is an insulator with a direct gap of 2.2 eV. The Mulliken charges are also analyzed to characterize the bonding property. After the structural relaxation, the optical properties are studied. It is found that the dielectric function of E Vert x and EVert y are isotropic, whereas the EVert x and EVert z are anisotropic. The effect of pressure on the energy-loss function in the ultraviolet region becomes more obvious as the pressure increases. Furthermore, the dynamical properties under different pressures are investigated using the finite displacement method. We find that the P3121 phase of BaZnO2 is dynamically stable under the pressure ranging from 0 GPa to 30 GPa. The phonon dispersion curves, phonon density of states, vibrational modes and atoms that contribute to these vibrations at {{\\varvec{Γ }}} point under different pressures are also reported in this work. Finally, by employing the quasi-harmonic approximation, the thermodynamic properties such as the temperature dependence of the thermal expansion coefficient, specific heat, entropy and Gibbs free energy under different pressures are investigated. It is found that the influences of the temperature on the heat capacity are much more significant than that of the pressure on it.

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

NASA Astrophysics Data System (ADS)

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

2012-06-01

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

Size dependence of yield strength simulated by a dislocation-density function dynamics approach

NASA Astrophysics Data System (ADS)

Leung, P. S. S.; Leung, H. S.; Cheng, B.; Ngan, A. H. W.

2015-04-01

The size dependence of the strength of nano- and micron-sized crystals is studied using a new simulation approach in which the dynamics of the density functions of dislocations are modeled. Since any quantity of dislocations can be represented by a density, this approach can handle large systems containing large quantities of dislocations, which may handicap discrete dislocation dynamics schemes due to the excessive computation time involved. For this reason, pillar sizes spanning a large range, from the sub-micron to micron regimes, can be simulated. The simulation results reveal the power-law relationship between strength and specimen size up to a certain size, beyond which the strength varies much more slowly with size. For specimens smaller than ∼4000b, their strength is found to be controlled by the dislocation depletion condition, in which the total dislocation density remains almost constant throughout the loading process. In specimens larger than ∼4000b, the initial dislocation distribution is of critical importance since the presence of dislocation entanglements is found to obstruct deformation in the neighboring regions within a distance of ∼2000b. This length scale suggests that the effects of dense dislocation clusters are greater in intermediate-sized specimens (e.g. 4000b and 8000b) than in larger specimens (e.g. 16 000b), according to the weakest-link concept.

Effect of wetting-layer density of states on the gain and phase recovery dynamics of quantum-dot semiconductor optical amplifiers

NASA Astrophysics Data System (ADS)

Kim, Jungho; Yu, Bong-Ahn

2015-03-01

We numerically investigate the effect of the wetting-layer (WL) density of states on the gain and phase recovery dynamics of quantum-dot semiconductor optical amplifiers in both electrical and optical pumping schemes by solving 1088 coupled rate equations. The temporal variations of the ultrafast gain and phase recovery responses at the ground state (GS) are calculated as a function of the WL density of states. The ultrafast gain recovery responses do not significantly depend on the WL density of states in the electrical pumping scheme and the three optical pumping schemes such as the optical pumping to the WL, the optical pumping to the excited state ensemble, and the optical pumping to the GS ensemble. The ultrafast phase recovery responses are also not significantly affected by the WL density of states except the optical pumping to the WL, where the phase recovery component caused by the WL becomes slowed down as the WL density of states increases.

Critical density of a soliton gas

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

El, G. A., E-mail: g.el@lboro.ac.uk

We quantify the notion of a dense soliton gas by establishing an upper bound for the integrated density of states of the quantum-mechanical Schrödinger operator associated with the Korteweg–de Vries soliton gas dynamics. As a by-product of our derivation, we find the speed of sound in the soliton gas with Gaussian spectral distribution function.

Critical density of a soliton gas

NASA Astrophysics Data System (ADS)

El, G. A.

2016-02-01

We quantify the notion of a dense soliton gas by establishing an upper bound for the integrated density of states of the quantum-mechanical Schrödinger operator associated with the Korteweg-de Vries soliton gas dynamics. As a by-product of our derivation, we find the speed of sound in the soliton gas with Gaussian spectral distribution function.

A Density Functional Approach to Polarizable Models: A Kim-Gordon-Response Density Interaction Potential for Molecular Simulations

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

Tabacchi, G; Hutter, J; Mundy, C

2005-04-07

A combined linear response--frozen electron density model has been implemented in a molecular dynamics scheme derived from an extended Lagrangian formalism. This approach is based on a partition of the electronic charge distribution into a frozen region described by Kim-Gordon theory, and a response contribution determined by the instaneous ionic configuration of the system. The method is free from empirical pair-potentials and the parameterization protocol involves only calculations on properly chosen subsystems. They apply this method to a series of alkali halides in different physical phases and are able to reproduce experimental structural and thermodynamic properties with an accuracy comparablemore » to Kohn-Sham density functional calculations.« less

Communication: Improved ab initio molecular dynamics by minimally biasing with experimental data

NASA Astrophysics Data System (ADS)

White, Andrew D.; Knight, Chris; Hocky, Glen M.; Voth, Gregory A.

2017-01-01

Accounting for electrons and nuclei simultaneously is a powerful capability of ab initio molecular dynamics (AIMD). However, AIMD is often unable to accurately reproduce properties of systems such as water due to inaccuracies in the underlying electronic density functionals. This shortcoming is often addressed by added empirical corrections and/or increasing the simulation temperature. We present here a maximum-entropy approach to directly incorporate limited experimental data via a minimal bias. Biased AIMD simulations of water and an excess proton in water are shown to give significantly improved properties both for observables which were biased to match experimental data and for unbiased observables. This approach also yields new physical insight into inaccuracies in the underlying density functional theory as utilized in the unbiased AIMD.

Communication: Improved ab initio molecular dynamics by minimally biasing with experimental data.

PubMed

White, Andrew D; Knight, Chris; Hocky, Glen M; Voth, Gregory A

2017-01-28

Accounting for electrons and nuclei simultaneously is a powerful capability of ab initio molecular dynamics (AIMD). However, AIMD is often unable to accurately reproduce properties of systems such as water due to inaccuracies in the underlying electronic density functionals. This shortcoming is often addressed by added empirical corrections and/or increasing the simulation temperature. We present here a maximum-entropy approach to directly incorporate limited experimental data via a minimal bias. Biased AIMD simulations of water and an excess proton in water are shown to give significantly improved properties both for observables which were biased to match experimental data and for unbiased observables. This approach also yields new physical insight into inaccuracies in the underlying density functional theory as utilized in the unbiased AIMD.

Ab initio theory and modeling of water.

PubMed

Chen, Mohan; Ko, Hsin-Yu; Remsing, Richard C; Calegari Andrade, Marcos F; Santra, Biswajit; Sun, Zhaoru; Selloni, Annabella; Car, Roberto; Klein, Michael L; Perdew, John P; Wu, Xifan

2017-10-10

Water is of the utmost importance for life and technology. However, a genuinely predictive ab initio model of water has eluded scientists. We demonstrate that a fully ab initio approach, relying on the strongly constrained and appropriately normed (SCAN) density functional, provides such a description of water. SCAN accurately describes the balance among covalent bonds, hydrogen bonds, and van der Waals interactions that dictates the structure and dynamics of liquid water. Notably, SCAN captures the density difference between water and ice I h at ambient conditions, as well as many important structural, electronic, and dynamic properties of liquid water. These successful predictions of the versatile SCAN functional open the gates to study complex processes in aqueous phase chemistry and the interactions of water with other materials in an efficient, accurate, and predictive, ab initio manner.

Ab initio theory and modeling of water

PubMed Central

Chen, Mohan; Ko, Hsin-Yu; Remsing, Richard C.; Calegari Andrade, Marcos F.; Santra, Biswajit; Sun, Zhaoru; Selloni, Annabella; Car, Roberto; Klein, Michael L.; Perdew, John P.; Wu, Xifan

2017-01-01

Water is of the utmost importance for life and technology. However, a genuinely predictive ab initio model of water has eluded scientists. We demonstrate that a fully ab initio approach, relying on the strongly constrained and appropriately normed (SCAN) density functional, provides such a description of water. SCAN accurately describes the balance among covalent bonds, hydrogen bonds, and van der Waals interactions that dictates the structure and dynamics of liquid water. Notably, SCAN captures the density difference between water and ice Ih at ambient conditions, as well as many important structural, electronic, and dynamic properties of liquid water. These successful predictions of the versatile SCAN functional open the gates to study complex processes in aqueous phase chemistry and the interactions of water with other materials in an efficient, accurate, and predictive, ab initio manner. PMID:28973868

Vibrational Properties of Hydrogen-Bonded Systems Using the Multireference Generalization to the "On-the-Fly" Electronic Structure within Quantum Wavepacket ab Initio Molecular Dynamics (QWAIMD).

PubMed

Li, Junjie; Li, Xiaohu; Iyengar, Srinivasan S

2014-06-10

We discuss a multiconfigurational treatment of the "on-the-fly" electronic structure within the quantum wavepacket ab initio molecular dynamics (QWAIMD) method for coupled treatment of quantum nuclear effects with electronic structural effects. Here, multiple single-particle electronic density matrices are simultaneously propagated with a quantum nuclear wavepacket and other classical nuclear degrees of freedom. The multiple density matrices are coupled through a nonorthogonal configuration interaction (NOCI) procedure to construct the instantaneous potential surface. An adaptive-mesh-guided set of basis functions composed of Gaussian primitives are used to simplify the electronic structure calculations. Specifically, with the replacement of the atom-centered basis functions positioned on the centers of the quantum-mechanically treated nuclei by a mesh-guided band of basis functions, the two-electron integrals used to compute the electronic structure potential surface become independent of the quantum nuclear variable and hence reusable along the entire Cartesian grid representing the quantum nuclear coordinates. This reduces the computational complexity involved in obtaining a potential surface and facilitates the interpretation of the individual density matrices as representative diabatic states. The parametric nuclear position dependence of the diabatic states is evaluated at the initial time-step using a Shannon-entropy-based sampling function that depends on an approximation to the quantum nuclear wavepacket and the potential surface. This development is meant as a precursor to an on-the-fly fully multireference electronic structure procedure embedded, on-the-fly, within a quantum nuclear dynamics formalism. We benchmark the current development by computing structural, dynamic, and spectroscopic features for a series of bihalide hydrogen-bonded systems: FHF(-), ClHCl(-), BrHBr(-), and BrHCl(-). We find that the donor-acceptor structural features are in good agreement with experiments. Spectroscopic features are computed using a unified velocity/flux autocorrelation function and include vibrational fundamentals and combination bands. These agree well with experiments and other theories.

Quantum power functional theory for many-body dynamics

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

Schmidt, Matthias, E-mail: Matthias.Schmidt@uni-bayreuth.de

2015-11-07

We construct a one-body variational theory for the time evolution of nonrelativistic quantum many-body systems. The position- and time-dependent one-body density, particle current, and time derivative of the current act as three variational fields. The generating (power rate) functional is minimized by the true current time derivative. The corresponding Euler-Lagrange equation, together with the continuity equation for the density, forms a closed set of one-body equations of motion. Space- and time-nonlocal one-body forces are generated by the superadiabatic contribution to the functional. The theory applies to many-electron systems.

X-ray absorption in insulators with non-Hermitian real-time time-dependent density functional theory.

PubMed

Fernando, Ranelka G; Balhoff, Mary C; Lopata, Kenneth

2015-02-10

Non-Hermitian real-time time-dependent density functional theory was used to compute the Si L-edge X-ray absorption spectrum of α-quartz using an embedded finite cluster model and atom-centered basis sets. Using tuned range-separated functionals and molecular orbital-based imaginary absorbing potentials, the excited states spanning the pre-edge to ∼20 eV above the ionization edge were obtained in good agreement with experimental data. This approach is generalizable to TDDFT studies of core-level spectroscopy and dynamics in a wide range of materials.

Prediction of Liquefaction Potential of Dredge Fill Sand by DCP and Dynamic Probing

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

Alam, Md. Jahangir; Azad, Abul Kalam; Rahman, Ziaur

2008-07-08

From many research it is proved that liquefaction potential of sand is function of mainly relative density and confining pressure. During routine site investigations, high-quality sampling and laboratory testing of sands are not feasible because of inevitable sample disturbance effects and budgetary constraints. On the other hand quality control of sand fill can be done by determining in situ density of sand in layer by layer which is expensive and time consuming. In this paper TRL DCP (Transportation Research Laboratory Dynamic Cone Penetration) and DPL (Dynamic Probing Light) are calibrated to predict the relative density of sand deposit. For thismore » purpose sand of known relative density is prepared in a calibration chamber which is a mild steel cylinder with diameter 0.5 m and height 1.0 m. Relative density of sand is varied by controlling height of fall and diameter of hole of sand discharge bowl. After filling, every time DPL and DCP tests are performed and for every blow the penetration of cone is recorded. N10 is then calculated from penetration records. Thus a database is compiled where N10 and relative densities are known. A correlation is made between N{sub 10} and relative density for two types of sand. A good correlation of N{sub 10} and relative density is found.« less

Predictions of Crystal Structures from First Principles

DTIC Science & Technology

2007-06-01

RDX crystal in hoped that the problem could be resolved by the molecular dynamics simulations . The fully ab initio development of density functional... Molecular Dynamics Simulations of RDX i.e., without any use of experimental results (except that Crystal the geometry of monomers was derived from X-ray...applied in molecular dynamics simulations of the RDX system, due to its size, is intractable by any high-level ab crystal. We performed isothermal

Parametrically coupled fermionic oscillators: Correlation functions and phase-space description

NASA Astrophysics Data System (ADS)

Ghosh, Arnab

2015-01-01

A fermionic analog of a parametric amplifier is used to describe the joint quantum state of the two interacting fermionic modes. Based on a two-mode generalization of the time-dependent density operator, time evolution of the fermionic density operator is determined in terms of its two-mode Wigner and P function. It is shown that the equation of motion of the Wigner function corresponds to a fermionic analog of Liouville's equation. The equilibrium density operator for fermionic fields developed by Cahill and Glauber is thus extended to a dynamical context to show that the mathematical structures of both the correlation functions and the weight factors closely resemble their bosonic counterpart. It has been shown that the fermionic correlation functions are marked by a characteristic upper bound due to Fermi statistics, which can be verified in the matter wave counterpart of photon down-conversion experiments.

Kinetic theory for strongly coupled Coulomb systems

NASA Astrophysics Data System (ADS)

Dufty, James; Wrighton, Jeffrey

2018-01-01

The calculation of dynamical properties for matter under extreme conditions is a challenging task. The popular Kubo-Greenwood model exploits elements from equilibrium density-functional theory (DFT) that allow a detailed treatment of electron correlations, but its origin is largely phenomenological; traditional kinetic theories have a more secure foundation but are limited to weak ion-electron interactions. The objective here is to show how a combination of the two evolves naturally from the short-time limit for the generator of the effective single-electron dynamics governing time correlation functions without such limitations. This provides a theoretical context for the current DFT-related approach, the Kubo-Greenwood model, while showing the nature of its corrections. The method is to calculate the short-time dynamics in the single-electron subspace for a given configuration of the ions. This differs from the usual kinetic theory approach in which an average over the ions is performed as well. In this way the effective ion-electron interaction includes strong Coulomb coupling and is shown to be determined from DFT. The correlation functions have the form of the random-phase approximation for an inhomogeneous system but with renormalized ion-electron and electron-electron potentials. The dynamic structure function, density response function, and electrical conductivity are calculated as examples. The static local field corrections in the dielectric function are identified in this way. The current analysis is limited to semiclassical electrons (quantum statistical potentials), so important quantum conditions are excluded. However, a quantization of the kinetic theory is identified for broader application while awaiting its detailed derivation.

Electron dynamics inside a vacuum tube diode through linear differential equations

NASA Astrophysics Data System (ADS)

González, Gabriel; Orozco, Fco. Javier González; Orozco

2014-04-01

In this paper we analyze the motion of charged particles in a vacuum tube diode by solving linear differential equations. Our analysis is based on expressing the volume charge density as a function of the current density and coordinates only, i.e. ρ=ρ(J,z), while in the usual scheme the volume charge density is expressed as a function of the current density and electrostatic potential, i.e. ρ=ρ(J,V). We show that, in the case of slow varying charge density, the space-charge-limited current is reduced up to 50%. Our approach gives the well-known behavior of the classical current density proportional to the three-halves power of the bias potential and inversely proportional to the square of the gap distance between electrodes, and does not require the solution of the nonlinear differential equation normally associated with the Child-Langmuir formulation.

Subsystem real-time time dependent density functional theory.

PubMed

Krishtal, Alisa; Ceresoli, Davide; Pavanello, Michele

2015-04-21

We present the extension of Frozen Density Embedding (FDE) formulation of subsystem Density Functional Theory (DFT) to real-time Time Dependent Density Functional Theory (rt-TDDFT). FDE is a DFT-in-DFT embedding method that allows to partition a larger Kohn-Sham system into a set of smaller, coupled Kohn-Sham systems. Additional to the computational advantage, FDE provides physical insight into the properties of embedded systems and the coupling interactions between them. The extension to rt-TDDFT is done straightforwardly by evolving the Kohn-Sham subsystems in time simultaneously, while updating the embedding potential between the systems at every time step. Two main applications are presented: the explicit excitation energy transfer in real time between subsystems is demonstrated for the case of the Na4 cluster and the effect of the embedding on optical spectra of coupled chromophores. In particular, the importance of including the full dynamic response in the embedding potential is demonstrated.

Magnetic behavior study of samarium nitride using density functional theory

NASA Astrophysics Data System (ADS)

Som, Narayan N.; Mankad, Venu H.; Dabhi, Shweta D.; Patel, Anjali; Jha, Prafulla K.

2018-02-01

In this work, the state-of-art density functional theory is employed to study the structural, electronic and magnetic properties of samarium nitride (SmN). We have performed calculation for both ferromagnetic and antiferromagnetic states in rock-salt phase. The calculated results of optimized lattice parameter and magnetic moment agree well with the available experimental and theoretical values. From energy band diagram and electronic density of states, we observe a half-metallic behaviour in FM phase of rock salt SmN in while metallicity in AFM I and AFM III phases. We present and discuss our current understanding of the possible half-metallicity together with the magnetic ordering in SmN. The calculated phonon dispersion curves shows dynamical stability of the considered structures. The phonon density of states and Eliashberg functional have also been analysed to understand the superconductivity in SmN.

Hierarchy of forward-backward stochastic Schrödinger equation

NASA Astrophysics Data System (ADS)

Ke, Yaling; Zhao, Yi

2016-07-01

Driven by the impetus to simulate quantum dynamics in photosynthetic complexes or even larger molecular aggregates, we have established a hierarchy of forward-backward stochastic Schrödinger equation in the light of stochastic unravelling of the symmetric part of the influence functional in the path-integral formalism of reduced density operator. The method is numerically exact and is suited for Debye-Drude spectral density, Ohmic spectral density with an algebraic or exponential cutoff, as well as discrete vibrational modes. The power of this method is verified by performing the calculations of time-dependent population differences in the valuable spin-boson model from zero to high temperatures. By simulating excitation energy transfer dynamics of the realistic full FMO trimer, some important features are revealed.

Electronic-structure and quantum dynamical study of the photochromism of the aromatic Schiff base salicylideneaniline

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

Ortiz-Sanchez, Juan Manuel; Gelabert, Ricard; Moreno, Miquel

2008-12-07

The ultrafast proton transfer dynamics of salicylideneaniline has been theoretically analyzed in the ground and first singlet excited electronic states using density functional theory (DFT) and time-dependent DFT calculations, which predict a ({pi},{pi}*) barrierless excited state intramolecular proton transfer (ESIPT). In addition to this, the photochemistry of salicylideneaniline is experimentally known to present fast depopulation processes of the photoexcited species before and after the proton transfer reaction. Such processes are explained by means of conical intersections between the ground and first singlet ({pi},{pi}*) excited electronic states. The electronic energies obtained by the time-dependent density functional theory formalism have been fittedmore » to a monodimensional potential energy surface in order to perform quantum dynamics study of the processes. Our results show that the proton transfer and deactivation of the photoexcited species before the ESIPT processes are completed within 49.6 and 37.7 fs, respectively, which is in remarkable good agreement with experiments.« less

A divide-conquer-recombine algorithmic paradigm for large spatiotemporal quantum molecular dynamics simulations

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

Shimojo, Fuyuki; Hattori, Shinnosuke; Department of Physics, Kumamoto University, Kumamoto 860-8555

We introduce an extension of the divide-and-conquer (DC) algorithmic paradigm called divide-conquer-recombine (DCR) to perform large quantum molecular dynamics (QMD) simulations on massively parallel supercomputers, in which interatomic forces are computed quantum mechanically in the framework of density functional theory (DFT). In DCR, the DC phase constructs globally informed, overlapping local-domain solutions, which in the recombine phase are synthesized into a global solution encompassing large spatiotemporal scales. For the DC phase, we design a lean divide-and-conquer (LDC) DFT algorithm, which significantly reduces the prefactor of the O(N) computational cost for N electrons by applying a density-adaptive boundary condition at themore » peripheries of the DC domains. Our globally scalable and locally efficient solver is based on a hybrid real-reciprocal space approach that combines: (1) a highly scalable real-space multigrid to represent the global charge density; and (2) a numerically efficient plane-wave basis for local electronic wave functions and charge density within each domain. Hybrid space-band decomposition is used to implement the LDC-DFT algorithm on parallel computers. A benchmark test on an IBM Blue Gene/Q computer exhibits an isogranular parallel efficiency of 0.984 on 786 432 cores for a 50.3 × 10{sup 6}-atom SiC system. As a test of production runs, LDC-DFT-based QMD simulation involving 16 661 atoms is performed on the Blue Gene/Q to study on-demand production of hydrogen gas from water using LiAl alloy particles. As an example of the recombine phase, LDC-DFT electronic structures are used as a basis set to describe global photoexcitation dynamics with nonadiabatic QMD (NAQMD) and kinetic Monte Carlo (KMC) methods. The NAQMD simulations are based on the linear response time-dependent density functional theory to describe electronic excited states and a surface-hopping approach to describe transitions between the excited states. A series of techniques are employed for efficiently calculating the long-range exact exchange correction and excited-state forces. The NAQMD trajectories are analyzed to extract the rates of various excitonic processes, which are then used in KMC simulation to study the dynamics of the global exciton flow network. This has allowed the study of large-scale photoexcitation dynamics in 6400-atom amorphous molecular solid, reaching the experimental time scales.« less

Density functional theory of gas-liquid phase separation in dilute binary mixtures

NASA Astrophysics Data System (ADS)

Okamoto, Ryuichi; Onuki, Akira

2016-06-01

We examine statics and dynamics of phase-separated states of dilute binary mixtures using density functional theory. In our systems, the difference of the solvation chemical potential between liquid and gas Δ {μ\\text{s}} (the Gibbs energy of transfer) is considerably larger than the thermal energy {{k}\\text{B}}T for each solute particle and the attractive interaction among the solute particles is weaker than that among the solvent particles. In these conditions, the saturated vapor pressure increases by {{k}\\text{B}}Tn2\\ell\\exp ≤ft(Δ {μ\\text{s}}/{{k}\\text{B}}T\\right) , where n2\\ell is the solute density added in liquid. For \\exp ≤ft(Δ {μ\\text{s}}/{{k}\\text{B}}T\\right)\\gg 1 , phase separation is induced at low solute densities in liquid and the new phase remains in gaseous states, even when the liquid pressure is outside the coexistence curve of the solvent. This explains the widely observed formation of stable nanobubbles in ambient water with a dissolved gas. We calculate the density and stress profiles across planar and spherical interfaces, where the surface tension decreases with increasing interfacial solute adsorption. We realize stable solute-rich bubbles with radius about 30 nm, which minimize the free energy functional. We then study dynamics around such a bubble after a decompression of the surrounding liquid, where the bubble undergoes a damped oscillation. In addition, we present some exact and approximate expressions for the surface tension and the interfacial stress tensor.

Combining two-body density functionals with multiconfigurational wavefunctions: diatomic molecules

NASA Astrophysics Data System (ADS)

McDouall, Joseph J. W.

The MCSCF method provides a correct zero-order wavefunction for all regions of molecular potential energy surfaces. To obtain quantitative accuracy a proper treatment of the dynamic correlation problem must be implemented. Traditionally this has been achieved through multireference variants of perturbation theory, configuration interaction and coupled cluster theory. The computational cost of such techniques makes them prohibitive for all but the smallest molecular problems. Reported here is an investigation into the efficacy of two-body density functionals in providing the dynamic correlation energy for MCSCF reference states. Tests were made on the two-body density functionals of Colle and Salvetti (CS), Moscardó and San-Fabián (MSF), and Moscardó and Pérez-Jiménez (MPJ5) in predicting the equilibrium bond lengths, harmonic frequencies and dissociation energies of fifteen diatomic molecules (3B2, 3BN, 2BS, 1C2, 2CN, 1CO, 1F2, 1FCl, 1N2, 3NCl, 3O2, 1PN, 3Si2, 3SiO, 3SO) using full valence-shell CASSCF reference wavefunctions. Also studied were modifications of these functionals recently suggested by Miehlich, Stoll and Savin (MSS) and Gräfenstein and Cremer (GC). The results obtained show accuracy comparable with and typically superior to the popular Kohn-Sham BLYP and B3LYP methods. However, the latter methods are not applicable in all regions of a potential energy surface, and even predict incorrect ground states for some systems. The use of two-body density functionals with MCSCF reference states does not share this shortcoming.

Dynamic least-squares kernel density modeling of Fokker-Planck equations with application to neural population.

PubMed

Shotorban, Babak

2010-04-01

The dynamic least-squares kernel density (LSQKD) model [C. Pantano and B. Shotorban, Phys. Rev. E 76, 066705 (2007)] is used to solve the Fokker-Planck equations. In this model the probability density function (PDF) is approximated by a linear combination of basis functions with unknown parameters whose governing equations are determined by a global least-squares approximation of the PDF in the phase space. In this work basis functions are set to be Gaussian for which the mean, variance, and covariances are governed by a set of partial differential equations (PDEs) or ordinary differential equations (ODEs) depending on what phase-space variables are approximated by Gaussian functions. Three sample problems of univariate double-well potential, bivariate bistable neurodynamical system [G. Deco and D. Martí, Phys. Rev. E 75, 031913 (2007)], and bivariate Brownian particles in a nonuniform gas are studied. The LSQKD is verified for these problems as its results are compared against the results of the method of characteristics in nondiffusive cases and the stochastic particle method in diffusive cases. For the double-well potential problem it is observed that for low to moderate diffusivity the dynamic LSQKD well predicts the stationary PDF for which there is an exact solution. A similar observation is made for the bistable neurodynamical system. In both these problems least-squares approximation is made on all phase-space variables resulting in a set of ODEs with time as the independent variable for the Gaussian function parameters. In the problem of Brownian particles in a nonuniform gas, this approximation is made only for the particle velocity variable leading to a set of PDEs with time and particle position as independent variables. Solving these PDEs, a very good performance by LSQKD is observed for a wide range of diffusivities.

The structural, electronic and dynamic properties of the L1{sub 2}- type Co{sub 3}Ti alloy

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

Arikan, Nihat; Özduran, Mustafa

2014-10-06

The structural, electronic and dynamic properties of the cubic Co{sub 3}Ti alloy in L1{sub 2} structure have been investigated using a pseudopotential plane wave (PP-PW) method within the generalized gradient approximation proposed by Perdew–Burke–Ernzerhof (GGA-PBE). The structural properties, including the lattice constant, the bulk modulus and its pressure derivative agree reasonably with the previous results. The density of state (DOS), projected density of state (PDOS) and electronic band structure are also reported. The DOS shows that Co{sub 3}Ti alloy has a metallic character since the energy bands cross the Fermi level. The density of states at Fermi level mainly comesmore » from the Co-3d states. Phonon dispersion curves and their corresponding total densities of states were obtained using a linear response in the framework of the density functional perturbation theory. All computed phonon frequencies are no imaginer and thus, Co{sub 3}Ti alloy is dynamically stable. The zone center phonon modes have been founded to be 9.307, 9.626 and 13.891 THz for Co{sub 3}Ti.« less

Plane wave density functional molecular dynamics study of exothermic reactions of Al/CuO thermites

NASA Astrophysics Data System (ADS)

Oloriegbe, Suleiman; Sewell, Thomas; Chen, Zhen; Jiang, Shan; Gan, Yong

2014-03-01

Exothermic reactions between nanosize aluminum (Al) and copper oxide (CuO) structures are of current interest because of their high reaction enthalpy and energy density which exceed those of traditional monomolecular energetic compounds such as TNT, RDX, and HMX. In this work, molecular dynamics simulations with forces obtained from plane wave density functional theory are used to investigate the atomic-scale and electronic processes that occur during the fast thermite reactions between Al and CuO nanostructures under adiabatic conditions. Aluminum surfaces in contact with O-exposed and Cu-exposed CuO surfaces are studied. Starting from initial temperature T = 800 K, we have observed: faster chemical reaction at the oxygen-rich interface during the initial 0.5 ps, linear temperature rise, and fast oxygen diffusion into the Al region with the rate 1.87 X 10-3 cm2/s. The density-derived electrostatic and chemical method is used to evaluate the net atomic charges and charge transfer during the important redox processes. High charge density around the oxygen-exposed interface may be responsible for the faster initial reactions at that interface. The overall reaction rate, determined using the time evolution of Cu-O charge orbital overlap population, is approximately first order.

First-principles electron dynamics control simulation of diamond under femtosecond laser pulse train irradiation.

PubMed

Wang, Cong; Jiang, Lan; Wang, Feng; Li, Xin; Yuan, Yanping; Xiao, Hai; Tsai, Hai-Lung; Lu, Yongfeng

2012-07-11

A real-time and real-space time-dependent density functional is applied to simulate the nonlinear electron-photon interactions during shaped femtosecond laser pulse train ablation of diamond. Effects of the key pulse train parameters such as the pulse separation, spatial/temporal pulse energy distribution and pulse number per train on the electron excitation and energy absorption are discussed. The calculations show that photon-electron interactions and transient localized electron dynamics can be controlled including photon absorption, electron excitation, electron density, and free electron distribution by the ultrafast laser pulse train.

Molecular Dynamics Modeling of Thermal Properties of Aluminum Near Melting Line

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

Karavaev, A. V.; Dremov, V. V.; Sapozhnikov, F. A.

2006-08-03

In this work we present results of calculations of thermal properties of solid and liquid phases of aluminum at different densities and temperatures using classical molecular dynamics with EAM potential function. Dependencies of heat capacity CV on temperature and density have been analyzed. It was shown that when temperature increases, heat capacity CV behavior deviates from that by Dulong-Petit law. It may be explained by influence of anharmonicity of crystal lattice vibrations. Comparison of heat capacity CV of liquid phase with Grover's model has been performed. Dependency of aluminum melting temperature on pressure has been acquired.

Towards a formal definition of static and dynamic electronic correlations.

PubMed

Benavides-Riveros, Carlos L; Lathiotakis, Nektarios N; Marques, Miguel A L

2017-05-24

Some of the most spectacular failures of density-functional and Hartree-Fock theories are related to an incorrect description of the so-called static electron correlation. Motivated by recent progress in the N-representability problem of the one-body density matrix for pure states, we propose a method to quantify the static contribution to the electronic correlation. By studying several molecular systems we show that our proposal correlates well with our intuition of static and dynamic electron correlation. Our results bring out the paramount importance of the occupancy of the highest occupied natural spin-orbital in such quantification.

A density functional theory study on the thermodynamic and dynamic properties of anthraquinone analogue cathode materials for rechargeable lithium ion batteries.

PubMed

Yang, Shu-Jing; Qin, Xiao-Ya; He, Rongxing; Shen, Wei; Li, Ming; Zhao, Liu-Bin

2017-05-21

Organic redox compounds have become the emerging electrode materials for rechargeable lithium ion batteries. The high electrochemical performance provides organic electrode materials with great opportunities to be applied in electric energy storage devices. Among the different types of organic materials, conjugated carbonyl compounds are the most promising type at present, because only they can simultaneously achieve, high energy density, high cycling stability, and high power density. In this research, a series of heteroatom substituted anthraquinone (AQ) derivatives were designed theoretically so that the high theoretical capacity of AQ remained. The discharge and charge mechanism as well as the thermodynamic and dynamic properties of AQ and its derivatives were investigated using first-principles density functional theory. Using heteroatom substitution, both the thermodynamic and dynamic properties of AQ as cathode materials could be largely improved. Among these conjugated carboxyl compounds, BDOZD and BDIOZD with a simultaneously high theoretical capacity and high working potential exhibit the largest energy density of about 780 W h kg -1 , which is 41% larger than that of AQ. The PQD with the smallest value of λ gives the largest charge transfer rate constant, which is about four times as large as the prototype molecule, AQ. The most interesting finding is that the lithium ion transfer plays a very important role in influencing both the discharge potential and electrochemical charge transfer rate. The present study illustrates that theoretical calculations provide a highly effective way to discover potential materials for use with rechargeable lithium ion batteries.

Equation of state and some structural and dynamical properties of the confined Lennard-Jones fluid into carbon nanotube: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Abbaspour, Mohsen; Akbarzadeh, Hamed; Salemi, Sirous; Abroodi, Mousarreza

2016-11-01

By considering the anisotropic pressure tensor, two separate equations of state (EoS) as functions of the density, temperature, and carbon nanotube (CNT) diameter have been proposed for the radial and axial directions for the confined Lennard-Jones (LJ) fluid into (11,11), (12,10), and (19,0) CNTs from 120 to 600 K using molecular dynamics (MD) simulations. We have also investigated the effects of the pore size, pore loading, chirality, and temperature on some of the structural and dynamical properties of the confined LJ fluid into (11,11), (12,10), (19,0), and (19,19) CNTs such as the radial density profile and self-diffusion coefficient. We have also determined the EoS for the confined LJ fluid into double and triple walled CNTs.

Combinations of coupled cluster, density functionals, and the random phase approximation for describing static and dynamic correlation, and van der Waals interactions

NASA Astrophysics Data System (ADS)

Garza, Alejandro J.; Bulik, Ireneusz W.; Alencar, Ana G. Sousa; Sun, Jianwei; Perdew, John P.; Scuseria, Gustavo E.

2016-04-01

Contrary to standard coupled cluster doubles (CCD) and Brueckner doubles (BD), singlet-paired analogues of CCD and BD (denoted here as CCD0 and BD0) do not break down when static correlation is present, but neglect substantial amounts of dynamic correlation. In fact, CCD0 and BD0 do not account for any contributions from multielectron excitations involving only same-spin electrons at all. We exploit this feature to add - without introducing double counting, self-interaction, or increase in cost - the missing correlation to these methods via meta-GGA (generalised gradient approximation) density functionals (Tao-Perdew-Staroverov-Scuseria and strongly constrained and appropriately normed). Furthermore, we improve upon these CCD0+DFT blends by invoking range separation: the short- and long-range correlations absent in CCD0/BD0 are evaluated with density functional theory and the direct random phase approximation, respectively. This corrects the description of long-range van der Waals forces. Comprehensive benchmarking shows that the combinations presented here are very accurate for weakly correlated systems, while also providing a reasonable description of strongly correlated problems without resorting to symmetry breaking.

Few-particle quantum dynamics-comparing nonequilibrium Green functions with the generalized Kadanoff-Baym ansatz to density operator theory

NASA Astrophysics Data System (ADS)

Hermanns, S.; Balzer, K.; Bonitz, M.

2013-03-01

The nonequilibrium description of quantum systems requires, for more than two or three particles, the use of a reduced description to be numerically tractable. Two possible approaches are based on either reduced density matrices or nonequilibrium Green functions (NEGF). Both concepts are formulated in terms of hierarchies of coupled equations—the Bogoliubov-Born-Green-Kirkwood-Yvon (BBGKY) hierarchy for the reduced density operators and the Martin-Schwinger-hierarchy (MS) for the Green functions, respectively. In both cases, similar approximations are introduced to decouple the hierarchy, yet still many questions regarding the correspondence of both approaches remain open. Here we analyze this correspondence by studying the generalized Kadanoff-Baym ansatz (GKBA) that reduces the NEGF to a single-time theory. Starting from the BBGKY-hierarchy we present the approximations that are necessary to recover the GKBA result both, with Hartree-Fock propagators (HF-GKBA) and propagators in second Born approximation. To test the quality of the HF-GKBA, we study the dynamics of a 4-electron Hubbard nanocluster starting from a strong nonequilibrium initial state and compare to exact results and the Wang-Cassing approximation to the BBGKY hierarchy presented recently by Akbari et al. [1].

Time-dependent dynamical behavior of surface tension on rotating fluids under microgravity environment

NASA Technical Reports Server (NTRS)

Hung, R. J.; Tsao, Y. D.; Hong, B. B.; Leslie, F. W.

1988-01-01

Time dependent evolutions of the profile of free surface (bubble shapes) for a cylindrical container partially filled with a Newtonian fluid of constant density, rotating about its axis of symmetry, have been studied. Numerical computations of the dynamics of bubble shapes have been carried out with the following situations: (1) linear functions of spin-up and spin-down in low and microgravity environments, (2) step functions of spin-up and spin-down in a low gravity environment, and (3) sinusoidal function oscillation of gravity environment in high and low rotating cylinder speeds.

Ordering dynamics of self-propelled particles in an inhomogeneous medium

NASA Astrophysics Data System (ADS)

Das, Rakesh; Mishra, Shradha; Puri, Sanjay

2018-02-01

Ordering dynamics of self-propelled particles in an inhomogeneous medium in two dimensions is studied. We write coarse-grained hydrodynamic equations of motion for density and polarisation fields in the presence of an external random disorder field, which is quenched in time. The strength of inhomogeneity is tuned from zero disorder (clean system) to large disorder. In the clean system, the polarisation field grows algebraically as LP ∼ t0.5 . The density field does not show clean power-law growth; however, it follows Lρ ∼ t0.8 approximately. In the inhomogeneous system, we find a disorder-dependent growth. For both the density and the polarisation, growth slows down with increasing strength of disorder. The polarisation shows a disorder-dependent power-law growth LP(t,Δ) ∼ t1/\\bar zP(Δ) for intermediate times. At late times, there is a crossover to logarithmic growth LP(t,Δ) ∼ (\\ln t)1/\\varphi , where φ is a disorder-independent exponent. Two-point correlation functions for the polarisation show dynamical scaling, but the density does not.

Structural, electronic, and dynamical properties of liquid water by ab initio molecular dynamics based on SCAN functional within the canonical ensemble

NASA Astrophysics Data System (ADS)

Zheng, Lixin; Chen, Mohan; Sun, Zhaoru; Ko, Hsin-Yu; Santra, Biswajit; Dhuvad, Pratikkumar; Wu, Xifan

2018-04-01

We perform ab initio molecular dynamics (AIMD) simulation of liquid water in the canonical ensemble at ambient conditions using the strongly constrained and appropriately normed (SCAN) meta-generalized-gradient approximation (GGA) functional approximation and carry out systematic comparisons with the results obtained from the GGA-level Perdew-Burke-Ernzerhof (PBE) functional and Tkatchenko-Scheffler van der Waals (vdW) dispersion correction inclusive PBE functional. We analyze various properties of liquid water including radial distribution functions, oxygen-oxygen-oxygen triplet angular distribution, tetrahedrality, hydrogen bonds, diffusion coefficients, ring statistics, density of states, band gaps, and dipole moments. We find that the SCAN functional is generally more accurate than the other two functionals for liquid water by not only capturing the intermediate-range vdW interactions but also mitigating the overly strong hydrogen bonds prescribed in PBE simulations. We also compare the results of SCAN-based AIMD simulations in the canonical and isothermal-isobaric ensembles. Our results suggest that SCAN provides a reliable description for most structural, electronic, and dynamical properties in liquid water.

The use and misuse of aircraft and missile RCS statistics

NASA Astrophysics Data System (ADS)

Bishop, Lee R.

1991-07-01

Both static and dynamic radar cross sections measurements are used for RCS predictions, but the static data are less complete than the dynamic. Integrated dynamics RCS data also have limitations for prediction radar detection performance. When raw static data are properly used, good first-order detection estimates are possible. The research to develop more-usable RCS statistics is reviewed, and windowing techniques for creating probability density functions from static RCS data are discussed.

Comparison of Molecular Dynamics with Classical Density Functional and Poisson–Boltzmann Theories of the Electric Double Layer in Nanochannels

PubMed Central

2012-01-01

Comparisons are made among Molecular Dynamics (MD), Classical Density Functional Theory (c-DFT), and Poisson–Boltzmann (PB) modeling of the electric double layer (EDL) for the nonprimitive three component model (3CM) in which the two ion species and solvent molecules are all of finite size. Unlike previous comparisons between c-DFT and Monte Carlo (MC), the present 3CM incorporates Lennard-Jones interactions rather than hard-sphere and hard-wall repulsions. c-DFT and MD results are compared over normalized surface charges ranging from 0.2 to 1.75 and bulk ion concentrations from 10 mM to 1 M. Agreement between the two, assessed by electric surface potential and ion density profiles, is found to be quite good. Wall potentials predicted by PB begin to depart significantly from c-DFT and MD for charge densities exceeding 0.3. Successive layers are observed to charge in a sequential manner such that the solvent becomes fully excluded from each layer before the onset of the next layer. Ultimately, this layer filling phenomenon results in fluid structures, Debye lengths, and electric surface potentials vastly different from the classical PB predictions. PMID:23316120

Modeling and Density Estimation of an Urban Freeway Network Based on Dynamic Graph Hybrid Automata

PubMed Central

Chen, Yangzhou; Guo, Yuqi; Wang, Ying

2017-01-01

In this paper, in order to describe complex network systems, we firstly propose a general modeling framework by combining a dynamic graph with hybrid automata and thus name it Dynamic Graph Hybrid Automata (DGHA). Then we apply this framework to model traffic flow over an urban freeway network by embedding the Cell Transmission Model (CTM) into the DGHA. With a modeling procedure, we adopt a dual digraph of road network structure to describe the road topology, use linear hybrid automata to describe multi-modes of dynamic densities in road segments and transform the nonlinear expressions of the transmitted traffic flow between two road segments into piecewise linear functions in terms of multi-mode switchings. This modeling procedure is modularized and rule-based, and thus is easily-extensible with the help of a combination algorithm for the dynamics of traffic flow. It can describe the dynamics of traffic flow over an urban freeway network with arbitrary topology structures and sizes. Next we analyze mode types and number in the model of the whole freeway network, and deduce a Piecewise Affine Linear System (PWALS) model. Furthermore, based on the PWALS model, a multi-mode switched state observer is designed to estimate the traffic densities of the freeway network, where a set of observer gain matrices are computed by using the Lyapunov function approach. As an example, we utilize the PWALS model and the corresponding switched state observer to traffic flow over Beijing third ring road. In order to clearly interpret the principle of the proposed method and avoid computational complexity, we adopt a simplified version of Beijing third ring road. Practical application for a large-scale road network will be implemented by decentralized modeling approach and distributed observer designing in the future research. PMID:28353664

Modeling and Density Estimation of an Urban Freeway Network Based on Dynamic Graph Hybrid Automata.

PubMed

Chen, Yangzhou; Guo, Yuqi; Wang, Ying

2017-03-29

In this paper, in order to describe complex network systems, we firstly propose a general modeling framework by combining a dynamic graph with hybrid automata and thus name it Dynamic Graph Hybrid Automata (DGHA). Then we apply this framework to model traffic flow over an urban freeway network by embedding the Cell Transmission Model (CTM) into the DGHA. With a modeling procedure, we adopt a dual digraph of road network structure to describe the road topology, use linear hybrid automata to describe multi-modes of dynamic densities in road segments and transform the nonlinear expressions of the transmitted traffic flow between two road segments into piecewise linear functions in terms of multi-mode switchings. This modeling procedure is modularized and rule-based, and thus is easily-extensible with the help of a combination algorithm for the dynamics of traffic flow. It can describe the dynamics of traffic flow over an urban freeway network with arbitrary topology structures and sizes. Next we analyze mode types and number in the model of the whole freeway network, and deduce a Piecewise Affine Linear System (PWALS) model. Furthermore, based on the PWALS model, a multi-mode switched state observer is designed to estimate the traffic densities of the freeway network, where a set of observer gain matrices are computed by using the Lyapunov function approach. As an example, we utilize the PWALS model and the corresponding switched state observer to traffic flow over Beijing third ring road. In order to clearly interpret the principle of the proposed method and avoid computational complexity, we adopt a simplified version of Beijing third ring road. Practical application for a large-scale road network will be implemented by decentralized modeling approach and distributed observer designing in the future research.

Effects of prey density, temperature and predator diversity on nonconsumptive predator-driven mortality in a freshwater food web.

PubMed

Veselý, Lukáš; Boukal, David S; Buřič, Miloš; Kozák, Pavel; Kouba, Antonín; Sentis, Arnaud

2017-12-22

Nonconsumptive predator-driven mortality (NCM), defined as prey mortality due to predation that does not result in prey consumption, is an underestimated component of predator-prey interactions with possible implications for population dynamics and ecosystem functioning. However, the biotic and abiotic factors influencing this mortality component remain largely unexplored, leaving a gap in our understanding of the impacts of environmental change on ecological communities. We investigated the effects of temperature, prey density, and predator diversity and density on NCM in an aquatic food web module composed of dragonfly larvae (Aeshna cyanea) and marbled crayfish (Procambarus fallax f. virginalis) preying on common carp (Cyprinus carpio) fry. We found that NCM increased with prey density and depended on the functional diversity and density of the predator community. Warming significantly reduced NCM only in the dragonfly larvae but the magnitude depended on dragonfly larvae density. Our results indicate that energy transfer across trophic levels is more efficient due to lower NCM in functionally diverse predator communities, at lower resource densities and at higher temperatures. This suggests that environmental changes such as climate warming and reduced resource availability could increase the efficiency of energy transfer in food webs only if functionally diverse predator communities are conserved.

r- and K-selection in fluctuating populations is determined by the evolutionary trade-off between two fitness measures: Growth rate and lifetime reproductive success.

PubMed

Engen, Steinar; Saether, Bernt-Erik

2017-01-01

In a stable environment, evolution maximizes growth rates in populations that are not density regulated and the carrying capacity in the case of density regulation. In a fluctuating environment, evolution maximizes a function of growth rate, carrying capacity and environmental variance, tending to r-selection and K-selection under large and small environmental noise, respectively. Here we analyze a model in which birth and death rates depend on density through the same function but with independent strength of density dependence. As a special case, both functions may be linear, corresponding to logistic dynamics. It is shown that evolution maximizes a function of the deterministic growth rate r 0 and the lifetime reproductive success (LRS) R 0 , both defined at small densities, as well as the environmental variance. Under large noise this function is dominated by r 0 and average lifetimes are small, whereas R 0 dominates and lifetimes are larger under small noise. Thus, K-selection is closely linked to selection for large R 0 so that evolution tends to maximize LRS in a stable environment. Consequently, different quantities (r 0 and R 0 ) tend to be maximized at low and high densities, respectively, favoring density-dependent changes in the optimal life history. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

High density liquid structure enhancement in glass forming aqueous solution of LiCl.

PubMed

Camisasca, G; De Marzio, M; Rovere, M; Gallo, P

2018-06-14

We investigate using molecular dynamics simulations the dynamical and structural properties of LiCl:6H 2 O aqueous solution upon supercooling. This ionic solution is a glass forming liquid of relevant interest in connection with the study of the anomalies of supercooled water. The LiCl:6H 2 O solution is easily supercooled and the liquid state can be maintained over a large decreasing temperature range. We performed simulations from ambient to 200 K in order to investigate how the presence of the salt modifies the behavior of supercooled water. The study of the relaxation time of the self-density correlation function shows that the system follows the prediction of the mode coupling theory and behaves like a fragile liquid in all the range explored. The analysis of the changes in the water structure induced by the salt shows that while the salt preserves the water hydrogen bonds in the system, it strongly affects the tetrahedral hydrogen bond network. Following the interpretation of the anomalies of water in terms of a two-state model, the modifications of the oxygen radial distribution function and the angular distribution function of the hydrogen bonds in water indicate that LiCl has the role of enhancing the high density liquid component of water with respect to the low density component. This is in agreement with recent experiments on aqueous ionic solutions.

High density liquid structure enhancement in glass forming aqueous solution of LiCl

NASA Astrophysics Data System (ADS)

Camisasca, G.; De Marzio, M.; Rovere, M.; Gallo, P.

2018-06-01

We investigate using molecular dynamics simulations the dynamical and structural properties of LiCl:6H2O aqueous solution upon supercooling. This ionic solution is a glass forming liquid of relevant interest in connection with the study of the anomalies of supercooled water. The LiCl:6H2O solution is easily supercooled and the liquid state can be maintained over a large decreasing temperature range. We performed simulations from ambient to 200 K in order to investigate how the presence of the salt modifies the behavior of supercooled water. The study of the relaxation time of the self-density correlation function shows that the system follows the prediction of the mode coupling theory and behaves like a fragile liquid in all the range explored. The analysis of the changes in the water structure induced by the salt shows that while the salt preserves the water hydrogen bonds in the system, it strongly affects the tetrahedral hydrogen bond network. Following the interpretation of the anomalies of water in terms of a two-state model, the modifications of the oxygen radial distribution function and the angular distribution function of the hydrogen bonds in water indicate that LiCl has the role of enhancing the high density liquid component of water with respect to the low density component. This is in agreement with recent experiments on aqueous ionic solutions.

A predator-prey model with a holling type I functional response including a predator mutual interference

USGS Publications Warehouse

Seo, G.; DeAngelis, D.L.

2011-01-01

The most widely used functional response in describing predator-prey relationships is the Holling type II functional response, where per capita predation is a smooth, increasing, and saturating function of prey density. Beddington and DeAngelis modified the Holling type II response to include interference of predators that increases with predator density. Here we introduce a predator-interference term into a Holling type I functional response. We explain the ecological rationale for the response and note that the phase plane configuration of the predator and prey isoclines differs greatly from that of the Beddington-DeAngelis response; for example, in having three possible interior equilibria rather than one. In fact, this new functional response seems to be quite unique. We used analytical and numerical methods to show that the resulting system shows a much richer dynamical behavior than the Beddington-DeAngelis response, or other typically used functional responses. For example, cyclic-fold, saddle-fold, homoclinic saddle connection, and multiple crossing bifurcations can all occur. We then use a smooth approximation to the Holling type I functional response with predator mutual interference to show that these dynamical properties do not result from the lack of smoothness, but rather from subtle differences in the functional responses. ?? 2011 Springer Science+Business Media, LLC.

Statistical Decoupling of a Lagrangian Fluid Parcel in Newtonian Cosmology

NASA Astrophysics Data System (ADS)

Wang, Xin; Szalay, Alex

2016-03-01

The Lagrangian dynamics of a single fluid element within a self-gravitational matter field is intrinsically non-local due to the presence of the tidal force. This complicates the theoretical investigation of the nonlinear evolution of various cosmic objects, e.g., dark matter halos, in the context of Lagrangian fluid dynamics, since fluid parcels with given initial density and shape may evolve differently depending on their environments. In this paper, we provide a statistical solution that could decouple this environmental dependence. After deriving the evolution equation for the probability distribution of the matter field, our method produces a set of closed ordinary differential equations whose solution is uniquely determined by the initial condition of the fluid element. Mathematically, it corresponds to the projected characteristic curve of the transport equation of the density-weighted probability density function (ρPDF). Consequently it is guaranteed that the one-point ρPDF would be preserved by evolving these local, yet nonlinear, curves with the same set of initial data as the real system. Physically, these trajectories describe the mean evolution averaged over all environments by substituting the tidal tensor with its conditional average. For Gaussian distributed dynamical variables, this mean tidal tensor is simply proportional to the velocity shear tensor, and the dynamical system would recover the prediction of the Zel’dovich approximation (ZA) with the further assumption of the linearized continuity equation. For a weakly non-Gaussian field, the averaged tidal tensor could be expanded perturbatively as a function of all relevant dynamical variables whose coefficients are determined by the statistics of the field.

STATISTICAL DECOUPLING OF A LAGRANGIAN FLUID PARCEL IN NEWTONIAN COSMOLOGY

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

Wang, Xin; Szalay, Alex, E-mail: xwang@cita.utoronto.ca

The Lagrangian dynamics of a single fluid element within a self-gravitational matter field is intrinsically non-local due to the presence of the tidal force. This complicates the theoretical investigation of the nonlinear evolution of various cosmic objects, e.g., dark matter halos, in the context of Lagrangian fluid dynamics, since fluid parcels with given initial density and shape may evolve differently depending on their environments. In this paper, we provide a statistical solution that could decouple this environmental dependence. After deriving the evolution equation for the probability distribution of the matter field, our method produces a set of closed ordinary differentialmore » equations whose solution is uniquely determined by the initial condition of the fluid element. Mathematically, it corresponds to the projected characteristic curve of the transport equation of the density-weighted probability density function (ρPDF). Consequently it is guaranteed that the one-point ρPDF would be preserved by evolving these local, yet nonlinear, curves with the same set of initial data as the real system. Physically, these trajectories describe the mean evolution averaged over all environments by substituting the tidal tensor with its conditional average. For Gaussian distributed dynamical variables, this mean tidal tensor is simply proportional to the velocity shear tensor, and the dynamical system would recover the prediction of the Zel’dovich approximation (ZA) with the further assumption of the linearized continuity equation. For a weakly non-Gaussian field, the averaged tidal tensor could be expanded perturbatively as a function of all relevant dynamical variables whose coefficients are determined by the statistics of the field.« less

Electron correlation and the self-interaction error of density functional theory

NASA Astrophysics Data System (ADS)

Polo, Victor; Kraka, Elfi; Cremer, Dieter

The self-interaction error (SIE) of commonly used DFT functionals has been systematically investigated by comparing the electron density distribution ρ( r ) generated by self-interaction corrected DFT (SIC-DFT) with a series of reference densities obtained by DFT or wavefunction theory (WFT) methods that cover typical electron correlation effects. Although the SIE of GGA functionals is considerably smaller than that of LDA functionals, it has significant consequences for the coverage of electron correlation effects at the DFT level of theory. The exchange SIE mimics long range (non-dynamic) pair correlation effects, and is responsible for the fact that the electron density of DFT exchange-only calculations resembles often that of MP4, MP2 or even CCSD(T) calculations. Changes in the electron density caused by SICDFT exchange are comparable with those that are associated with HF exchange. Correlation functionals contract the density towards the bond and the valence region, thus taking negative charge out of the van der Waals region where these effects are exaggerated by the influence of the SIE of the correlation functional. Hence, SIC-DFT leads in total to a relatively strong redistribution of negative charge from van der Waals, non-bonding, and valence regions of heavy atoms to the bond regions. These changes, although much stronger, resemble those obtained when comparing the densities of hybrid functionals such as B3LYP with the corresponding GGA functional BLYP. Hence, the balanced mixing of local and non-local exchange and correlation effects as it is achieved by hybrid functionals mimics SIC-DFT and can be considered as an economic way to include some SIC into standard DFT. However, the investigation shows also that the SIC-DFT description of molecules is unreliable because the standard functionals used were optimized for DFT including the SIE.

Inelastic neutron scattering study of phonon density of states in nanostructured Si1 xGex thermoelectrics

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

Dhital, Chetan; Abernathy, Douglas L; Zhu, Gaohua

2012-01-01

Inelastic neutron scattering measurements are utilized to explore relative changes in the generalized phonon density of states of nanocrystalline Si1 xGex thermoelectric materials prepared via ball-milling and hot-pressing techniques. Dynamic signatures of Ge clustering can be inferred from the data by referencing the resulting spectra to a density functional theoretical model assuming homogeneous alloying via the virtual-crystal approximation. Comparisons are also presented between as-milled Si nanopowder and bulk, polycrystalline Si where a preferential low-energy enhancement and lifetime broadening of the phonon density of states appear in the nanopowder. Negligible differences are however observed between the phonon spectra of bulk Simore » andhot-pressed, nanostructured Si samples suggesting that changes to the single-phonon dynamics above 4 meV play only a secondary role in the modified heat conduction of this compound.« less

Bypassing the malfunction junction in warm dense matter simulations

NASA Astrophysics Data System (ADS)

Cangi, Attila; Pribram-Jones, Aurora

2015-03-01

Simulation of warm dense matter requires computational methods that capture both quantum and classical behavior efficiently under high-temperature and high-density conditions. The state-of-the-art approach to model electrons and ions under those conditions is density functional theory molecular dynamics, but this method's computational cost skyrockets as temperatures and densities increase. We propose finite-temperature potential functional theory as an in-principle-exact alternative that suffers no such drawback. In analogy to the zero-temperature theory developed previously, we derive an orbital-free free energy approximation through a coupling-constant formalism. Our density approximation and its associated free energy approximation demonstrate the method's accuracy and efficiency. A.C. has been partially supported by NSF Grant CHE-1112442. A.P.J. is supported by DOE Grant DE-FG02-97ER25308.

Atomic structure of self-organizing iridium induced nanowires on Ge(001)

NASA Astrophysics Data System (ADS)

Kabanov, N. S.; Heimbuch, R.; Zandvliet, H. J. W.; Saletsky, A. M.; Klavsyuk, A. L.

2017-05-01

The atomic structure of self-organizing iridium (Ir) induced nanowires on Ge(001) is studied by density functional theory (DFT) calculations and variable-temperature scanning tunneling microscopy. The Ir induced nanowires are aligned in a direction perpendicular to the Ge(001) substrate dimer rows, have a width of two atoms and are completely kink-less. Density functional theory calculations show that the Ir atoms prefer to dive into the Ge(001) substrate and push up the neighboring Ge substrate atoms. The nanowires are composed of Ge atoms and not Ir atoms as previously assumed. The regions in the vicinity of the nanowires are very dynamic, even at temperatures as low as 77 K. Time-resolved scanning tunneling microscopy measurements reveal that this dynamics is caused by buckled Ge substrate dimers that flip back and forth between their two buckled configurations.

Carbonic anhydrase inhibition of Schiff base derivative of imino-methyl-naphthalen-2-ol: Synthesis, structure elucidation, molecular docking, dynamic simulation and density functional theory calculations

NASA Astrophysics Data System (ADS)

Abbas, Saghir; Nasir, Hafiza Huma; Zaib, Sumera; Ali, Saqib; Mahmood, Tariq; Ayub, Khurshid; Tahir, Muhammad Nawaz; Iqbal, Jamshed

2018-03-01

In the present study, we have designed and synthesized a Schiff base derivative 3 and characterized by FT-IR, 1H and 13C NMR spectroscopy. Single crystal X-ray diffraction and NMR studies were also performed. The synthetic compound was screened for its inhibitory potential against carbonic anhydrase II. The experimental results were validated by molecular docking and dynamic simulations of compound 3 in the active pocket of enzyme. Important binding interactions with the key residues in the active site of the carbonic anhydrase enzyme were revealed. Moreover, supramolecular assembly of the title compound was analyzed by density functional theory (DFT) calculations. These studies rendered a more clear understanding for the demonstration of novel molecular mechanism involved in CA II inhibition by the synthesized compound.

Germanium multiphase equation of state

DOE PAGES

Crockett, Scott D.; Lorenzi-Venneri, Giulia De; Kress, Joel D.; ...

2014-05-07

A new SESAME multiphase germanium equation of state (EOS) has been developed using the best available experimental data and density functional theory (DFT) calculations. The equilibrium EOS includes the Ge I (diamond), the Ge II (β-Sn) and the liquid phases. The foundation of the EOS is based on density functional theory calculations which are used to determine the cold curve and the Debye temperature. Results are compared to Hugoniot data through the solid-solid and solid-liquid transitions. We propose some experiments to better understand the dynamics of this element

Automated identification of functional dynamic networks from X-ray crystallography

PubMed Central

van den Bedem, Henry; Bhabha, Gira; Yang, Kun; Wright, Peter E.; Fraser, James S.

2013-01-01

Protein function often depends on the exchange between conformational substates. Allosteric ligand binding or distal mutations can stabilize specific active site conformations and consequently alter protein function. In addition to comparing independently determined X-ray crystal structures, alternative conformations observed at low levels of electron density have the potential to provide mechanistic insights into conformational dynamics. Here, we report a new multi-conformer contact network algorithm (CONTACT) that identifies networks of conformationally heterogeneous residues directly from high-resolution X-ray crystallography data. Contact networks in Escherichia coli dihydrofolate reductase (ecDHFR) predict the long-range pattern of NMR chemical shift perturbations of an allosteric mutation. A comparison of contact networks in wild type and mutant ecDHFR suggests how mutations that alter optimized networks of coordinated motions can impair catalytic function. Thus, CONTACT-guided mutagenesis will allow the structure-dynamics-function relationship to be exploited in protein engineering and design. PMID:23913260

Mass Transport in the Warm, Dense Matter and High-Energy Density Regimes

NASA Astrophysics Data System (ADS)

Kress, J. D.; Burakovsky, L.; Ticknor, C.; Collins, L. A.; Lambert, F.

2011-10-01

Large-scale hydrodynamical simulations of fluids and plasmas under extreme conditions require knowledge of certain microscopic properties such as diffusion and viscosity in addition to the equation-of-state. To determine these dynamical properties, we employ quantum molecular dynamical (MD) simulations on large samples of atoms. The method has several advantages: 1) static, dynamical, and optical properties are produced consistently from the same simulations, and 2) mixture properties arise in a natural way since all intra- and inter-particle interactions are properly represented. We utilize two forms of density functional theory: 1) Kohn-Sham (KS-DFT) and 2) orbital-free (OF-DFT). KS-DFT is computationally intense due to its reliance on an orbital representation. As the temperature rises, the Thomas-Fermi approximation in OF-DFT begins to represent accurately the density functional, and provides an efficient and systematic means for extending the quantum simulations to very hot conditions. We have performed KS-DFT and OF-DFT calculations of the self-diffusion, mutual diffusion and shear viscosity for Al, Li, H, and LiH. We examine trends in these quantities and compare to more approximate forms such as the one-component plasma model. We also determine the validity of mixing rules that combine the properties of pure species into a composite result.

Multiphase aluminum equations of state via density functional theory

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

Sjostrom, Travis; Crockett, Scott; Rudin, Sven

2016-10-03

We have performed density functional theory (DFT) based calculations for aluminum in extreme conditions of both pressure and temperature, up to five times compressed ambient density, and over 1 000 000 K in temperature. In order to cover such a domain, DFT methods including phonon calculations, quantum molecular dynamics, and orbital-free DFT are employed. Our results are then used to construct a SESAME equation of state for the aluminum 1100 alloy, encompassing the fcc, hcp, and bcc solid phases as well as the liquid regime. We also provide extensive comparison with experiment, and based on this we also provide amore » slightly modified equation of state for the aluminum 6061 alloy.« less

Double density dynamics: realizing a joint distribution of a physical system and a parameter system

NASA Astrophysics Data System (ADS)

Fukuda, Ikuo; Moritsugu, Kei

2015-11-01

To perform a variety of types of molecular dynamics simulations, we created a deterministic method termed ‘double density dynamics’ (DDD), which realizes an arbitrary distribution for both physical variables and their associated parameters simultaneously. Specifically, we constructed an ordinary differential equation that has an invariant density relating to a joint distribution of the physical system and the parameter system. A generalized density function leads to a physical system that develops under nonequilibrium environment-describing superstatistics. The joint distribution density of the physical system and the parameter system appears as the Radon-Nikodym derivative of a distribution that is created by a scaled long-time average, generated from the flow of the differential equation under an ergodic assumption. The general mathematical framework is fully discussed to address the theoretical possibility of our method, and a numerical example representing a 1D harmonic oscillator is provided to validate the method being applied to the temperature parameters.

STED Imaging of Golgi Dynamics with Cer-SiR: A Two-Component, Photostable, High-Density Lipid Probe for Live Cells.

PubMed

Erdmann, Roman S; Toomre, Derek; Schepartz, Alanna

2017-01-01

Long time-lapse super-resolution imaging in live cells requires a labeling strategy that combines a bright, photostable fluorophore with a high-density localization probe. Lipids are ideal high-density localization probes, as they are >100 times more abundant than most membrane-bound proteins and simultaneously demark the boundaries of cellular organelles. Here, we describe Cer-SiR, a two-component, high-density lipid probe that is exceptionally photostable. Cer-SiR is generated in cells via a bioorthogonal reaction of two components: a ceramide lipid tagged with trans-cyclooctene (Cer-TCO) and a reactive, photostable Si-rhodamine dye (SiR-Tz). These components assemble within the Golgi apparatus of live cells to form Cer-SiR. Cer-SiR is benign to cellular function, localizes within the Golgi at a high density, and is sufficiently photostable to enable visualization of Golgi structure and dynamics by 3D confocal or long time-lapse STED microscopy.

Stomata size and spatial pattern effects on leaf gas exchange - a quantitative assessment of plant evolutionary choices

NASA Astrophysics Data System (ADS)

Or, Dani; Assouline, Shmuel; Aminzadeh, Milad; Haghighi, Erfan; Schymanski, Stan; Lehmann, Peter

2014-05-01

Land plants developed a dynamically gas-permeable layer at their leaf surfaces to allow CO2 uptake for photosynthesis while controlling water vapor loss through numerous adjustable openings (stomata) in the impervious leaf epidermis. Details of stomata structure, density and function may vary greatly among different plant families and respond to local environmental conditions, yet they share basic traits in dynamically controlling gaseous exchange rates by varying stomata apertures. We implement a pore scale gas diffusion model to quantitatively interpret the functionality of different combinations of stomata size and pattern on leaf gas exchange and thermal management based on data from fossil records and contemporary data sets. Considering all available data we draw several general conclusions concerning stomata design considerations: (1) the sizes and densities of stomata in the available fossil record leaves were designed to evaporate at rates in the range 0.75≤e/e0 ≤0.99 (relative to free water evaporation); (2) examination of evaporation curves show that for a given stomata size, the density (jointly defining the leaf evaporating area when fully open) was chosen to enable a high sensitivity in reducing evaporation rate with incremental stomatal closure, nevertheless, results show the design includes safety margins to account for different wind conditions (boundary layer thickness); (3) scaled for mean vapor flux, the size of stomata plays a minor role in the uniformity of leaf thermal field for a given stomata density. These principles enable rationale assessment of plant response to raising CO2, and provide a physical framework for considering the consequences of different stomata patterns (patchy) on leaf gas exchange (and thermal regime). In contrast with present quantitative description of traits and functionality of these dynamic covers in terms of gaseous diffusion resistance (or conductance), where stomata size, density and spatial pattern are lumped into a single effective resistance parameter, the present approach enables derivation of nuanced insights and offers predictive capabilities that link changes in stomata structure and geometrical attributes to quantifying environmental influences and feedbacks on leaf structure and function.

Dynamics of polymers: A mean-field theory

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

Fredrickson, Glenn H.; Materials Research Laboratory, University of California, Santa Barbara, California 93106; Department of Materials, University of California, Santa Barbara, California 93106

2014-02-28

We derive a general mean-field theory of inhomogeneous polymer dynamics; a theory whose form has been speculated and widely applied, but not heretofore derived. Our approach involves a functional integral representation of a Martin-Siggia-Rose (MSR) type description of the exact many-chain dynamics. A saddle point approximation to the generating functional, involving conditions where the MSR action is stationary with respect to a collective density field ρ and a conjugate MSR response field ϕ, produces the desired dynamical mean-field theory. Besides clarifying the proper structure of mean-field theory out of equilibrium, our results have implications for numerical studies of polymer dynamicsmore » involving hybrid particle-field simulation techniques such as the single-chain in mean-field method.« less

Communication: a density functional with accurate fractional-charge and fractional-spin behaviour for s-electrons.

PubMed

Johnson, Erin R; Contreras-García, Julia

2011-08-28

We develop a new density-functional approach combining physical insight from chemical structure with treatment of multi-reference character by real-space modeling of the exchange-correlation hole. We are able to recover, for the first time, correct fractional-charge and fractional-spin behaviour for atoms of groups 1 and 2. Based on Becke's non-dynamical correlation functional [A. D. Becke, J. Chem. Phys. 119, 2972 (2003)] and explicitly accounting for core-valence separation and pairing effects, this method is able to accurately describe dissociation and strong correlation in s-shell many-electron systems. © 2011 American Institute of Physics

Lattice dynamics calculations based on density-functional perturbation theory in real space

NASA Astrophysics Data System (ADS)

Shang, Honghui; Carbogno, Christian; Rinke, Patrick; Scheffler, Matthias

2017-06-01

A real-space formalism for density-functional perturbation theory (DFPT) is derived and applied for the computation of harmonic vibrational properties in molecules and solids. The practical implementation using numeric atom-centered orbitals as basis functions is demonstrated exemplarily for the all-electron Fritz Haber Institute ab initio molecular simulations (FHI-aims) package. The convergence of the calculations with respect to numerical parameters is carefully investigated and a systematic comparison with finite-difference approaches is performed both for finite (molecules) and extended (periodic) systems. Finally, the scaling tests and scalability tests on massively parallel computer systems demonstrate the computational efficiency.

A DYNAMIC DENSITY FUNCTIONAL THEORY APPROACH TO DIFFUSION IN WHITE DWARFS AND NEUTRON STAR ENVELOPES

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

Diaw, A.; Murillo, M. S.

2016-09-20

We develop a multicomponent hydrodynamic model based on moments of the Born–Bogolyubov–Green–Kirkwood–Yvon hierarchy equations for physical conditions relevant to astrophysical plasmas. These equations incorporate strong correlations through a density functional theory closure, while transport enters through a relaxation approximation. This approach enables the introduction of Coulomb coupling correction terms into the standard Burgers equations. The diffusive currents for these strongly coupled plasmas is self-consistently derived. The settling of impurities and its impact on cooling can be greatly affected by strong Coulomb coupling, which we show can be quantified using the direct correlation function.

Charge Separation and Exciton Dynamics at Polymer/ZnO Interface from First-Principles Simulations.

PubMed

Wu, Guangfen; Li, Zi; Zhang, Xu; Lu, Gang

2014-08-07

Charge separation and exciton dynamics play a crucial role in determining the performance of excitonic photovoltaics. Using time-dependent density functional theory with a range-separated exchange-correlation functional as well as nonadiabatic ab initio molecular dynamics, we have studied the formation and dynamics of charge-transfer (CT) excitons at polymer/ZnO interface. The interfacial atomic structure, exciton density of states and conversions between exciton species are examined from first-principles. The exciton dynamics exhibits both adiabatic and nonadiabatic characters. While the adiabatic transitions are facilitated by C═C vibrations along the polymer (P3HT) backbone, the nonadiabatic transitions are realized by exciton hopping between the excited states. We find that the localized ZnO surface states lead to localized low-energy CT states and poor charge separation. In contrast, the surface states of crystalline C60 are indistinguishable from the bulk states, resulting in delocalized CT states and efficient charge separation in polymer/fullerene (P3HT/PCBM) heterojunctions. The hot CT states are found to cool down in an ultrafast time scale and may not play a major role in charge separation of P3HT/ZnO. Finally we suggest that the dimensions of nanostructured acceptors can be tuned to obtain both efficient charge separation and high open circuit voltages.

Modeling of Firn Compaction for Estimating Ice-Sheet Mass Change from Observed Ice-Sheet Elevation Change

NASA Technical Reports Server (NTRS)

Li, Jun; Zwally, H. Jay

2011-01-01

Changes in ice-sheet surface elevation are caused by a combination of ice-dynamic imbalance, ablation, temporal variations in accumulation rate, firn compaction and underlying bedrock motion. Thus, deriving the rate of ice-sheet mass change from measured surface elevation change requires information on the rate of firn compaction and bedrock motion, which do not involve changes in mass, and requires an appropriate firn density to associate with elevation changes induced by recent accumulation rate variability. We use a 25 year record of surface temperature and a parameterization for accumulation change as a function of temperature to drive a firn compaction model. We apply this formulation to ICESat measurements of surface elevation change at three locations on the Greenland ice sheet in order to separate the accumulation-driven changes from the ice-dynamic/ablation-driven changes, and thus to derive the corresponding mass change. Our calculated densities for the accumulation-driven changes range from 410 to 610 kg/cu m, which along with 900 kg/cu m for the dynamic/ablation-driven changes gives average densities ranging from 680 to 790 kg/cu m. We show that using an average (or "effective") density to convert elevation change to mass change is not valid where the accumulation and the dynamic elevation changes are of opposite sign.

Structural, electronic, mechanical, and dynamical properties of graphene oxides: A first principles study

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

Dabhi, Shweta D.; Gupta, Sanjay D.; Jha, Prafulla K., E-mail: prafullaj@yahoo.com

We report the results of a theoretical study on the structural, electronic, mechanical, and vibrational properties of some graphene oxide models (GDO, a-GMO, z-GMO, ep-GMO and mix-GMO) at ambient pressure. The calculations are based on the ab-initio plane-wave pseudo potential density functional theory, within the generalized gradient approximations for the exchange and correlation functional. The calculated values of lattice parameters, bulk modulus, and its first order pressure derivative are in good agreement with other reports. A linear response approach to the density functional theory is used to derive the phonon frequencies. We discuss the contribution of the phonons in themore » dynamical stability of graphene oxides and detailed analysis of zone centre phonon modes in all the above mentioned models. Our study demonstrates a wide range of energy gap available in the considered models of graphene oxide and hence the possibility of their use in nanodevices.« less

Bonding and structure in dense multi-component molecular mixtures

DOE PAGES

Meyer, Edmund R.; Ticknor, Christopher; Bethkenhagen, Mandy; ...

2015-10-30

We have performed finite-temperature density functional theory molecular dynamics simulations on dense methane, ammonia, and water mixtures (CH 4:NH 3:H 2O) for various compositions and temperatures (2000 K ≤ T ≤ 10000 K) that span a set of possible conditions in the interiors of ice-giant exoplanets. The equation-of-state, pair distribution functions, and bond autocorrelation functions (BACF) were used to probe the structure and dynamics of these complex fluids. In particular, an improvement to the choice of the cutoff in the BACF was developed that allowed analysis refinements for density and temperature effects. We note the relative changes in the naturemore » of these systems engendered by variations in the concentration ratios. As a result, a basic tenet emerges from all these comparisons that varying the relative amounts of the three heavy components (C,N,O) can effect considerable changes in the nature of the fluid and may in turn have ramifications for the structure and composition of various planetary layers.« less

Dynamic programming for optimization of timber production and grazing in ponderosa pine

Treesearch

Kurt H. Riitters; J. Douglas Brodie; David W. Hann

1982-01-01

Dynamic programming procedures are presented for optimizing thinning and rotation of even-aged ponderosa pine by using the four descriptors: age, basal area, number of trees, and time since thinning. Because both timber yield and grazing yield are functions of stand density, the two outputs-forage and timber-can both be optimized. The soil expectation values for single...

Trajectory-based nonadiabatic dynamics with time-dependent density functional theory.

PubMed

Curchod, Basile F E; Rothlisberger, Ursula; Tavernelli, Ivano

2013-05-10

Understanding the fate of an electronically excited molecule constitutes an important task for theoretical chemistry, and practical implications range from the interpretation of atto- and femtosecond spectroscopy to the development of light-driven molecular machines, the control of photochemical reactions, and the possibility of capturing sunlight energy. However, many challenging conceptual and technical problems are involved in the description of these phenomena such as 1) the failure of the well-known Born-Oppenheimer approximation; 2) the need for accurate electronic properties such as potential energy surfaces, excited nuclear forces, or nonadiabatic coupling terms; and 3) the necessity of describing the dynamics of the photoexcited nuclear wavepacket. This review provides an overview of the current methods to address points 1) and 3) and shows how time-dependent density functional theory (TDDFT) and its linear-response extension can be used for point 2). First, the derivation of Ehrenfest dynamics and nonadiabatic Bohmian dynamics is discussed and linked to Tully's trajectory surface hopping. Second, the coupling of these trajectory-based nonadiabatic schemes with TDDFT is described in detail with special emphasis on the derivation of the required electronic structure properties. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Communication: Two-step explosion processes of highly charged fullerene cations C{sub 60}{sup q+} (q = 20–60)

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

Yamazaki, Kaoru; Nakamura, Takashi; Kanno, Manabu

2014-09-28

To establish the fundamental understanding of the fragmentation dynamics of highly positive charged nano- and bio-materials, we carried out on-the-fly classical trajectory calculations on the fragmentation dynamics of C{sub 60}{sup q+} (q = 20–60). We used the UB3LYP/3-21G level of density functional theory and the self-consistent charge density-functional based tight-binding theory. For q ≥ 20, we found that a two-step explosion mechanism governs the fragmentation dynamics: C{sub 60}{sup q+} first ejects singly and multiply charged fast atomic cations C{sup z+} (z ≥ 1) via Coulomb explosions on a timescale of 10 fs to stabilize the remaining core cluster. Thermal evaporationsmore » of slow atomic and molecular fragments from the core cluster subsequently occur on a timescale of 100 fs to 1 ps. Increasing the charge q makes the fragments smaller. This two-step mechanism governs the fragmentation dynamics in the most likely case that the initial kinetic energy accumulated upon ionization to C{sub 60}{sup q+} by ion impact or X-ray free electron laser is larger than 100 eV.« less

A semi-analytic dynamical friction model for cored galaxies

NASA Astrophysics Data System (ADS)

Petts, J. A.; Read, J. I.; Gualandris, A.

2016-11-01

We present a dynamical friction model based on Chandrasekhar's formula that reproduces the fast inspiral and stalling experienced by satellites orbiting galaxies with a large constant density core. We show that the fast inspiral phase does not owe to resonance. Rather, it owes to the background velocity distribution function for the constant density core being dissimilar from the usually assumed Maxwellian distribution. Using the correct background velocity distribution function and our semi-analytic model from previous work, we are able to correctly reproduce the infall rate in both cored and cusped potentials. However, in the case of large cores, our model is no longer able to correctly capture core-stalling. We show that this stalling owes to the tidal radius of the satellite approaching the size of the core. By switching off dynamical friction when rt(r) = r (where rt is the tidal radius at the satellite's position), we arrive at a model which reproduces the N-body results remarkably well. Since the tidal radius can be very large for constant density background distributions, our model recovers the result that stalling can occur for Ms/Menc ≪ 1, where Ms and Menc are the mass of the satellite and the enclosed galaxy mass, respectively. Finally, we include the contribution to dynamical friction that comes from stars moving faster than the satellite. This next-to-leading order effect becomes the dominant driver of inspiral near the core region, prior to stalling.

Critical dynamic approach to stationary states in complex systems

NASA Astrophysics Data System (ADS)

Rozenfeld, A. F.; Laneri, K.; Albano, E. V.

2007-04-01

A dynamic scaling Ansatz for the approach to stationary states in complex systems is proposed and tested by means of extensive simulations applied to both the Bak-Sneppen (BS) model, which exhibits robust Self-Organised Critical (SOC) behaviour, and the Game of Life (GOL) of J. Conway, whose critical behaviour is under debate. Considering the dynamic scaling behaviour of the density of sites (ρ(t)), it is shown that i) by starting the dynamic measurements with configurations such that ρ(t=0) →0, one observes an initial increase of the density with exponents θ= 0.12(2) and θ= 0.11(2) for the BS and GOL models, respectively; ii) by using initial configurations with ρ(t=0) →1, the density decays with exponents δ= 0.47(2) and δ= 0.28(2) for the BS and GOL models, respectively. It is also shown that the temporal autocorrelation decays with exponents Ca = 0.35(2) (Ca = 0.35(5)) for the BS (GOL) model. By using these dynamically determined critical exponents and suitable scaling relationships, we also obtain the dynamic exponents z = 2.10(5) (z = 2.10(5)) for the BS (GOL) model. Based on this evidence we conclude that the dynamic approach to stationary states of the investigated models can be described by suitable power-law functions of time with well-defined exponents.

Structure and Entanglement Factors on Dynamics of Polymer-Grafted Nanoparticles

DOE PAGES

Liu, Siqi; Senses, Erkan; Jiao, Yang; ...

2016-04-15

Nanoparticles functionalized with long polymer chains at low graft density are interesting systems to study structure–dynamic relationships in polymer nanocomposites since they are shown to aggregate into strings in both solution and melts and also into spheres and branched aggregates in the presence of free polymer chains. Our work investigates structure and entanglement effects in composites of polystyrene-grafted iron oxide nanoparticles by measuring particle relaxations using X-ray photon correlation spectroscopy. And for particles within highly ordered strings and aggregated systems, they experience a dynamically heterogeneous environment displaying hyperdiffusive relaxation commonly observed in jammed soft glassy systems. Furthermore, particle dynamics ismore » diffusive for branched aggregated structures which could be caused by less penetration of long matrix chains into brushes. These results suggest that particle motion is dictated by the strong interactions of chains grafted at low density with the host matrix polymer.« less

Weakly Nonergodic Dynamics in the Gross-Pitaevskii Lattice

NASA Astrophysics Data System (ADS)

Mithun, Thudiyangal; Kati, Yagmur; Danieli, Carlo; Flach, Sergej

2018-05-01

The microcanonical Gross-Pitaevskii (also known as the semiclassical Bose-Hubbard) lattice model dynamics is characterized by a pair of energy and norm densities. The grand canonical Gibbs distribution fails to describe a part of the density space, due to the boundedness of its kinetic energy spectrum. We define Poincaré equilibrium manifolds and compute the statistics of microcanonical excursion times off them. The tails of the distribution functions quantify the proximity of the many-body dynamics to a weakly nonergodic phase, which occurs when the average excursion time is infinite. We find that a crossover to weakly nonergodic dynamics takes place inside the non-Gibbs phase, being unnoticed by the largest Lyapunov exponent. In the ergodic part of the non-Gibbs phase, the Gibbs distribution should be replaced by an unknown modified one. We relate our findings to the corresponding integrable limit, close to which the actions are interacting through a short range coupling network.

The effect of the size of the system, aspect ratio and impurities concentration on the dynamic of emergent magnetic monopoles in artificial spin ice systems

NASA Astrophysics Data System (ADS)

León, Alejandro

2013-08-01

In this work we study the dynamical properties of a finite array of nanomagnets in artificial kagome spin ice at room temperature. The dynamic response of the array of nanomagnets is studied by implementing a "frustrated celular autómata" (FCA), based in the charge model and dipolar model. The FCA simulations allow us to study in real-time and deterministic way, the dynamic of the system, with minimal computational resource. The update function is defined according to the coordination number of vertices in the system. Our results show that for a set geometric parameters of the array of nanomagnets, the system exhibits high density of Dirac strings and high density emergent magnetic monopoles. A study of the effect of disorder in the arrangement of nanomagnets is incorporated in this work.

Second-order perturbation theory with a density matrix renormalization group self-consistent field reference function: theory and application to the study of chromium dimer.

PubMed

Kurashige, Yuki; Yanai, Takeshi

2011-09-07

We present a second-order perturbation theory based on a density matrix renormalization group self-consistent field (DMRG-SCF) reference function. The method reproduces the solution of the complete active space with second-order perturbation theory (CASPT2) when the DMRG reference function is represented by a sufficiently large number of renormalized many-body basis, thereby being named DMRG-CASPT2 method. The DMRG-SCF is able to describe non-dynamical correlation with large active space that is insurmountable to the conventional CASSCF method, while the second-order perturbation theory provides an efficient description of dynamical correlation effects. The capability of our implementation is demonstrated for an application to the potential energy curve of the chromium dimer, which is one of the most demanding multireference systems that require best electronic structure treatment for non-dynamical and dynamical correlation as well as large basis sets. The DMRG-CASPT2/cc-pwCV5Z calculations were performed with a large (3d double-shell) active space consisting of 28 orbitals. Our approach using large-size DMRG reference addressed the problems of why the dissociation energy is largely overestimated by CASPT2 with the small active space consisting of 12 orbitals (3d4s), and also is oversensitive to the choice of the zeroth-order Hamiltonian. © 2011 American Institute of Physics

Fluid dynamic propagation of initial baryon number perturbations on a Bjorken flow background

DOE PAGES

Floerchinger, Stefan; Martinez, Mauricio

2015-12-11

Baryon number density perturbations offer a possible route to experimentally measure baryon number susceptibilities and heat conductivity of the quark gluon plasma. We study the fluid dynamical evolution of local and event-by-event fluctuations of baryon number density, flow velocity, and energy density on top of a (generalized) Bjorken expansion. To that end we use a background-fluctuation splitting and a Bessel-Fourier decomposition for the fluctuating part of the fluid dynamical fields with respect to the azimuthal angle, the radius in the transverse plane, and rapidity. Here, we examine how the time evolution of linear perturbations depends on the equation of statemore » as well as on shear viscosity, bulk viscosity, and heat conductivity for modes with different azimuthal, radial, and rapidity wave numbers. Finally we discuss how this information is accessible to experiments in terms of the transverse and rapidity dependence of correlation functions for baryonic particles in high energy nuclear collisions.« less

The thermal-wave model: A Schroedinger-like equation for charged particle beam dynamics

NASA Technical Reports Server (NTRS)

Fedele, Renato; Miele, G.

1994-01-01

We review some results on longitudinal beam dynamics obtained in the framework of the Thermal Wave Model (TWM). In this model, which has recently shown the capability to describe both longitudinal and transverse dynamics of charged particle beams, the beam dynamics is ruled by Schroedinger-like equations for the beam wave functions, whose squared modulus is proportional to the beam density profile. Remarkably, the role of the Planck constant is played by a diffractive constant epsilon, the emittance, which has a thermal nature.

Theoretical investigation of the structural, electronic, dynamical and thermal properties of YSn3 and YPb3

NASA Astrophysics Data System (ADS)

Kılıçarslan, Aynur; Salmankurt, Bahadır; Duman, Sıtkı

2017-02-01

We have performed an ab initio study of the structural, electronic, dynamical and thermal properties of the cubic AuCu3-type YSn3 and YPb3 by using the density functional theory, plane-wave pseudopotential method and a linear response scheme, within the generalized gradient approximation. An analysis of the electronic density of states at the Fermi level is found to be governed by the p states of Sn and Pb atoms with some contributions from the d states of Y atoms. The obtained phonon figures indicate that these material are dynamically stable in the cubic structure. Due to the metallic behavior of the compounds, the calculated zone-center phonon modes are triply degenerate. Also the thermal properties have been examined.

A molecular dynamics study on the interaction between epoxy and functionalized graphene sheets

NASA Astrophysics Data System (ADS)

Melro, L. S.; Pyrz, R.; Jensen, L. R.

2016-07-01

The interaction between graphene and epoxy resin was studied using molecular dynamics simulations. The interfacial shear strength and pull out force were calculated for functionalised graphene layers (carboxyl, carbonyl, and hydroxyl) and epoxy composites interfaces. The influence of functional groups, as well as their distribution and coverage density on the graphene sheets were also analysed through the determination of the Young's modulus. Functionalisation proved to be detrimental to the mechanical properties, nonetheless according to interfacial studies the interaction between graphene and epoxy resin increases.

Dynamical consequences of compositional and thermal density stratification beneath spreading centers

NASA Technical Reports Server (NTRS)

Sotin, C.; Parmentier, E. M.

1989-01-01

Dynamical consequences of compositional buoyancy and the combined effects of compositional and thermal buoyancy on mantle flow and crustal production are explored. The results show that for a low enough mantle viscosity, buoyant upwelling can significantly enhance the crustal thickness relative to that which would be produced by plate spreading alone, while for a mantle viscosity of 10 to the 22nd Pa s, upwelling due to plate spreading is dominant and crustal thickness is predicted to be a function of spreading rate. The results indicate that thermal and compositional density variations result in opposing buoyancy forces that can cause time-dependent upwelling.

Comparison of electron transport calculations in warm dense matter using the Ziman formula

DOE PAGES

Burrill, D. J.; Feinblum, D. V.; Charest, M. R. J.; ...

2016-02-10

The Ziman formulation of electrical conductivity is tested in warm and hot dense matter using the pseudo-atom molecular dynamics method. Several implementation options that have been widely used in the literature are systematically tested through a comparison to the accurate, but expensive Kohn–Sham density functional theory molecular dynamics (KS-DFT-MD) calculations. As a result, the comparison is made for several elements and mixtures and for a wide range of temperatures and densities, and reveals a preferred method that generally gives very good agreement with the KS-DFT-MD results, but at a fraction of the computational cost.

The Structure of Liquid and Amorphous Hafnia.

PubMed

Gallington, Leighanne C; Ghadar, Yasaman; Skinner, Lawrie B; Weber, J K Richard; Ushakov, Sergey V; Navrotsky, Alexandra; Vazquez-Mayagoitia, Alvaro; Neuefeind, Joerg C; Stan, Marius; Low, John J; Benmore, Chris J

2017-11-10

Understanding the atomic structure of amorphous solids is important in predicting and tuning their macroscopic behavior. Here, we use a combination of high-energy X-ray diffraction, neutron diffraction, and molecular dynamics simulations to benchmark the atomic interactions in the high temperature stable liquid and low-density amorphous solid states of hafnia. The diffraction results reveal an average Hf-O coordination number of ~7 exists in both the liquid and amorphous nanoparticle forms studied. The measured pair distribution functions are compared to those generated from several simulation models in the literature. We have also performed ab initio and classical molecular dynamics simulations that show density has a strong effect on the polyhedral connectivity. The liquid shows a broad distribution of Hf-Hf interactions, while the formation of low-density amorphous nanoclusters can reproduce the sharp split peak in the Hf-Hf partial pair distribution function observed in experiment. The agglomeration of amorphous nanoparticles condensed from the gas phase is associated with the formation of both edge-sharing and corner-sharing HfO 6,7 polyhedra resembling that observed in the monoclinic phase.

The Structure of Liquid and Amorphous Hafnia

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

Gallington, Leighanne; Ghadar, Yasaman; Skinner, Lawrie

Understanding the atomic structure of amorphous solids is important in predicting and tuning their macroscopic behavior. Here, we use a combination of high-energy X-ray diffraction, neutron diffraction, and molecular dynamics simulations to benchmark the atomic interactions in the high temperature stable liquid and low-density amorphous solid states of hafnia. The diffraction results reveal an average Hf–O coordination number of ~7 exists in both the liquid and amorphous nanoparticle forms studied. The measured pair distribution functions are compared to those generated from several simulation models in the literature. We have also performed ab initio and classical molecular dynamics simulations that showmore » density has a strong effect on the polyhedral connectivity. The liquid shows a broad distribution of Hf–Hf interactions, while the formation of low-density amorphous nanoclusters can reproduce the sharp split peak in the Hf–Hf partial pair distribution function observed in experiment. The agglomeration of amorphous nanoparticles condensed from the gas phase is associated with the formation of both edge-sharing and corner-sharing HfO 6,7 polyhedra resembling that observed in the monoclinic phase.« less

The Structure of Liquid and Amorphous Hafnia

DOE PAGES

Gallington, Leighanne; Ghadar, Yasaman; Skinner, Lawrie; ...

2017-11-10

Understanding the atomic structure of amorphous solids is important in predicting and tuning their macroscopic behavior. Here, we use a combination of high-energy X-ray diffraction, neutron diffraction, and molecular dynamics simulations to benchmark the atomic interactions in the high temperature stable liquid and low-density amorphous solid states of hafnia. The diffraction results reveal an average Hf–O coordination number of ~7 exists in both the liquid and amorphous nanoparticle forms studied. The measured pair distribution functions are compared to those generated from several simulation models in the literature. We have also performed ab initio and classical molecular dynamics simulations that showmore » density has a strong effect on the polyhedral connectivity. The liquid shows a broad distribution of Hf–Hf interactions, while the formation of low-density amorphous nanoclusters can reproduce the sharp split peak in the Hf–Hf partial pair distribution function observed in experiment. The agglomeration of amorphous nanoparticles condensed from the gas phase is associated with the formation of both edge-sharing and corner-sharing HfO 6,7 polyhedra resembling that observed in the monoclinic phase.« less

Predator diversity and environmental change modify the strengths of trophic and nontrophic interactions.

PubMed

Sentis, Arnaud; Gémard, Charlène; Jaugeon, Baptiste; Boukal, David S

2017-07-01

Understanding the dependence of species interaction strengths on environmental factors and species diversity is crucial to predict community dynamics and persistence in a rapidly changing world. Nontrophic (e.g. predator interference) and trophic components together determine species interaction strengths, but the effects of environmental factors on these two components remain largely unknown. This impedes our ability to fully understand the links between environmental drivers and species interactions. Here, we used a dynamical modelling framework based on measured predator functional responses to investigate the effects of predator diversity, prey density, and temperature on trophic and nontrophic interaction strengths within a freshwater food web. We found that (i) species interaction strengths cannot be predicted from trophic interactions alone, (ii) nontrophic interaction strengths vary strongly among predator assemblages, (iii) temperature has opposite effects on trophic and nontrophic interaction strengths, and (iv) trophic interaction strengths decrease with prey density, whereas the dependence of nontrophic interaction strengths on prey density is concave up. Interestingly, the qualitative impacts of temperature and prey density on the strengths of trophic and nontrophic interactions were independent of predator identity, suggesting a general pattern. Our results indicate that taking multiple environmental factors and the nonlinearity of density-dependent species interactions into account is an important step towards a better understanding of the effects of environmental variations on complex ecological communities. The functional response approach used in this study opens new avenues for (i) the quantification of the relative importance of the trophic and nontrophic components in species interactions and (ii) a better understanding how environmental factors affect these interactions and the dynamics of ecological communities. © 2016 John Wiley & Sons Ltd.

Time-Dependent Density Functional Theory for Open Systems and Its Applications.

PubMed

Chen, Shuguang; Kwok, YanHo; Chen, GuanHua

2018-02-20

Photovoltaic devices, electrochemical cells, catalysis processes, light emitting diodes, scanning tunneling microscopes, molecular electronics, and related devices have one thing in common: open quantum systems where energy and matter are not conserved. Traditionally quantum chemistry is confined to isolated and closed systems, while quantum dissipation theory studies open quantum systems. The key quantity in quantum dissipation theory is the reduced system density matrix. As the reduced system density matrix is an O(M! × M!) matrix, where M is the number of the particles of the system of interest, quantum dissipation theory can only be employed to simulate systems of a few particles or degrees of freedom. It is thus important to combine quantum chemistry and quantum dissipation theory so that realistic open quantum systems can be simulated from first-principles. We have developed a first-principles method to simulate the dynamics of open electronic systems, the time-dependent density functional theory for open systems (TDDFT-OS). Instead of the reduced system density matrix, the key quantity is the reduced single-electron density matrix, which is an N × N matrix where N is the number of the atomic bases of the system of interest. As the dimension of the key quantity is drastically reduced, the TDDFT-OS can thus be used to simulate the dynamics of realistic open electronic systems and efficient numerical algorithms have been developed. As an application, we apply the method to study how quantum interference develops in a molecular transistor in time domain. We include electron-phonon interaction in our simulation and show that quantum interference in the given system is robust against nuclear vibration not only in the steady state but also in the transient dynamics. As another application, by combining TDDFT-OS with Ehrenfest dynamics, we study current-induced dissociation of water molecules under scanning tunneling microscopy and follow its time dependent dynamics. Given the rapid development in ultrafast experiments with atomic resolution in recent years, time dependent simulation of open electronic systems will be useful to gain insight and understanding of such experiments. This Account will mainly focus on the practical aspects of the TDDFT-OS method, describing the numerical implementation and demonstrating the method with applications.

Dynamic plasmonic colour display

NASA Astrophysics Data System (ADS)

Duan, Xiaoyang; Kamin, Simon; Liu, Na

2017-02-01

Plasmonic colour printing based on engineered metasurfaces has revolutionized colour display science due to its unprecedented subwavelength resolution and high-density optical data storage. However, advanced plasmonic displays with novel functionalities including dynamic multicolour printing, animations, and highly secure encryption have remained in their infancy. Here we demonstrate a dynamic plasmonic colour display technique that enables all the aforementioned functionalities using catalytic magnesium metasurfaces. Controlled hydrogenation and dehydrogenation of the constituent magnesium nanoparticles, which serve as dynamic pixels, allow for plasmonic colour printing, tuning, erasing and restoration of colour. Different dynamic pixels feature distinct colour transformation kinetics, enabling plasmonic animations. Through smart material processing, information encoded on selected pixels, which are indiscernible to both optical and scanning electron microscopies, can only be read out using hydrogen as a decoding key, suggesting a new generation of information encryption and anti-counterfeiting applications.

Dynamic plasmonic colour display.

PubMed

Duan, Xiaoyang; Kamin, Simon; Liu, Na

2017-02-24

Plasmonic colour printing based on engineered metasurfaces has revolutionized colour display science due to its unprecedented subwavelength resolution and high-density optical data storage. However, advanced plasmonic displays with novel functionalities including dynamic multicolour printing, animations, and highly secure encryption have remained in their infancy. Here we demonstrate a dynamic plasmonic colour display technique that enables all the aforementioned functionalities using catalytic magnesium metasurfaces. Controlled hydrogenation and dehydrogenation of the constituent magnesium nanoparticles, which serve as dynamic pixels, allow for plasmonic colour printing, tuning, erasing and restoration of colour. Different dynamic pixels feature distinct colour transformation kinetics, enabling plasmonic animations. Through smart material processing, information encoded on selected pixels, which are indiscernible to both optical and scanning electron microscopies, can only be read out using hydrogen as a decoding key, suggesting a new generation of information encryption and anti-counterfeiting applications.

Dynamic plasmonic colour display

PubMed Central

Duan, Xiaoyang; Kamin, Simon; Liu, Na

2017-01-01

Plasmonic colour printing based on engineered metasurfaces has revolutionized colour display science due to its unprecedented subwavelength resolution and high-density optical data storage. However, advanced plasmonic displays with novel functionalities including dynamic multicolour printing, animations, and highly secure encryption have remained in their infancy. Here we demonstrate a dynamic plasmonic colour display technique that enables all the aforementioned functionalities using catalytic magnesium metasurfaces. Controlled hydrogenation and dehydrogenation of the constituent magnesium nanoparticles, which serve as dynamic pixels, allow for plasmonic colour printing, tuning, erasing and restoration of colour. Different dynamic pixels feature distinct colour transformation kinetics, enabling plasmonic animations. Through smart material processing, information encoded on selected pixels, which are indiscernible to both optical and scanning electron microscopies, can only be read out using hydrogen as a decoding key, suggesting a new generation of information encryption and anti-counterfeiting applications. PMID:28232722

Density-dependence as a size-independent regulatory mechanism.

PubMed

de Vladar, Harold P

2006-01-21

The growth function of populations is central in biomathematics. The main dogma is the existence of density-dependence mechanisms, which can be modelled with distinct functional forms that depend on the size of the population. One important class of regulatory functions is the theta-logistic, which generalizes the logistic equation. Using this model as a motivation, this paper introduces a simple dynamical reformulation that generalizes many growth functions. The reformulation consists of two equations, one for population size, and one for the growth rate. Furthermore, the model shows that although population is density-dependent, the dynamics of the growth rate does not depend either on population size, nor on the carrying capacity. Actually, the growth equation is uncoupled from the population size equation, and the model has only two parameters, a Malthusian parameter rho and a competition coefficient theta. Distinct sign combinations of these parameters reproduce not only the family of theta-logistics, but also the van Bertalanffy, Gompertz and Potential Growth equations, among other possibilities. It is also shown that, except for two critical points, there is a general size-scaling relation that includes those appearing in the most important allometric theories, including the recently proposed Metabolic Theory of Ecology. With this model, several issues of general interest are discussed such as the growth of animal population, extinctions, cell growth and allometry, and the effect of environment over a population.

Edge reconstruction in armchair phosphorene nanoribbons revealed by discontinuous Galerkin density functional theory.

PubMed

Hu, Wei; Lin, Lin; Yang, Chao

2015-12-21

With the help of our recently developed massively parallel DGDFT (Discontinuous Galerkin Density Functional Theory) methodology, we perform large-scale Kohn-Sham density functional theory calculations on phosphorene nanoribbons with armchair edges (ACPNRs) containing a few thousands to ten thousand atoms. The use of DGDFT allows us to systematically achieve a conventional plane wave basis set type of accuracy, but with a much smaller number (about 15) of adaptive local basis (ALB) functions per atom for this system. The relatively small number of degrees of freedom required to represent the Kohn-Sham Hamiltonian, together with the use of the pole expansion the selected inversion (PEXSI) technique that circumvents the need to diagonalize the Hamiltonian, results in a highly efficient and scalable computational scheme for analyzing the electronic structures of ACPNRs as well as their dynamics. The total wall clock time for calculating the electronic structures of large-scale ACPNRs containing 1080-10,800 atoms is only 10-25 s per self-consistent field (SCF) iteration, with accuracy fully comparable to that obtained from conventional planewave DFT calculations. For the ACPNR system, we observe that the DGDFT methodology can scale to 5000-50,000 processors. We use DGDFT based ab initio molecular dynamics (AIMD) calculations to study the thermodynamic stability of ACPNRs. Our calculations reveal that a 2 × 1 edge reconstruction appears in ACPNRs at room temperature.

Generalized-active-space pair-density functional theory: an efficient method to study large, strongly correlated, conjugated systems

DOE PAGES

Ghosh, Soumen; Cramer, Christopher J.; Truhlar, Donald G.; ...

2017-01-19

Predicting ground- and excited-state properties of open-shell organic molecules by electronic structure theory can be challenging because an accurate treatment has to correctly describe both static and dynamic electron correlation. Strongly correlated systems, i.e., systems with near-degeneracy correlation effects, are particularly troublesome. Multiconfigurational wave function methods based on an active space are adequate in principle, but it is impractical to capture most of the dynamic correlation in these methods for systems characterized by many active electrons. Here, we recently developed a new method called multiconfiguration pair-density functional theory (MC-PDFT), that combines the advantages of wave function theory and density functionalmore » theory to provide a more practical treatment of strongly correlated systems. Here we present calculations of the singlet–triplet gaps in oligoacenes ranging from naphthalene to dodecacene. Calculations were performed for unprecedently large orbitally optimized active spaces of 50 electrons in 50 orbitals, and we test a range of active spaces and active space partitions, including four kinds of frontier orbital partitions. We show that MC-PDFT can predict the singlet–triplet splittings for oligoacenes consistent with the best available and much more expensive methods, and indeed MC-PDFT may constitute the benchmark against which those other models should be compared, given the absence of experimental data.« less

Generalized-active-space pair-density functional theory: an efficient method to study large, strongly correlated, conjugated systems

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

Ghosh, Soumen; Cramer, Christopher J.; Truhlar, Donald G.

Predicting ground- and excited-state properties of open-shell organic molecules by electronic structure theory can be challenging because an accurate treatment has to correctly describe both static and dynamic electron correlation. Strongly correlated systems, i.e., systems with near-degeneracy correlation effects, are particularly troublesome. Multiconfigurational wave function methods based on an active space are adequate in principle, but it is impractical to capture most of the dynamic correlation in these methods for systems characterized by many active electrons. Here, we recently developed a new method called multiconfiguration pair-density functional theory (MC-PDFT), that combines the advantages of wave function theory and density functionalmore » theory to provide a more practical treatment of strongly correlated systems. Here we present calculations of the singlet–triplet gaps in oligoacenes ranging from naphthalene to dodecacene. Calculations were performed for unprecedently large orbitally optimized active spaces of 50 electrons in 50 orbitals, and we test a range of active spaces and active space partitions, including four kinds of frontier orbital partitions. We show that MC-PDFT can predict the singlet–triplet splittings for oligoacenes consistent with the best available and much more expensive methods, and indeed MC-PDFT may constitute the benchmark against which those other models should be compared, given the absence of experimental data.« less

Stability of mechanical joints in launching vehicles: Local and global stationary values of energy density

NASA Astrophysics Data System (ADS)

Chue, Ching-Hwei

A method was developed for predicting the behavior of mechanical joints in launch vehicles with particular emphasis placed on how the combined effects of loading, geometry, and materials could be optimized in terms of structure instability and/or integrity. What was considered to be essential is the fluctuation of the volume energy density with time in the structure. The peaks and valleys of the volume energy density function will be associated with failure by fracture and/or yielding while the distance between their local and global stationary values govern the structure instability. The Solid Rocket Booster (SRB) of the space shuttle was analyzed under axisymmetric and non-axisymmetric loadings. A semi-analytical finite element program was developed for solving the case of non-axisymmetric loading. Following a dynamic stress analysis, contours of the volume energy density in the structure were obtained as a function of time. The magnitudes and locations of these stationary values were then calculated locally and globally and related to possible failure by fracture. In the case of axisymmetric flight, the local and global instability behavior do not change appreciably. Fluctuations in the energy density and the dynamic stability length parameter become appreciable when the non-axisymmetric loads are considered. The magnitude of the energy in the shell structure is sensitive to alterations in the gas pressure induced by the solid propellant.

Statistical properties of a filtered Poisson process with additive random noise: distributions, correlations and moment estimation

NASA Astrophysics Data System (ADS)

Theodorsen, A.; E Garcia, O.; Rypdal, M.

2017-05-01

Filtered Poisson processes are often used as reference models for intermittent fluctuations in physical systems. Such a process is here extended by adding a noise term, either as a purely additive term to the process or as a dynamical term in a stochastic differential equation. The lowest order moments, probability density function, auto-correlation function and power spectral density are derived and used to identify and compare the effects of the two different noise terms. Monte-Carlo studies of synthetic time series are used to investigate the accuracy of model parameter estimation and to identify methods for distinguishing the noise types. It is shown that the probability density function and the three lowest order moments provide accurate estimations of the model parameters, but are unable to separate the noise types. The auto-correlation function and the power spectral density also provide methods for estimating the model parameters, as well as being capable of identifying the noise type. The number of times the signal crosses a prescribed threshold level in the positive direction also promises to be able to differentiate the noise type.

Hydrogen bonding in malonaldehyde: a density functional and reparametrized semiempirical approach

NASA Astrophysics Data System (ADS)

Kovačević, Goran; Hrenar, Tomica; Došlić, Nadja

2003-08-01

Intramolecular proton transfer in malonaldehyde (MA) has been investigated by density functional theory (DFT). The DFT results were used for the construction of a high quality semiempirical potential energy surface with a reparametrized PM3 Hamiltonian. A two-step reparameterization procedure is proposed in which (i) the PM3-MAIS core-core functions for the O-H and H-H interactions were used and a new functional form for the O-O correction function was proposed and (ii) a set of specific reaction parameters (SRP) has been obtained via genetic algorithm optimization. The quality of the reparametrized semiempirical potential energy surfaces was tested by calculating the tunneling splitting of vibrational levels and the anharmonic vibrational frequencies of the system. The applicability to multi-dimensional dynamics in large molecular systems is discussed.

Relation between the Dynamics of Glassy Clusters and Characteristic Features of their Energy Landscape

NASA Astrophysics Data System (ADS)

De, Sandip; Schaefer, Bastian; Sadeghi, Ali; Sicher, Michael; Kanhere, D. G.; Goedecker, Stefan

2014-02-01

Based on a recently introduced metric for measuring distances between configurations, we introduce distance-energy (DE) plots to characterize the potential energy surface of clusters. Producing such plots is computationally feasible on the density functional level since it requires only a few hundred stable low energy configurations including the global minimum. By using standard criteria based on disconnectivity graphs and the dynamics of Lennard-Jones clusters, we show that the DE plots convey the necessary information about the character of the potential energy surface and allow us to distinguish between glassy and nonglassy systems. We then apply this analysis to real clusters at the density functional theory level and show that both glassy and nonglassy clusters can be found in simulations. It turns out that among our investigated clusters only those can be synthesized experimentally which exhibit a nonglassy landscape.

Nuclear spin relaxation due to chemical shift anisotropy of gas-phase 129Xe.

PubMed

Hanni, Matti; Lantto, Perttu; Vaara, Juha

2011-08-14

Nuclear spin relaxation provides detailed dynamical information on molecular systems and materials. Here, first-principles modeling of the chemical shift anisotropy (CSA) relaxation time for the prototypic monoatomic (129)Xe gas is carried out, both complementing and predicting the results of NMR measurements. Our approach is based on molecular dynamics simulations combined with pre-parametrized ab initio binary nuclear shielding tensors, an "NMR force field". By using the Redfield relaxation formalism, the simulated CSA time correlation functions lead to spectral density functions that, for the first time, quantitatively determine the experimental spin-lattice relaxation times T(1). The quality requirements on both the Xe-Xe interaction potential and binary shielding tensor are investigated in the context of CSA T(1). Persistent dimers Xe(2) are found to be responsible for the CSA relaxation mechanism in the low-density limit of the gas, completely in line with the earlier experimental findings.

On the emergence of a generalised Gamma distribution. Application to traded volume in financial markets

NASA Astrophysics Data System (ADS)

Duarte Queirós, S. M.

2005-08-01

This letter reports on a stochastic dynamical scenario whose associated stationary probability density function is exactly a generalised form, with a power law instead of exponencial decay, of the ubiquitous Gamma distribution. This generalisation, also known as F-distribution, was empirically proposed for the first time to adjust for high-frequency stock traded volume distributions in financial markets and verified in experiments with granular material. The dynamical assumption presented herein is based on local temporal fluctuations of the average value of the observable under study. This proposal is related to superstatistics and thus to the current nonextensive statistical mechanics framework. For the specific case of stock traded volume, we connect the local fluctuations in the mean stock traded volume with the typical herding behaviour presented by financial traders. Last of all, NASDAQ 1 and 2 minute stock traded volume sequences and probability density functions are numerically reproduced.

Probabilistic DHP adaptive critic for nonlinear stochastic control systems.

PubMed

Herzallah, Randa

2013-06-01

Following the recently developed algorithms for fully probabilistic control design for general dynamic stochastic systems (Herzallah & Káarnáy, 2011; Kárný, 1996), this paper presents the solution to the probabilistic dual heuristic programming (DHP) adaptive critic method (Herzallah & Káarnáy, 2011) and randomized control algorithm for stochastic nonlinear dynamical systems. The purpose of the randomized control input design is to make the joint probability density function of the closed loop system as close as possible to a predetermined ideal joint probability density function. This paper completes the previous work (Herzallah & Káarnáy, 2011; Kárný, 1996) by formulating and solving the fully probabilistic control design problem on the more general case of nonlinear stochastic discrete time systems. A simulated example is used to demonstrate the use of the algorithm and encouraging results have been obtained. Copyright © 2013 Elsevier Ltd. All rights reserved.

An ab initio molecular dynamics and density functional theory study of the formation of phosphate chains from metathiophosphates.

PubMed

Mosey, Nicholas J; Woo, Tom K

2006-09-04

The reactions that occur between metathiophosphate (MTP) molecules are identified and examined through ab initio molecular dynamics simulations and static quantum chemical calculations at the density functional level of theory. The simulations show that certain types of MTPs can react to yield phosphate chains, while others only dimerize. These differences are rationalized in terms of reaction energies and the electronic structures of these molecules. In the reaction leading to the formation of phosphate chains, the reactive center, a tri-coordinate phosphorus atom, is continually regenerated. A polymerization mechanism linking MTPs to phosphate chains is developed on the basis of these results. This information sheds light on the underlying processes that may be responsible for the formation of phosphates under high-temperature conditions and may prove useful in the development of protocols for the rational synthesis of complex phosphate structures.

Mapping the temperature-dependent conformational landscapes of the dynamic enzymes cyclophilin A and urease

NASA Astrophysics Data System (ADS)

Thorne, Robert; Keedy, Daniel; Warkentin, Matthew; Fraser, James; Moreau, David; Atakisi, Hakan; Rau, Peter

Proteins populate complex, temperature-dependent ensembles of conformations that enable their function. Yet in X-ray crystallographic studies, roughly 98% of structures have been determined at 100 K, and most refined to only a single conformation. A combination of experimental methods enabled by studies of ice formation and computational methods for mining low-density features in electron density maps have been applied to determine the evolution of the conformational landscapes of the enzymes cyclophilin A and urease between 300 K and 100 K. Minority conformations of most side chains depopulate on cooling from 300 to ~200 K, below which subsequent conformational evolution is quenched. The characteristic temperatures for this depopulation are highly heterogeneous throughout each enzyme. The temperature-dependent ensemble of the active site flap in urease has also been mapped. These all-atom, site-resolved measurements and analyses rule out one interpretation of the protein-solvent glass transition, and give an alternative interpretation of a dynamical transition identified in site-averaged experiments. They demonstrate a powerful approach to structural characterization of the dynamic underpinnings of protein function. Supported by NSF MCB-1330685.

A review of theoretical study of graphene chemical vapor deposition synthesis on metals: nucleation, growth, and the role of hydrogen and oxygen

NASA Astrophysics Data System (ADS)

Rezwan Habib, Mohammad; Liang, Tao; Yu, Xuegong; Pi, Xiaodong; Liu, Yingchun; Xu, Mingsheng

2018-03-01

Graphene has attracted intense research interest due to its extraordinary properties and great application potential. Various methods have been proposed for the synthesis of graphene, among which chemical vapor deposition has drawn a great deal of attention for synthesizing large-area and high-quality graphene. Theoretical understanding of the synthesis mechanism is crucial for optimizing the experimental design for desired graphene production. In this review, we discuss the three fundamental steps of graphene synthesis in details, i.e. (1) decomposition of carbon feedstocks and formation of various active carbon species, (2) nucleation, and (3) attachment and extension. We provide a complete scenario of graphene synthesis on metal surfaces at atomistic level by means of density functional theory, molecular dynamics (MD), Monte Carlo (MC) and their combination and interface with other simulation methods such as quantum mechanical molecular dynamics, density functional tight binding molecular dynamics, and combination of MD and MC. We also address the latest investigation of the influences of the hydrogen and oxygen on the synthesis and the quality of the synthesized graphene.

Nuclear Fission: from more phenomenology and adjusted parameters to more fundamental theory and increased predictive power

NASA Astrophysics Data System (ADS)

Bulgac, Aurel; Jin, Shi; Magierski, Piotr; Roche, Kenneth; Schunck, Nicolas; Stetcu, Ionel

2017-11-01

Two major recent developments in theory and computational resources created the favorable conditions for achieving a microscopic description of fission dynamics in classically allowed regions of the collective potential energy surface, almost eighty years after its discovery in 1939 by Hahn and Strassmann [1]. The first major development was in theory, the extension of the Time-Dependent Density Functional Theory (TDDFT) [2-5] to superfluid fermion systems [6]. The second development was in computing, the emergence of powerful enough supercomputers capable of solving the complex systems of equations describing the time evolution in three dimensions without any restrictions of hundreds of strongly interacting nucleons. Thus the conditions have been created to renounce phenomenological models and incomplete microscopic treatments with uncontrollable approximations and/or assumptions in the description of the complex dynamics of fission. Even though the available nuclear energy density functionals (NEDFs) are phenomenological still, their accuracy is improving steadily and the prospects of being able to perform calculations of the nuclear fission dynamics and to predict many properties of the fission fragments, otherwise not possible to extract from experiments.

A search for two types of transverse excitations in liquid polyvalent metals at ambient pressure: An ab initio molecular dynamics study of collective excitations in liquid Al, Tl and Ni

NASA Astrophysics Data System (ADS)

Bryk, Taras; Demchuk, Taras; Jakse, Noël; Wax, Jean-François

2018-02-01

Recent findings of pressure-induced emergence of unusual high-frequency contribution to transverse current spectral functions in several simple liquid metals at high pressures raised a question whether similar features can be observed in liquid metals at ambient conditions. We report here analysis of ab initio molecular dynamics-derived longitudinal (L) and transverse (T) current spectral functions and corresponding dispersions of collective excitations in liquid polyvalent metals Al, Tl, Ni. We have not found evidences of the second branch of high-frequency transverse modes in liquid Al and Ni, while in the case of liquid Tl they were clearly present in transverse dynamics. The vibrational density of states for liquid Tl has a pronounced high-frequency shoulder, which is located right in the frequency range of the second high-frequency transverse branch, while for liquid Al and Ni the vibrational density of states has only a weak indication of possible high-frequency shoulder. The origin of specific behavior of transverse excitations in liquid Tl is discussed.

Structure of cold nuclear matter at subnuclear densities by quantum molecular dynamics

NASA Astrophysics Data System (ADS)

Watanabe, Gentaro; Sato, Katsuhiko; Yasuoka, Kenji; Ebisuzaki, Toshikazu

2003-09-01

Structure of cold nuclear matter at subnuclear densities for the proton fraction x=0.5, 0.3, and 0.1 is investigated by quantum molecular dynamics (QMD) simulations. We demonstrate that the phases with slablike and rodlike nuclei, etc. can be formed dynamically from hot uniform nuclear matter without any assumptions on nuclear shape, and also systematically analyze the structure of cold matter using two-point correlation functions and Minkowski functionals. In our simulations, we also observe intermediate phases, which have complicated nuclear shapes. It has been found out that these phases can be characterized as those with negative Euler characteristic. Our result implies the existence of these kinds of phases in addition to the simple “pasta” phases in neutron star crusts and supernova inner cores. In addition, we investigate the properties of the effective QMD interaction used in the present work to examine the validity of our results. The resultant energy per nucleon ɛn of the pure neutron matter, the proton chemical μ(0)p in pure neutron matter and the nuclear surface tension Esurf are generally reasonable in comparison with other nuclear interactions.

Quantum dynamics modeled by interacting trajectories

NASA Astrophysics Data System (ADS)

Cruz-Rodríguez, L.; Uranga-Piña, L.; Martínez-Mesa, A.; Meier, C.

2018-03-01

We present quantum dynamical simulations based on the propagation of interacting trajectories where the effect of the quantum potential is mimicked by effective pseudo-particle interactions. The method is applied to several quantum systems, both for bound and scattering problems. For the bound systems, the quantum ground state density and zero point energy are shown to be perfectly obtained by the interacting trajectories. In the case of time-dependent quantum scattering, the Eckart barrier and uphill ramp are considered, with transmission coefficients in very good agreement with standard quantum calculations. Finally, we show that via wave function synthesis along the trajectories, correlation functions and energy spectra can be obtained based on the dynamics of interacting trajectories.

Tetragonal and collapsed-tetragonal phases of CaFe2As2 : A view from angle-resolved photoemission and dynamical mean-field theory

NASA Astrophysics Data System (ADS)

van Roekeghem, Ambroise; Richard, Pierre; Shi, Xun; Wu, Shangfei; Zeng, Lingkun; Saparov, Bayrammurad; Ohtsubo, Yoshiyuki; Qian, Tian; Sefat, Athena S.; Biermann, Silke; Ding, Hong

2016-06-01

We present a study of the tetragonal to collapsed-tetragonal transition of CaFe2As2 using angle-resolved photoemission spectroscopy and dynamical mean field theory-based electronic structure calculations. We observe that the collapsed-tetragonal phase exhibits reduced correlations and a higher coherence temperature due to the stronger Fe-As hybridization. Furthermore, a comparison of measured photoemission spectra and theoretical spectral functions shows that momentum-dependent corrections to the density functional band structure are essential for the description of low-energy quasiparticle dispersions. We introduce those using the recently proposed combined "screened exchange + dynamical mean field theory" scheme.

III-Nitride, SiC and Diamond Materials for Electronic Devices. Symposium Held April 8-12 1996, San Francisco, California, U.S.A. Volume 423.

DTIC Science & Technology

1996-12-01

gallium, nitrogen and gallium nitride structures. Thus it can be shown to be transferable and efficient for predictive molecular -dynamic simulations on...potentials and forces for the molecular dynamics simulations are derived by means of a density-functional based nonorthogonal tight-binding (DF-TB) scheme...LDA). Molecular -dynamics simulations for determining the different reconstructions of the SiC surface use the slab method (two-dimensional periodic

Influence of spatial heterogeneity on the type of zooplankton functional response: A study based on field observations

NASA Astrophysics Data System (ADS)

Morozov, Andrew; Arashkevich, Elena; Reigstad, Marit; Falk-Petersen, Stig

2008-10-01

Mathematical models of plankton dynamics are sensitive to the choice of type of zooplankton functional response, i.e., to how the rate of intake of food varies with the food density. Conventionally, the conclusion on the actual type of functional response for a given zooplankton species is made based upon laboratory analysis on experimental feeding. In this paper, we show that such an approach can be too simplistic and misleading. Based on real ocean data obtained from three expeditions of R/V Jan Mayen in the Barents Sea in 2003-2005, we demonstrate that vertical heterogeneity in algal distribution as well as active vertical movement of herbivorous zooplankton can modify the type of trophic response completely. In particular, we found that the rate of average intake of algae by Calanus glacialis exhibits a Holling type III response, instead of Holling type I or II found previously in laboratory experiments. We argue that this conceptual discrepancy is due to the ability of the zooplankton to feed in layers with high algal density and to avoid depths with lower algal density. Since theoretical studies would predict enhancing in system stability in the case of Holling type III, our results may be of importance for understanding the main factors controlling plankton dynamics.

Estimation of Nanodiamond Surface Charge Density from Zeta Potential and Molecular Dynamics Simulations.

PubMed

Ge, Zhenpeng; Wang, Yi

2017-04-20

Molecular dynamics simulations of nanoparticles (NPs) are increasingly used to study their interactions with various biological macromolecules. Such simulations generally require detailed knowledge of the surface composition of the NP under investigation. Even for some well-characterized nanoparticles, however, this knowledge is not always available. An example is nanodiamond, a nanoscale diamond particle with surface dominated by oxygen-containing functional groups. In this work, we explore using the harmonic restraint method developed by Venable et al., to estimate the surface charge density (σ) of nanodiamonds. Based on the Gouy-Chapman theory, we convert the experimentally determined zeta potential of a nanodiamond to an effective charge density (σ eff ), and then use the latter to estimate σ via molecular dynamics simulations. Through scanning a series of nanodiamond models, we show that the above method provides a straightforward protocol to determine the surface charge density of relatively large (> ∼100 nm) NPs. Overall, our results suggest that despite certain limitation, the above protocol can be readily employed to guide the model construction for MD simulations, which is particularly useful when only limited experimental information on the NP surface composition is available to a modeler.

PYFLOW_2.0: a computer program for calculating flow properties and impact parameters of past dilute pyroclastic density currents based on field data

NASA Astrophysics Data System (ADS)

Dioguardi, Fabio; Mele, Daniela

2018-03-01

This paper presents PYFLOW_2.0, a hazard tool for the calculation of the impact parameters of dilute pyroclastic density currents (DPDCs). DPDCs represent the dilute turbulent type of gravity flows that occur during explosive volcanic eruptions; their hazard is the result of their mobility and the capability to laterally impact buildings and infrastructures and to transport variable amounts of volcanic ash along the path. Starting from data coming from the analysis of deposits formed by DPDCs, PYFLOW_2.0 calculates the flow properties (e.g., velocity, bulk density, thickness) and impact parameters (dynamic pressure, deposition time) at the location of the sampled outcrop. Given the inherent uncertainties related to sampling, laboratory analyses, and modeling assumptions, the program provides ranges of variations and probability density functions of the impact parameters rather than single specific values; from these functions, the user can interrogate the program to obtain the value of the computed impact parameter at any specified exceedance probability. In this paper, the sedimentological models implemented in PYFLOW_2.0 are presented, program functionalities are briefly introduced, and two application examples are discussed so as to show the capabilities of the software in quantifying the impact of the analyzed DPDCs in terms of dynamic pressure, volcanic ash concentration, and residence time in the atmosphere. The software and user's manual are made available as a downloadable electronic supplement.

Discontinuous Galerkin finite element method for solving population density functions of cortical pyramidal and thalamic neuronal populations.

PubMed

Huang, Chih-Hsu; Lin, Chou-Ching K; Ju, Ming-Shaung

2015-02-01

Compared with the Monte Carlo method, the population density method is efficient for modeling collective dynamics of neuronal populations in human brain. In this method, a population density function describes the probabilistic distribution of states of all neurons in the population and it is governed by a hyperbolic partial differential equation. In the past, the problem was mainly solved by using the finite difference method. In a previous study, a continuous Galerkin finite element method was found better than the finite difference method for solving the hyperbolic partial differential equation; however, the population density function often has discontinuity and both methods suffer from a numerical stability problem. The goal of this study is to improve the numerical stability of the solution using discontinuous Galerkin finite element method. To test the performance of the new approach, interaction of a population of cortical pyramidal neurons and a population of thalamic neurons was simulated. The numerical results showed good agreement between results of discontinuous Galerkin finite element and Monte Carlo methods. The convergence and accuracy of the solutions are excellent. The numerical stability problem could be resolved using the discontinuous Galerkin finite element method which has total-variation-diminishing property. The efficient approach will be employed to simulate the electroencephalogram or dynamics of thalamocortical network which involves three populations, namely, thalamic reticular neurons, thalamocortical neurons and cortical pyramidal neurons. Copyright © 2014 Elsevier Ltd. All rights reserved.

Measuring the stellar luminosity function and spatial density profile of the inner 0.5 pc of the Milky Way nuclear star cluster

NASA Astrophysics Data System (ADS)

Do, Tuan; Ghez, Andrea; Lu, Jessica R.; Morris, Mark R.; Yelda, Sylvana; Martinez, Gregory D.; Peter, Annika H. G.; Wright, Shelley; Bullock, James; Kaplinghat, Manoj; Matthews, K.

2012-07-01

We report on measurements of the luminosity function of early (young) and late-type (old) stars in the central 0.5 pc of the Milky Way nuclear star cluster as well as the density profiles of both components. The young (~ 6 Myr) and old stars (> 1 Gyr) in this region provide different physical probes of the environment around a supermassive black hole; the luminosity function of the young stars offers us a way to measure the initial mass function from star formation in an extreme environment, while the density profile of the old stars offers us a probe of the dynamical interaction of a star cluster with a massive black hole. The two stellar populations are separated through a near-infrared spectroscopic survey using the integral-field spectrograph OSIRIS on Keck II behind the laser guide star adaptive optics system. This spectroscopic survey is able to separate early-type (young) and late-type (old) stars with a completeness of 50% at K' = 15.5. We describe our method of completeness correction using a combination of star planting simulations and Bayesian inference. The completeness corrected luminosity function of the early-type stars contains significantly more young stars at faint magnitudes compared to previous surveys with similar depth. In addition, by using proper motion and radial velocity measurements along with anisotropic spherical Jeans modeling of the cluster, it is possible to measure the spatial density profile of the old stars, which has been difficult to constrain with number counts alone. The most probable model shows that the spatial density profile, n(r) propto r-γ, to be shallow with γ = 0.4 ± 0.2, which is much flatter than the dynamically relaxed case of γ = 3/2 to 7/4, but does rule out a 'hole' in the distribution of old stars. We show, for the first time, that the spatial density profile, the black hole mass, and velocity anisotropy can be fit simultaneously to obtain a black hole mass that is consistent with that derived from individual orbits of stars at distances < 1000 AU from the Galactic center.

Drift of Phase Fluctuations in the ABC Model

NASA Astrophysics Data System (ADS)

Bertini, Lorenzo; Buttà, Paolo

2013-07-01

In a recent work, Bodineau and Derrida analyzed the phase fluctuations in the ABC model. In particular, they computed the asymptotic variance and, on the basis of numerical simulations, they conjectured the presence of a drift, which they guessed to be an antisymmetric function of the three densities. By assuming the validity of the fluctuating hydrodynamic approximation, we prove the presence of such a drift, providing an analytical expression for it. This expression is then shown to be an antisymmetric function of the three densities. The antisymmetry of the drift can also be inferred from a symmetry property of the underlying microscopic dynamics.

Optimal positions and parameters of translational and rotational mass dampers in beams subjected to random excitation

NASA Astrophysics Data System (ADS)

Łatas, Waldemar

2018-01-01

The problem of vibrations of the beam with the attached system of translational and rotational dynamic mass dampers subjected to random excitations with peaked power spectral densities, is presented in the hereby paper. The Euler-Bernoulli beam model is applied, while for solving the equation of motion the Galerkin method and the Laplace time transform are used. The obtained transfer functions allow to determine power spectral densities of the beam deflection and other dependent variables. Numerical examples present simple optimization problems of mass dampers parameters for local and global objective functions.

Objective Molecular Dynamics with Self-consistent Charge Density Functional Tight-Binding (SCC-DFTB) Method

NASA Astrophysics Data System (ADS)

Dumitrica, Traian; Hourahine, Ben; Aradi, Balint; Frauenheim, Thomas

We discus the coupling of the objective boundary conditions into the SCC density functional-based tight binding code DFTB+. The implementation is enabled by a generalization to the helical case of the classical Ewald method, specifically by Ewald-like formulas that do not rely on a unit cell with translational symmetry. The robustness of the method in addressing complex hetero-nuclear nano- and bio-fibrous systems is demonstrated with illustrative simulations on a helical boron nitride nanotube, a screw dislocated zinc oxide nanowire, and an ideal double-strand DNA. Work supported by NSF CMMI 1332228.

Muscle anatomy and dynamic muscle function in osteogenesis imperfecta type I.

PubMed

Veilleux, Louis-Nicolas; Lemay, Martin; Pouliot-Laforte, Annie; Cheung, Moira S; Glorieux, Francis H; Rauch, Frank

2014-02-01

Results of previous studies suggested that children and adolescents with osteogenesis imperfecta (OI) type I have a muscle force deficit. However, muscle function has only been assessed by static isometric force tests and not in more natural conditions such as dynamic force and power tests. The purpose of this study was to assess lower extremity dynamic muscle function and muscle anatomy in OI type I. The study was performed in the outpatient department of a pediatric orthopedic hospital. A total of 54 individuals with OI type I (6-21 years; 20 male) and 54 age- and sex-matched controls took part in this study. Calf muscle cross-sectional area and density were measured by peripheral quantitative computed tomography. Lower extremity muscle function (peak force per body weight and peak power per body mass) was measured by jumping mechanography through 5 tests: multiple two-legged hopping, multiple one-legged hopping, single two-legged jump, chair-rise test, and heel-rise test. Compared with age- and sex-matched controls, patients with OI type I had smaller muscle size (P = .04) but normal muscle density (P = .21). They also had lower average peak force and lower specific force (peak force/muscle cross-sectional area; all P < .008). Average peak power was lower in patients with OI type I but not significantly so (all P > .054). Children and adolescents with OI type I have, on average, a significant force deficit in the lower limb as measured by dynamic force tests. Nonetheless, these data also show that OI type I is compatible with normal muscle performance in some individuals.

Large deviation function for a driven underdamped particle in a periodic potential

NASA Astrophysics Data System (ADS)

Fischer, Lukas P.; Pietzonka, Patrick; Seifert, Udo

2018-02-01

Employing large deviation theory, we explore current fluctuations of underdamped Brownian motion for the paradigmatic example of a single particle in a one-dimensional periodic potential. Two different approaches to the large deviation function of the particle current are presented. First, we derive an explicit expression for the large deviation functional of the empirical phase space density, which replaces the level 2.5 functional used for overdamped dynamics. Using this approach, we obtain several bounds on the large deviation function of the particle current. We compare these to bounds for overdamped dynamics that have recently been derived, motivated by the thermodynamic uncertainty relation. Second, we provide a method to calculate the large deviation function via the cumulant generating function. We use this method to assess the tightness of the bounds in a numerical case study for a cosine potential.

Spectral functions of strongly correlated extended systems via an exact quantum embedding

NASA Astrophysics Data System (ADS)

Booth, George H.; Chan, Garnet Kin-Lic

2015-04-01

Density matrix embedding theory (DMET) [Phys. Rev. Lett. 109, 186404 (2012), 10.1103/PhysRevLett.109.186404], introduced an approach to quantum cluster embedding methods whereby the mapping of strongly correlated bulk problems to an impurity with finite set of bath states was rigorously formulated to exactly reproduce the entanglement of the ground state. The formalism provided similar physics to dynamical mean-field theory at a tiny fraction of the cost but was inherently limited by the construction of a bath designed to reproduce ground-state, static properties. Here, we generalize the concept of quantum embedding to dynamic properties and demonstrate accurate bulk spectral functions at similarly small computational cost. The proposed spectral DMET utilizes the Schmidt decomposition of a response vector, mapping the bulk dynamic correlation functions to that of a quantum impurity cluster coupled to a set of frequency-dependent bath states. The resultant spectral functions are obtained on the real-frequency axis, without bath discretization error, and allows for the construction of arbitrary dynamic correlation functions. We demonstrate the method on the one- (1D) and two-dimensional (2D) Hubbard model, where we obtain zero temperature and thermodynamic limit spectral functions, and show the trivial extension to two-particle Green's functions. This advance therefore extends the scope and applicability of DMET in condensed-matter problems as a computationally tractable route to correlated spectral functions of extended systems and provides a competitive alternative to dynamical mean-field theory for dynamic quantities.

Comparative study of cluster Ag17Cu2 by instantaneous normal mode analysis and by isothermal Brownian-type molecular dynamics simulation.

PubMed

Tang, Ping-Han; Wu, Ten-Ming; Yen, Tsung-Wen; Lai, S K; Hsu, P J

2011-09-07

We perform isothermal Brownian-type molecular dynamics simulations to obtain the velocity autocorrelation function and its time Fourier-transformed power spectral density for the metallic cluster Ag(17)Cu(2). The temperature dependences of these dynamical quantities from T = 0 to 1500 K were examined and across this temperature range the cluster melting temperature T(m), which we define to be the principal maximum position of the specific heat is determined. The instantaneous normal mode analysis is then used to dissect the cluster dynamics by calculating the vibrational instantaneous normal mode density of states and hence its frequency integrated value I(j) which is an ensemble average of all vibrational projection operators for the jth atom in the cluster. In addition to comparing the results with simulation data, we look more closely at the entities I(j) of all atoms using the point group symmetry and diagnose their temperature variations. We find that I(j) exhibit features that may be used to deduce T(m), which turns out to agree very well with those inferred from the power spectral density and specific heat. © 2011 American Institute of Physics

Large-scale galaxy flow from a non-gravitational impulse

NASA Technical Reports Server (NTRS)

Hogan, Craig J.; Kaiser, Nick

1989-01-01

A theory is presented describing linear perturbations of an expanding universe containing multiple, independently perturbed, collisionless, gravitationally coupled constituents. Solutions are found in the limit where one initially unperturbed component dominates the total density. The theory is applied to perturbations generated by a nongravitational process in one or more of the light components, as would occur in explosive or radiation-pressure-instability theories of galaxy formation. The apparent dynamical density parameter and correlations between density and velocity amplitude for various populations, are evaluated as a function of cosmic scale factor.

What drives interaction strengths in complex food webs? A test with feeding rates of a generalist stream predator.

PubMed

Preston, Daniel L; Henderson, Jeremy S; Falke, Landon P; Segui, Leah M; Layden, Tamara J; Novak, Mark

2018-05-08

Describing the mechanisms that drive variation in species interaction strengths is central to understanding, predicting, and managing community dynamics. Multiple factors have been linked to trophic interaction strength variation, including species densities, species traits, and abiotic factors. Yet most empirical tests of the relative roles of multiple mechanisms that drive variation have been limited to simplified experiments that may diverge from the dynamics of natural food webs. Here, we used a field-based observational approach to quantify the roles of prey density, predator density, predator-prey body-mass ratios, prey identity, and abiotic factors in driving variation in feeding rates of reticulate sculpin (Cottus perplexus). We combined data on over 6,000 predator-prey observations with prey identification time functions to estimate 289 prey-specific feeding rates at nine stream sites in Oregon. Feeding rates on 57 prey types showed an approximately log-normal distribution, with few strong and many weak interactions. Model selection indicated that prey density, followed by prey identity, were the two most important predictors of prey-specific sculpin feeding rates. Feeding rates showed a positive relationship with prey taxon densities that was inconsistent with predator saturation predicted by current functional response models. Feeding rates also exhibited four orders-of-magnitude in variation across prey taxonomic orders, with the lowest feeding rates observed on prey with significant anti-predator defenses. Body-mass ratios were the third most important predictor variable, showing a hump-shaped relationship with the highest feeding rates at intermediate ratios. Sculpin density was negatively correlated with feeding rates, consistent with the presence of intraspecific predator interference. Our results highlight how multiple co-occurring drivers shape trophic interactions in nature and underscore ways in which simplified experiments or reliance on scaling laws alone may lead to biased inferences about the structure and dynamics of species-rich food webs. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Why do gallium clusters have a higher melting point than the bulk?

PubMed

Chacko, S; Joshi, Kavita; Kanhere, D G; Blundell, S A

2004-04-02

Density functional molecular dynamical simulations have been performed on Ga17 and Ga13 clusters to understand the recently observed higher-than-bulk melting temperatures in small gallium clusters [Phys. Rev. Lett. 91, 215508 (2003)

Renormalized dynamics of the Dean-Kawasaki model

NASA Astrophysics Data System (ADS)

Bidhoodi, Neeta; Das, Shankar P.

2015-07-01

We study the model of a supercooled liquid for which the equation of motion for the coarse-grained density ρ (x ,t ) is the nonlinear diffusion equation originally proposed by Dean and Kawasaki, respectively, for Brownian and Newtonian dynamics of fluid particles. Using a Martin-Siggia-Rose (MSR) field theory we study the renormalization of the dynamics in a self-consistent form in terms of the so-called self-energy matrix Σ . The appropriate model for the renormalized dynamics involves an extended set of field variables {ρ ,θ } , linked through a nonlinear constraint. The latter incorporates, in a nonperturbative manner, the effects of an infinite number of density nonlinearities in the dynamics. We show that the contributing element of Σ which renormalizes the bare diffusion constant D0 to DR is same as that proposed by Kawasaki and Miyazima [Z. Phys. B Condens. Matter 103, 423 (1997), 10.1007/s002570050396]. DR sharply decreases with increasing density. We consider the likelihood of a ergodic-nonergodic (ENE) transition in the model beyond a critical point. The transition is characterized by the long-time limit of the density correlation freezing at a nonzero value. From our analysis we identify an element of Σ which arises from the above-mentioned nonlinear constraint and is key to the viability of the ENE transition. If this self-energy would be zero, then the model supports a sharp ENE transition with DR=0 as predicted by Kawasaki and Miyazima. With the full model having nonzero value for this self-energy, the density autocorrelation function decays to zero in the long-time limit. Hence the ENE transition is not supported in the model.

Multiconfigurational short-range density-functional theory for open-shell systems

NASA Astrophysics Data System (ADS)

Hedegârd, Erik Donovan; Toulouse, Julien; Jensen, Hans Jørgen Aagaard

2018-06-01

Many chemical systems cannot be described by quantum chemistry methods based on a single-reference wave function. Accurate predictions of energetic and spectroscopic properties require a delicate balance between describing the most important configurations (static correlation) and obtaining dynamical correlation efficiently. The former is most naturally done through a multiconfigurational (MC) wave function, whereas the latter can be done by, e.g., perturbation theory. We have employed a different strategy, namely, a hybrid between multiconfigurational wave functions and density-functional theory (DFT) based on range separation. The method is denoted by MC short-range DFT (MC-srDFT) and is more efficient than perturbative approaches as it capitalizes on the efficient treatment of the (short-range) dynamical correlation by DFT approximations. In turn, the method also improves DFT with standard approximations through the ability of multiconfigurational wave functions to recover large parts of the static correlation. Until now, our implementation was restricted to closed-shell systems, and to lift this restriction, we present here the generalization of MC-srDFT to open-shell cases. The additional terms required to treat open-shell systems are derived and implemented in the DALTON program. This new method for open-shell systems is illustrated on dioxygen and [Fe(H2O)6]3+.

Beyond the dynamic density functional theory for steady currents: application to driven colloidal particles in a channel.

PubMed

Tarazona, P; Marini Bettolo Marconi, Umberto

2008-04-28

Motivated by recent studies on the dynamics of colloidal solutions in narrow channels, we consider the steady state properties of an assembly of noninteracting particles subject to the action of a traveling potential moving at a constant speed, while the solvent is modeled by a heat bath at rest in the laboratory frame. Here, since the description we propose takes into account the inertia of the colloidal particles, it is necessary to consider the evolution of both positions and momenta and study the governing equation for the one-particle phase-space distribution. First, we derive the asymptotic form of its solutions as an expansion in Hermite polynomials and their generic properties, such as the force and energy balance, and then we particularize our study to the case of an inverted parabolic potential barrier. We numerically obtain the steady state density and temperature profile and show that the expansion is rapidly convergent for large values of the friction constant and small drifting velocities. On the one hand, the present results confirm the previous studies based on the dynamic density functional theory (DDFT): On the other hand, when the friction constant is large, it display effects such as the presence of a wake behind the barrier and a strong inhomogeneity in the temperature field which are beyond the DDFT description.

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

Versino, Daniele; Bronkhorst, Curt Allan

The computational formulation of a micro-mechanical material model for the dynamic failure of ductile metals is presented in this paper. The statistical nature of porosity initiation is accounted for by introducing an arbitrary probability density function which describes the pores nucleation pressures. Each micropore within the representative volume element is modeled as a thick spherical shell made of plastically incompressible material. The treatment of porosity by a distribution of thick-walled spheres also allows for the inclusion of micro-inertia effects under conditions of shock and dynamic loading. The second order ordinary differential equation governing the microscopic porosity evolution is solved withmore » a robust implicit procedure. A new Chebyshev collocation method is employed to approximate the porosity distribution and remapping is used to optimize memory usage. The adaptive approximation of the porosity distribution leads to a reduction of computational time and memory usage of up to two orders of magnitude. Moreover, the proposed model affords consistent performance: changing the nucleation pressure probability density function and/or the applied strain rate does not reduce accuracy or computational efficiency of the material model. The numerical performance of the model and algorithms presented is tested against three problems for high density tantalum: single void, one-dimensional uniaxial strain, and two-dimensional plate impact. Here, the results using the integration and algorithmic advances suggest a significant improvement in computational efficiency and accuracy over previous treatments for dynamic loading conditions.« less

Phase space explorations in time dependent density functional theory

NASA Astrophysics Data System (ADS)

Rajam, Aruna K.

Time dependent density functional theory (TDDFT) is one of the useful tools for the study of the dynamic behavior of correlated electronic systems under the influence of external potentials. The success of this formally exact theory practically relies on approximations for the exchange-correlation potential which is a complicated functional of the co-ordinate density, non-local in space and time. Adiabatic approximations (such as ALDA), which are local in time, are most commonly used in the increasing applications of the field. Going beyond ALDA, has been proved difficult leading to mathematical inconsistencies. We explore the regions where the theory faces challenges, and try to answer some of them via the insights from two electron model systems. In this thesis work we propose a phase-space extension of the TDDFT. We want to answer the challenges the theory is facing currently by exploring the one-body phase-space. We give a general introduction to this theory and its mathematical background in the first chapter. In second chapter, we carryout a detailed study of instantaneous phase-space densities and argue that the functionals of distributions can be a better alternative to the nonlocality issue of the exchange-correlation potentials. For this we study in detail the interacting and the non-interacting phase-space distributions for Hookes atom model. The applicability of ALDA-based TDDFT for the dynamics in strongfields can become severely problematic due to the failure of single-Slater determinant picture.. In the third chapter, we analyze how the phase-space distributions can shine some light into this problem. We do a comparative study of Kohn-Sham and interacting phase-space and momentum distributions for single ionization and double ionization systems. Using a simple model of two-electron systems, we have showed that the momentum distribution computed directly from the exact KS system contains spurious oscillations: a non-classical description of the essentially classical two-electron dynamics. In Time dependent density matrix functional theory (TDDMFT), the evolution scheme of the 1RDM (first order reduced density matrix) contains second-order reduced density matrix (2RDM), which has to be expressed in terms of 1RDMs. Any non-correlated approximations (Hartree-Fock) for 2RDM would fail to capture the natural occupations of the system. In our fourth chapter, we show that by applying the quasi-classical and semi-classical approximations one can capture the natural occupations of the excited systems. We study a time-dependent Moshinsky atom model for this. The fifth chapter contains a comparative work on the existing non-local exchange-correlation kernels that are based on current density response frame work and the co-moving frame work. We show that the two approaches though coinciding with each other in linear response regime, actually turn out to be different in non-linear regime.

Immigration Rates during Population Density Reduction in a Coral Reef Fish

PubMed Central

Turgeon, Katrine; Kramer, Donald L.

2016-01-01

Although the importance of density-dependent dispersal has been recognized in theory, few empirical studies have examined how immigration changes over a wide range of densities. In a replicated experiment using a novel approach allowing within-site comparison, we examined changes in immigration rate following the gradual removal of territorial damselfish from a limited area within a much larger patch of continuous habitat. In all sites, immigration occurred at intermediate densities but did not occur before the start of removals and only rarely as density approached zero. In the combined data and in 5 of 7 sites, the number of immigrants was a hump-shaped function of density. This is the first experimental evidence for hump-shaped, density-dependent immigration. This pattern may be more widespread than previously recognized because studies over more limited density ranges have identified positive density dependence at low densities and negative density dependence at high densities. Positive density dependence at low density can arise from limits to the number of potential immigrants and from behavioral preferences for settling near conspecifics. Negative density dependence at high density can arise from competition for resources, especially high quality territories. The potential for non-linear effects of local density on immigration needs to be recognized for robust predictions of conservation reserve function, harvest impacts, pest control, and the dynamics of fragmented populations. PMID:27271081

On the phase diagram of water with density functional theory potentials: the melting temperature of Ice I-h with the Perdew-Burke-Ernzerhof and Becke-Lee-Yang-Parr functionals

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

Yoo, Soohaeng; Zeng, Xiao Cheng; Xantheas, Sotiris S.

2009-06-11

The melting temperature (Tm) of ice Ih was determined from constant enthalphy (NPH) Born-Oppenheimer Molecular Dynamics (BOMD) simulations to be 417±3 K for the Perdew-Burke-Ernzerhof (PBE) and 411±4 K for the Becke-Lee-Yang-Parr (BLYP) density functionals using a coexisting ice (Ih)-liquid phase at constant pressures of P = 2,500 and 10,000 bar and a density ρ = 1 g/cm3, respectively. This suggests that ambient condition simulations at ρ = 1 g/cm3 will rather describe a supercooled state that is overstructured when compared to liquid water. This work was supported by the US Department of Energy Office of Basic Energy Sciences' Chemicalmore » Sciences program. Pacific Northwest National Laboratory is operated by Battelle for the US Department of Energy.« less

Quantum wavepacket ab initio molecular dynamics: an approach for computing dynamically averaged vibrational spectra including critical nuclear quantum effects.

PubMed

Sumner, Isaiah; Iyengar, Srinivasan S

2007-10-18

We have introduced a computational methodology to study vibrational spectroscopy in clusters inclusive of critical nuclear quantum effects. This approach is based on the recently developed quantum wavepacket ab initio molecular dynamics method that combines quantum wavepacket dynamics with ab initio molecular dynamics. The computational efficiency of the dynamical procedure is drastically improved (by several orders of magnitude) through the utilization of wavelet-based techniques combined with the previously introduced time-dependent deterministic sampling procedure measure to achieve stable, picosecond length, quantum-classical dynamics of electrons and nuclei in clusters. The dynamical information is employed to construct a novel cumulative flux/velocity correlation function, where the wavepacket flux from the quantized particle is combined with classical nuclear velocities to obtain the vibrational density of states. The approach is demonstrated by computing the vibrational density of states of [Cl-H-Cl]-, inclusive of critical quantum nuclear effects, and our results are in good agreement with experiment. A general hierarchical procedure is also provided, based on electronic structure harmonic frequencies, classical ab initio molecular dynamics, computation of nuclear quantum-mechanical eigenstates, and employing quantum wavepacket ab initio dynamics to understand vibrational spectroscopy in hydrogen-bonded clusters that display large degrees of anharmonicities.

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

Liu, Siqi; Senses, Erkan; Jiao, Yang

Nanoparticles functionalized with long polymer chains at low graft density are interesting systems to study structure–dynamic relationships in polymer nanocomposites since they are shown to aggregate into strings in both solution and melts and also into spheres and branched aggregates in the presence of free polymer chains. Our work investigates structure and entanglement effects in composites of polystyrene-grafted iron oxide nanoparticles by measuring particle relaxations using X-ray photon correlation spectroscopy. And for particles within highly ordered strings and aggregated systems, they experience a dynamically heterogeneous environment displaying hyperdiffusive relaxation commonly observed in jammed soft glassy systems. Furthermore, particle dynamics ismore » diffusive for branched aggregated structures which could be caused by less penetration of long matrix chains into brushes. These results suggest that particle motion is dictated by the strong interactions of chains grafted at low density with the host matrix polymer.« less

Multilayer-MCTDH approach to the energy transfer dynamics in the LH2 antenna complex

NASA Astrophysics Data System (ADS)

Shibl, Mohamed F.; Schulze, Jan; Al-Marri, Mohammed J.; Kühn, Oliver

2017-09-01

The multilayer multiconfiguration time-dependent Hartree method is used to study the coupled exciton-vibrational dynamics in a high-dimensional nonameric model of the LH2 antenna complex of purple bacteria. The exciton-vibrational coupling is parametrized within the Huang-Rhys model according to phonon and intramolecular vibrational modes derived from an experimental bacteriochlorophyll spectral density. In contrast to reduced density matrix approaches, the Schrödinger equation is solved explicitly, giving access to the full wave function. This facilitates an unbiased analysis in terms of the coupled dynamics of excitonic and vibrational degrees of freedom. For the present system, we identify spectator modes for the B800 to B800 transfer and we find a non-additive effect of phonon and intramolecular vibrational modes on the B800 to B850 exciton transfer.

Liquid li structure and dynamics: A comparison between OFDFT and second nearest-neighbor embedded-atom method

DOE PAGES

Chen, Mohan; Vella, Joseph R.; Panagiotopoulos, Athanassios Z.; ...

2015-04-08

The structure and dynamics of liquid lithium are studied using two simulation methods: orbital-free (OF) first-principles molecular dynamics (MD), which employs OF density functional theory (DFT), and classical MD utilizing a second nearest-neighbor embedded-atom method potential. The properties we studied include the dynamic structure factor, the self-diffusion coefficient, the dispersion relation, the viscosity, and the bond angle distribution function. Our simulation results were compared to available experimental data when possible. Each method has distinct advantages and disadvantages. For example, OFDFT gives better agreement with experimental dynamic structure factors, yet is more computationally demanding than classical simulations. Classical simulations can accessmore » a broader temperature range and longer time scales. The combination of first-principles and classical simulations is a powerful tool for studying properties of liquid lithium.« less

Conformation and dynamics of the ligand shell of a water-soluble Au102 nanoparticle.

PubMed

Salorinne, Kirsi; Malola, Sami; Wong, O Andrea; Rithner, Christopher D; Chen, Xi; Ackerson, Christopher J; Häkkinen, Hannu

2016-01-21

Inorganic nanoparticles, stabilized by a passivating layer of organic molecules, form a versatile class of nanostructured materials with potential applications in material chemistry, nanoscale physics, nanomedicine and structural biology. While the structure of the nanoparticle core is often known to atomic precision, gaining precise structural and dynamical information on the organic layer poses a major challenge. Here we report a full assignment of (1)H and (13)C NMR shifts to all ligands of a water-soluble, atomically precise, 102-atom gold nanoparticle stabilized by 44 para-mercaptobenzoic acid ligands in solution, by using a combination of multidimensional NMR methods, density functional theory calculations and molecular dynamics simulations. Molecular dynamics simulations augment the data by giving information about the ligand disorder and visualization of possible distinct ligand conformations of the most dynamic ligands. The method demonstrated here opens a way to controllable strategies for functionalization of ligated nanoparticles for applications.

Conformation and dynamics of the ligand shell of a water-soluble Au102 nanoparticle

PubMed Central

Salorinne, Kirsi; Malola, Sami; Wong, O. Andrea; Rithner, Christopher D.; Chen, Xi; Ackerson, Christopher J.; Häkkinen, Hannu

2016-01-01

Inorganic nanoparticles, stabilized by a passivating layer of organic molecules, form a versatile class of nanostructured materials with potential applications in material chemistry, nanoscale physics, nanomedicine and structural biology. While the structure of the nanoparticle core is often known to atomic precision, gaining precise structural and dynamical information on the organic layer poses a major challenge. Here we report a full assignment of 1H and 13C NMR shifts to all ligands of a water-soluble, atomically precise, 102-atom gold nanoparticle stabilized by 44 para-mercaptobenzoic acid ligands in solution, by using a combination of multidimensional NMR methods, density functional theory calculations and molecular dynamics simulations. Molecular dynamics simulations augment the data by giving information about the ligand disorder and visualization of possible distinct ligand conformations of the most dynamic ligands. The method demonstrated here opens a way to controllable strategies for functionalization of ligated nanoparticles for applications. PMID:26791253

Dynamical class of a two-dimensional plasmonic Dirac system.

PubMed

Silva, Érica de Mello

2015-10-01

A current goal in plasmonic science and technology is to figure out how to manage the relaxational dynamics of surface plasmons in graphene since its damping constitutes a hinder for the realization of graphene-based plasmonic devices. In this sense we believe it might be of interest to enlarge the knowledge on the dynamical class of two-dimensional plasmonic Dirac systems. According to the recurrence relations method, different systems are said to be dynamically equivalent if they have identical relaxation functions at all times, and such commonality may lead to deep connections between seemingly unrelated physical systems. We employ the recurrence relations approach to obtain relaxation and memory functions of density fluctuations and show that a two-dimensional plasmonic Dirac system at long wavelength and zero temperature belongs to the same dynamical class of standard two-dimensional electron gas and classical harmonic oscillator chain with an impurity mass.

Universality classes of fluctuation dynamics in hierarchical complex systems

NASA Astrophysics Data System (ADS)

Macêdo, A. M. S.; González, Iván R. Roa; Salazar, D. S. P.; Vasconcelos, G. L.

2017-03-01

A unified approach is proposed to describe the statistics of the short-time dynamics of multiscale complex systems. The probability density function of the relevant time series (signal) is represented as a statistical superposition of a large time-scale distribution weighted by the distribution of certain internal variables that characterize the slowly changing background. The dynamics of the background is formulated as a hierarchical stochastic model whose form is derived from simple physical constraints, which in turn restrict the dynamics to only two possible classes. The probability distributions of both the signal and the background have simple representations in terms of Meijer G functions. The two universality classes for the background dynamics manifest themselves in the signal distribution as two types of tails: power law and stretched exponential, respectively. A detailed analysis of empirical data from classical turbulence and financial markets shows excellent agreement with the theory.

Warm Dense Matter Demonstrating Non-Drude Conductivity from Observations of Nonlinear Plasmon Damping

NASA Astrophysics Data System (ADS)

Witte, Bastian B. L.

2017-10-01

The thermal and electrical conductivity, equation of state and the spectral opacity in warm dense matter (WDM) are essential properties for modeling, e.g., fusion experiments or the magnetic field generation in planets. In the last decade it has been shown that x-ray Thomson scattering (XRTS) is an effective tool to determine plasma parameters like temperature and density in the WDM regime. Recently, the electrical conductivity was extracted from XRTS experiments for the first time. The spectrally resolved scattering data of aluminum, isochorically heated by the Linac Coherent Light Source (LCLS), show strong dependence on electron correlations. Therefore, the damping of plasmons, the collective electron oscillations, has to be treated beyond perturbation theory. We present results for the dynamic transport properties in warm dense aluminum using density-functional-theory molecular dynamics (DFT-MD) simulations. The choice of the exchange-correlation (XC) functional, describing the interactions in the electronic subsystem, has significant impact on the ionization energy of bound electrons and the dynamic dielectric function. Our newly developed method for the calculation of XRTS signals including plasmon and bound-free transitions is based on transition matrix elements together with ionic contributions using uniquely DFT-MD simulations. The results show excellent agreement with the LCLS data if hybrid functionals are applied. The experimental finding of nonlinear plasmon damping is caused by the non-Drude conductivity in warm dense aluminum. Here, we show further validation by comparing with x-ray absorption data. These findings enable new insights into the impact of XC functionals on calculated properties of WDM and allow detailed predictions for future experiments at the unprecedented densities on the NIF. This work was performed in collaboration with P. Sperling, S.H. Glenzer, R. Redmer and was supported by the DFG via the Collaborative Research Center SFB 652 and the DOE Office of Science, Fusion Energy Science under Grant No. FWP 100182.

A non-JKL density matrix functional for intergeminal correlation between closed-shell geminals from analysis of natural orbital configuration interaction expansions

NASA Astrophysics Data System (ADS)

van Meer, R.; Gritsenko, O. V.; Baerends, E. J.

2018-03-01

Almost all functionals that are currently used in density matrix functional theory have been created by some a priori ansatz that generates approximations to the second-order reduced density matrix (2RDM). In this paper, a more consistent approach is used: we analyze the 2RDMs (in the natural orbital basis) of rather accurate multi-reference configuration interaction expansions for several small molecules (CH4, NH3, H2O, FH, and N2) and use the knowledge gained to generate new functionals. The analysis shows that a geminal-like structure is present in the 2RDMs, even though no geminal theory has been applied from the onset. It is also shown that the leading non-geminal dynamical correlation contributions are generated by a specific set of double excitations. The corresponding determinants give rise to non-JKL (non Coulomb/Exchange like) multipole-multipole dispersive attractive terms between geminals. Due to the proximity of the geminals, these dispersion terms are large and cannot be omitted, proving pure JKL functionals to be essentially deficient. A second correction emerges from the observation that the "normal" geminal-like exchange between geminals breaks down when one breaks multiple bonds. This problem can be fixed by doubling the exchange between bond broken geminals, effectively restoring the often physically correct high-spin configurations on the bond broken fragments. Both of these corrections have been added to the commonly used antisymmetrized product of strongly orthogonal geminals functional. The resulting non-JKL functional Extended Löwdin-Shull Dynamical-Multibond is capable of reproducing complete active space self-consistent field curves, in which one active orbital is used for each valence electron.

A Balanced Approach to Adaptive Probability Density Estimation.

PubMed

Kovacs, Julio A; Helmick, Cailee; Wriggers, Willy

2017-01-01

Our development of a Fast (Mutual) Information Matching (FIM) of molecular dynamics time series data led us to the general problem of how to accurately estimate the probability density function of a random variable, especially in cases of very uneven samples. Here, we propose a novel Balanced Adaptive Density Estimation (BADE) method that effectively optimizes the amount of smoothing at each point. To do this, BADE relies on an efficient nearest-neighbor search which results in good scaling for large data sizes. Our tests on simulated data show that BADE exhibits equal or better accuracy than existing methods, and visual tests on univariate and bivariate experimental data show that the results are also aesthetically pleasing. This is due in part to the use of a visual criterion for setting the smoothing level of the density estimate. Our results suggest that BADE offers an attractive new take on the fundamental density estimation problem in statistics. We have applied it on molecular dynamics simulations of membrane pore formation. We also expect BADE to be generally useful for low-dimensional applications in other statistical application domains such as bioinformatics, signal processing and econometrics.

The interacting effects of temperature and food chain length on trophic abundance and ecosystem function.

PubMed

Beveridge, Oliver S; Humphries, Stuart; Petchey, Owen L

2010-05-01

1. While much is known about the independent effects of trophic structure and temperature on density and ecosystem processes, less is known about the interaction(s) between the two. 2. We manipulated the temperature of laboratory-based bacteria-protist communities that contained communities with one, two, or three trophic levels, and recorded species' densities and bacterial decomposition. 3. Temperature, food chain length and their interaction produced significant responses in microbial density and bacterial decomposition. Prey and resource density expressed different patterns of temperature dependency during different phases of population dynamics. The addition of a predator altered the temperature-density relationship of prey, from a unimodal trend to a negative one. Bacterial decomposition was greatest in the presence of consumers at higher temperatures. 4. These results are qualitatively consistent with a recent model of direct and indirect temperature effects on resource-consumer population dynamics. Results highlight and reinforce the importance of indirect effects of temperature mediated through trophic interactions. Understanding and predicting the consequences of environmental change will require that indirect effects, trophic structure, and individual species' tolerances be incorporated into theory and models.

Recombination dynamics in In{sub x}Ga{sub 1−x}N quantum wells—Contribution of excited subband recombination to carrier leakage

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

Schulz, T.; Markurt, T.; Albrecht, M.

2014-11-03

The recombination dynamics of In{sub x}Ga{sub 1−x}N single quantum wells are investigated. By comparing the photoluminescence (PL) decay spectra with simulated emission spectra obtained by a Schrödinger-Poisson approach, we give evidence that recombination from higher subbands contributes the emission of the quantum well at high excitation densities. This recombination path appears as a shoulder on the high energy side of the spectrum at high charge carrier densities and exhibits decay in the range of ps. Due to the lower confinement of the excited subband states, a distinct proportion of the probability density function lies outside the quantum well, thus contributingmore » to charge carrier loss. By estimating the current density in our time resolved PL experiments, we show that the onset of this loss mechanism occurs in the droop relevant regime above 20 A/cm{sup 2}.« less

Reversible near-infrared light directed reflection in a self-organized helical superstructure loaded with upconversion nanoparticles.

PubMed

Wang, Ling; Dong, Hao; Li, Yannian; Xue, Chenming; Sun, Ling-Dong; Yan, Chun-Hua; Li, Quan

2014-03-26

Adding external, dynamic control to self-organized superstructures with desired functionalities is an important leap necessary in leveraging the fascinating molecular systems for applications. Here, the new light-driven chiral molecular switch and upconversion nanoparticles, doped in a liquid crystal media, were able to self-organize into an optically tunable helical superstructure. The resulting nanoparticle impregnated helical superstructure was found to exhibit unprecedented reversible near-infrared (NIR) light-guided tunable behavior only by modulating the excitation power density of a continuous-wave NIR laser (980 nm). Upon irradiation by the NIR laser at the high power density, the reflection wavelength of the photonic superstructure red-shifted, whereas its reverse process occurred upon irradiation by the same laser but with the lower power density. Furthermore, reversible dynamic NIR-light-driven red, green, and blue reflections in a single thin film, achieved only by varying the power density of the NIR light, were for the first time demonstrated.

Wave function continuity and the diagonal Born-Oppenheimer correction at conical intersections

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

Meek, Garrett A.; Levine, Benjamin G., E-mail: levine@chemistry.msu.edu

2016-05-14

We demonstrate that though exact in principle, the expansion of the total molecular wave function as a sum over adiabatic Born-Oppenheimer (BO) vibronic states makes inclusion of the second-derivative nonadiabatic energy term near conical intersections practically problematic. In order to construct a well-behaved molecular wave function that has density at a conical intersection, the individual BO vibronic states in the summation must be discontinuous. When the second-derivative nonadiabatic terms are added to the Hamiltonian, singularities in the diagonal BO corrections (DBOCs) of the individual BO states arise from these discontinuities. In contrast to the well-known singularities in the first-derivative couplingsmore » at conical intersections, these singularities are non-integrable, resulting in undefined DBOC matrix elements. Though these singularities suggest that the exact molecular wave function may not have density at the conical intersection point, there is no physical basis for this constraint. Instead, the singularities are artifacts of the chosen basis of discontinuous functions. We also demonstrate that continuity of the total molecular wave function does not require continuity of the individual adiabatic nuclear wave functions. We classify nonadiabatic molecular dynamics methods according to the constraints placed on wave function continuity and analyze their formal properties. Based on our analysis, it is recommended that the DBOC be neglected when employing mixed quantum-classical methods and certain approximate quantum dynamical methods in the adiabatic representation.« less

Wave function continuity and the diagonal Born-Oppenheimer correction at conical intersections

NASA Astrophysics Data System (ADS)

Meek, Garrett A.; Levine, Benjamin G.

2016-05-01

We demonstrate that though exact in principle, the expansion of the total molecular wave function as a sum over adiabatic Born-Oppenheimer (BO) vibronic states makes inclusion of the second-derivative nonadiabatic energy term near conical intersections practically problematic. In order to construct a well-behaved molecular wave function that has density at a conical intersection, the individual BO vibronic states in the summation must be discontinuous. When the second-derivative nonadiabatic terms are added to the Hamiltonian, singularities in the diagonal BO corrections (DBOCs) of the individual BO states arise from these discontinuities. In contrast to the well-known singularities in the first-derivative couplings at conical intersections, these singularities are non-integrable, resulting in undefined DBOC matrix elements. Though these singularities suggest that the exact molecular wave function may not have density at the conical intersection point, there is no physical basis for this constraint. Instead, the singularities are artifacts of the chosen basis of discontinuous functions. We also demonstrate that continuity of the total molecular wave function does not require continuity of the individual adiabatic nuclear wave functions. We classify nonadiabatic molecular dynamics methods according to the constraints placed on wave function continuity and analyze their formal properties. Based on our analysis, it is recommended that the DBOC be neglected when employing mixed quantum-classical methods and certain approximate quantum dynamical methods in the adiabatic representation.

Wave function continuity and the diagonal Born-Oppenheimer correction at conical intersections.

PubMed

Meek, Garrett A; Levine, Benjamin G

2016-05-14

We demonstrate that though exact in principle, the expansion of the total molecular wave function as a sum over adiabatic Born-Oppenheimer (BO) vibronic states makes inclusion of the second-derivative nonadiabatic energy term near conical intersections practically problematic. In order to construct a well-behaved molecular wave function that has density at a conical intersection, the individual BO vibronic states in the summation must be discontinuous. When the second-derivative nonadiabatic terms are added to the Hamiltonian, singularities in the diagonal BO corrections (DBOCs) of the individual BO states arise from these discontinuities. In contrast to the well-known singularities in the first-derivative couplings at conical intersections, these singularities are non-integrable, resulting in undefined DBOC matrix elements. Though these singularities suggest that the exact molecular wave function may not have density at the conical intersection point, there is no physical basis for this constraint. Instead, the singularities are artifacts of the chosen basis of discontinuous functions. We also demonstrate that continuity of the total molecular wave function does not require continuity of the individual adiabatic nuclear wave functions. We classify nonadiabatic molecular dynamics methods according to the constraints placed on wave function continuity and analyze their formal properties. Based on our analysis, it is recommended that the DBOC be neglected when employing mixed quantum-classical methods and certain approximate quantum dynamical methods in the adiabatic representation.

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.

Optimization of constrained density functional theory

NASA Astrophysics Data System (ADS)

O'Regan, David D.; Teobaldi, Gilberto

2016-07-01

Constrained density functional theory (cDFT) is a versatile electronic structure method that enables ground-state calculations to be performed subject to physical constraints. It thereby broadens their applicability and utility. Automated Lagrange multiplier optimization is necessary for multiple constraints to be applied efficiently in cDFT, for it to be used in tandem with geometry optimization, or with molecular dynamics. In order to facilitate this, we comprehensively develop the connection between cDFT energy derivatives and response functions, providing a rigorous assessment of the uniqueness and character of cDFT stationary points while accounting for electronic interactions and screening. In particular, we provide a nonperturbative proof that stable stationary points of linear density constraints occur only at energy maxima with respect to their Lagrange multipliers. We show that multiple solutions, hysteresis, and energy discontinuities may occur in cDFT. Expressions are derived, in terms of convenient by-products of cDFT optimization, for quantities such as the dielectric function and a condition number quantifying ill definition in multiple constraint cDFT.

A H-infinity Fault Detection and Diagnosis Scheme for Discrete Nonlinear System Using Output Probability Density Estimation

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

Zhang Yumin; Lum, Kai-Yew; Wang Qingguo

In this paper, a H-infinity fault detection and diagnosis (FDD) scheme for a class of discrete nonlinear system fault using output probability density estimation is presented. Unlike classical FDD problems, the measured output of the system is viewed as a stochastic process and its square root probability density function (PDF) is modeled with B-spline functions, which leads to a deterministic space-time dynamic model including nonlinearities, uncertainties. A weighting mean value is given as an integral function of the square root PDF along space direction, which leads a function only about time and can be used to construct residual signal. Thus,more » the classical nonlinear filter approach can be used to detect and diagnose the fault in system. A feasible detection criterion is obtained at first, and a new H-infinity adaptive fault diagnosis algorithm is further investigated to estimate the fault. Simulation example is given to demonstrate the effectiveness of the proposed approaches.« less

A H-infinity Fault Detection and Diagnosis Scheme for Discrete Nonlinear System Using Output Probability Density Estimation

NASA Astrophysics Data System (ADS)

Zhang, Yumin; Wang, Qing-Guo; Lum, Kai-Yew

2009-03-01

In this paper, a H-infinity fault detection and diagnosis (FDD) scheme for a class of discrete nonlinear system fault using output probability density estimation is presented. Unlike classical FDD problems, the measured output of the system is viewed as a stochastic process and its square root probability density function (PDF) is modeled with B-spline functions, which leads to a deterministic space-time dynamic model including nonlinearities, uncertainties. A weighting mean value is given as an integral function of the square root PDF along space direction, which leads a function only about time and can be used to construct residual signal. Thus, the classical nonlinear filter approach can be used to detect and diagnose the fault in system. A feasible detection criterion is obtained at first, and a new H-infinity adaptive fault diagnosis algorithm is further investigated to estimate the fault. Simulation example is given to demonstrate the effectiveness of the proposed approaches.

Oxygen reduction on a Pt(111) catalyst in HT-PEM fuel cells by density functional theory

NASA Astrophysics Data System (ADS)

Sun, Hong; Li, Jie; Almheiri, Saif; Xiao, Jianyu

2017-08-01

The oxygen reduction reaction plays an important role in the performance of high-temperature proton exchange membrane (HT-PEM) fuel cells. In this study, a molecular dynamics model, which is based on the density functional theory and couples the system's energy, the exchange-correlation energy functional, the charge density distribution function, and the simplified Kohn-Sham equation, was developed to simulate the oxygen reduction reaction on a Pt(111) surface. Additionally, an electrochemical reaction system on the basis of a four-electron reaction mechanism was also developed for this simulation. The reaction path of the oxygen reduction reaction, the product structure of each reaction step and the system's energy were simulated. It is found that the first step reaction of the first hydrogen ion with the oxygen molecule is the controlling step of the overall reaction. Increasing the operating temperature speeds up the first step reaction rate and slightly decreases its reaction energy barrier. Our results provide insight into the working principles of HT-PEM fuel cells.

Ab initio molecular dynamics simulation study of successive hydrogenation reactions of carbon monoxide producing methanol

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

Pham, Thi Nu; Ono, Shota; Ohno, Kaoru, E-mail: ohno@ynu.ac.jp

Doing ab initio molecular dynamics simulations, we demonstrate a possibility of hydrogenation of carbon monoxide producing methanol step by step. At first, the hydrogen atom reacts with the carbon monoxide molecule at the excited state forming the formyl radical. Formaldehyde was formed after adding one more hydrogen atom to the system. Finally, absorption of two hydrogen atoms to formaldehyde produces methanol molecule. This study is performed by using the all-electron mixed basis approach based on the time dependent density functional theory within the adiabatic local density approximation for an electronic ground-state configuration and the one-shot GW approximation for an electronicmore » excited state configuration.« less

Radiation pressure dynamics in planetary exospheres - A 'natural' framework

NASA Technical Reports Server (NTRS)

Bishop, James; Chamberlain, Joseph W.

1989-01-01

Exospheric theory is reformulated to provide for the analysis of dynamical underpinning of exospheric features. The formulation is based on the parabolic-cylindrical separability of the Hamiltonian that describes particle motions in the combined fields of planetary gravity and solar radiation pressure. An approximate solution for trajectory evolution in terms of orbital elements is derived and the role of the exopause in the tail phenomenon is discussed. Also, an expression is obtained for the bound constituent atom densities at outer planetocoronal positions along the planet-sun axis for the case of an evaporative, uniform exobase. This expression is used to estimate midnight density enhancements as a function of radial distance for the terrestrial planets.

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

Zhu, Yuanyuan; Sushko, Peter V.; Melzer, Daniel

A novel pathway of increasing the surface density of catalytically active oxygen radical sites on a MoVTeNb oxide (M1 phase) catalyst during alkane oxidative dehydrogenation is reported. The novel sites form when a fraction of Te4+ is reduced and emitted from the M1 crystals under catalytic operating conditions, without compromising structural integrity of the catalyst framework. Density functional theory calculations show this Te reduction induces multiple inter-related electron transfers, and the associated cooperative effects lead to the formation of O- radicals. The in situ observations identify complex dynamic changes in the catalyst on an atomistic level, highlighting a new waymore » to tailor structure and dynamics for highly active catalysts.« less

Functional response of wolves preying on barren-ground caribou in a multiple-prey ecosystem

USGS Publications Warehouse

Dale, B.W.; Adams, Layne G.; Bowyer, R.T.

1994-01-01

1. We investigated the functional response of wolves (Canis lupus) to varying abundance of ungulate prey to test the hypothesis that switching from alternate prey to preferred prey results in regulation of a caribou (Rangifer tarandus) population at low densities. 2. We determined prey selection, kill rates, and prey abundance for four wolf packs during three 30-day periods in March 1989, March 1990, November 1990, and created a simple discrete model to evaluate the potential for the expected numerical and observed functional responses of wolves to regulate caribou populations. 3. We observed a quickly decelerating type II functional response that, in the absence of numerical response, implicates an anti-regulatory effect of wolf predation on barren-ground caribou dynamics. 4. There was little potential for regulation caused by the multiplicative effect of increasing functional and numerical responses because of presence of alternative prey. This resulted in high wolf:caribou ratios at low prey densities which precluded the effects of an increasing functional response. 5. Inversely density-dependent predation by other predators, such as bears, reduces the potential for predators to regulate caribou populations at low densities, and small reductions in predation by one predator may have disproportionately large effects on the total predation rate.

Use of a stochastic approach for description of water balance and runoff production dynamics

NASA Astrophysics Data System (ADS)

Gioia, A.; Manfreda, S.; Iacobellis, V.; Fiorentino, M.

2009-04-01

The present study exploits an analytical model (Manfreda, NHESS [2008]) for the description of the probability density function of soil water balance and runoff generation over a set of river basins belonging to Southern Italy. The model is based on a stochastic differential equation where the rainfall forcing is interpreted as an additive noise in the soil water balance; the watershed heterogeneity is described exploiting the conceptual lumped watershed Xinanjiang model (widely used in China) that uses a parabolic curve for the distribution of the soil water storage capacity (Zhao et al. [1980]). The model, characterized by parameters that depend on soil, vegetation and basin morphology, allowed to derive the probability density function of the relative saturation and the surface runoff of a basin accounting for the spatial heterogeneity in soil water storage. Its application on some river basins belonging to regions of Southern Italy, gives interesting insights for the investigation of the role played by the dynamical interaction between climate, soil, and vegetation in soil moisture and runoff production dynamics. Manfreda, S., Runoff Generation Dynamics within a Humid River Basin, Natural Hazard and Earth System Sciences, 8, 1349-1357, 2008. Zhao, R. -J., Zhang, Y. L., and Fang, L. R.: The Xinanjiang model, Hydrological Forecasting Proceedings Oxford Symposium, IAHS Pub. 129, 351-356, 1980.

Stochastic dynamics in a two-dimensional oscillator near a saddle-node bifurcation

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

Inchiosa, M. E.; In, V.; Bulsara, A. R.

We study the oscillator equations describing a particular class of nonlinear amplifier, exemplified in this work by a two-junction superconducting quantum interference device. This class of dynamic system is described by a potential energy function that can admit minima (corresponding to stable solutions of the dynamic equations), or {open_quotes}running states{close_quotes} wherein the system is biased so that the potential minima disappear and the solutions display spontaneous oscillations. Just beyond the onset of the spontaneous oscillations, the system is known to show significantly enhanced sensitivity to very weak magnetic signals. The global phase space structure allows us to apply a centermore » manifold technique to approximate analytically the oscillatory behavior just past the (saddle-node) bifurcation and compute the oscillation period, which obeys standard scaling laws. In this regime, the dynamics can be represented by an {open_quotes}integrate-fire{close_quotes} model drawn from the computational neuroscience repertoire; in fact, we obtain an {open_quotes}interspike interval{close_quotes} probability density function and an associated power spectral density (computed via Renewal theory) that agree very well with the results obtained via numerical simulations. Notably, driving the system with one or more time sinusoids produces a noise-lowering injection locking effect and/or heterodyning.« less

Large Deviations in Weakly Interacting Boundary Driven Lattice Gases

NASA Astrophysics Data System (ADS)

van Wijland, Frédéric; Rácz, Zoltán

2005-01-01

One-dimensional, boundary-driven lattice gases with local interactions are studied in the weakly interacting limit. The density profiles and the correlation functions are calculated to first order in the interaction strength for zero-range and short-range processes differing only in the specifics of the detailed-balance dynamics. Furthermore, the effective free-energy (large-deviation function) and the integrated current distribution are also found to this order. From the former, we find that the boundary drive generates long-range correlations only for the short-range dynamics while the latter provides support to an additivity principle recently proposed by Bodineau and Derrida.

Development and application of an empirical probability distribution for the prediction error of re-entry body maximum dynamic pressure

NASA Technical Reports Server (NTRS)

Lanzi, R. James; Vincent, Brett T.

1993-01-01

The relationship between actual and predicted re-entry maximum dynamic pressure is characterized using a probability density function and a cumulative distribution function derived from sounding rocket flight data. This paper explores the properties of this distribution and demonstrates applications of this data with observed sounding rocket re-entry body damage characteristics to assess probabilities of sustaining various levels of heating damage. The results from this paper effectively bridge the gap existing in sounding rocket reentry analysis between the known damage level/flight environment relationships and the predicted flight environment.

Computing rates of Markov models of voltage-gated ion channels by inverting partial differential equations governing the probability density functions of the conducting and non-conducting states.

PubMed

Tveito, Aslak; Lines, Glenn T; Edwards, Andrew G; McCulloch, Andrew

2016-07-01

Markov models are ubiquitously used to represent the function of single ion channels. However, solving the inverse problem to construct a Markov model of single channel dynamics from bilayer or patch-clamp recordings remains challenging, particularly for channels involving complex gating processes. Methods for solving the inverse problem are generally based on data from voltage clamp measurements. Here, we describe an alternative approach to this problem based on measurements of voltage traces. The voltage traces define probability density functions of the functional states of an ion channel. These probability density functions can also be computed by solving a deterministic system of partial differential equations. The inversion is based on tuning the rates of the Markov models used in the deterministic system of partial differential equations such that the solution mimics the properties of the probability density function gathered from (pseudo) experimental data as well as possible. The optimization is done by defining a cost function to measure the difference between the deterministic solution and the solution based on experimental data. By evoking the properties of this function, it is possible to infer whether the rates of the Markov model are identifiable by our method. We present applications to Markov model well-known from the literature. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Many-body formulation of carriers capture time in quantum dots applicable in device simulation codes

NASA Astrophysics Data System (ADS)

Vallone, Marco

2010-03-01

We present an application of Green's functions formalism to calculate in a simplified but rigorous way electrons and holes capture time in quantum dots in closed form as function of carrier density, levels confinement potential, and temperature. Carrier-carrier (Auger) scattering and single LO-phonon emission are both addressed accounting for dynamic effects of the potential screening in the single plasmon pole approximation of the dielectric function. Regarding the LO-phonons interaction, the formulation evidences the role of the dynamic screening from wetting-layer carriers in comparison with its static limit, describes the interplay between screening and Fermi band filling, and offers simple expressions for capture time, suitable for modeling implementation.

A Gaussian theory for fluctuations in simple liquids.

PubMed

Krüger, Matthias; Dean, David S

2017-04-07

Assuming an effective quadratic Hamiltonian, we derive an approximate, linear stochastic equation of motion for the density-fluctuations in liquids, composed of overdamped Brownian particles. From this approach, time dependent two point correlation functions (such as the intermediate scattering function) are derived. We show that this correlation function is exact at short times, for any interaction and, in particular, for arbitrary external potentials so that it applies to confined systems. Furthermore, we discuss the relation of this approach to previous ones, such as dynamical density functional theory as well as the formally exact treatment. This approach, inspired by the well known Landau-Ginzburg Hamiltonians, and the corresponding "Model B" equation of motion, may be seen as its microscopic version, containing information about the details on the particle level.

Assessing exchange-correlation functionals for elasticity and thermodynamics of α -ZrW2O8 : A density functional perturbation theory study

NASA Astrophysics Data System (ADS)

Weck, Philippe F.; Kim, Eunja; Greathouse, Jeffery A.; Gordon, Margaret E.; Bryan, Charles R.

2018-04-01

Elastic and thermodynamic properties of negative thermal expansion (NTE) α -ZrW2O8 have been calculated using PBEsol and PBE exchange-correlation functionals within the framework of density functional perturbation theory (DFPT). Measured elastic constants are reproduced within ∼ 2 % with PBEsol and ∼ 6 % with PBE. The thermal evolution of the Grüneisen parameter computed within the quasi-harmonic approximation exhibits negative values below the Debye temperature, consistent with observation. The standard molar heat capacity is predicted to be CP0 = 192.2 and 193.8 J mol-1K-1 with PBEsol and PBE, respectively. These results suggest superior accuracy of DFPT/PBEsol for studying the lattice dynamics, elasticity and thermodynamics of NTE materials.

A Gaussian theory for fluctuations in simple liquids

NASA Astrophysics Data System (ADS)

Krüger, Matthias; Dean, David S.

2017-04-01

Assuming an effective quadratic Hamiltonian, we derive an approximate, linear stochastic equation of motion for the density-fluctuations in liquids, composed of overdamped Brownian particles. From this approach, time dependent two point correlation functions (such as the intermediate scattering function) are derived. We show that this correlation function is exact at short times, for any interaction and, in particular, for arbitrary external potentials so that it applies to confined systems. Furthermore, we discuss the relation of this approach to previous ones, such as dynamical density functional theory as well as the formally exact treatment. This approach, inspired by the well known Landau-Ginzburg Hamiltonians, and the corresponding "Model B" equation of motion, may be seen as its microscopic version, containing information about the details on the particle level.

The glass transition temperature of thin films: A molecular dynamics study for a bead-spring model.

PubMed

Stevenson, Craig S; Curro, John G; McCoy, John D

2017-05-28

Molecular dynamics simulations were carried out on free-standing liquid films of different thicknesses h using a bead-spring model of 10 beads per chain. The glass transition temperatures, T g , of the various films were determined from plots of the internal energy versus temperature. We used these simulations to test the validity of our earlier conjecture that the glass transition of a confined liquid could be approximated by pre-averaging over the non-uniform density profile of the film. Using the density profiles from our simulations, we computed the average density of the free-standing films as a function of temperature. In all our film simulations we found, within the error of the simulation, that T g of the film occurred at the same density (or packing fraction) as the bulk system at the bulk glass transition temperature T g B . By equating these densities at their respective glass transition temperatures, as suggested by the simulations, we deduced that T g /T g B is proportional to h 0 /h. This is consistent with previous simulations and experimental data. Moreover, the parameter h 0 is determinable in our model from the density profile of the films.

EEG-Based Quantification of Cortical Current Density and Dynamic Causal Connectivity Generalized across Subjects Performing BCI-Monitored Cognitive Tasks

PubMed Central

Courellis, Hristos; Mullen, Tim; Poizner, Howard; Cauwenberghs, Gert; Iversen, John R.

2017-01-01

Quantification of dynamic causal interactions among brain regions constitutes an important component of conducting research and developing applications in experimental and translational neuroscience. Furthermore, cortical networks with dynamic causal connectivity in brain-computer interface (BCI) applications offer a more comprehensive view of brain states implicated in behavior than do individual brain regions. However, models of cortical network dynamics are difficult to generalize across subjects because current electroencephalography (EEG) signal analysis techniques are limited in their ability to reliably localize sources across subjects. We propose an algorithmic and computational framework for identifying cortical networks across subjects in which dynamic causal connectivity is modeled among user-selected cortical regions of interest (ROIs). We demonstrate the strength of the proposed framework using a “reach/saccade to spatial target” cognitive task performed by 10 right-handed individuals. Modeling of causal cortical interactions was accomplished through measurement of cortical activity using (EEG), application of independent component clustering to identify cortical ROIs as network nodes, estimation of cortical current density using cortically constrained low resolution electromagnetic brain tomography (cLORETA), multivariate autoregressive (MVAR) modeling of representative cortical activity signals from each ROI, and quantification of the dynamic causal interaction among the identified ROIs using the Short-time direct Directed Transfer function (SdDTF). The resulting cortical network and the computed causal dynamics among its nodes exhibited physiologically plausible behavior, consistent with past results reported in the literature. This physiological plausibility of the results strengthens the framework's applicability in reliably capturing complex brain functionality, which is required by applications, such as diagnostics and BCI. PMID:28566997

Watching excitons move: the time-dependent transition density matrix

NASA Astrophysics Data System (ADS)

Ullrich, Carsten

2012-02-01

Time-dependent density-functional theory allows one to calculate excitation energies and the associated transition densities in principle exactly. The transition density matrix (TDM) provides additional information on electron-hole localization and coherence of specific excitations of the many-body system. We have extended the TDM concept into the real-time domain in order to visualize the excited-state dynamics in conjugated molecules. The time-dependent TDM is defined as an implicit density functional, and can be approximately obtained from the time-dependent Kohn-Sham orbitals. The quality of this approximation is assessed in simple model systems. A computational scheme for real molecular systems is presented: the time-dependent Kohn-Sham equations are solved with the OCTOPUS code and the time-dependent Kohn-Sham TDM is calculated using a spatial partitioning scheme. The method is applied to show in real time how locally created electron-hole pairs spread out over neighboring conjugated molecular chains. The coupling mechanism, electron-hole coherence, and the possibility of charge separation are discussed.

Local Fitting of the Kohn-Sham Density in a Gaussian and Plane Waves Scheme for Large-Scale Density Functional Theory Simulations.

PubMed

Golze, Dorothea; Iannuzzi, Marcella; Hutter, Jürg

2017-05-09

A local resolution-of-the-identity (LRI) approach is introduced in combination with the Gaussian and plane waves (GPW) scheme to enable large-scale Kohn-Sham density functional theory calculations. In GPW, the computational bottleneck is typically the description of the total charge density on real-space grids. Introducing the LRI approximation, the linear scaling of the GPW approach with respect to system size is retained, while the prefactor for the grid operations is reduced. The density fitting is an O(N) scaling process implemented by approximating the atomic pair densities by an expansion in one-center fit functions. The computational cost for the grid-based operations becomes negligible in LRIGPW. The self-consistent field iteration is up to 30 times faster for periodic systems dependent on the symmetry of the simulation cell and on the density of grid points. However, due to the overhead introduced by the local density fitting, single point calculations and complete molecular dynamics steps, including the calculation of the forces, are effectively accelerated by up to a factor of ∼10. The accuracy of LRIGPW is assessed for different systems and properties, showing that total energies, reaction energies, intramolecular and intermolecular structure parameters are well reproduced. LRIGPW yields also high quality results for extended condensed phase systems such as liquid water, ice XV, and molecular crystals.

The large-scale gravitational bias from the quasi-linear regime.

NASA Astrophysics Data System (ADS)

Bernardeau, F.

1996-08-01

It is known that in gravitational instability scenarios the nonlinear dynamics induces non-Gaussian features in cosmological density fields that can be investigated with perturbation theory. Here, I derive the expression of the joint moments of cosmological density fields taken at two different locations. The results are valid when the density fields are filtered with a top-hat filter window function, and when the distance between the two cells is large compared to the smoothing length. In particular I show that it is possible to get the generating function of the coefficients C_p,q_ defined by <δ^p^({vec}(x)_1_)δ^q^({vec}(x)_2_)>_c_=C_p,q_ <δ^2^({vec}(x))>^p+q-2^ <δ({vec}(x)_1_)δ({vec}(x)_2_)> where δ({vec}(x)) is the local smoothed density field. It is then possible to reconstruct the joint density probability distribution function (PDF), generalizing for two points what has been obtained previously for the one-point density PDF. I discuss the validity of the large separation approximation in an explicit numerical Monte Carlo integration of the C_2,1_ parameter as a function of |{vec}(x)_1_-{vec}(x)_2_|. A straightforward application is the calculation of the large-scale ``bias'' properties of the over-dense (or under-dense) regions. The properties and the shape of the bias function are presented in details and successfully compared with numerical results obtained in an N-body simulation with CDM initial conditions.

Collision-induced light scattering in a thin xenon layer between graphite slabs - MD study.

PubMed

Dawid, A; Górny, K; Wojcieszyk, D; Dendzik, Z; Gburski, Z

2014-08-14

The collision-induced light scattering many-body correlation functions and their spectra in thin xenon layer located between two parallel graphite slabs have been investigated by molecular dynamics computer simulations. The results have been obtained at three different distances (densities) between graphite slabs. Our simulations show the increased intensity of the interaction-induced light scattering spectra at low frequencies for xenon atoms in confined space, in comparison to the bulk xenon sample. Moreover, we show substantial dependence of the interaction-induced light scattering correlation functions of xenon on the distances between graphite slabs. The dynamics of xenon atoms in a confined space was also investigated by calculating the mean square displacement functions and related diffusion coefficients. The structural property of confined xenon layer was studied by calculating the density profile, perpendicular to the graphite slabs. Building of a fluid phase of xenon in the innermost part of the slot was observed. The nonlinear dependence of xenon diffusion coefficient on the separation distance between graphite slabs has been found. Copyright © 2014. Published by Elsevier B.V.

Dynamical density functional theory for arbitrary-shape colloidal fluids including inertia and hydrodynamic interactions

NASA Astrophysics Data System (ADS)

Duran-Olivencia, Miguel A.; Goddard, Ben; Kalliadasis, Serafim

2015-11-01

Over the last few decades the classical density-functional theory (DFT) and its dynamic extensions (DDFTs) have become a remarkably powerful tool in the study of colloidal fluids. Recently there has been extensive research to generalise all previous DDFTs finally yielding a general DDFT equation (for spherical particles) which takes into account both inertia and hydrodynamic interactions (HI) which strongly influence non-equilibrium properties. The present work will be devoted to a further generalisation of such a framework to systems of anisotropic particles. To this end, the kinetic equation for the Brownian particle distribution function is derived starting from the Liouville equation and making use of Zwanzig's projection-operator techniques. By averaging over all but one particle, a DDFT equation is finally obtained with some similarities to that for spherical colloids. However, there is now an inevitable translational-rotational coupling which affects the diffusivity of asymmetric particles. Lastly, in the overdamped (high friction) limit the theory is notably simplified leading to a DDFT equation which agrees with previous derivations. We acknowledge financial support from European Research Council via Advanced Grant No. 247031.

Room-temperature d0 ferromagnetism in carbon-doped Y2O3 for spintronic applications: A density functional theory study

NASA Astrophysics Data System (ADS)

Chakraborty, Brahmananda; Nandi, Prithwish K.; Kawazoe, Yoshiyuki; Ramaniah, Lavanya M.

2018-05-01

Through density functional theory simulations with the generalized gradient approximation, confirmed by the more sophisticated hybrid functional, we predict the triggering of d0 ferromagnetism in C doped Y2O3 at a hole density of 3.36 ×1021c m-3 (one order less than the critical hole density of ZnO) having magnetic moment of 2.0 μB per defect with ferromagnetic coupling large enough to promote room-temperature ferromagnetism. The persistence of ferromagnetism at room temperature is established through computation of the Curie temperature by the mean field approximation and ab initio molecular dynamics simulations. The induced magnetic moment is mainly contributed by the 2 p orbital of the impurity C and the 2 p orbital of O and we quantitatively and extensively demonstrate through the analysis of density of states and ferromagnetic coupling that the Stoner criterion is satisfied to activate room-temperature ferromagnetism. As the system is stable at room temperature, C doped Y2O3 has feasible defect formation energy and ferromagnetism survives for the choice of hybrid exchange functional, and at room temperature we strongly believe that C doped Y2O3 can be tailored as a room-temperature diluted magnetic semiconductor for spintronic applications.

Composite polarizability and the construction of an invariant function of refraction and mass density for solutions.

PubMed

Szymański, Krzysztof; Petrache, Horia I

2011-04-14

Re-examination of dynamical ionic polarizabilities in water solutions leads to the formulation of a solution function r(c), which combines the indices of refraction and mass densities of solutions. We show that this function should be independent of ionic concentration if the composite polarizabilities of hydrated solute clusters are constant. Using existing experimental data for a number of aqueous salt and organic solutions, we find that the r(c) function is either constant or varies linearly with concentration, in most cases with negligible slope. We use this function to compare ionic polarizabilities of crystals and aqueous solutions and to highlight how solute polarizabilities at infinite dilution scale with the electronic valence shell of cations and anions. The proposed r(c) function can be used generally to verify the consistency of experimental measurements and of simulation results, and it provides a test of assumptions in current theories of ionic polarizabilities.

Light-front representation of chiral dynamics with Δ isobar and large-N c relations

DOE PAGES

Granados, C.; Weiss, C.

2016-06-13

Transverse densities describe the spatial distribution of electromagnetic current in the nucleon at fixed light-front time. At peripheral distances b = O(M π –1) the densities are governed by chiral dynamics and can be calculated model-independently using chiral effective field theory (EFT). Recent work has shown that the EFT results can be represented in first-quantized form, as overlap integrals of chiral light-front wave functions describing the transition of the nucleon to soft-pion-nucleon intermediate states, resulting in a quantum-mechanical picture of the peripheral transverse densities. We now extend this representation to include intermediate states with Δ isobars and implement relations basedmore » on the large-N c limit of QCD. We derive the wave function overlap formulas for the Δ contributions to the peripheral transverse densities by way of a three-dimensional reduction of relativistic chiral EFT expressions. Our procedure effectively maintains rotational invariance and avoids the ambiguities with higher-spin particles in the light-front time-ordered approach. We study the interplay of πN and πΔ intermediate states in the quantum-mechanical picture of the densities in a transversely polarized nucleon. We show that the correct N c-scaling of the charge and magnetization densities emerges as the result of the particular combination of currents generated by intermediate states with degenerate N and Δ. The off-shell behavior of the chiral EFT is summarized in contact terms and can be studied easily. As a result, the methods developed here can be applied to other peripheral densities and to moments of the nucleon's generalized parton distributions.« less

The effect of area size and predation on the time to extinction of prairie vole populations. simulation studies via SERDYCA: a Spatially-Explicit Individual-Based Model of Rodent Dynamics

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

Kostova, T; Carlsen, T

2003-11-21

We present a spatially-explicit individual-based computational model of rodent dynamics, customized for the prairie vole species, M. Ochrogaster. The model is based on trophic relationships and represents important features such as territorial competition, mating behavior, density-dependent predation and dispersal out of the modeled spatial region. Vegetation growth and vole fecundity are dependent on climatic components. The results of simulations show that the model correctly predicts the overall temporal dynamics of the population density. Time-series analysis shows a very good match between the periods corresponding to the peak population density frequencies predicted by the model and the ones reported in themore » literature. The model is used to study the relation between persistence, landscape area and predation. We introduce the notions of average time to extinction (ATE) and persistence frequency to quantify persistence. While the ATE decreases with decrease of area, it is a bell-shaped function of the predation level: increasing for 'small' and decreasing for 'large' predation levels.« less

Orbital-free extension to Kohn-Sham density functional theory equation of state calculations: Application to silicon dioxide

DOE PAGES

Sjostrom, Travis; Crockett, Scott

2015-09-02

The liquid regime equation of state of silicon dioxide SiO 2 is calculated via quantum molecular dynamics in the density range of 5 to 15 g/cc and with temperatures from 0.5 to 100 eV, including the α-quartz and stishovite phase Hugoniot curves. Below 8 eV calculations are based on Kohn-Sham density functional theory (DFT), and above 8 eV a new orbital-free DFT formulation, presented here, based on matching Kohn-Sham DFT calculations is employed. Recent experimental shock data are found to be in very good agreement with the current results. Finally both experimental and simulation data are used in constructing amore » new liquid regime equation of state table for SiO 2.« less

Gaussian polarizable-ion tight binding.

PubMed

Boleininger, Max; Guilbert, Anne Ay; Horsfield, Andrew P

2016-10-14

To interpret ultrafast dynamics experiments on large molecules, computer simulation is required due to the complex response to the laser field. We present a method capable of efficiently computing the static electronic response of large systems to external electric fields. This is achieved by extending the density-functional tight binding method to include larger basis sets and by multipole expansion of the charge density into electrostatically interacting Gaussian distributions. Polarizabilities for a range of hydrocarbon molecules are computed for a multipole expansion up to quadrupole order, giving excellent agreement with experimental values, with average errors similar to those from density functional theory, but at a small fraction of the cost. We apply the model in conjunction with the polarizable-point-dipoles model to estimate the internal fields in amorphous poly(3-hexylthiophene-2,5-diyl).

Gaussian polarizable-ion tight binding

NASA Astrophysics Data System (ADS)

Boleininger, Max; Guilbert, Anne AY; Horsfield, Andrew P.

2016-10-01

To interpret ultrafast dynamics experiments on large molecules, computer simulation is required due to the complex response to the laser field. We present a method capable of efficiently computing the static electronic response of large systems to external electric fields. This is achieved by extending the density-functional tight binding method to include larger basis sets and by multipole expansion of the charge density into electrostatically interacting Gaussian distributions. Polarizabilities for a range of hydrocarbon molecules are computed for a multipole expansion up to quadrupole order, giving excellent agreement with experimental values, with average errors similar to those from density functional theory, but at a small fraction of the cost. We apply the model in conjunction with the polarizable-point-dipoles model to estimate the internal fields in amorphous poly(3-hexylthiophene-2,5-diyl).

Modeling ecological traps for the control of feral pigs

PubMed Central

Dexter, Nick; McLeod, Steven R

2015-01-01

Ecological traps are habitat sinks that are preferred by dispersing animals but have higher mortality or reduced fecundity compared to source habitats. Theory suggests that if mortality rates are sufficiently high, then ecological traps can result in extinction. An ecological trap may be created when pest animals are controlled in one area, but not in another area of equal habitat quality, and when there is density-dependent immigration from the high-density uncontrolled area to the low-density controlled area. We used a logistic population model to explore how varying the proportion of habitat controlled, control mortality rate, and strength of density-dependent immigration for feral pigs could affect the long-term population abundance and time to extinction. Increasing control mortality, the proportion of habitat controlled and the strength of density-dependent immigration decreased abundance both within and outside the area controlled. At higher levels of these parameters, extinction was achieved for feral pigs. We extended the analysis with a more complex stochastic, interactive model of feral pig dynamics in the Australian rangelands to examine how the same variables as the logistic model affected long-term abundance in the controlled and uncontrolled area and time to extinction. Compared to the logistic model of feral pig dynamics, the stochastic interactive model predicted lower abundances and extinction at lower control mortalities and proportions of habitat controlled. To improve the realism of the stochastic interactive model, we substituted fixed mortality rates with a density-dependent control mortality function, empirically derived from helicopter shooting exercises in Australia. Compared to the stochastic interactive model with fixed mortality rates, the model with the density-dependent control mortality function did not predict as substantial decline in abundance in controlled or uncontrolled areas or extinction for any combination of variables. These models demonstrate that pest eradication is theoretically possible without the pest being controlled throughout its range because of density-dependent immigration into the area controlled. The stronger the density-dependent immigration, the better the overall control in controlled and uncontrolled habitat combined. However, the stronger the density-dependent immigration, the poorer the control in the area controlled. For feral pigs, incorporating environmental stochasticity improves the prospects for eradication, but adding a realistic density-dependent control function eliminates these prospects. PMID:26045954

Do understorey or overstorey traits drive tree encroachment on a drained raised bog?

PubMed

Jagodziński, A M; Horodecki, P; Rawlik, K; Dyderski, M K

2017-07-01

One of the most important threats to peatland ecosystems is drainage, resulting in encroachment of woody species. Our main aim was to check which features - overstorey or understorey vegetation - are more important for shaping the seedling bank of pioneer trees colonising peatlands (Pinus sylvestris and Betula pubescens). We hypothesised that tree stand parameters will be more important predictors of natural regeneration density than understorey vegetation parameters, and the former will be negatively correlated with species diversity and richness and also with functional richness and functional dispersion, which indicate a high level of habitat filtering. The study was conducted in the 'Zielone Bagna' nature reserve (NW Poland). We assessed the structure of tree stands and natural regeneration (of B. pubescens and P. sylvestris) and vegetation species composition. Random forest and DCA were applied to assess relationships between variables studied. Understorey vegetation traits affected tree seedling density (up to 0.5-m height) more than tree stand traits. Density of older seedlings depended more on tree stand traits. We did not find statistically significant relationships between natural regeneration densities and functional diversity components, except for functional richness, which was positively correlated with density of the youngest tree seedlings. Seedling densities were higher in plots with lower functional dispersion and functional divergence, which indicated that habitat filtering is more important than competition. Presence of an abundant seedling bank is crucial for the process of woody species encroachment on drained peatlands, thus its dynamics should be monitored in protected areas. © 2017 German Botanical Society and The Royal Botanical Society of the Netherlands.

Quantum molecular dynamics of warm dense iron and a five-phase equation of state

NASA Astrophysics Data System (ADS)

Sjostrom, Travis; Crockett, Scott

2018-05-01

Through quantum molecular dynamics (QMD), utilizing both Kohn-Sham (orbital-based) and orbital-free density functional theory, we calculate the equation of state of warm dense iron in the density range 7 -30 g/cm 3 and temperatures from 1 to 100 eV. A critical examination of the iron pseudopotential is made, from which we find a significant improvement at high pressure to the previous QMD calculations of Wang et al. [Phys. Rev. E 89, 023101 (2014), 10.1103/PhysRevE.89.023101]. Our results also significantly extend the ranges of density and temperature that were attempted in that prior work. We calculate the shock Hugoniot and find very good agreement with experimental results to pressures over 20 TPa. These results are then incorporated with previous studies to generate a five-phase equation of state for iron.

How Actuated Particles Effectively Capture Biomolecular Targets

PubMed Central

2017-01-01

Because of their high surface-to-volume ratio and adaptable surface functionalization, particles are widely used in bioanalytical methods to capture molecular targets. In this article, a comprehensive study is reported of the effectiveness of protein capture by actuated magnetic particles. Association rate constants are quantified in experiments as well as in Brownian dynamics simulations for different particle actuation configurations. The data reveal how the association rate depends on the particle velocity, particle density, and particle assembly characteristics. Interestingly, single particles appear to exhibit target depletion zones near their surface, caused by the high density of capture molecules. The depletion effects are even more limiting in cases with high particle densities. The depletion effects are overcome and protein capture rates are enhanced by applying dynamic particle actuation, resulting in an increase in the association rate constants by up to 2 orders of magnitude. PMID:28192952

Ultrafast semi-metallic layer formation in detonating nitromethane

NASA Astrophysics Data System (ADS)

Reed, Evan; Manaa, M. Riad; Fried, Laurence; Glaesemann, Kurt; Joannopoulos, John

2008-03-01

We present the first quantum molecular dynamics simulations behind a detonation front (up to 0.2 ns) of the explosive nitromethane (CH3NO2) represented by the density-functional-based tight-binding method (DFTB). This simulation is enabled by our recently developed multi-scale shock wave molecular dynamics technique (MSST) that opens the door to longer duration simulations by several orders of magnitude. The electronic density of states around the Fermi energy initially increases as metastable material states are produced but then later decreases, perhaps unexpectedly. These changes indicate that the shock front is characterized by an increase in optical thickness and conductivity followed by a reduction around 100 picoseconds behind the front. We find that a significant population of intermediate metastable molecules are charged and charged species play an important role in the density of states evolution. The transient transformation to a semi-metallic state can be understood within the Anderson picture of metallization.

Committor of elementary reactions on multistate systems

NASA Astrophysics Data System (ADS)

Király, Péter; Kiss, Dóra Judit; Tóth, Gergely

2018-04-01

In our study, we extend the committor concept on multi-minima systems, where more than one reaction may proceed, but the feasible data evaluation needs the projection onto partial reactions. The elementary reaction committor and the corresponding probability density of the reactive trajectories are defined and calculated on a three-hole two-dimensional model system explored by single-particle Langevin dynamics. We propose a method to visualize more elementary reaction committor functions or probability densities of reactive trajectories on a single plot that helps to identify the most important reaction channels and the nonreactive domains simultaneously. We suggest a weighting for the energy-committor plots that correctly shows the limits of both the minimal energy path and the average energy concepts. The methods also performed well on the analysis of molecular dynamics trajectories of 2-chlorobutane, where an elementary reaction committor, the probability densities, the potential energy/committor, and the free-energy/committor curves are presented.

Quench dynamics of the spin-imbalanced Fermi-Hubbard model in one dimension

NASA Astrophysics Data System (ADS)

Yin, Xiao; Radzihovsky, Leo

2016-12-01

We study a nonequilibrium dynamics of a one-dimensional spin-imbalanced Fermi-Hubbard model following a quantum quench of on-site interaction, realizable, for example, in Feshbach-resonant atomic Fermi gases. We focus on the post-quench evolution starting from the initial BCS and Fulde-Ferrell-Larkin-Ovchinnikov (FFLO) ground states and analyze the corresponding spin-singlet, spin-triplet, density-density, and magnetization-magnetization correlation functions. We find that beyond a light-cone crossover time, rich post-quench dynamics leads to thermalized and pre-thermalized stationary states that display strong dependence on the initial ground state. For initially gapped BCS state, the long-time stationary state resembles thermalization with the effective temperature set by the initial value of the Hubbard interaction. In contrast, while the initial gapless FFLO state reaches a stationary pre-thermalized form, it remains far from equilibrium. We suggest that such post-quench dynamics can be used as a fingerprint for identification and study of the FFLO phase.

Adsorption of hairy particles with mobile ligands: Molecular dynamics and density functional study

NASA Astrophysics Data System (ADS)

Borówko, M.; Sokołowski, S.; Staszewski, T.; Pizio, O.

2018-01-01

We study models of hairy nanoparticles in contact with a hard wall. Each particle is built of a spherical core with a number of ligands attached to it and each ligand is composed of several spherical, tangentially jointed segments. The number of segments is the same for all ligands. Particular models differ by the numbers of ligands and of segments per ligand, but the total number of segments is constant. Moreover, our model assumes that the ligands are tethered to the core in such a manner that they can "slide" over the core surface. Using molecular dynamics simulations we investigate the differences in the structure of a system close to the wall. In order to characterize the distribution of the ligands around the core, we have calculated the end-to-end distances of the ligands and the lengths and orientation of the mass dipoles. Additionally, we also employed a density functional approach to obtain the density profiles. We have found that if the number of ligands is not too high, the proposed version of the theory is capable to predict the structure of the system with a reasonable accuracy.

Study of correlations from Ab-Initio Simulations of Liquid Water

NASA Astrophysics Data System (ADS)

Soto, Adrian; Fernandez-Serra, Marivi; Lu, Deyu; Yoo, Shinjae

An accurate understanding of the dynamics and the structure of H2O molecules in the liquid phase is of extreme importance both from a fundamental and from a practical standpoint. Despite the successes of Molecular Dynamics (MD) with Density Functional Theory (DFT), liquid water remains an extremely difficult material to simulate accurately and efficiently because of fine balance between the covalent O-H bond, the hydrogen bond and the attractive the van der Waals forces. Small errors in those produce dramatic changes in the macroscopic properties of the liquid or in its structural properties. Different density functionals produce answers that differ by as much as 35% in ambient conditions, with none producing quantitative results in agreement with experiment at different mass densities. In order to understand these differences we perform an exhaustive scanning of the geometrical coordinates of MD simulations and study their statistical correlations with the simulation output quantities using advanced correlation analyses and machine learning techniques. This work was partially supported by DOE Award No. DE-FG02-09ER16052, by DOE Early Career Award No. DE-SC0003871, by BNL LDRD 16-039 project and BNL Contract No. DE-SC0012704.

Study of correlations from Ab-Initio Simulations of Liquid Water

NASA Astrophysics Data System (ADS)

Soto, Adrian; Fernandez-Serra, Marivi; Lu, Deyu; Yoo, Shinjae

An accurate understanding of the dynamics and the structure of H2O molecules in the liquid phase is of extreme importance both from a fundamental and from a practical standpoint. Despite the successes of Molecular Dynamics (MD) with Density Functional Theory (DFT), liquid water remains an extremely difficult material to simulate accurately and efficiently because of fine balance between the covalent O-H bond, the hydrogen bond and the attractive the van der Waals forces. Small errors in those produce dramatic changes in the macroscopic properties of the liquid or in its structural properties. Different density functionals produce answers that differ by as much as 35% in ambient conditions, with none producing quantitative results in agreement with experiment at different mass densities [J. Chem Phys. 139, 194502(2013)]. In order to understand these differences we perform an exhaustive scanning of the geometrical coordinates of MD simulations and study their statistical correlations with the simulation output quantities using advanced correlation analyses and machine learning techniques. This work was partially supported by DOE Award No. DE-FG02-09ER16052, by DOE Early Career Award No. DE-SC0003871, by BNL LDRD 16-039 project and BNL Contract No. DE-SC0012704.

Importance of strong-correlation on the lattice dynamics of light-actinides Th-Pa alloy

NASA Astrophysics Data System (ADS)

de La Peã+/-A Seaman, Omar; Heid, Rolf; Bohnen, Klaus-Peter

We have studied the structural, electronic, and lattice dynamics of the Th1-xPax actinide alloy. This system have been analyzed within the framework of density functional perturbation theory, using a mixed-basis pseudopotential method and the virtual crystal approximation (VCA) for modeling the alloy. In particular, the energetics is analyzed as the ground-state crystal structure is changed form fcc to bct, as well as the electronic density of states (DOS), and the phonon frequencies. Such properties have been calculated with and without strong correlations effects through the LDA+U formalism. Although the strong-correlation does not influence on a great manner the Th properties, such effects are more important as the content increases towards Pa, affecting even the definition of the ground-state crystal structure for Pa (experimentally determined as bct). The evolution of the density of states at the Fermi level (N (EF)) and the phonon frequencies as a function of Pa-content are presented and discussed in detail, aiming to understand their influence on the electron-phonon coupling for the Th-Pa alloy. This research was supported by Conacyt-México under project No. CB2013-221807-F.

Role of oxygen functional groups for structure and dynamics of interfacial water on low rank coal surface: a molecular dynamics simulation

NASA Astrophysics Data System (ADS)

You, Xiaofang; Wei, Hengbin; Zhu, Xianchang; Lyu, Xianjun; Li, Lin

2018-07-01

Molecular dynamics simulations were employed to study the effects of oxygen functional groups for structure and dynamics properties of interfacial water molecules on the subbituminous coal surface. Because of complex composition and structure, the graphite surface modified by hydroxyl, carboxyl and carbonyl groups was used to represent the surface model of subbituminous coal according to XPS results, and the composing proportion for hydroxyl, carbonyl and carboxyl is 25:3:5. The hydration energy with -386.28 kJ/mol means that the adsorption process between water and coal surface is spontaneous. Density profiles for oxygen atoms and hydrogen atoms indicate that the coal surface properties affect the structural and dynamic characteristics of the interfacial water molecules. The interfacial water exhibits much more ordering than bulk water. The results of radial distribution functions, mean square displacement and local self-diffusion coefficient for water molecule related to three oxygen moieties confirmed that the water molecules prefer to absorb with carboxylic groups, and adsorption of water molecules at the hydroxyl and carbonyl is similar.

Inference of Time-Evolving Coupled Dynamical Systems in the Presence of Noise

NASA Astrophysics Data System (ADS)

Stankovski, Tomislav; Duggento, Andrea; McClintock, Peter V. E.; Stefanovska, Aneta

2012-07-01

A new method is introduced for analysis of interactions between time-dependent coupled oscillators, based on the signals they generate. It distinguishes unsynchronized dynamics from noise-induced phase slips and enables the evolution of the coupling functions and other parameters to be followed. It is based on phase dynamics, with Bayesian inference of the time-evolving parameters achieved by shaping the prior densities to incorporate knowledge of previous samples. The method is tested numerically and applied to reveal and quantify the time-varying nature of cardiorespiratory interactions.

A nonadditive methanol force field: Bulk liquid and liquid-vapor interfacial properties via molecular dynamics simulations using a fluctuating charge model

NASA Astrophysics Data System (ADS)

Patel, Sandeep; Brooks, Charles L.

2005-01-01

We study the bulk and interfacial properties of methanol via molecular dynamics simulations using a CHARMM (Chemistry at HARvard Molecular Mechanics) fluctuating charge force field. We discuss the parametrization of the electrostatic model as part of the ongoing CHARMM development for polarizable protein force fields. The bulk liquid properties are in agreement with available experimental data and competitive with existing fixed-charge and polarizable force fields. The liquid density and vaporization enthalpy are determined to be 0.809 g/cm3 and 8.9 kcal/mol compared to the experimental values of 0.787 g/cm3 and 8.94 kcal/mol, respectively. The liquid structure as indicated by radial distribution functions is in keeping with the most recent neutron diffraction results; the force field shows a slightly more ordered liquid, necessarily arising from the enhanced condensed phase electrostatics (as evidenced by an induced liquid phase dipole moment of 0.7 D), although the average coordination with two neighboring molecules is consistent with the experimental diffraction study as well as with recent density functional molecular dynamics calculations. The predicted surface tension of 19.66±1.03 dyn/cm is slightly lower than the experimental value of 22.6 dyn/cm, but still competitive with classical force fields. The interface demonstrates the preferential molecular orientation of molecules as observed via nonlinear optical spectroscopic methods. Finally, via canonical molecular dynamics simulations, we assess the model's ability to reproduce the vapor-liquid equilibrium from 298 to 423 K, the simulation data then used to obtain estimates of the model's critical temperature and density. The model predicts a critical temperature of 470.1 K and critical density of 0.312 g/cm3 compared to the experimental values of 512.65 K and 0.279 g/cm3, respectively. The model underestimates the critical temperature by 8% and overestimates the critical density by 10%, and in this sense is roughly equivalent to the underlying fixed-charge CHARMM22 force field.

Application of Molecular Dynamics Simulations in Molecular Property Prediction I: Density and Heat of Vaporization

PubMed Central

Wang, Junmei; Tingjun, Hou

2011-01-01

Molecular mechanical force field (FF) methods are useful in studying condensed phase properties. They are complementary to experiment and can often go beyond experiment in atomic details. Even a FF is specific for studying structures, dynamics and functions of biomolecules, it is still important for the FF to accurately reproduce the experimental liquid properties of small molecules that represent the chemical moieties of biomolecules. Otherwise, the force field may not describe the structures and energies of macromolecules in aqueous solutions properly. In this work, we have carried out a systematic study to evaluate the General AMBER Force Field (GAFF) in studying densities and heats of vaporization for a large set of organic molecules that covers the most common chemical functional groups. The latest techniques, such as the particle mesh Ewald (PME) for calculating electrostatic energies, and Langevin dynamics for scaling temperatures, have been applied in the molecular dynamics (MD) simulations. For density, the average percent error (APE) of 71 organic compounds is 4.43% when compared to the experimental values. More encouragingly, the APE drops to 3.43% after the exclusion of two outliers and four other compounds for which the experimental densities have been measured with pressures higher than 1.0 atm. For heat of vaporization, several protocols have been investigated and the best one, P4/ntt0, achieves an average unsigned error (AUE) and a root-mean-square error (RMSE) of 0.93 and 1.20 kcal/mol, respectively. How to reduce the prediction errors through proper van der Waals (vdW) parameterization has been discussed. An encouraging finding in vdW parameterization is that both densities and heats of vaporization approach their “ideal” values in a synchronous fashion when vdW parameters are tuned. The following hydration free energy calculation using thermodynamic integration further justifies the vdW refinement. We conclude that simple vdW parameterization can significantly reduce the prediction errors. We believe that GAFF can greatly improve its performance in predicting liquid properties of organic molecules after a systematic vdW parameterization, which will be reported in a separate paper. PMID:21857814

Strong influence of coadsorbate interaction on CO desorption dynamics on Ru(0001) probed by ultrafast x-ray spectroscopy and ab initio simulations

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

Xin, H.; LaRue, J.; Oberg, H.

2015-04-16

We show that coadsorbed oxygen atoms have a dramatic influence on the CO desorption dynamics from Ru(0001). In contrast to the precursor-mediated desorption mechanism on Ru(0001), the presence of surface oxygen modifies the electronic structure of Ru atoms such that CO desorption occurs predominantly via the direct pathway. This phenomenon is directly observed in an ultrafast pump-probe experiment using a soft x-ray free-electron laser to monitor the dynamic evolution of the valence electronic structure of the surface species. This is supported with the potential of mean force along the CO desorption path obtained from density-functional theory calculations. Charge density distributionmore » and frozen-orbital analysis suggest that the oxygen-induced reduction of the Pauli repulsion, and consequent increase of the dative interaction between the CO 5σ and the charged Ru atom, is the electronic origin of the distinct desorption dynamics. Ab initio molecular dynamics simulations of CO desorption from Ru(0001) and oxygen-coadsorbed Ru(0001) provide further insights into the surface bond-breaking process.« less

Prediction of Excitation Energies for Conjugated Oligomers and Polymers from Time-Dependent Density Functional Theory

PubMed Central

Tao, Jianmin; Tretiak, Sergei; Zhu, Jian-Xin

2010-01-01

With technological advances, light-emitting conjugated oligomers and polymers have become competitive candidates in the commercial market of light-emitting diodes for display and other technologies, due to the ultralow cost, light weight, and flexibility. Prediction of excitation energies of these systems plays a crucial role in the understanding of their optical properties and device design. In this review article, we discuss the calculation of excitation energies with time-dependent density functional theory, which is one of the most successful methods in the investigation of the dynamical response of molecular systems to external perturbation, owing to its high computational efficiency.

Effective charges of ionic liquid determined self-consistently through combination of molecular dynamics simulation and density-functional theory.

PubMed

Ishizuka, Ryosuke; Matubayasi, Nobuyuki

2017-11-15

A self-consistent scheme combining the molecular dynamics (MD) simulation and density functional theory (DFT) was recently proposed to incorporate the effects of the charge transfer and polarization of ions into non-poralizable force fields of ionic liquids for improved description of energetics and dynamics. The purpose of the present work is to analyze the detailed setups of the MD/DFT scheme by focusing on how the basis set, exchange-correlation (XC) functional, charge-fitting method or force field for the intramolecular and Lennard-Jones interactions affects the MD/DFT results of 1,3-dimethylimidazolium bis(trifluoromethylsulfonyl) imide ( [C1mim][NTf2]) and 1-ethyl-3-methylimidazolium glycinate ( [C2mim][Gly]). It was found that the double-zeta valence polarized or larger size of basis set is required for the convergence of the effective charge of the ion. The choice of the XC functional was further not influential as far as the generalized gradient approximation is used. The charge-fitting method and force field govern the accuracy of the MD/DFT scheme, on the other hand. We examined the charge-fitting methods of Blöchl, the iterative Hirshfeld (Hirshfeld-I), and REPEAT in combination with Lopes et al.'s force field and general AMBER force field. There is no single combination of charge fitting and force field that provides good agreements with the experiments, while the MD/DFT scheme reduces the effective charges of the ions and leads to better description of energetics and dynamics compared to the original force field with unit charges. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Photoluminescence Dynamics of Aryl sp 3 Defect States in Single-Walled Carbon Nanotubes

DOE PAGES

Hartmann, Nicolai F.; Velizhanin, Kirill A.; Haroz, Erik H.; ...

2016-08-16

Photoluminescent defect states introduced by sp 3 functionalization of semiconducting carbon nanotubes are rapidly emerging as important routes for boosting emission quantum yields and introducing new functionality. Knowledge of the relaxation dynamics of these states is required for understanding how functionalizing agents (molecular dopants) may be designed to access specific behaviors. We measure photoluminescence (PL) decay dynamics of sp 3 defect states introduced by aryl functionalization of the carbon nanotube surface. Results are given for five different nanotube chiralities, each doped with a range of aryl functionality. We find the PL decays of these sp 3 defect states are biexponential,more » with both components relaxing on timescales of ~ 100 ps. Exciton trapping at defects is found to increases PL lifetimes by a factor of 5-10, in comparison to those for the free exciton. A significant chirality dependence is observed in the decay times, ranging from 77 ps for (7,5) nanotubes to > 600 ps for (5,4) structures. The strong correlation of time constants with emission energy indicates relaxation occurs via multiphonon decay processes, with close agreement to theoretical expectations. Variation of the aryl dopant further modulates decay times by 10-15%. The aryl defects also affect PL lifetimes of the free E 11 exciton. Shortening of the E 11 bright state lifetime as defect density increases provides further confirmation that defects act as exciton traps. A similar shortening of the E11 dark exciton lifetime is found as defect density increases, providing strong experimental evidence that dark excitons are also trapped at such defect sites.« less

Photoluminescence Dynamics of Aryl sp 3 Defect States in Single-Walled Carbon Nanotubes

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

Hartmann, Nicolai F.; Velizhanin, Kirill A.; Haroz, Erik H.

Photoluminescent defect states introduced by sp 3 functionalization of semiconducting carbon nanotubes are rapidly emerging as important routes for boosting emission quantum yields and introducing new functionality. Knowledge of the relaxation dynamics of these states is required for understanding how functionalizing agents (molecular dopants) may be designed to access specific behaviors. We measure photoluminescence (PL) decay dynamics of sp 3 defect states introduced by aryl functionalization of the carbon nanotube surface. Results are given for five different nanotube chiralities, each doped with a range of aryl functionality. We find the PL decays of these sp 3 defect states are biexponential,more » with both components relaxing on timescales of ~ 100 ps. Exciton trapping at defects is found to increases PL lifetimes by a factor of 5-10, in comparison to those for the free exciton. A significant chirality dependence is observed in the decay times, ranging from 77 ps for (7,5) nanotubes to > 600 ps for (5,4) structures. The strong correlation of time constants with emission energy indicates relaxation occurs via multiphonon decay processes, with close agreement to theoretical expectations. Variation of the aryl dopant further modulates decay times by 10-15%. The aryl defects also affect PL lifetimes of the free E 11 exciton. Shortening of the E 11 bright state lifetime as defect density increases provides further confirmation that defects act as exciton traps. A similar shortening of the E11 dark exciton lifetime is found as defect density increases, providing strong experimental evidence that dark excitons are also trapped at such defect sites.« less

High-pressure and high-temperature physical properties of LiF studied by density functional theory calculations and molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Sun, Xiao-Wei; Liu, Zi-Jiang; Quan, Wei-Long; Song, Ting; Khenata, Rabah; Bin-Omran, Saad

2018-05-01

Using the revised Perdew-Burke-Ernzerhof generalized gradient approximation based on first-principles plane-wave pseudopotential density functional theory, the high-pressure structural phase transition of LiF is explored. From the analysis of Gibbs free energies, we find that no phase transition occurs for LiF in the presented pressure range from 0 to 1000 GPa, and this result is consistent with the theoretical prediction obtained via ab initio calculations [N.A. Smirnov, Phys. Rev. B 83 (2011) 014109]. Using the classical molecular dynamics technique with effective pair potentials which consist of the Coulomb, dispersion, and repulsion interaction, the melting phase diagram of LiF is determined. The obtained normalized volumes under pressure are in good agreement with our density functional theory results and the available experimental data. Meanwhile, with the help of the quasi-harmonic Debye model in which the phononic effects are considered, the thermodynamic properties of interest, including the volume thermal expansion coefficient, isothermal bulk modulus and its first and second pressure derivatives, heat capacity at constant volume, entropy, Debye temperature, and Grüneisen parameter of LiF are predicted systematically. All the properties of LiF with the stable NaCl-type structure in the temperature range of 0-4900 K and the pressure up to 1000 GPa are summarized.

Time-dependent vibrational spectral analysis of first principles trajectory of methylamine with wavelet transform.

PubMed

Biswas, Sohag; Mallik, Bhabani S

2017-04-12

The fluctuation dynamics of amine stretching frequencies, hydrogen bonds, dangling N-D bonds, and the orientation profile of the amine group of methylamine (MA) were investigated under ambient conditions by means of dispersion-corrected density functional theory-based first principles molecular dynamics (FPMD) simulations. Along with the dynamical properties, various equilibrium properties such as radial distribution function, spatial distribution function, combined radial and angular distribution functions and hydrogen bonding were also calculated. The instantaneous stretching frequencies of amine groups were obtained by wavelet transform of the trajectory obtained from FPMD simulations. The frequency-structure correlation reveals that the amine stretching frequency is weakly correlated with the nearest nitrogen-deuterium distance. The frequency-frequency correlation function has a short time scale of around 110 fs and a longer time scale of about 1.15 ps. It was found that the short time scale originates from the underdamped motion of intact hydrogen bonds of MA pairs. However, the long time scale of the vibrational spectral diffusion of N-D modes is determined by the overall dynamics of hydrogen bonds as well as the dangling ND groups and the inertial rotation of the amine group of the molecule.

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.

Anomalous and non-Gaussian diffusion in Hertzian spheres

NASA Astrophysics Data System (ADS)

Ouyang, Wenze; Sun, Bin; Sun, Zhiwei; Xu, Shenghua

2018-09-01

By means of molecular dynamics simulations, we study the non-Gaussian diffusion in the fluid of Hertzian spheres. The time dependent non-Gaussian parameter, as an indicator of the dynamic heterogeneity, is increased with the increasing of temperature. When the temperature is high enough, the dynamic heterogeneity becomes very significant, and it seems counterintuitive that the maximum of non-Gaussian parameter and the position of its peak decrease monotonically with the increasing of density. By fitting the curves of self intermediate scattering function, we find that the character relaxation time τα is surprisingly not coupled with the time τmax where the non-Gaussian parameter reaches to a maximum. The intriguing features of non-Gaussian diffusion at high enough temperatures can be associated with the weakly correlated mean-field behavior of Hertzian spheres. Especially the time τmax is nearly inversely proportional to the density at extremely high temperatures.

Mass transport properties of Pu/DT mixtures from orbital free molecular dynamics simulations

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

Kress, Joel David; Ticknor, Christopher; Collins, Lee A.

2015-09-16

Mass transport properties (shear viscosity and diffusion coefficients) for Pu/DT mixtures were calculated with Orbital Free Molecular Dynamics (OFMD). The results were fitted to simple functions of mass density (for ρ=10.4 to 62.4 g/cm 3) and temperature (for T=100 up to 3,000 eV) for Pu/DT mixtures consisting of 100/0, 25/75, 50/50, and 75/25 by number.

Quantum Critical Point revisited by the Dynamical Mean Field Theory

NASA Astrophysics Data System (ADS)

Xu, Wenhu; Kotliar, Gabriel; Tsvelik, Alexei

Dynamical mean field theory is used to study the quantum critical point (QCP) in the doped Hubbard model on a square lattice. The QCP is characterized by a universal scaling form of the self energy and a spin density wave instability at an incommensurate wave vector. The scaling form unifies the low energy kink and the high energy waterfall feature in the spectral function, while the spin dynamics includes both the critical incommensurate and high energy antiferromagnetic paramagnons. We use the frequency dependent four-point correlation function of spin operators to calculate the momentum dependent correction to the electron self energy. Our results reveal a substantial difference with the calculations based on the Spin-Fermion model which indicates that the frequency dependence of the the quasiparitcle-paramagnon vertices is an important factor. The authors are supported by Center for Computational Design of Functional Strongly Correlated Materials and Theoretical Spectroscopy under DOE Grant DE-FOA-0001276.

Electron dynamics in complex environments with real-time time dependent density functional theory in a QM-MM framework.

PubMed

Morzan, Uriel N; Ramírez, Francisco F; Oviedo, M Belén; Sánchez, Cristián G; Scherlis, Damián A; Lebrero, Mariano C González

2014-04-28

This article presents a time dependent density functional theory (TDDFT) implementation to propagate the Kohn-Sham equations in real time, including the effects of a molecular environment through a Quantum-Mechanics Molecular-Mechanics (QM-MM) hamiltonian. The code delivers an all-electron description employing Gaussian basis functions, and incorporates the Amber force-field in the QM-MM treatment. The most expensive parts of the computation, comprising the commutators between the hamiltonian and the density matrix-required to propagate the electron dynamics-, and the evaluation of the exchange-correlation energy, were migrated to the CUDA platform to run on graphics processing units, which remarkably accelerates the performance of the code. The method was validated by reproducing linear-response TDDFT results for the absorption spectra of several molecular species. Two different schemes were tested to propagate the quantum dynamics: (i) a leap-frog Verlet algorithm, and (ii) the Magnus expansion to first-order. These two approaches were confronted, to find that the Magnus scheme is more efficient by a factor of six in small molecules. Interestingly, the presence of iron was found to seriously limitate the length of the integration time step, due to the high frequencies associated with the core-electrons. This highlights the importance of pseudopotentials to alleviate the cost of the propagation of the inner states when heavy nuclei are present. Finally, the methodology was applied to investigate the shifts induced by the chemical environment on the most intense UV absorption bands of two model systems of general relevance: the formamide molecule in water solution, and the carboxy-heme group in Flavohemoglobin. In both cases, shifts of several nanometers are observed, consistently with the available experimental data.

Statistical properties of swarms of self-propelled particles with repulsions across the order-disorder transition

NASA Astrophysics Data System (ADS)

Romenskyy, Maksym; Lobaskin, Vladimir

2013-03-01

We study dynamic self-organisation and order-disorder transitions in a two-dimensional system of self-propelled particles. Our model is a variation of the Vicsek model, where particles align the motion to their neighbours but repel each other at short distances. We use computer simulations to measure the orientational order parameter for particle velocities as a function of intensity of internal noise or particle density. We show that in addition to the transition to an ordered state on increasing the particle density, as reported previously, there exists a transition into a disordered phase at the higher densities, which can be attributed to the destructive action of the repulsions. We demonstrate that the transition into the ordered phase is accompanied by the onset of algebraic behaviour of the two-point velocity correlation function and by a non-monotonous variation of the velocity relaxation time. The critical exponent for the decay of the velocity correlation function in the ordered phase depends on particle concentration at low densities but assumes a universal value in more dense systems.

Development of a Multicenter Density Functional Tight Binding Model for Plutonium Surface Hydriding.

PubMed

Goldman, Nir; Aradi, Bálint; Lindsey, Rebecca K; Fried, Laurence E

2018-05-08

We detail the creation of a multicenter density functional tight binding (DFTB) model for hydrogen on δ-plutonium, using a framework of new Slater-Koster interaction parameters and a repulsive energy based on the Chebyshev Interaction Model for Efficient Simulation (ChIMES), where two- and three-center atomic interactions are represented by linear combinations of Chebyshev polynomials. We find that our DFTB/ChIMES model yields a total electron density of states for bulk δ-Pu that compares well to that from Density Functional Theory, as well as to a grid of energy calculations representing approximate H 2 dissociation paths on the δ-Pu (100) surface. We then perform molecular dynamics simulations and minimum energy pathway calculations to determine the energetics of surface dissociation and subsurface diffusion on the (100) and (111) surfaces. Our approach allows for the efficient creation of multicenter repulsive energies with a relatively small investment in initial DFT calculations. Our efforts are particularly pertinent to studies that rely on quantum calculations for interpretation and validation, such as experimental determination of chemical reactivity both on surfaces and in condensed phases.

Linear and quadratic static response functions and structure functions in Yukawa liquids.

PubMed

Magyar, Péter; Donkó, Zoltán; Kalman, Gabor J; Golden, Kenneth I

2014-08-01

We compute linear and quadratic static density response functions of three-dimensional Yukawa liquids by applying an external perturbation potential in molecular dynamics simulations. The response functions are also obtained from the equilibrium fluctuations (static structure factors) in the system via the fluctuation-dissipation theorems. The good agreement of the quadratic response functions, obtained in the two different ways, confirms the quadratic fluctuation-dissipation theorem. We also find that the three-point structure function may be factorizable into two-point structure functions, leading to a cluster representation of the equilibrium triplet correlation function.

Density-based clustering analyses to identify heterogeneous cellular sub-populations

NASA Astrophysics Data System (ADS)

Heaster, Tiffany M.; Walsh, Alex J.; Landman, Bennett A.; Skala, Melissa C.

2017-02-01

Autofluorescence microscopy of NAD(P)H and FAD provides functional metabolic measurements at the single-cell level. Here, density-based clustering algorithms were applied to metabolic autofluorescence measurements to identify cell-level heterogeneity in tumor cell cultures. The performance of the density-based clustering algorithm, DENCLUE, was tested in samples with known heterogeneity (co-cultures of breast carcinoma lines). DENCLUE was found to better represent the distribution of cell clusters compared to Gaussian mixture modeling. Overall, DENCLUE is a promising approach to quantify cell-level heterogeneity, and could be used to understand single cell population dynamics in cancer progression and treatment.

Droplets and the three-phase contact line at the nano-scale. Statics and dynamics

NASA Astrophysics Data System (ADS)

Yatsyshin, Petr; Sibley, David; Savva, Nikos; Kalliadasis, Serafim

2014-11-01

Understanding the behaviour of the solid-liquid-vapour contact line at the scale of several tens of molecular diameters is important in wetting hydrodynamics with applications in micro- and nano-fluidics, including the design of lab-on-a-chip devices and surfaces with specific wetting properties. Due to the fluid inhomogeneity at the nano-scale, the application of continuum-mechanical approaches is limited, and a natural way to remedy this is to seek descriptions accounting for the non-local molecular-level interactions. Density Functional Theory (DFT) for fluids offers a statistical-mechanical framework based on expressing the free energy of the fluid-solid pair as a functional of the spatially varying fluid density. DFT allows us to investigate small drops deposited on planar substrates whilst keeping track of the microscopic structural details of the fluid. Starting from a model of intermolecular forces, we systematically obtain interfaces, surface tensions, and the microscopic contact angle. Using a dynamic extension of equilibrium DFT, we investigate the diffusion-driven evolution of the three-phase contact line to gain insight into the dynamic behaviour of the microscopic contact angle, which is still under debate.

Hypervelocity Impact Test Fragment Modeling: Modifications to the Fragment Rotation Analysis and Lightcurve Code

NASA Technical Reports Server (NTRS)

Gouge, Michael F.

2011-01-01

Hypervelocity impact tests on test satellites are performed by members of the orbital debris scientific community in order to understand and typify the on-orbit collision breakup process. By analysis of these test satellite fragments, the fragment size and mass distributions are derived and incorporated into various orbital debris models. These same fragments are currently being put to new use using emerging technologies. Digital models of these fragments are created using a laser scanner. A group of computer programs referred to as the Fragment Rotation Analysis and Lightcurve code uses these digital representations in a multitude of ways that describe, measure, and model on-orbit fragments and fragment behavior. The Dynamic Rotation subroutine generates all of the possible reflected intensities from a scanned fragment as if it were observed to rotate dynamically while in orbit about the Earth. This calls an additional subroutine that graphically displays the intensities and the resulting frequency of those intensities as a range of solar phase angles in a Probability Density Function plot. This document reports the additions and modifications to the subset of the Fragment Rotation Analysis and Lightcurve concerned with the Dynamic Rotation and Probability Density Function plotting subroutines.

Identification of parameters through which surface chemistry determines the lifetimes of hot electrons in small Au nanoparticles

PubMed Central

Aruda, Kenneth O.; Tagliazucchi, Mario; Sweeney, Christina M.; Hannah, Daniel C.; Schatz, George C.; Weiss, Emily A.

2013-01-01

This paper describes measurements of the dynamics of hot electron cooling in photoexcited gold nanoparticles (Au NPs) with diameters of ∼3.5 nm, and passivated with either a hexadecylamine or hexadecanethiolate adlayer, using ultrafast transient absorption spectroscopy. Fits of these dynamics with temperature-dependent Mie theory reveal that both the electronic heat capacity and the electron–phonon coupling constant are larger for the thiolated NPs than for the aminated NPs, by 40% and 30%, respectively. Density functional theory calculations on ligand-functionalized Au slabs show that the increase in these quantities is due to an increased electronic density of states near the Fermi level upon ligand exchange from amines to thiolates. The lifetime of hot electrons, which have thermalized from the initial plasmon excitation, increases with increasing electronic heat capacity, but decreases with increasing electron–phonon coupling, so the effects of changing surface chemistry on these two quantities partially cancel to yield a hot electron lifetime of thiolated NPs that is only 20% longer than that of aminated NPs. This analysis also reveals that incorporation of a temperature-dependent electron–phonon coupling constant is necessary to adequately fit the dynamics of electron cooling. PMID:23440215

Ion beam sputter etching and deposition of fluoropolymers

NASA Technical Reports Server (NTRS)

Banks, B. A.; Sovey, J. S.; Miller, T. B.; Crandall, K. S.

1978-01-01

Fluoropolymer etching and deposition techniques including thermal evaporation, RF sputtering, plasma polymerization, and ion beam sputtering are reviewed. Etching and deposition mechanism and material characteristics are discussed. Ion beam sputter etch rates for polytetrafluoroethylene (PTFE) were determined as a function of ion energy, current density and ion beam power density. Peel strengths were measured for epoxy bonds to various ion beam sputtered fluoropolymers. Coefficients of static and dynamic friction were measured for fluoropolymers deposited from ion bombarded PTFE.

Microstructure and Dynamic Failure Properties of Freeze-Cast Materials for Thermobaric Warhead Cases

DTIC Science & Technology

2012-12-01

Function LLNL Lawrence Livermore National Laboratory PDF Probability Density Function PMMA Poly(Methyl Methacrylate) RM Reactive Materials SEM...FREEZE CAST MATERIALS Freeze casting technology combines compounds such as aluminum oxide and poly(methyl methacrylate) ( PMMA ) to develop a...Subsequently, the porous structure can be infiltrated with a variety of materials, such as a standard polymer like PMMA . This hybrid material is believed

Pressure effects on the relaxation of an excited nitromethane molecule in an argon bath

NASA Astrophysics Data System (ADS)

Rivera-Rivera, Luis A.; Wagner, Albert F.; Sewell, Thomas D.; Thompson, Donald L.

2015-01-01

Classical molecular dynamics simulations were performed to study the relaxation of nitromethane in an Ar bath (of 1000 atoms) at 300 K and pressures 10, 50, 75, 100, 125, 150, 300, and 400 atm. The molecule was instantaneously excited by statistically distributing 50 kcal/mol among the internal degrees of freedom. At each pressure, 1000 trajectories were integrated for 1000 ps, except for 10 atm, for which the integration time was 5000 ps. The computed ensemble-averaged rotational energy decay is ˜100 times faster than the vibrational energy decay. Both rotational and vibrational decay curves can be satisfactorily fit with the Lendvay-Schatz function, which involves two parameters: one for the initial rate and one for the curvature of the decay curve. The decay curves for all pressures exhibit positive curvature implying the rate slows as the molecule loses energy. The initial rotational relaxation rate is directly proportional to density over the interval of simulated densities, but the initial vibrational relaxation rate decreases with increasing density relative to the extrapolation of the limiting low-pressure proportionality to density. The initial vibrational relaxation rate and curvature are fit as functions of density. For the initial vibrational relaxation rate, the functional form of the fit arises from a combinatorial model for the frequency of nitromethane "simultaneously" colliding with multiple Ar atoms. Roll-off of the initial rate from its low-density extrapolation occurs because the cross section for collision events with L Ar atoms increases with L more slowly than L times the cross section for collision events with one Ar atom. The resulting density-dependent functions of the initial rate and curvature represent, reasonably well, all the vibrational decay curves except at the lowest density for which the functions overestimate the rate of decay. The decay over all gas phase densities is predicted by extrapolating the fits to condensed-phase densities.

Pressure effects on the relaxation of an excited nitromethane molecule in an argon bath

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

Rivera-Rivera, Luis A.; Wagner, Albert F.; Sewell, Thomas D.

2015-01-07

Classical molecular dynamics simulations were performed to study the relaxation of nitromethane in an Ar bath (of 1000 atoms) at 300 K and pressures 10, 50, 75, 100, 125, 150, 300, and 400 atm. The molecule was instantaneously excited by statistically distributing 50 kcal/mol among the internal degrees of freedom. At each pressure, 1000 trajectories were integrated for 1000 ps, except for 10 atm, for which the integration time was 5000 ps. The computed ensemble-averaged rotational energy decay is similar to 100 times faster than the vibrational energy decay. Both rotational and vibrational decay curves can be satisfactorily fit withmore » the Lendvay-Schatz function, which involves two parameters: one for the initial rate and one for the curvature of the decay curve. The decay curves for all pressures exhibit positive curvature implying the rate slows as the molecule loses energy. The initial rotational relaxation rate is directly proportional to density over the interval of simulated densities, but the initial vibrational relaxation rate decreases with increasing density relative to the extrapolation of the limiting low-pressure proportionality to density. The initial vibrational relaxation rate and curvature are fit as functions of density. For the initial vibrational relaxation rate, the functional form of the fit arises from a combinatorial model for the frequency of nitromethane "simultaneously" colliding with multiple Ar atoms. Roll-off of the initial rate from its low-density extrapolation occurs because the cross section for collision events with L Ar atoms increases with L more slowly than L times the cross section for collision events with one Ar atom. The resulting density-dependent functions of the initial rate and curvature represent, reasonably well, all the vibrational decay curves except at the lowest density for which the functions overestimate the rate of decay. The decay over all gas phase densities is predicted by extrapolating the fits to condensed-phase densities. (C) 2015 AIP Publishing LLC.« less

Pressure effects on the relaxation of an excited nitromethane molecule in an argon bath.

PubMed

Rivera-Rivera, Luis A; Wagner, Albert F; Sewell, Thomas D; Thompson, Donald L

2015-01-07

Classical molecular dynamics simulations were performed to study the relaxation of nitromethane in an Ar bath (of 1000 atoms) at 300 K and pressures 10, 50, 75, 100, 125, 150, 300, and 400 atm. The molecule was instantaneously excited by statistically distributing 50 kcal/mol among the internal degrees of freedom. At each pressure, 1000 trajectories were integrated for 1000 ps, except for 10 atm, for which the integration time was 5000 ps. The computed ensemble-averaged rotational energy decay is ∼100 times faster than the vibrational energy decay. Both rotational and vibrational decay curves can be satisfactorily fit with the Lendvay-Schatz function, which involves two parameters: one for the initial rate and one for the curvature of the decay curve. The decay curves for all pressures exhibit positive curvature implying the rate slows as the molecule loses energy. The initial rotational relaxation rate is directly proportional to density over the interval of simulated densities, but the initial vibrational relaxation rate decreases with increasing density relative to the extrapolation of the limiting low-pressure proportionality to density. The initial vibrational relaxation rate and curvature are fit as functions of density. For the initial vibrational relaxation rate, the functional form of the fit arises from a combinatorial model for the frequency of nitromethane "simultaneously" colliding with multiple Ar atoms. Roll-off of the initial rate from its low-density extrapolation occurs because the cross section for collision events with L Ar atoms increases with L more slowly than L times the cross section for collision events with one Ar atom. The resulting density-dependent functions of the initial rate and curvature represent, reasonably well, all the vibrational decay curves except at the lowest density for which the functions overestimate the rate of decay. The decay over all gas phase densities is predicted by extrapolating the fits to condensed-phase densities.

Pressure effects on the relaxation of an excited nitromethane molecule in an argon bath

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

Rivera-Rivera, Luis A.; Sewell, Thomas D.; Thompson, Donald L.

2015-01-07

Classical molecular dynamics simulations were performed to study the relaxation of nitromethane in an Ar bath (of 1000 atoms) at 300 K and pressures 10, 50, 75, 100, 125, 150, 300, and 400 atm. The molecule was instantaneously excited by statistically distributing 50 kcal/mol among the internal degrees of freedom. At each pressure, 1000 trajectories were integrated for 1000 ps, except for 10 atm, for which the integration time was 5000 ps. The computed ensemble-averaged rotational energy decay is ∼100 times faster than the vibrational energy decay. Both rotational and vibrational decay curves can be satisfactorily fit with the Lendvay-Schatzmore » function, which involves two parameters: one for the initial rate and one for the curvature of the decay curve. The decay curves for all pressures exhibit positive curvature implying the rate slows as the molecule loses energy. The initial rotational relaxation rate is directly proportional to density over the interval of simulated densities, but the initial vibrational relaxation rate decreases with increasing density relative to the extrapolation of the limiting low-pressure proportionality to density. The initial vibrational relaxation rate and curvature are fit as functions of density. For the initial vibrational relaxation rate, the functional form of the fit arises from a combinatorial model for the frequency of nitromethane “simultaneously” colliding with multiple Ar atoms. Roll-off of the initial rate from its low-density extrapolation occurs because the cross section for collision events with L Ar atoms increases with L more slowly than L times the cross section for collision events with one Ar atom. The resulting density-dependent functions of the initial rate and curvature represent, reasonably well, all the vibrational decay curves except at the lowest density for which the functions overestimate the rate of decay. The decay over all gas phase densities is predicted by extrapolating the fits to condensed-phase densities.« less

Watching proteins function with picosecond X-ray crystallography and molecular dynamics simulations.

NASA Astrophysics Data System (ADS)

Anfinrud, Philip

2006-03-01

Time-resolved electron density maps of myoglobin, a ligand-binding heme protein, have been stitched together into movies that unveil with < 2-å spatial resolution and 150-ps time-resolution the correlated protein motions that accompany and/or mediate ligand migration within the hydrophobic interior of a protein. A joint analysis of all-atom molecular dynamics (MD) calculations and picosecond time-resolved X-ray structures provides single-molecule insights into mechanisms of protein function. Ensemble-averaged MD simulations of the L29F mutant of myoglobin following ligand dissociation reproduce the direction, amplitude, and timescales of crystallographically-determined structural changes. This close agreement with experiments at comparable resolution in space and time validates the individual MD trajectories, which identify and structurally characterize a conformational switch that directs dissociated ligands to one of two nearby protein cavities. This unique combination of simulation and experiment unveils functional protein motions and illustrates at an atomic level relationships among protein structure, dynamics, and function. In collaboration with Friedrich Schotte and Gerhard Hummer, NIH.

Parasitism alters three power laws of scaling in a metazoan community: Taylor’s law, density-mass allometry, and variance-mass allometry

PubMed Central

Lagrue, Clément; Poulin, Robert; Cohen, Joel E.

2015-01-01

How do the lifestyles (free-living unparasitized, free-living parasitized, and parasitic) of animal species affect major ecological power-law relationships? We investigated this question in metazoan communities in lakes of Otago, New Zealand. In 13,752 samples comprising 1,037,058 organisms, we found that species of different lifestyles differed in taxonomic distribution and body mass and were well described by three power laws: a spatial Taylor’s law (the spatial variance in population density was a power-law function of the spatial mean population density); density-mass allometry (the spatial mean population density was a power-law function of mean body mass); and variance-mass allometry (the spatial variance in population density was a power-law function of mean body mass). To our knowledge, this constitutes the first empirical confirmation of variance-mass allometry for any animal community. We found that the parameter values of all three relationships differed for species with different lifestyles in the same communities. Taylor's law and density-mass allometry accurately predicted the form and parameter values of variance-mass allometry. We conclude that species of different lifestyles in these metazoan communities obeyed the same major ecological power-law relationships but did so with parameters specific to each lifestyle, probably reflecting differences among lifestyles in population dynamics and spatial distribution. PMID:25550506

Parasitism alters three power laws of scaling in a metazoan community: Taylor's law, density-mass allometry, and variance-mass allometry.

PubMed

Lagrue, Clément; Poulin, Robert; Cohen, Joel E

2015-02-10

How do the lifestyles (free-living unparasitized, free-living parasitized, and parasitic) of animal species affect major ecological power-law relationships? We investigated this question in metazoan communities in lakes of Otago, New Zealand. In 13,752 samples comprising 1,037,058 organisms, we found that species of different lifestyles differed in taxonomic distribution and body mass and were well described by three power laws: a spatial Taylor's law (the spatial variance in population density was a power-law function of the spatial mean population density); density-mass allometry (the spatial mean population density was a power-law function of mean body mass); and variance-mass allometry (the spatial variance in population density was a power-law function of mean body mass). To our knowledge, this constitutes the first empirical confirmation of variance-mass allometry for any animal community. We found that the parameter values of all three relationships differed for species with different lifestyles in the same communities. Taylor's law and density-mass allometry accurately predicted the form and parameter values of variance-mass allometry. We conclude that species of different lifestyles in these metazoan communities obeyed the same major ecological power-law relationships but did so with parameters specific to each lifestyle, probably reflecting differences among lifestyles in population dynamics and spatial distribution.

A computationally efficient ductile damage model accounting for nucleation and micro-inertia at high triaxialities

DOE PAGES

Versino, Daniele; Bronkhorst, Curt Allan

2018-01-31

The computational formulation of a micro-mechanical material model for the dynamic failure of ductile metals is presented in this paper. The statistical nature of porosity initiation is accounted for by introducing an arbitrary probability density function which describes the pores nucleation pressures. Each micropore within the representative volume element is modeled as a thick spherical shell made of plastically incompressible material. The treatment of porosity by a distribution of thick-walled spheres also allows for the inclusion of micro-inertia effects under conditions of shock and dynamic loading. The second order ordinary differential equation governing the microscopic porosity evolution is solved withmore » a robust implicit procedure. A new Chebyshev collocation method is employed to approximate the porosity distribution and remapping is used to optimize memory usage. The adaptive approximation of the porosity distribution leads to a reduction of computational time and memory usage of up to two orders of magnitude. Moreover, the proposed model affords consistent performance: changing the nucleation pressure probability density function and/or the applied strain rate does not reduce accuracy or computational efficiency of the material model. The numerical performance of the model and algorithms presented is tested against three problems for high density tantalum: single void, one-dimensional uniaxial strain, and two-dimensional plate impact. Here, the results using the integration and algorithmic advances suggest a significant improvement in computational efficiency and accuracy over previous treatments for dynamic loading conditions.« less

The interface of SrTiO3 and H2O from density functional theory molecular dynamics

PubMed Central

Spijker, P.; Foster, A. S.

2016-01-01

We use dispersion-corrected density functional theory molecular dynamics simulations to predict the ionic, electronic and vibrational properties of the SrTiO3/H2O solid–liquid interface. Approximately 50% of surface oxygens on the planar SrO termination are hydroxylated at all studied levels of water coverage, the corresponding number being 15% for the planar TiO2 termination and 5% on the stepped TiO2-terminated surface. The lateral ordering of the hydration structure is largely controlled by covalent-like surface cation to H2O bonding and surface corrugation. We find a featureless electronic density of states in and around the band gap energy region at the solid–liquid interface. The vibrational spectrum indicates redshifting of the O–H stretching band due to surface-to-liquid hydrogen bonding and blueshifting due to high-frequency stretching vibrations of OH fragments within the liquid, as well as strong suppression of the OH stretching band on the stepped surface. We find highly varying rates of proton transfer above different SrTiO3 surfaces, owing to differences in hydrogen bond strength and the degree of dissociation of incident water. Trends in proton dynamics and the mode of H2O adsorption among studied surfaces can be explained by the differential ionicity of the Ti–O and Sr–O bonds in the SrTiO3 crystal. PMID:27713660

Glass polymorphism in amorphous germanium probed by first-principles computer simulations

NASA Astrophysics Data System (ADS)

Mancini, G.; Celino, M.; Iesari, F.; Di Cicco, A.

2016-01-01

The low-density (LDA) to high-density (HDA) transformation in amorphous Ge at high pressure is studied by first-principles molecular dynamics simulations in the framework of density functional theory. Previous experiments are accurately reproduced, including the presence of a well-defined LDA-HDA transition above 8 GPa. The LDA-HDA density increase is found to be about 14%. Pair and bond-angle distributions are obtained in the 0-16 GPa pressure range and allowed us a detailed analysis of the transition. The local fourfold coordination is transformed in an average HDA sixfold coordination associated with different local geometries as confirmed by coordination number analysis and shape of the bond-angle distributions.

Convolutionless Nakajima-Zwanzig equations for stochastic analysis in nonlinear dynamical systems.

PubMed

Venturi, D; Karniadakis, G E

2014-06-08

Determining the statistical properties of stochastic nonlinear systems is of major interest across many disciplines. Currently, there are no general efficient methods to deal with this challenging problem that involves high dimensionality, low regularity and random frequencies. We propose a framework for stochastic analysis in nonlinear dynamical systems based on goal-oriented probability density function (PDF) methods. The key idea stems from techniques of irreversible statistical mechanics, and it relies on deriving evolution equations for the PDF of quantities of interest, e.g. functionals of the solution to systems of stochastic ordinary and partial differential equations. Such quantities could be low-dimensional objects in infinite dimensional phase spaces. We develop the goal-oriented PDF method in the context of the time-convolutionless Nakajima-Zwanzig-Mori formalism. We address the question of approximation of reduced-order density equations by multi-level coarse graining, perturbation series and operator cumulant resummation. Numerical examples are presented for stochastic resonance and stochastic advection-reaction problems.

Multi-charge-state molecular dynamics and self-diffusion coefficient in the warm dense matter regime

NASA Astrophysics Data System (ADS)

Fu, Yongsheng; Hou, Yong; Kang, Dongdong; Gao, Cheng; Jin, Fengtao; Yuan, Jianmin

2018-01-01

We present a multi-ion molecular dynamics (MIMD) simulation and apply it to calculating the self-diffusion coefficients of ions with different charge-states in the warm dense matter (WDM) regime. First, the method is used for the self-consistent calculation of electron structures of different charge-state ions in the ion sphere, with the ion-sphere radii being determined by the plasma density and the ion charges. The ionic fraction is then obtained by solving the Saha equation, taking account of interactions among different charge-state ions in the system, and ion-ion pair potentials are computed using the modified Gordon-Kim method in the framework of temperature-dependent density functional theory on the basis of the electron structures. Finally, MIMD is used to calculate ionic self-diffusion coefficients from the velocity correlation function according to the Green-Kubo relation. A comparison with the results of the average-atom model shows that different statistical processes will influence the ionic diffusion coefficient in the WDM regime.

Simulating Excitons in MoS2 with Time-Dependent Density Functional Theory

NASA Astrophysics Data System (ADS)

Flamant, Cedric; Kolesov, Grigory; Kaxiras, Efthimios

Monolayer molybdenum disulfide, owing to its graphene-like two-dimensional geometry whilst still having a finite bandgap, is a material of great interest in condensed matter physics and for potential application in electronic devices. In particular, MoS2 exhibits significant excitonic effects, a desirable quality for fundamental many-body research. Time-dependent density functional theory (TD-DFT) allows us to simulate dynamical effects as well as temperature-based effects in a natural way given the direct treatment of the time evolution of the system. We present a TD-DFT study of monolayer MoS2 exciton dynamics, examining various qualitative and quantitative predictions in pure samples and in the presence of defects. In particular, we generate an absorption spectrum through simulated pulse excitation for comparison to experiment and also analyze the response of the exciton in an external electric field.In this work we also discuss the electronic structure of the exciton in MoS2 with and without vacancies.

Local phase transitions in driven colloidal suspensions

NASA Astrophysics Data System (ADS)

Scacchi, A.; Brader, J. M.

2018-02-01

Using dynamical density functional theory and Brownian dynamics simulations, we investigate the influence of a driven tracer particle on the density distribution of a colloidal suspension at a thermodynamic state point close to the liquid side of the binodal. In bulk systems, we find that a localised region of the colloid-poor phase, a 'cavitation bubble', forms behind the moving tracer. The extent of the cavitation bubble is investigated as a function of both the size and velocity of the tracer. The addition of a confining boundary enables us to investigate the interaction between the local phase instability at the substrate and that at the particle surface. When both the substrate and tracer interact repulsively with the colloids we observe the formation of a colloid-poor bridge between the substrate and the tracer. When a shear flow is applied parallel to the substrate the bridge becomes distorted and, at sufficiently high shear-rates, disconnects from the substrate to form a cavitation bubble.

Convolutionless Nakajima–Zwanzig equations for stochastic analysis in nonlinear dynamical systems

PubMed Central

Venturi, D.; Karniadakis, G. E.

2014-01-01

Determining the statistical properties of stochastic nonlinear systems is of major interest across many disciplines. Currently, there are no general efficient methods to deal with this challenging problem that involves high dimensionality, low regularity and random frequencies. We propose a framework for stochastic analysis in nonlinear dynamical systems based on goal-oriented probability density function (PDF) methods. The key idea stems from techniques of irreversible statistical mechanics, and it relies on deriving evolution equations for the PDF of quantities of interest, e.g. functionals of the solution to systems of stochastic ordinary and partial differential equations. Such quantities could be low-dimensional objects in infinite dimensional phase spaces. We develop the goal-oriented PDF method in the context of the time-convolutionless Nakajima–Zwanzig–Mori formalism. We address the question of approximation of reduced-order density equations by multi-level coarse graining, perturbation series and operator cumulant resummation. Numerical examples are presented for stochastic resonance and stochastic advection–reaction problems. PMID:24910519

Nonequilibrium phase transitions of sheared colloidal microphases: Results from dynamical density functional theory

NASA Astrophysics Data System (ADS)

Stopper, Daniel; Roth, Roland

2018-06-01

By means of classical density functional theory and its dynamical extension, we consider a colloidal fluid with spherically symmetric competing interactions, which are well known to exhibit a rich bulk phase behavior. This includes complex three-dimensional periodically ordered cluster phases such as lamellae, two-dimensional hexagonally packed cylinders, gyroid structures, or spherical micelles. While the bulk phase behavior has been studied extensively in earlier work, in this paper we focus on such structures confined between planar repulsive walls under shear flow. For sufficiently high shear rates, we observe that microphase separation can become fully suppressed. For lower shear rates, however, we find that, e.g., the gyroid structure undergoes a kinetic phase transition to a hexagonally packed cylindrical phase, which is found experimentally and theoretically in amphiphilic block copolymer systems. As such, besides the known similarities between the latter and colloidal systems regarding the equilibrium phase behavior, our work reveals further intriguing nonequilibrium relations between copolymer melts and colloidal fluids with competing interactions.

High Density or Urban Sprawl: What Works Best in Biology?

PubMed

Oreopoulos, John; Gray-Owen, Scott D; Yip, Christopher M

2017-02-28

With new approaches in imaging-from new tools or reagents to processing algorithms-come unique opportunities and challenges to our understanding of biological processes, structures, and dynamics. Although innovations in super-resolution imaging are affording novel perspectives into how molecules structurally associate and localize in response to, or in order to initiate, specific signaling events in the cell, questions arise as to how to interpret these observations in the context of biological function. Just as each neighborhood in a city has its own unique vibe, culture, and indeed density, recent work has shown that membrane receptor behavior and action is governed by their localization and association state. There is tremendous potential in developing strategies for tracking how the populations of these molecular neighborhoods change dynamically.

Analyzing fragment production in mass-asymmetric reactions as a function of density dependent part of symmetry energy

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

Kaur, Amandeep; Deepshikha; Vinayak, Karan Singh

2016-07-15

We performed a theoretical investigation of different mass-asymmetric reactions to access the direct impact of the density-dependent part of symmetry energy on multifragmentation. The simulations are performed for a specific set of reactions having same system mass and N/Z content, using isospin-dependent quantum molecular dynamics model to estimate the quantitative dependence of fragment production on themass-asymmetry factor (τ) for various symmetry energy forms. The dynamics associated with different mass-asymmetric reactions is explored and the direct role of symmetry energy is checked. Also a comparison with the experimental data (asymmetric reaction) is presented for a different equation of states (symmetry energymore » forms).« less

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

NASA Astrophysics Data System (ADS)

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

2016-04-01

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

The Self-Organization of a Spoken Word

PubMed Central

Holden, John G.; Rajaraman, Srinivasan

2012-01-01

Pronunciation time probability density and hazard functions from large speeded word naming data sets were assessed for empirical patterns consistent with multiplicative and reciprocal feedback dynamics – interaction dominant dynamics. Lognormal and inverse power law distributions are associated with multiplicative and interdependent dynamics in many natural systems. Mixtures of lognormal and inverse power law distributions offered better descriptions of the participant’s distributions than the ex-Gaussian or ex-Wald – alternatives corresponding to additive, superposed, component processes. The evidence for interaction dominant dynamics suggests fundamental links between the observed coordinative synergies that support speech production and the shapes of pronunciation time distributions. PMID:22783213

Assessing exchange-correlation functionals for elasticity and thermodynamics of α - ZrW 2 O 8 : A density functional perturbation theory study

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

Weck, Philippe F.; Kim, Eunja; Greathouse, Jeffery A.

Elastic and thermodynamic properties of negative thermal expansion (NTE) αα-ZrW2O8 have been calculated using PBEsol and PBE exchange-correlation functionals within the framework of density functional perturbation theory (DFPT). Measured elastic constants are reproduced within ~2% with PBEsol and 6% with PBE. The thermal evolution of the Grüneisen parameter computed within the quasi-harmonic approximation exhibits negative values below the Debye temperature, consistent with observation. The standard molar heat capacity is predicted to be Cmore » $$O\\atop{P}$$=192.2 and 193.8 J mol -1K -1 with PBEsol and PBE, respectively. These results suggest superior accuracy of DFPT/PBEsol for studying the lattice dynamics, elasticity and thermodynamics of NTE materials.« less

Assessing exchange-correlation functionals for elasticity and thermodynamics of α - ZrW 2 O 8 : A density functional perturbation theory study

DOE PAGES

Weck, Philippe F.; Kim, Eunja; Greathouse, Jeffery A.; ...

2018-03-15

Elastic and thermodynamic properties of negative thermal expansion (NTE) αα-ZrW2O8 have been calculated using PBEsol and PBE exchange-correlation functionals within the framework of density functional perturbation theory (DFPT). Measured elastic constants are reproduced within ~2% with PBEsol and 6% with PBE. The thermal evolution of the Grüneisen parameter computed within the quasi-harmonic approximation exhibits negative values below the Debye temperature, consistent with observation. The standard molar heat capacity is predicted to be Cmore » $$O\\atop{P}$$=192.2 and 193.8 J mol -1K -1 with PBEsol and PBE, respectively. These results suggest superior accuracy of DFPT/PBEsol for studying the lattice dynamics, elasticity and thermodynamics of NTE materials.« less

Quantum molecular dynamics study on the proton exchange, ionic structures, and transport properties of warm dense hydrogen-deuterium mixtures

NASA Astrophysics Data System (ADS)

Liu, Lei; Li, Zhi-Guo; Dai, Jia-Yu; Chen, Qi-Feng; Chen, Xiang-Rong

2018-06-01

Comprehensive knowledge of physical properties such as equation of state (EOS), proton exchange, dynamic structures, diffusion coefficients, and viscosities of hydrogen-deuterium mixtures with densities from 0.1 to 5 g /cm3 and temperatures from 1 to 50 kK has been presented via quantum molecular dynamics (QMD) simulations. The existing multi-shock experimental EOS provides an important benchmark to evaluate exchange-correlation functionals. The comparison of simulations with experiments indicates that a nonlocal van der Waals density functional (vdW-DF1) produces excellent results. Fraction analysis of molecules using a weighted integral over pair distribution functions was performed. A dissociation diagram together with a boundary where the proton exchange (H2+D2⇌2 HD ) occurs was generated, which shows evidence that the HD molecules form as the H2 and D2 molecules are almost 50% dissociated. The mechanism of proton exchange can be interpreted as a process of dissociation followed by recombination. The ionic structures at extreme conditions were analyzed by the effective coordination number model. High-order cluster, circle, and chain structures can be founded in the strongly coupled warm dense regime. The present QMD diffusion coefficient and viscosity can be used to benchmark two analytical one-component plasma (OCP) models: the Coulomb and Yukawa OCP models.

Subcycle dynamics of high-order-harmonic generation of He atoms excited by attosecond pulses and driven by near-infrared laser fields: A self-interaction-free time-dependent density-functional-theory approach

NASA Astrophysics Data System (ADS)

Heslar, John; Telnov, Dmitry A.; Chu, Shih-I.

2014-05-01

In the framework of the self-interaction-free time-dependent density-functional theory, we have performed three-dimensional (3D) ab initio calculations of He atoms in near-infrared (NIR) laser fields subject to excitation by a single extreme ultraviolet (XUV) attosecond pulse (SAP). We have explored the dynamical behavior of the subcycle high harmonic generation (HHG) for transitions from the excited states to the ground state and found oscillation structures with respect to the time delay between the SAP and NIR fields. The oscillatory pattern in the photon emission spectra has a period of ˜1.3 fs which is half of the NIR laser optical cycle, similar to that recently measured in the experiments on transient absorption of He [M. Chini et al., Sci. Rep. 3, 1105 (2013), 10.1038/srep01105]. We present the photon emission spectra from 1s2p, 1s3p, 1s4p, 1s5p, and 1s6p excited states as functions of the time delay. We explore the subcycle Stark shift phenomenon in NIR fields and its influence on the photon emission process. Our analysis reveals several interesting features of the subcycle HHG dynamics and we identify the mechanisms responsible for the observed peak splitting in the photon emission spectra.

First-principles investigations on ionization and thermal conductivity of polystyrene for inertial confinement fusion applications

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

Hu, S. X., E-mail: shu@lle.rochester.edu; Goncharov, V. N.; McCrory, R. L.

2016-04-15

Using quantum molecular-dynamics (QMD) methods based on the density functional theory, we have performed first-principles investigations of the ionization and thermal conductivity of polystyrene (CH) over a wide range of plasma conditions (ρ = 0.5 to 100 g/cm{sup 3} and T = 15 625 to 500 000 K). The ionization data from orbital-free molecular-dynamics calculations have been fitted with a “Saha-type” model as a function of the CH plasma density and temperature, which gives an increasing ionization as the CH density increases even at low temperatures (T < 50 eV). The orbital-free molecular dynamics method is only used to gauge the average ionization behavior of CH under the average-atommore » model in conjunction with the pressure-matching mixing rule. The thermal conductivities (κ{sub QMD}) of CH, derived directly from the Kohn–Sham molecular-dynamics calculations, are then analytically fitted with a generalized Coulomb logarithm [(lnΛ){sub QMD}] over a wide range of plasma conditions. When compared with the traditional ionization and thermal conductivity models used in radiation–hydrodynamics codes for inertial confinement fusion simulations, the QMD results show a large difference in the low-temperature regime in which strong coupling and electron degeneracy play an essential role in determining plasma properties. Hydrodynamic simulations of cryogenic deuterium–tritium targets with CH ablators on OMEGA and the National Ignition Facility using the QMD-derived ionization and thermal conductivity of CH have predicted ∼20% variation in target performance in terms of hot-spot pressure and neutron yield (gain) with respect to traditional model simulations.« less

Pairing-induced speedup of nuclear spontaneous fission

NASA Astrophysics Data System (ADS)

Sadhukhan, Jhilam; Dobaczewski, J.; Nazarewicz, W.; Sheikh, J. A.; Baran, A.

2014-12-01

Background: Collective inertia is strongly influenced at the level crossing at which the quantum system changes its microscopic configuration diabatically. Pairing correlations tend to make the large-amplitude nuclear collective motion more adiabatic by reducing the effect of these configuration changes. Competition between pairing and level crossing is thus expected to have a profound impact on spontaneous fission lifetimes. Purpose: To elucidate the role of nucleonic pairing on spontaneous fission, we study the dynamic fission trajectories of 264Fm and 240Pu using the state-of-the-art self-consistent framework. Methods: We employ the superfluid nuclear density functional theory with the Skyrme energy density functional SkM* and a density-dependent pairing interaction. Along with shape variables, proton and neutron pairing correlations are taken as collective coordinates. The collective inertia tensor is calculated within the nonperturbative cranking approximation. The fission paths are obtained by using the least action principle in a four-dimensional collective space of shape and pairing coordinates. Results: Pairing correlations are enhanced along the minimum-action fission path. For the symmetric fission of 264Fm, where the effect of triaxiality on the fission barrier is large, the geometry of the fission pathway in the space of the shape degrees of freedom is weakly impacted by pairing. This is not the case for 240Pu, where pairing fluctuations restore the axial symmetry of the dynamic fission trajectory. Conclusions: The minimum-action fission path is strongly impacted by nucleonic pairing. In some cases, the dynamical coupling between shape and pairing degrees of freedom can lead to a dramatic departure from the static picture. Consequently, in the dynamical description of nuclear fission, particle-particle correlations should be considered on the same footing as those associated with shape degrees of freedom.

Pairing-induced speedup of nuclear spontaneous fission

DOE PAGES

Sadhukhan, Jhilam; Dobaczewski, J.; Nazarewicz, W.; ...

2014-12-22

Collective inertia is strongly influenced at the level crossing at which the quantum system changes its microscopic configuration diabatically. Pairing correlations tend to make the large-amplitude nuclear collective motion more adiabatic by reducing the effect of these configuration changes. Competition between pairing and level crossing is thus expected to have a profound impact on spontaneous fission lifetimes. To elucidate the role of nucleonic pairing on spontaneous fission, we study the dynamic fission trajectories of 264Fm and 240Pu using the state-of-the-art self-consistent framework. We employ the superfluid nuclear density functional theory with the Skyrme energy density functional SkM* and a density-dependentmore » pairing interaction. Along with shape variables, proton and neutron pairing correlations are taken as collective coordinates. The collective inertia tensor is calculated within the nonperturbative cranking approximation. The fission paths are obtained by using the least action principle in a four-dimensional collective space of shape and pairing coordinates. Pairing correlations are enhanced along the minimum-action fission path. For the symmetric fission of 264Fm, where the effect of triaxiality on the fission barrier is large, the geometry of the fission pathway in the space of the shape degrees of freedom is weakly impacted by pairing. This is not the case for 240Pu, where pairing fluctuations restore the axial symmetry of the dynamic fission trajectory. The minimum-action fission path is strongly impacted by nucleonic pairing. In some cases, the dynamical coupling between shape and pairing degrees of freedom can lead to a dramatic departure from the static picture. As a result, in the dynamical description of nuclear fission, particle-particle correlations should be considered on the same footing as those associated with shape degrees of freedom.« less

Time-series analysis of lung texture on bone-suppressed dynamic chest radiograph for the evaluation of pulmonary function: a preliminary study

NASA Astrophysics Data System (ADS)

Tanaka, Rie; Matsuda, Hiroaki; Sanada, Shigeru

2017-03-01

The density of lung tissue changes as demonstrated on imagery is dependent on the relative increases and decreases in the volume of air and lung vessels per unit volume of lung. Therefore, a time-series analysis of lung texture can be used to evaluate relative pulmonary function. This study was performed to assess a time-series analysis of lung texture on dynamic chest radiographs during respiration, and to demonstrate its usefulness in the diagnosis of pulmonary impairments. Sequential chest radiographs of 30 patients were obtained using a dynamic flat-panel detector (FPD; 100 kV, 0.2 mAs/pulse, 15 frames/s, SID = 2.0 m; Prototype, Konica Minolta). Imaging was performed during respiration, and 210 images were obtained over 14 seconds. Commercial bone suppression image-processing software (Clear Read Bone Suppression; Riverain Technologies, Miamisburg, Ohio, USA) was applied to the sequential chest radiographs to create corresponding bone suppression images. Average pixel values, standard deviation (SD), kurtosis, and skewness were calculated based on a density histogram analysis in lung regions. Regions of interest (ROIs) were manually located in the lungs, and the same ROIs were traced by the template matching technique during respiration. Average pixel value effectively differentiated regions with ventilatory defects and normal lung tissue. The average pixel values in normal areas changed dynamically in synchronization with the respiratory phase, whereas those in regions of ventilatory defects indicated reduced variations in pixel value. There were no significant differences between ventilatory defects and normal lung tissue in the other parameters. We confirmed that time-series analysis of lung texture was useful for the evaluation of pulmonary function in dynamic chest radiography during respiration. Pulmonary impairments were detected as reduced changes in pixel value. This technique is a simple, cost-effective diagnostic tool for the evaluation of regional pulmonary function.

Resource-driven changes to host population stability alter the evolution of virulence and transmission.

PubMed

Hite, Jessica L; Cressler, Clayton E

2018-05-05

What drives the evolution of parasite life-history traits? Recent studies suggest that linking within- and between-host processes can provide key insight into both disease dynamics and parasite evolution. Still, it remains difficult to understand how to pinpoint the critical factors connecting these cross-scale feedbacks, particularly under non-equilibrium conditions; many natural host populations inherently fluctuate and parasites themselves can strongly alter the stability of host populations. Here, we develop a general model framework that mechanistically links resources to parasite evolution across a gradient of stable and unstable conditions. First, we dynamically link resources and between-host processes (host density, stability, transmission) to virulence evolution, using a 'non-nested' model. Then, we consider a 'nested' model where population-level processes (transmission and virulence) depend on resource-driven changes to individual-level (within-host) processes (energetics, immune function, parasite production). Contrary to 'non-nested' model predictions, the 'nested' model reveals complex effects of host population dynamics on parasite evolution, including regions of evolutionary bistability; evolution can push parasites towards strongly or weakly stabilizing strategies. This bistability results from dynamic feedbacks between resource-driven changes to host density, host immune function and parasite production. Together, these results highlight how cross-scale feedbacks can provide key insights into the structuring role of parasites and parasite evolution.This article is part of the theme issue 'Anthropogenic resource subsidies and host-parasite dynamics in wildlife'. © 2018 The Author(s).

Probing the structural and dynamical properties of liquid water with models including non-local electron correlation

NASA Astrophysics Data System (ADS)

Del Ben, Mauro; Hutter, Jürg; VandeVondele, Joost

2015-08-01

Water is a ubiquitous liquid that displays a wide range of anomalous properties and has a delicate structure that challenges experiment and simulation alike. The various intermolecular interactions that play an important role, such as repulsion, polarization, hydrogen bonding, and van der Waals interactions, are often difficult to reproduce faithfully in atomistic models. Here, electronic structure theories including all these interactions at equal footing, which requires the inclusion of non-local electron correlation, are used to describe structure and dynamics of bulk liquid water. Isobaric-isothermal (NpT) ensemble simulations based on the Random Phase Approximation (RPA) yield excellent density (0.994 g/ml) and fair radial distribution functions, while various other density functional approximations produce scattered results (0.8-1.2 g/ml). Molecular dynamics simulation in the microcanonical (NVE) ensemble based on Møller-Plesset perturbation theory (MP2) yields dynamical properties in the condensed phase, namely, the infrared spectrum and diffusion constant. At the MP2 and RPA levels of theory, ice is correctly predicted to float on water, resolving one of the anomalies as resulting from a delicate balance between van der Waals and hydrogen bonding interactions. For several properties, obtaining quantitative agreement with experiment requires correction for nuclear quantum effects (NQEs), highlighting their importance, for structure, dynamics, and electronic properties. A computed NQE shift of 0.6 eV for the band gap and absorption spectrum illustrates the latter. Giving access to both structure and dynamics of condensed phase systems, non-local electron correlation will increasingly be used to study systems where weak interactions are of paramount importance.

Single-molecule interfacial electron transfer dynamics in solar energy conversion

NASA Astrophysics Data System (ADS)

Dhital, Bharat

This dissertation work investigated the parameters affecting the interfacial electron transfer (ET) dynamics in dye-semiconductor nanoparticles (NPs) system by using single-molecule fluorescence spectroscopy and imaging combined with electrochemistry. The influence of the molecule-substrate electronic coupling, the molecular structure, binding geometry on the surface and the molecule-attachment surface chemistry on interfacial charge transfer processes was studied on zinc porphyrin-TiO2 NP systems. The fluorescence blinking measurement on TiO2 NP demonstrated that electronic coupling regulates dynamics of charge transfer processes at the interface depending on the conformation of molecule on the surface. Moreover, semiconductor surface charge induced electronic coupling of molecule which is electrostatically adsorbed on the semiconductor surface also predominantly alters the ET dynamics. Furthermore, interfacial electric field and electron accepting state density dependent ET dynamics has been dissected in zinc porphyrin-TiO2 NP system by observing the single-molecule fluorescence blinking dynamics and fluorescence lifetime with and without applied bias. The significant difference in fluorescence fluctuation and lifetime suggested the modulation of charge transfer dynamics at the interface with external electric field perturbation. Quasi-continuous distribution of fluorescence intensity with applied negative potential was attributed to the faster charge recombination due to reduced density of electron accepting states. The driving force and electron accepting state density ET dependent dynamics has also been probed in zinc porphyrin-TiO2 NP and zinc porphyrin-indium tin oxide (ITO) systems. Study of a molecule adsorbed on two different semiconductors (ITO and TiO2), with large difference in electron densities and distinct driving forces, allows us to observe the changes in rates of back electron transfer process reflected by the suppressed fluorescence blinking of molecule on ITO surface. Finally, the electric field effect on the interface properties has been probed by using surface-enhanced Raman spectroscopy and supported by density functional theory calculations in alizarin-TiO2 system. The perturbation, created by the external potential, has been observed to cause a shift and/or splitting interfacial bond vibrational mode, typical indicator of the coupling energy changes between alizarin and TiO2. Such splitting provides evidence for electric field-dependent electronic coupling changes that have a significant impact on the interfacial electron transfer dynamics.

Molecular dynamics simulation of liquid structure for undercooled Zr-Nb alloys assisted with electrostatic levitation experiments

NASA Astrophysics Data System (ADS)

Yang, S. J.; Hu, L.; Wang, L.; Wei, B.

2018-06-01

The liquid structures of undercooled Zr90Nb10, Zr70Nb30 and Zr50Nb50 alloys were studied by molecular dynamics simulation combined with electrostatic levitation experiments. The densities of three alloys were measured by electrostatic levitation to modify the Zr-Nb potential functions by adjusting parameters in potential functions. In simulation, the atomic packing in Zr-Nb alloys was more ordered at lower temperatures. The Voronoi tessellation analyses indicated Nb-centered clusters were easier to form than Zr-centered clusters although the Nb content was less than 50%. The partial pair distribution functions showed that the interactions among Zr atoms are quite different to that among Nb atoms.

Simulation of Charged Systems in Heterogeneous Dielectric Media via a True Energy Functional

NASA Astrophysics Data System (ADS)

Jadhao, Vikram; Solis, Francisco J.; de la Cruz, Monica Olvera

2012-11-01

For charged systems in heterogeneous dielectric media, a key obstacle for molecular dynamics (MD) simulations is the need to solve the Poisson equation in the media. This obstacle can be bypassed using MD methods that treat the local polarization charge density as a dynamic variable, but such approaches require access to a true free energy functional, one that evaluates to the equilibrium electrostatic energy at its minimum. In this Letter, we derive the needed functional. As an application, we develop a Car-Parrinello MD method for the simulation of free charges present near a spherical emulsion droplet separating two immiscible liquids with different dielectric constants. Our results show the presence of nonmonotonic ionic profiles in the dielectric with a lower dielectric constant.

Acoustic dynamics of supercooled indomethacin probed by Brillouin light scattering.

PubMed

De Panfilis, S; Pogna, E A A; Virga, A; Scopigno, T

2014-07-21

Acoustics dynamics of the molecular glass-former indomethacin (IMC) have been investigated by Brillouin light scattering (BLS) at GHz frequencies. Elastic response of the system has been tracked from the melting temperature down to the glass transition through the supercooled liquid. Both the structural arrest and the vibrational dynamics are described by modeling the experimentally determined dynamic structure factor within the framework of the Langevin equation, through a simplified choice of memory function which allows one to determine sound velocity and the acoustic attenuation coefficient as a function of temperature. The density fluctuation spectra in the glassy phase, as probed by BLS, are compared with time-domain results from photoacoustics experiments. The arising scenario is discussed in the context of current literature reporting inelastic X-ray scattering and BLS in platelet geometry. The link between the probed elastic properties and the non-ergodicity factor of the glass phase is finally scrutinized.

Lattice dynamical and dielectric properties of L-amino acids

NASA Astrophysics Data System (ADS)

Tulip, P. R.; Clark, S. J.

2006-08-01

We present the results of ab initio calculations of the lattice dynamical and dielectric properties of the L-amino acids L-alanine, L-leucine, and L-isoleucine. Normal-mode frequencies and dielectric permittivity tensors are obtained using density-functional perturbation theory implemented within the plane-wave pseudopotential approximation. IR spectra are calculated and are used to analyze the effects of intermolecular interactions and zwitterionization upon the lattice dynamics. It is found that vibronic modes associated with the carboxy and amino functional groups undergo modification from their free-molecule values due to the presence of hydrogen bonds. The role of macroscopic electric fields set up by zone-center normal modes in the lattice dynamics is investigated by analysis of the Born effective charge. Calculated permittivity tensors are found to be greater than would be obtained by a naive use of the isolated molecular values, indicating the role of intermolecular interactions in increasing molecular polarizability.

Phonon Softening due to Melting of the Ferromagnetic Order in Elemental Iron

NASA Astrophysics Data System (ADS)

Han, Qiang; Birol, Turan; Haule, Kristjan

2018-05-01

We study the fundamental question of the lattice dynamics of a metallic ferromagnet in the regime where the static long-range magnetic order is replaced by the fluctuating local moments embedded in a metallic host. We use the ab initio density functional theory + embedded dynamical mean-field theory functional approach to address the dynamic stability of iron polymorphs and the phonon softening with an increased temperature. We show that the nonharmonic and inhomogeneous phonon softening measured in iron is a result of the melting of the long-range ferromagnetic order and is unrelated to the first-order structural transition from the bcc to the fcc phase, as is usually assumed. We predict that the bcc structure is dynamically stable at all temperatures at normal pressure and is thermodynamically unstable only between the bcc-α and the bcc-δ phases of iron.

Thermodynamics of RNA structures by Wang–Landau sampling

PubMed Central

Lou, Feng; Clote, Peter

2010-01-01

Motivation: Thermodynamics-based dynamic programming RNA secondary structure algorithms have been of immense importance in molecular biology, where applications range from the detection of novel selenoproteins using expressed sequence tag (EST) data, to the determination of microRNA genes and their targets. Dynamic programming algorithms have been developed to compute the minimum free energy secondary structure and partition function of a given RNA sequence, the minimum free-energy and partition function for the hybridization of two RNA molecules, etc. However, the applicability of dynamic programming methods depends on disallowing certain types of interactions (pseudoknots, zig-zags, etc.), as their inclusion renders structure prediction an nondeterministic polynomial time (NP)-complete problem. Nevertheless, such interactions have been observed in X-ray structures. Results: A non-Boltzmannian Monte Carlo algorithm was designed by Wang and Landau to estimate the density of states for complex systems, such as the Ising model, that exhibit a phase transition. In this article, we apply the Wang-Landau (WL) method to compute the density of states for secondary structures of a given RNA sequence, and for hybridizations of two RNA sequences. Our method is shown to be much faster than existent software, such as RNAsubopt. From density of states, we compute the partition function over all secondary structures and over all pseudoknot-free hybridizations. The advantage of the WL method is that by adding a function to evaluate the free energy of arbitary pseudoknotted structures and of arbitrary hybridizations, we can estimate thermodynamic parameters for situations known to be NP-complete. This extension to pseudoknots will be made in the sequel to this article; in contrast, the current article describes the WL algorithm applied to pseudoknot-free secondary structures and hybridizations. Availability: The WL RNA hybridization web server is under construction at http://bioinformatics.bc.edu/clotelab/. Contact: clote@bc.edu PMID:20529917

Molecular dynamics simulation of the ionic liquid N-octylpyridinium tetrafluoroborate and acetonitrile: Thermodynamic and structural properties

NASA Astrophysics Data System (ADS)

Zhou, Siwen; Zhu, Guanglai; Kang, Xianqu; Li, Qiang; Sha, Maolin; Cui, Zhifeng; Xu, Xinsheng

2018-06-01

Using molecular dynamics simulation, the research obtained the thermodynamic properties and microstructures of the mixture of N-octylpyridinium tetrafluoroborate and acetonitrile, including density, self-diffusion coefficients, excess properties, radial distribution functions (RDFs) and spatial distribution functions (SDFs). Both RDFs and SDFs indicate that the local microstructure of the polar region is different from the nonpolar region with different mole fraction of ionic liquids. Acetonitrile could increase the order of the polar regions. While with acetonitrile increasing, the orderliness of the nonpolar region increases firstly and then decreases. In relatively dilute solution, ionic liquids were dispersed to form small aggregates wrapped by acetonitrile.

Nonlinear dynamics of the cellular-automaton ``game of Life''

NASA Astrophysics Data System (ADS)

Garcia, J. B. C.; Gomes, M. A. F.; Jyh, T. I.; Ren, T. I.; Sales, T. R. M.

1993-11-01

A statistical analysis of the ``game of Life'' due to Conway [Berlekamp, Conway, and Guy, Winning Ways for Your Mathematical Plays (Academic, New York, 1982), Vol. 2] is reported. The results are based on extensive computer simulations starting with uncorrelated distributions of live sites at t=0. The number n(s,t) of clusters of s live sites at time t, the mean cluster size s¯(t), and the diversity of sizes among other statistical functions are obtained. The dependence of the statistical functions with the initial density of live sites is examined. Several scaling relations as well as static and dynamic critical exponents are found.

A regional-scale, high resolution dynamical malaria model that accounts for population density, climate and surface hydrology.

PubMed

Tompkins, Adrian M; Ermert, Volker

2013-02-18

The relative roles of climate variability and population related effects in malaria transmission could be better understood if regional-scale dynamical malaria models could account for these factors. A new dynamical community malaria model is introduced that accounts for the temperature and rainfall influences on the parasite and vector life cycles which are finely resolved in order to correctly represent the delay between the rains and the malaria season. The rainfall drives a simple but physically based representation of the surface hydrology. The model accounts for the population density in the calculation of daily biting rates. Model simulations of entomological inoculation rate and circumsporozoite protein rate compare well to data from field studies from a wide range of locations in West Africa that encompass both seasonal endemic and epidemic fringe areas. A focus on Bobo-Dioulasso shows the ability of the model to represent the differences in transmission rates between rural and peri-urban areas in addition to the seasonality of malaria. Fine spatial resolution regional integrations for Eastern Africa reproduce the malaria atlas project (MAP) spatial distribution of the parasite ratio, and integrations for West and Eastern Africa show that the model grossly reproduces the reduction in parasite ratio as a function of population density observed in a large number of field surveys, although it underestimates malaria prevalence at high densities probably due to the neglect of population migration. A new dynamical community malaria model is publicly available that accounts for climate and population density to simulate malaria transmission on a regional scale. The model structure facilitates future development to incorporate migration, immunity and interventions.

A regional-scale, high resolution dynamical malaria model that accounts for population density, climate and surface hydrology

PubMed Central

2013-01-01

Background The relative roles of climate variability and population related effects in malaria transmission could be better understood if regional-scale dynamical malaria models could account for these factors. Methods A new dynamical community malaria model is introduced that accounts for the temperature and rainfall influences on the parasite and vector life cycles which are finely resolved in order to correctly represent the delay between the rains and the malaria season. The rainfall drives a simple but physically based representation of the surface hydrology. The model accounts for the population density in the calculation of daily biting rates. Results Model simulations of entomological inoculation rate and circumsporozoite protein rate compare well to data from field studies from a wide range of locations in West Africa that encompass both seasonal endemic and epidemic fringe areas. A focus on Bobo-Dioulasso shows the ability of the model to represent the differences in transmission rates between rural and peri-urban areas in addition to the seasonality of malaria. Fine spatial resolution regional integrations for Eastern Africa reproduce the malaria atlas project (MAP) spatial distribution of the parasite ratio, and integrations for West and Eastern Africa show that the model grossly reproduces the reduction in parasite ratio as a function of population density observed in a large number of field surveys, although it underestimates malaria prevalence at high densities probably due to the neglect of population migration. Conclusions A new dynamical community malaria model is publicly available that accounts for climate and population density to simulate malaria transmission on a regional scale. The model structure facilitates future development to incorporate migration, immunity and interventions. PMID:23419192

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.