Nonequilibrium Chromosome Looping via Molecular Slip Links

Science.gov (United States)

Brackley, C. A.; Johnson, J.; Michieletto, D.; Morozov, A. N.; Nicodemi, M.; Cook, P. R.; Marenduzzo, D.

2017-09-01

We propose a model for the formation of chromatin loops based on the diffusive sliding of molecular slip links. These mimic the behavior of molecules like cohesin, which, along with the CTCF protein, stabilize loops which contribute to organizing the genome. By combining 3D Brownian dynamics simulations and 1D exactly solvable nonequilibrium models, we show that diffusive sliding is sufficient to account for the strong bias in favor of convergent CTCF-mediated chromosome loops observed experimentally. We also find that the diffusive motion of multiple slip links along chromatin is rectified by an intriguing ratchet effect that arises if slip links bind to the chromatin at a preferred "loading site." This emergent collective behavior favors the extrusion of loops which are much larger than the ones formed by single slip links.

Site-discrimination by molecular imposters at dissymmetric molecular crystal surfaces

Science.gov (United States)

Poloni, Laura N.

The organization of atoms and molecules into crystalline forms is ubiquitous in nature and has been critical to the development of many technologies on which modern society relies. Classical crystal growth theory can describe atomic crystal growth, however, a description of molecular crystal growth is lacking. Molecular crystals are often characterized by anisotropic intermolecular interactions and dissymmetric crystal surfaces with anisotropic growth rates along different crystallographic directions. This thesis describes combination of experimental and computational techniques to relate crystal structure to surface structure and observed growth rates. Molecular imposters, also known as tailor-made impurities, can be used to control crystal growth for practical applications such as inhibition of pathological crystals, but can also be used to understand site specificity at crystal growth surfaces. The first part of this thesis builds on previous real-time in situ atomic force microscopy (AFM) observations of dislocation-actuated growth on the morphologically significant face of hexagonal L-cystine crystals, which aggregate in vivo to form kidney stones in patients suffering from cystinuria. The inhibitory effect of various L-cystine structural mimics (a.k.a. molecular imposters) was investigated through experimental and computational methods to identify the key structural factors responsible for molecular recognition between molecular imposters and L-cystine crystal surface sites. The investigation of L-cystine crystal growth in the presence of molecular imposters through a combination of kinetic analysis using in situ AFM, morphology analysis and birefringence measurements of bulk crystals, and molecular modeling of imposter binding to energetically inequivalent surface sites revealed that different molecular imposters inhibited crystal growth by a Cabrera-Vermilyea pinning mechanism and that imposters bind to a single binding site on the dissymmetric {1000} L

Conserving GW scheme for nonequilibrium quantum transport in molecular contacts

DEFF Research Database (Denmark)

Thygesen, Kristian Sommer; Rubio, Angel

2008-01-01

We give a detailed presentation of our recent scheme to include correlation effects in molecular transport calculations using the nonequilibrium Keldysh formalism. The scheme is general and can be used with any quasiparticle self-energy, but for practical reasons, we mainly specialize to the so......-called GW self-energy, widely used to describe the quasiparticle band structures and spectroscopic properties of extended and low-dimensional systems. We restrict the GW self-energy to a finite, central region containing the molecule, and we describe the leads by density functional theory (DFT). A minimal...

Dipole plasma in molecular crystals

International Nuclear Information System (INIS)

Kotel'nikov, Yu.E.; Kochelaev, B.I.

1976-01-01

Collective oscillations in a system of electric dipoles of molecular crystals are investigated. It has been proved in the exciton approximation that in an elementary cell of a molecular crystal with one molecule there may exist energy fluctuations of the ''dipole'' plasma, analogous to plasma oscillations in the charged Fermi liquid

Nonequilibrium molecular dynamics simulation of coupling between nanoparticles and base-fluid in a nanofluid

International Nuclear Information System (INIS)

Kang, Hongbo; Zhang, Yuwen; Yang, Mo; Li, Ling

2012-01-01

The intent of this study is to examine nonequilibrium heat transfer in a copper–argon nanofluid by molecular dynamics simulation. Two different methods, the physical definition method and the curve fitting method, are introduced to calculate the coupling factor between nanoparticles and base fluid. The results show that the coupling factors obtained by these two methods are consistent. The coupling factor is proportional to the volume fraction of the nanoparticle and inversely proportional to nanoparticle diameter. In the temperature range of 90–200 K, the coupling factor is not affected by temperature. The nanoparticle aggregation results in a decrease of the coupling factor. -- Highlights: ► Nonequilibrium heat transfer in a copper–argon nanofluid is investigated by molecular dynamics simulation. ► The coupling factor is proportion to the volume fraction of the nanoparticle and inverse proportion to nanoparticle diameter. ► In the temperature range of 90–200 K, there is no temperature effect on the coupling factor. ► The nanoparticle aggregation results in a decrease of the coupling factor.

A corrected NEGF + DFT approach for calculating electronic transport through molecular devices: Filling bound states and patching the non-equilibrium integration

International Nuclear Information System (INIS)

Li Rui; Zhang Jiaxing; Hou Shimin; Qian Zekan; Shen Ziyong; Zhao Xingyu; Xue Zengquan

2007-01-01

We discuss two problems in the conventional approach for studying charge transport in molecular electronic devices that is based on the non-equilibrium Green's function formalism and density functional theory, i.e., the bound states and the numerical integration of the non-equilibrium density matrix. A scheme of filling the bound states in the bias window and a method of patching the non-equilibrium integration are proposed, both of which are referred to as the non-equilibrium correction. The discussion is illustrated by means of calculations on a model system consisting of a 4,4 bipyridine molecule connected to two semi-infinite gold monatomic chains

Non-equilibrium dynamics from RPMD and CMD.

Science.gov (United States)

Welsch, Ralph; Song, Kai; Shi, Qiang; Althorpe, Stuart C; Miller, Thomas F

2016-11-28

We investigate the calculation of approximate non-equilibrium quantum time correlation functions (TCFs) using two popular path-integral-based molecular dynamics methods, ring-polymer molecular dynamics (RPMD) and centroid molecular dynamics (CMD). It is shown that for the cases of a sudden vertical excitation and an initial momentum impulse, both RPMD and CMD yield non-equilibrium TCFs for linear operators that are exact for high temperatures, in the t = 0 limit, and for harmonic potentials; the subset of these conditions that are preserved for non-equilibrium TCFs of non-linear operators is also discussed. Furthermore, it is shown that for these non-equilibrium initial conditions, both methods retain the connection to Matsubara dynamics that has previously been established for equilibrium initial conditions. Comparison of non-equilibrium TCFs from RPMD and CMD to Matsubara dynamics at short times reveals the orders in time to which the methods agree. Specifically, for the position-autocorrelation function associated with sudden vertical excitation, RPMD and CMD agree with Matsubara dynamics up to O(t 4 ) and O(t 1 ), respectively; for the position-autocorrelation function associated with an initial momentum impulse, RPMD and CMD agree with Matsubara dynamics up to O(t 5 ) and O(t 2 ), respectively. Numerical tests using model potentials for a wide range of non-equilibrium initial conditions show that RPMD and CMD yield non-equilibrium TCFs with an accuracy that is comparable to that for equilibrium TCFs. RPMD is also used to investigate excited-state proton transfer in a system-bath model, and it is compared to numerically exact calculations performed using a recently developed version of the Liouville space hierarchical equation of motion approach; again, similar accuracy is observed for non-equilibrium and equilibrium initial conditions.

Modeling of ultrafast THz interactions in molecular crystals

DEFF Research Database (Denmark)

Pedersen, Pernille Klarskov; Clark, Stewart J.; Jepsen, Peter Uhd

2014-01-01

In this paper we present a numerical study of terahertz pulses interacting with crystals of cesium iodide. We model the molecular dynamics of the cesium iodide crystals with the Density Functional Theory software CASTEP, where ultrafast terahertz pulses are implemented to the CASTEP software...... to interact with molecular crystals. We investigate the molecular dynamics of cesium iodide crystals when interacting with realistic terahertz pulses of field strengths from 0 to 50 MV/cm. We find nonlinearities in the response of the CsI crystals at field strengths higher than 10 MV/cm....

Molecular beam studies of energy transfer in scattering from crystal surfaces

International Nuclear Information System (INIS)

Guthrie, W.L.

1983-01-01

The translational energy distributions and angular distributions of D 2 O produced from the reaction of incident D 2 and O 2 on a (111) platinum single crystal surface have been measured through the use of a molecular beam-surface scattering apparatus equipped with a time-of-flight spectrometer. The translation energies were measured over the surface temperature range T/sub s/ = 664 K - 913 K and at scattering angles of 7 0 and 40 0 from the surface normal. The D 2 O translational energy, , was found to be approximately half the equilibrium value over the temperature range examined, with /2k varying from 280 K to 480 K. These results are discussed in terms of a non-equilibrium desorption model. The two-photon ionization spectrometer was built to investigate the internal rotational and vibrational energy distributions of NO scattered from Pt(111) surfaces. The rotational energy distributions were measured over the crystal temperature range of T/sub s/ = 400 K - 1200 K. The translational energy distributions and angular distributions were measured using the time-of-flight spectrometer over the crystal temperature range of 400 K - 110 K and for beam translational energies of 0.046 eV, 0.11 eV and 0.24 eV, so that complete energy exchange information for translation, rotation and vibration is available for this gas-surface system. Significant energy transfer was observed in all three modes

Temperature control in molecular dynamic simulations of non-equilibrium processes

International Nuclear Information System (INIS)

Toton, Dawid; Lorenz, Christian D; Rompotis, Nikolaos; Martsinovich, Natalia; Kantorovich, Lev

2010-01-01

Thermostats are often used in various condensed matter problems, e.g. when a biological molecule undergoes a transformation in a solution, a crystal surface is irradiated with energetic particles, a crack propagates in a solid upon applied stress, two surfaces slide with respect to each other, an excited local phonon dissipates its energy into a crystal bulk, and so on. In all of these problems, as well as in many others, there is an energy transfer between different local parts of the entire system kept at a constant temperature. Very often, when modelling such processes using molecular dynamics simulations, thermostatting is done using strictly equilibrium approaches serving to describe the NVT ensemble. In this paper we critically discuss the applicability of such approaches to non-equilibrium problems, including those mentioned above, and stress that the correct temperature control can only be achieved if the method is based on the generalized Langevin equation (GLE). Specifically, we emphasize that a meaningful compromise between computational efficiency and a physically appropriate implementation of the NVT thermostat can be achieved, at least for solid state and surface problems, if the so-called stochastic boundary conditions (SBC), recently derived from the GLE (Kantorovich and Rompotis 2008 Phys. Rev. B 78 094305), are used. For SBC, the Langevin thermostat is only applied to the outer part of the simulated fragment of the entire system which borders the surrounding environment (not considered explicitly) serving as a heat bath. This point is illustrated by comparing the performance of the SBC and some of the equilibrium thermostats in two problems: (i) irradiation of the Si(001) surface with an energetic CaF 2 molecule using an ab initio density functional theory based method, and (ii) the tribology of two amorphous SiO 2 surfaces coated with self-assembled monolayers of methyl-terminated hydrocarbon alkoxylsilane molecules using a classical atomistic

Shear Viscosity of Benzene, Toluene, and p-Xylene by Non-equilibrium Molecular Dynamics Simulations

International Nuclear Information System (INIS)

Lee, Song Hi

2004-01-01

Green and Kubo showed that the phenomenological coefficients describing many transport processes and time dependent phenomena in general could be written as integrals over a certain type of function called a time correlation function. The Green-Kubo formulas are the formal expressions for hydrodynamic field variables and some of the thermodynamic properties in terms of the microscopic variables of an N-particle system. The identification of microscopic expressions for macroscopic variables is made by a process of comparison of the conservation equations of hydrodynamics with the microscopic equations of change for conserved densities. The importance of these formulas is three-fold: they provide an obvious method for calculating transport coefficients using computer simulation, a convenient starting point for constructing analytic theories for non-equilibrium processes, and an essential information for designing non-equilibrium molecular dynamics (NEMD) algorithm.

Monolayer atomic crystal molecular superlattices

Science.gov (United States)

Wang, Chen; He, Qiyuan; Halim, Udayabagya; Liu, Yuanyue; Zhu, Enbo; Lin, Zhaoyang; Xiao, Hai; Duan, Xidong; Feng, Ziying; Cheng, Rui; Weiss, Nathan O.; Ye, Guojun; Huang, Yun-Chiao; Wu, Hao; Cheng, Hung-Chieh; Shakir, Imran; Liao, Lei; Chen, Xianhui; Goddard, William A., III; Huang, Yu; Duan, Xiangfeng

2018-03-01

Artificial superlattices, based on van der Waals heterostructures of two-dimensional atomic crystals such as graphene or molybdenum disulfide, offer technological opportunities beyond the reach of existing materials. Typical strategies for creating such artificial superlattices rely on arduous layer-by-layer exfoliation and restacking, with limited yield and reproducibility. The bottom-up approach of using chemical-vapour deposition produces high-quality heterostructures but becomes increasingly difficult for high-order superlattices. The intercalation of selected two-dimensional atomic crystals with alkali metal ions offers an alternative way to superlattice structures, but these usually have poor stability and seriously altered electronic properties. Here we report an electrochemical molecular intercalation approach to a new class of stable superlattices in which monolayer atomic crystals alternate with molecular layers. Using black phosphorus as a model system, we show that intercalation with cetyl-trimethylammonium bromide produces monolayer phosphorene molecular superlattices in which the interlayer distance is more than double that in black phosphorus, effectively isolating the phosphorene monolayers. Electrical transport studies of transistors fabricated from the monolayer phosphorene molecular superlattice show an on/off current ratio exceeding 107, along with excellent mobility and superior stability. We further show that several different two-dimensional atomic crystals, such as molybdenum disulfide and tungsten diselenide, can be intercalated with quaternary ammonium molecules of varying sizes and symmetries to produce a broad class of superlattices with tailored molecular structures, interlayer distances, phase compositions, electronic and optical properties. These studies define a versatile material platform for fundamental studies and potential technological applications.

Amorphous ices explained in terms of nonequilibrium phase transitions in supercooled water

Science.gov (United States)

Limmer, David; Chandler, David

2013-03-01

We analyze the phase diagram of supercooled water out-of-equilibrium using concepts from space-time thermodynamics and the dynamic facilitation theory of the glass transition, together with molecular dynamics simulations. We find that when water is driven out-of-equilibrium, it can exist in multiple amorphous states. In contrast, we find that when water is at equilibrium, it can exist in only one liquid state. The amorphous non-equilibrium states are solids, distinguished from the liquid by their lack of mobility, and distinguished from each other by their different densities and local structure. This finding explains the experimentally observed polyamorphism of water as a class of nonequilibrium phenomena involving glasses of different densities. While the amorphous solids can be long lived, they are thermodynamically unstable. When allowed to relax to equilibrium, they crystallize with pathways that pass first through liquid state configurations and then to ordered ice.

Consequences of Molecular-Scale Non-Equilibrium Activity on the Dynamics and Mechanics of Self-Assembled Actin-Based Structures and Materials

Science.gov (United States)

Marshall Mccall, Patrick

Living cells are hierarchically self-organized forms of active soft matter: molecules on the nanometer scale form functional structures and organelles on the micron scale, which then compose cells on the scale of 10s of microns. While the biological functions of intracellular organelles are defined by the composition and properties of the structures themselves, how those bulk properties emerge from the properties and interactions of individual molecules remains poorly understood. Actin, a globular protein which self-assembles into dynamic semi-flexible polymers, is the basic structural material of cells and the major component of many functional organelles. In this thesis, I have used purified actin as a model system to explore the interplay between molecular-scale dynamics and organelle-scale functionality, with particular focus on the role of molecular-scale non-equilibrium activity. One of the most canonical forms of molecular-scale non-equilibrium activity is that of mechanoenzymes, also called motor proteins. These proteins utilized the free energy liberated by hydrolysis of ATP to perform mechanical work, thereby introducing non-equilibrium "active" stresses on the molecular scale. Combining experiments with mathematical modeling, we demonstrate in this thesis that non-equilibrium motor activity is sufficient to drive self-organization and pattern formation of the multimeric actin-binding motor protein Myosin II on 1D reconstituted actomyosin bundles. Like myosin, actin is itself an ATPase. However, nono-equilibrium ATP hydrolysis on actin is known to regulate the stability and assembly kinetics of actin filaments rather than generate active stresses per se. At the level of single actin filaments, the inhomogeneous nucleotide composition generated along the filament length by hydrolysis directs binding of regulatory proteins like cofilin, which mediate filament disassembly and thereby accelerate actin filament turnover. The concequences of this non-equilibrium

Prediction of molecular crystal structures

International Nuclear Information System (INIS)

Beyer, Theresa

2001-01-01

The ab initio prediction of molecular crystal structures is a scientific challenge. Reliability of first-principle prediction calculations would show a fundamental understanding of crystallisation. Crystal structure prediction is also of considerable practical importance as different crystalline arrangements of the same molecule in the solid state (polymorphs)are likely to have different physical properties. A method of crystal structure prediction based on lattice energy minimisation has been developed in this work. The choice of the intermolecular potential and of the molecular model is crucial for the results of such studies and both of these criteria have been investigated. An empirical atom-atom repulsion-dispersion potential for carboxylic acids has been derived and applied in a crystal structure prediction study of formic, benzoic and the polymorphic system of tetrolic acid. As many experimental crystal structure determinations at different temperatures are available for the polymorphic system of paracetamol (acetaminophen), the influence of the variations of the molecular model on the crystal structure lattice energy minima, has also been studied. The general problem of prediction methods based on the assumption that the experimental thermodynamically stable polymorph corresponds to the global lattice energy minimum, is that more hypothetical low lattice energy structures are found within a few kJ mol -1 of the global minimum than are likely to be experimentally observed polymorphs. This is illustrated by the results for molecule I, 3-oxabicyclo(3.2.0)hepta-1,4-diene, studied for the first international blindtest for small organic crystal structures organised by the Cambridge Crystallographic Data Centre (CCDC) in May 1999. To reduce the number of predicted polymorphs, additional factors to thermodynamic criteria have to be considered. Therefore the elastic constants and vapour growth morphologies have been calculated for the lowest lattice energy

Prediction of molecular crystal structures

Energy Technology Data Exchange (ETDEWEB)

Beyer, Theresa

2001-07-01

The ab initio prediction of molecular crystal structures is a scientific challenge. Reliability of first-principle prediction calculations would show a fundamental understanding of crystallisation. Crystal structure prediction is also of considerable practical importance as different crystalline arrangements of the same molecule in the solid state (polymorphs)are likely to have different physical properties. A method of crystal structure prediction based on lattice energy minimisation has been developed in this work. The choice of the intermolecular potential and of the molecular model is crucial for the results of such studies and both of these criteria have been investigated. An empirical atom-atom repulsion-dispersion potential for carboxylic acids has been derived and applied in a crystal structure prediction study of formic, benzoic and the polymorphic system of tetrolic acid. As many experimental crystal structure determinations at different temperatures are available for the polymorphic system of paracetamol (acetaminophen), the influence of the variations of the molecular model on the crystal structure lattice energy minima, has also been studied. The general problem of prediction methods based on the assumption that the experimental thermodynamically stable polymorph corresponds to the global lattice energy minimum, is that more hypothetical low lattice energy structures are found within a few kJ mol{sup -1} of the global minimum than are likely to be experimentally observed polymorphs. This is illustrated by the results for molecule I, 3-oxabicyclo(3.2.0)hepta-1,4-diene, studied for the first international blindtest for small organic crystal structures organised by the Cambridge Crystallographic Data Centre (CCDC) in May 1999. To reduce the number of predicted polymorphs, additional factors to thermodynamic criteria have to be considered. Therefore the elastic constants and vapour growth morphologies have been calculated for the lowest lattice energy

Investigation of PEG crystallization in frozen PEG-sucrose-water solutions. I. Characterization of the nonequilibrium behavior during freeze-thawing.

Science.gov (United States)

Bhatnagar, Bakul S; Martin, Susan M; Teagarden, Dirk L; Shalaev, Evgenyi Y; Suryanarayanan, Raj

2010-06-01

Our objective was to characterize the nonequilibrium thermal behavior of frozen aqueous solutions containing PEG and sucrose. Aqueous solutions of (i) sucrose (10%, w/v) with different concentrations of PEG (1-20%, w/v), and (ii) PEG (10%, w/v) with different concentrations of sucrose (2-20%, w/v), were cooled to -70 degrees C at 5 degrees C/min and heated to 25 degrees C at 2 degrees C/min in a differential scanning calorimeter. Annealing was performed at temperatures ranging from -50 to -20 degrees C for 2 or 6 h. Similar experiments were also performed in the low-temperature stage of a powder X-ray diffractometer. A limited number of additional DSC experiments were performed wherein the samples were cooled to -100 degrees C. In unannealed systems with a fixed sucrose concentration (10%, w/v), the T'g decreased from -35 to -48 degrees C when PEG concentration was increased from 1% to 20% (w/v). On annealing at -25 degrees C, PEG crystallized. This was evident from the increase in T'g and the appearance of a secondary melting endotherm in the DSC. Low-temperature XRD provided direct evidence of PEG crystallization. Annealing at temperatures crystallization and a devitrification event was observed above the T'g. In unannealed systems with a fixed PEG concentration (10%, w/v), the T'g increased from -50 to -40 degrees C when sucrose concentration was increased from 5% to 50%, w/v. As the annealing time increased (at -25 degrees C), the T'g approached that of a sucrose-water system, reflecting progressive PEG crystallization. A second glass transition at approximately -65 degrees C was evident in unannealed systems [10%, w/v sucrose and 10 (or 20%), w/v PEG] cooled to -100 degrees C. Investigation of the nonequilibrium behavior of frozen PEG-sucrose-water ternary system revealed phase separation in the freeze-concentrate. Annealing facilitated PEG crystallization. (c) 2010 Wiley-Liss, Inc. and the American Pharmacists Association

Molecular-dynamics study of propane-hydrate dissociation: Fluctuation-dissipation and non-equilibrium analysis.

Science.gov (United States)

Ghaani, Mohammad Reza; English, Niall J

2018-03-21

Equilibrium and non-equilibrium molecular-dynamics (MD) simulations have been performed to investigate thermal-driven break-up of planar propane-hydrate interfaces in contact with liquid water over the 260-320 K range. Two types of hydrate-surface water-lattice molecular termination were adopted, at the hydrate edge with water, for comparison: a 001-direct surface cleavage and one with completed cages. Statistically significant differences in melting temperatures and initial break-up rates were observed between both interface types. Dissociation rates were observed to be strongly dependent on temperature, with higher rates at larger over-temperatures vis-à-vis melting. A simple coupled mass and heat transfer model, developed previously, was applied to fit the observed dissociation profiles, and this helps us to identify clearly two distinct hydrate-decomposition régimes; following a highly temperature-dependent break-up phase, a second well-defined stage is essentially independent of temperature, in which the remaining nanoscale, de facto two-dimensional system's lattice framework is intrinsically unstable. Further equilibrium MD-analysis of the two-phase systems at their melting point, with consideration of the relaxation times gleaned from the auto-correlation functions of fluctuations in a number of enclathrated guest molecules, led to statistically significant differences between the two surface-termination cases; a consistent correlation emerged in both cases between the underlying, non-equilibrium, thermal-driven dissociation rates sampled directly from melting with that from an equilibrium-MD fluctuation-dissipation approach.

Communication: Influence of external static and alternating electric fields on water from long-time non-equilibrium ab initio molecular dynamics

Science.gov (United States)

Futera, Zdenek; English, Niall J.

2017-07-01

The response of water to externally applied electric fields is of central relevance in the modern world, where many extraneous electric fields are ubiquitous. Historically, the application of external fields in non-equilibrium molecular dynamics has been restricted, by and large, to relatively inexpensive, more or less sophisticated, empirical models. Here, we report long-time non-equilibrium ab initio molecular dynamics in both static and oscillating (time-dependent) external electric fields, therefore opening up a new vista in rigorous studies of electric-field effects on dynamical systems with the full arsenal of electronic-structure methods. In so doing, we apply this to liquid water with state-of-the-art non-local treatment of dispersion, and we compute a range of field effects on structural and dynamical properties, such as diffusivities and hydrogen-bond kinetics.

PREFACE: International Symposium on Non-Equilibrium Soft Matter 2010 International Symposium on Non-Equilibrium Soft Matter 2010

Science.gov (United States)

Kawakatsu, T.; Matsuyama, A.; Ohta, T.; Tanaka, H.; Tanaka, S.

2011-07-01

Soft matter is a rapidly growing interdisciplinary research field covering a range of subject areas including physics, chemistry, biology, mathematics and engineering. Some of the important universal features of these materials are their mesoscopic structures and their dynamics. Due to the existence of such large-scale structures, which nevertheless exhibit interactions of the order of the thermal energy, soft matter can readily be taken out of equilibrium by imposing a weak external field such as an electric field, a mechanical stress or a shear flow. The importance of the coexistence of microscopic molecular dynamics and the mesoscopic/macroscopic structures and flows requires us to develop hierarchical approaches to understand the nonlinear and nonequilibrium phenomena, which is one of the central issues of current soft matter research. This special section presents selected contributions from the 'International Symposium on Non-Equilibrium Soft Matter 2010' held from 17-20 August 2010 in Nara, Japan, which aimed to describe recent advances in soft matter research focusing especially on its nonequilibrium aspects. The topics discussed cover statics and dynamics of a wide variety of materials ranging from traditional soft matter like polymers, gels, emulsions, liquid crystals and colloids to biomaterials such as biopolymers and biomembranes. Among these studies, we highlighted the physics of biomembranes and vesicles, which has attracted great attention during the last decade; we organized a special session for this active field. The work presented in this issue deals with (1) structure formation in biomembranes and vesicles, (2) rheology of polymers and gels, (3) mesophases in block copolymers, (4) mesoscopic structures in liquid crystals and ionic liquids, and (5) nonequilibrium dynamics. This symposium was organized as part of a research project supported by the Grant-in-Aid for the priority area 'Soft Matter Physics' (2006-2010) from the Ministry of Education

Slow neutron scattering in molecular crystals. 5-4

International Nuclear Information System (INIS)

Inoue, Kazuhiko

1976-01-01

The utilization of incoherent inelastic neutron scattering (INS) as a probe for molecular crystals is reviewed. In particular, some typical examples of the measurement of incoherent inelastic neutron scattering spectra (INSS) in molecular crystals are presented in the first section of this report. The results of measurement are shown for theta-xylene, benzene, polypropylene oxide, deuteride, and formic acid. The second section presents an equation for the incoherent scattering cross section of a crystal by dividing the molecular motion into the outer and inner modes. Phonon expansion is also used for the easy understanding of the relation between the INSS and the dynamic characteristics of molecular crystals. In the third section, the measured results are analyzed on the basis of the theory presented in the previous section. And the difference between the van der Waals bond and the hydrogen bond is shortly discussed. (Aoki, K.)

Non-equilibrium responses of PFPE lubricants with various atomistic/molecular architecture at elevated temperature

Science.gov (United States)

Chung, Pil Seung; Song, Wonyup; Biegler, Lorenz T.; Jhon, Myung S.

2017-05-01

During the operation of hard disk drive (HDD), the perfluoropolyether (PFPE) lubricant experiences elastic or viscous shear/elongation deformations, which affect the performance and reliability of the HDD. Therefore, the viscoelastic responses of PFPE could provide a finger print analysis in designing optimal molecular architecture of lubricants to control the tribological phenomena. In this paper, we examine the rheological responses of PFPEs including storage (elastic) and loss (viscous) moduli (G' and G″) by monitoring the time-dependent-stress-strain relationship via non-equilibrium molecular dynamics simulations. We analyzed the rheological responses by using Cox-Merz rule, and investigated the molecular structural and thermal effects on the solid-like and liquid-like behaviors of PFPEs. The temperature dependence of the endgroup agglomeration phenomena was examined, where the functional endgroups are decoupled as the temperature increases. By analyzing the relaxation processes, the molecular rheological studies will provide the optimal lubricant selection criteria to enhance the HDD performance and reliability for the heat-assisted magnetic recording applications.

Non-equilibrium responses of PFPE lubricants with various atomistic/molecular architecture at elevated temperature

Directory of Open Access Journals (Sweden)

Pil Seung Chung

2017-05-01

Full Text Available During the operation of hard disk drive (HDD, the perfluoropolyether (PFPE lubricant experiences elastic or viscous shear/elongation deformations, which affect the performance and reliability of the HDD. Therefore, the viscoelastic responses of PFPE could provide a finger print analysis in designing optimal molecular architecture of lubricants to control the tribological phenomena. In this paper, we examine the rheological responses of PFPEs including storage (elastic and loss (viscous moduli (G′ and G″ by monitoring the time-dependent-stress-strain relationship via non-equilibrium molecular dynamics simulations. We analyzed the rheological responses by using Cox-Merz rule, and investigated the molecular structural and thermal effects on the solid-like and liquid-like behaviors of PFPEs. The temperature dependence of the endgroup agglomeration phenomena was examined, where the functional endgroups are decoupled as the temperature increases. By analyzing the relaxation processes, the molecular rheological studies will provide the optimal lubricant selection criteria to enhance the HDD performance and reliability for the heat-assisted magnetic recording applications.

Hole Mobility of Molecular β-Copper Phthalocyanine Crystal

International Nuclear Information System (INIS)

Pengmanayol, S.; Osotchan, T.; Suewattana, M.; Ingadapa, N.; Girdpun, J.

2011-01-01

A Monte Carlo approach is used to estimate hole mobilities in molecular β-copper phthalocyanine (CuPc) crystal for different applied electric field directions. Due to the crystal symmetry, the twelve neighboring molecules in the three-dimensional crystal are selected in the hopping rate calculation. Density functional theory is employed to derive the molecular interaction between the central and neighboring molecules for various applied electric fields. The derived molecular hopping rate is applied to 80 × 80 × 80 lattice sites under periodic boundary conditions. In order to achieve accurate statistics, each calculation includes 6561 particles with more than 10000 hopping steps under an applied electric field of 0.5–3.5 MV/cm. The results indicate that the molecular hopping strongly depends on the molecular orientation and neighboring sites related to the applied electric field direction. The estimated carrier mobility can be described by the percentage occupation in each neighboring site and the obtained hole mobility value is in the same range of the measured values of single crystal CuPc. The calculated mobility for applied electric field along the c crystal axis exhibits the highest values while the mobility along the b axis has the smallest value. (condensed matter: structure, mechanical and thermal properties)

Optical spectra and lattice dynamics of molecular crystals

CERN Document Server

Zhizhin, GN

1995-01-01

The current volume is a single topic volume on the optical spectra and lattice dynamics of molecular crystals. The book is divided into two parts. Part I covers both the theoretical and experimental investigations of organic crystals. Part II deals with the investigation of the structure, phase transitions and reorientational motion of molecules in organic crystals. In addition appendices are given which provide the parameters for the calculation of the lattice dynamics of molecular crystals, procedures for the calculation of frequency eigenvectors of utilizing computers, and the frequencies and eigenvectors of lattice modes for several organic crystals. Quite a large amount of Russian literature is cited, some of which has previously not been available to scientists in the West.

Molecular mechanisms of crystal growth

International Nuclear Information System (INIS)

Pina, C. M.

2000-01-01

In this paper I present an example of the research that the Mineral Surface Group of the Munster University is conducting in the field of Crystal Growth. Atomic Force Microscopy (Am) in situ observations of different barite (BaSO4) faces growing from aqueous solutions, in combination with computer simulations of the surface attachment of growth units allows us to test crystal growth models. Our results demonstrate the strong structural control that a crystal can exert on its own growth, revealing also the limitation of the classical crystal growth theories (two dimensional nucleation and spiral growth models) in providing a complete explanation for the growth behaviour at a molecular scale. (Author) 6 refs

Reverse Non-Equilibrium Molecular Dynamics Demonstrate That Surface Passivation Controls Thermal Transport at Semiconductor-Solvent Interfaces.

Science.gov (United States)

Hannah, Daniel C; Gezelter, J Daniel; Schaller, Richard D; Schatz, George C

2015-06-23

We examine the role played by surface structure and passivation in thermal transport at semiconductor/organic interfaces. Such interfaces dominate thermal transport in semiconductor nanomaterials owing to material dimensions much smaller than the bulk phonon mean free path. Utilizing reverse nonequilibrium molecular dynamics simulations, we calculate the interfacial thermal conductance (G) between a hexane solvent and chemically passivated wurtzite CdSe surfaces. In particular, we examine the dependence of G on the CdSe slab thickness, the particular exposed crystal facet, and the extent of surface passivation. Our results indicate a nonmonotonic dependence of G on ligand-grafting density, with interfaces generally exhibiting higher thermal conductance for increasing surface coverage up to ∼0.08 ligands/Å(2) (75-100% of a monolayer, depending on the particular exposed facet) and decreasing for still higher coverages. By analyzing orientational ordering and solvent penetration into the ligand layer, we show that a balance of competing effects is responsible for this nonmonotonic dependence. Although the various unpassivated CdSe surfaces exhibit similar G values, the crystal structure of an exposed facet nevertheless plays an important role in determining the interfacial thermal conductance of passivated surfaces, as the density of binding sites on a surface determines the ligand-grafting densities that may ultimately be achieved. We demonstrate that surface passivation can increase G relative to a bare surface by roughly 1 order of magnitude and that, for a given extent of passivation, thermal conductance can vary by up to a factor of ∼2 between different surfaces, suggesting that appropriately tailored nanostructures may direct heat flow in an anisotropic fashion for interface-limited thermal transport.

Non-equilibrium dynamics of open systems and fluctuation-dissipation theorems

Czech Academy of Sciences Publication Activity Database

Špička, Václav; Velický, B.; Kalvová, Anděla

2017-01-01

Roč. 65, 6-8 (2017), s. 1-23, č. článku 1700032. ISSN 0015-8208 Institutional support: RVO:68378271 Keywords : non-equilibrium * fluctuation-dissipation theorems * non-equilibrium Greens function * transient and steady state magnetic current * molecular bridge Subject RIV: BE - Theoretical Physics OBOR OECD: Atomic, molecular and chemical physics ( physics of atoms and molecules including collision, interaction with radiation, magnetic resonances, Mössbauer effect) Impact factor: 2.434, year: 2016

Nonequilibrium Molecular Energy Coupling and Conversion Mechanisms

Science.gov (United States)

2016-08-28

resolved temperature measurements, by pure rotational picosecond broadband Coherent Anti-Stokes Raman Spectroscopy ( CARS ), and kinetic modeling...rotational ps CARS for thermometry measurements in highly transient nonequilibrium plasmas. Rotational-translational temperatures are measured for time...primarily on localized flow heating on sub-acoustic time scale, and for assessing feasibility of high-speed aerodynamic flow control by vibrational

Adiabatic Hamiltonian deformation, linear response theory, and nonequilibrium molecular dynamics

International Nuclear Information System (INIS)

Hoover, W.G.

1980-01-01

Although Hamiltonians of various kinds have previously been used to derive Green-Kubo relations for the transport coefficients, the particular choice described is uniquely related to thermodynamics. This nonequilibrium Hamiltonian formulation of fluid flow provides pedagogically simple routes to nonequilibrium fluxes and distribution functions, to theoretical understanding of long-time effects, and to new numerical methods for simulating systems far from equilibrium. The same methods are now being applied to solid-phase problems. At the relatively high frequencies used in the viscous fluid calculations described, solids typically behave elastically. Lower frequencies lead to the formation of dislocations and other defects, making it possible to study plastic flow. A property of the nonequilibrium equations of motion which might be profitably explored is their effective irreversibility. Because only a few particles are necessary to generate irreversible behavior, simulations using adiabatic deformations of the kind described here could perhaps elucidate the instability in the equations of motion responsible for irreversibility

Transient magnetic currents through a molecular bridge: limits to reduction of non-equilibrium Green's functions to a generalized master equation

Czech Academy of Sciences Publication Activity Database

Kalvová, Anděla; Velický, B.; Špička, Václav

2017-01-01

Roč. 30, č. 3 (2017), s. 807-811 ISSN 1557-1939 Institutional support: RVO:68378271 Keywords : non-equilibrium * initial conditions * transient currents * molecular islands Subject RIV: BM - Solid Matter Physics ; Magnetism OBOR OECD: Condensed matter physics (including formerly solid state physics, supercond.) Impact factor: 1.180, year: 2016

Control of liquid crystal molecular orientation using ultrasound vibration

Energy Technology Data Exchange (ETDEWEB)

Taniguchi, Satoki [Faculty of Life and Medical Sciences, Doshisha University, 1-3 Tataramiyakodani, Kyotanabe, Kyoto 610-0321 (Japan); Wave Electronics Research Center, Doshisha University, 1-3 Tataramiyakodani, Kyotanabe, Kyoto 610-0321 (Japan); Koyama, Daisuke; Matsukawa, Mami [Wave Electronics Research Center, Doshisha University, 1-3 Tataramiyakodani, Kyotanabe, Kyoto 610-0321 (Japan); Faculty of Science and Engineering, Doshisha University, 1-3 Tataramiyakodani, Kyotanabe, Kyoto 610-0321 (Japan); Shimizu, Yuki; Emoto, Akira [Faculty of Science and Engineering, Doshisha University, 1-3 Tataramiyakodani, Kyotanabe, Kyoto 610-0321 (Japan); Nakamura, Kentaro [Precision and Intelligence Laboratory, Tokyo Institute of Technology, 4259-R2-26, Nagatsuta-cho, Midori-ku, Yokohama 226-8503 (Japan)

2016-03-07

We propose a technique to control the orientation of nematic liquid crystals using ultrasound and investigate the optical characteristics of the oriented samples. An ultrasonic liquid crystal cell with a thickness of 5–25 μm and two ultrasonic lead zirconate titanate transducers was fabricated. By exciting the ultrasonic transducers, the flexural vibration modes were generated on the cell. An acoustic radiation force to the liquid crystal layer was generated, changing the molecular orientation and thus the light transmission. By modulating the ultrasonic driving frequency and voltage, the spatial distribution of the molecular orientation of the liquid crystals could be controlled. The distribution of the transmitted light intensity depends on the thickness of the liquid crystal layer because the acoustic field in the liquid crystal layer is changed by the orientational film.

A computer-aided molecular design framework for crystallization solvent design

DEFF Research Database (Denmark)

Karunanithi, Arunprakash T.; Achenie, Luke E.K.; Gani, Rafiqul

2006-01-01

One of the key decisions in designing solution crystallization processes is the selection of solvents. In this paper, we present a computer-aided molecular design (CAMD) framework for the design and selection of solvents and/or anti-solvents for solution crystallization. The CAMD problem is formu......One of the key decisions in designing solution crystallization processes is the selection of solvents. In this paper, we present a computer-aided molecular design (CAMD) framework for the design and selection of solvents and/or anti-solvents for solution crystallization. The CAMD problem...... solvent molecules. Solvent design and selection for two types of solution crystallization processes namely cooling crystallization and drowning out crystallization are presented. In the first case study, the design of single compound solvent for crystallization of ibuprofen, which is an important...

Superradiance from crystals of molecular nanomagnets.

Science.gov (United States)

Chudnovsky, E M; Garanin, D A

2002-10-07

We show that crystals of molecular nanomagnets can exhibit giant magnetic relaxation due to the Dicke superradiance of electromagnetic waves. Rigorous theory is presented that combines superradiance with the Landau-Zener effect.

Molecular dynamics study of CO2 hydrate dissociation: Fluctuation-dissipation and non-equilibrium analysis.

Science.gov (United States)

English, Niall J; Clarke, Elaine T

2013-09-07

Equilibrium and non-equilibrium molecular dynamics (MD) simulations have been performed to investigate thermal-driven break-up of planar CO2 hydrate interfaces in liquid water at 300-320 K. Different guest compositions, at 85%, 95%, and 100% of maximum theoretical occupation, led to statistically-significant differences in the observed initial dissociation rates. The melting temperatures of each interface were estimated, and dissociation rates were observed to be strongly dependent on temperature, with higher dissociation rates at larger over-temperatures vis-à-vis melting. A simple coupled mass and heat transfer model developed previously was applied to fit the observed dissociation profiles, and this helps to identify clearly two distinct régimes of break-up; a second well-defined region is essentially independent of composition and temperature, in which the remaining nanoscale, de facto two-dimensional system's lattice framework is intrinsically unstable. From equilibrium MD of the two-phase systems at their melting point, the relaxation times of the auto-correlation functions of fluctuations in number of enclathrated guest molecules were used as a basis for comparison of the variation in the underlying, non-equilibrium, thermal-driven dissociation rates via Onsager's hypothesis, and statistically significant differences were found, confirming the value of a fluctuation-dissipation approach in this case.

Studies of the surface structures of molecular crystals and of adsorbed molecular monolayers on the (111) crystal faces of platinum and silver by low-energy electron diffraction

International Nuclear Information System (INIS)

Firment, L.E.

1977-01-01

The structures of molecular crystal surfaces were investigated for the first time by the use of low-energy electron diffraction (LEED). The experimental results from a variety of molecular crystals were examined and compared as a first step towards understanding the properties of these surfaces on a microscopic level. The method of sample preparation employed, vapor deposition onto metal single-crystal substrates at low temperatures in ultrahigh vacuum, allowed concurrent study of the structures of adsorbed monolayers on metal surfaces and of the growth processes of molecular films on metal substrates. The systems investigated were ice, ammonia, naphthalene, benzene, the n-paraffins (C 3 to C 8 ), cyclohexane, trioxane, acetic acid, propionic acid, methanol, and methylamine adsorbed and condensed on both Pt(111) and Ag(111) surfaces. Electron-beam-induced damage of the molecular surfaces was observed after electron exposures of 10 -4 A sec cm -2 at 20 eV. Aromatic molecular crystal samples were more resistant to damage than samples of saturated molecules. The quality and orientation of the grown molecular crystal films were influenced by substrate preparation and growth conditions. Forty ordered monolayer structures were observed. 110 figures, 22 tables, 162 references

Nonideal plasmas as non-equilibrium media

International Nuclear Information System (INIS)

Morozov, I V; Norman, G E; Valuev, A A; Valuev, I A

2003-01-01

Various aspects of the collective behaviour of non-equilibrium nonideal plasmas are studied. The relaxation of kinetic energy to the equilibrium state is simulated by the molecular dynamics (MD) method for two-component non-degenerate strongly non-equilibrium plasmas. The initial non-exponential stage, its duration and the subsequent exponential stage of the relaxation process are studied for a wide range of ion charge, nonideality parameter and ion mass. A simulation model of the nonideal plasma excited by an electron beam is proposed. An approach is developed to calculate the dynamic structure factor in non-stationary conditions. Instability increment is obtained from MD simulations

Equilibrium sampling by reweighting nonequilibrium simulation trajectories.

Science.gov (United States)

Yang, Cheng; Wan, Biao; Xu, Shun; Wang, Yanting; Zhou, Xin

2016-03-01

Based on equilibrium molecular simulations, it is usually difficult to efficiently visit the whole conformational space of complex systems, which are separated into some metastable regions by high free energy barriers. Nonequilibrium simulations could enhance transitions among these metastable regions and then be applied to sample equilibrium distributions in complex systems, since the associated nonequilibrium effects can be removed by employing the Jarzynski equality (JE). Here we present such a systematical method, named reweighted nonequilibrium ensemble dynamics (RNED), to efficiently sample equilibrium conformations. The RNED is a combination of the JE and our previous reweighted ensemble dynamics (RED) method. The original JE reproduces equilibrium from lots of nonequilibrium trajectories but requires that the initial distribution of these trajectories is equilibrium. The RED reweights many equilibrium trajectories from an arbitrary initial distribution to get the equilibrium distribution, whereas the RNED has both advantages of the two methods, reproducing equilibrium from lots of nonequilibrium simulation trajectories with an arbitrary initial conformational distribution. We illustrated the application of the RNED in a toy model and in a Lennard-Jones fluid to detect its liquid-solid phase coexistence. The results indicate that the RNED sufficiently extends the application of both the original JE and the RED in equilibrium sampling of complex systems.

Non-Equilibrium Solidification of Undercooled Metallic Melts

Directory of Open Access Journals (Sweden)

Dieter M. Herlach

2014-06-01

Full Text Available If a liquid is undercooled below its equilibrium melting temperature an excess Gibbs free energy is created. This gives access to solidification of metastable solids under non-equilibrium conditions. In the present work, techniques of containerless processing are applied. Electromagnetic and electrostatic levitation enable to freely suspend a liquid drop of a few millimeters in diameter. Heterogeneous nucleation on container walls is completely avoided leading to large undercoolings. The freely suspended drop is accessible for direct observation of rapid solidification under conditions far away from equilibrium by applying proper diagnostic means. Nucleation of metastable crystalline phases is monitored by X-ray diffraction using synchrotron radiation during non-equilibrium solidification. While nucleation preselects the crystallographic phase, subsequent crystal growth controls the microstructure evolution. Metastable microstructures are obtained from deeply undercooled melts as supersaturated solid solutions, disordered superlattice structures of intermetallics. Nucleation and crystal growth take place by heat and mass transport. Comparative experiments in reduced gravity allow for investigations on how forced convection can be used to alter the transport processes and design materials by using undercooling and convection as process parameters.

Generalized Langevin equation: An efficient approach to nonequilibrium molecular dynamics of open systems

Science.gov (United States)

Stella, L.; Lorenz, C. D.; Kantorovich, L.

2014-04-01

The generalized Langevin equation (GLE) has been recently suggested to simulate the time evolution of classical solid and molecular systems when considering general nonequilibrium processes. In this approach, a part of the whole system (an open system), which interacts and exchanges energy with its dissipative environment, is studied. Because the GLE is derived by projecting out exactly the harmonic environment, the coupling to it is realistic, while the equations of motion are non-Markovian. Although the GLE formalism has already found promising applications, e.g., in nanotribology and as a powerful thermostat for equilibration in classical molecular dynamics simulations, efficient algorithms to solve the GLE for realistic memory kernels are highly nontrivial, especially if the memory kernels decay nonexponentially. This is due to the fact that one has to generate a colored noise and take account of the memory effects in a consistent manner. In this paper, we present a simple, yet efficient, algorithm for solving the GLE for practical memory kernels and we demonstrate its capability for the exactly solvable case of a harmonic oscillator coupled to a Debye bath.

Uncovering molecular processes in crystal nucleation and growth by using molecular simulation.

Science.gov (United States)

Anwar, Jamshed; Zahn, Dirk

2011-02-25

Exploring nucleation processes by molecular simulation provides a mechanistic understanding at the atomic level and also enables kinetic and thermodynamic quantities to be estimated. However, whilst the potential for modeling crystal nucleation and growth processes is immense, there are specific technical challenges to modeling. In general, rare events, such as nucleation cannot be simulated using a direct "brute force" molecular dynamics approach. The limited time and length scales that are accessible by conventional molecular dynamics simulations have inspired a number of advances to tackle problems that were considered outside the scope of molecular simulation. While general insights and features could be explored from efficient generic models, new methods paved the way to realistic crystal nucleation scenarios. The association of single ions in solvent environments, the mechanisms of motif formation, ripening reactions, and the self-organization of nanocrystals can now be investigated at the molecular level. The analysis of interactions with growth-controlling additives gives a new understanding of functionalized nanocrystals and the precipitation of composite materials. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Beyond the second law entropy production and non-equilibrium systems

CERN Document Server

Lineweaver, Charles; Niven, Robert; Regenauer-Lieb, Klaus

2014-01-01

The Second Law, a cornerstone of thermodynamics, governs the average direction of dissipative, non-equilibrium processes. But it says nothing about their actual rates or the probability of fluctuations about the average. This interdisciplinary book, written and peer-reviewed by international experts, presents recent advances in the search for new non-equilibrium principles beyond the Second Law, and their applications to a wide range of systems across physics, chemistry and biology. Beyond The Second Law brings together traditionally isolated areas of non-equilibrium research and highlights potentially fruitful connections between them, with entropy production playing the unifying role. Key theoretical concepts include the Maximum Entropy Production principle, the Fluctuation Theorem, and the Maximum Entropy method of statistical inference. Applications of these principles are illustrated in such diverse fields as climatology, cosmology, crystal growth morphology, Earth system science, environmental physics, ...

Theory of piezoelectricity, electrostriction, and pyroelectricity in molecular crystals.

Science.gov (United States)

Munn, R W

2010-03-14

A microscopic theory is presented for piezoelectricity, electrostriction, and pyroelectricity in molecular crystals. The required coefficients are derived by combining a theoretical treatment of the dependence of molecular dipole moments on molecular displacement and a generalized elastic theory for internal strain.

Electrical properties of molecular crystals; Proprietes electriques des cristaux moleculaires

Energy Technology Data Exchange (ETDEWEB)

Barraud, A [Commissariat a l' Energie Atomique, Saclay (France). Centre d' Etudes Nucleaires

1968-07-01

This literature survey summarizes the electrical properties of molecular crystals: molecular crystal structure, transport and excitation mechanisms of charge-carriers, and differences compared to inorganic semi-conductors. The main results concerning the electrical conductivity of the most-studied molecular crystals are presented, together with the optical and photo-electrical properties of these crystals. Finally the different types of electrical measurements used are reviewed, as well as the limits of each method. (author) [French] Cette etude bibliographique resume les proprietes electriques des cristaux moleculaires: structure des cristaux moleculaires, mecanismes de transport et d'excitation des porteurs de charge et differences avec les semiconducteurs mineraux. Les principaux resultats sur la conductibilite electrique des cristaux moleculaires les plus etudies y sont exposes, ainsi que les proprietes optiques et photoelectriques de ces cristaux. Enfin les differents types de mesures electriques utilisees sont passees en revue ainsi que les limites de chaque methode. (auteur)

Electrical properties of molecular crystals; Proprietes electriques des cristaux moleculaires

Energy Technology Data Exchange (ETDEWEB)

Barraud, A. [Commissariat a l' Energie Atomique, Saclay (France). Centre d' Etudes Nucleaires

1968-07-01

This literature survey summarizes the electrical properties of molecular crystals: molecular crystal structure, transport and excitation mechanisms of charge-carriers, and differences compared to inorganic semi-conductors. The main results concerning the electrical conductivity of the most-studied molecular crystals are presented, together with the optical and photo-electrical properties of these crystals. Finally the different types of electrical measurements used are reviewed, as well as the limits of each method. (author) [French] Cette etude bibliographique resume les proprietes electriques des cristaux moleculaires: structure des cristaux moleculaires, mecanismes de transport et d'excitation des porteurs de charge et differences avec les semiconducteurs mineraux. Les principaux resultats sur la conductibilite electrique des cristaux moleculaires les plus etudies y sont exposes, ainsi que les proprietes optiques et photoelectriques de ces cristaux. Enfin les differents types de mesures electriques utilisees sont passees en revue ainsi que les limites de chaque methode. (auteur)

Molecular-Based Optical Diagnostics for Hypersonic Nonequilibrium Flows

Science.gov (United States)

Danehy, Paul; Bathel, Brett; Johansen, Craig; Winter, Michael; O'Byrne, Sean; Cutler, Andrew

2015-01-01

This presentation package consists of seven different talks rolled up into one. These talks are all invited orals presentations in a special session at the Aviation 2015 conference and represent contributions that were made to a recent AIAA book that will be published entitled 'Hypersonic Nonequilibrium Flows: Fundamentals and Recent Advances'. Slide 5 lists the individual presentations that will be given during the special session.

Plasticity induced phase transformation in molecular crystals

OpenAIRE

Koslowski, Marisol

2014-01-01

Solid state amorphization (SSA) can be achieved in crystalline materials including metal alloys, intermetallics, semiconductors, minerals and molecular crystals. Even though the mechanisms may differ in different materials, the crystalline to amorphous transformation occurs when the crystal reaches a metastable state in which its free energy is higher than that of the amorphous phase. SSA is observed in metal alloys because of interdiffusion of the crystalline elements during mechanical milli...

Nonlinear and Nonequilibrium Spin Injection in Magnetic Tunneling Junctions

Science.gov (United States)

Guo, Hong

2007-03-01

Quantitative analysis of charge and spin quantum transport in spintronic devices requires an atomistic first principles approach that can handle nonlinear and nonequilibrium transport conditions. We have developed an approach for this purpose based on real space density functional theory (DFT) carried out within the Keldysh nonequilibrium Green's function formalism (NEGF). We report theoretical analysis of nonlinear and nonequilibrium spin injection and quantum transport in Fe/MgO/Fe trilayer structures as a function of external bias voltage. Devices with well relaxed atomic structures and with FeO oxidization layers are investigated as a function of external bias voltage. We also report calculations of nonequilibrium spin injection into molecular layers and graphene. Comparisons to experimental data will be presented. Work in collaborations with: Derek Waldron, Vladimir Timochevski (McGill University); Ke Xia (Institute of Physics, Chinese Academy of Science, Beijing, China); Eric Zhu, Jian Wang (University of Hong Kong); Paul Haney, and Allan MacDonald (University of Texas at Austin).

Computer simulation of nonequilibrium processes

International Nuclear Information System (INIS)

Wallace, D.C.

1985-07-01

The underlying concepts of nonequilibrium statistical mechanics, and of irreversible thermodynamics, will be described. The question at hand is then, how are these concepts to be realize in computer simulations of many-particle systems. The answer will be given for dissipative deformation processes in solids, on three hierarchical levels: heterogeneous plastic flow, dislocation dynamics, an molecular dynamics. Aplication to the shock process will be discussed

NON-EQUILIBRIUM MOLECULAR DYNAMICS USED TO OBTAIN SORET COEFFICIENTS OF BINARY HYDROCARBON MIXTURES

Directory of Open Access Journals (Sweden)

F. A. Furtado

2015-09-01

Full Text Available AbstractThe Boundary Driven Non-Equilibrium Molecular Dynamics (BD-NEMD method is employed to evaluate Soret coefficients of binary mixtures. Using a n-decane/n-pentane mixture at 298 K, we study several parameters and conditions of the simulation procedure such as system size, time step size, frequency of perturbation, and the undesired warming up of the system during the simulation. The Soret coefficients obtained here deviated around 20% when comparing with experimental data and with simulated results from the literature. We showed that fluctuations in composition gradients and the consequent deviations of the Soret coefficient may be due to characteristic fluctuations of the composition gradient. Best results were obtained with the smallest time steps and without using a thermostat, which shows that there is room for improvement and/or development of new BD-NEMD algorithms.

Molecular morphology and crystallization in the quantum limit

DEFF Research Database (Denmark)

Bohr, Jakob

2002-01-01

The effects of phonons on crystallization and crystal morphology are investigated. It is shown that the commensuration of the lattice vibrations with the lattice will favor certain crystal morphologies. Vibrational effects can also be important for the molecular structure of chain molecules...... protein are estimated to differ by several electron volts. For a biomolecule, such energy is significant and may contribute to cold denaturing as seen for proteins. This is consistent with the empirical observation that cold denaturation is exothermic and hot denaturation endothermic....

The effect of non-equilibrium metal cooling on the interstellar medium

Science.gov (United States)

Capelo, Pedro R.; Bovino, Stefano; Lupi, Alessandro; Schleicher, Dominik R. G.; Grassi, Tommaso

2018-04-01

By using a novel interface between the modern smoothed particle hydrodynamics code GASOLINE2 and the chemistry package KROME, we follow the hydrodynamical and chemical evolution of an isolated galaxy. In order to assess the relevance of different physical parameters and prescriptions, we constructed a suite of 10 simulations, in which we vary the chemical network (primordial and metal species), how metal cooling is modelled (non-equilibrium versus equilibrium; optically thin versus thick approximation), the initial gas metallicity (from 10 to 100 per cent solar), and how molecular hydrogen forms on dust. This is the first work in which metal injection from supernovae, turbulent metal diffusion, and a metal network with non-equilibrium metal cooling are self-consistently included in a galaxy simulation. We find that properly modelling the chemical evolution of several metal species and the corresponding non-equilibrium metal cooling has important effects on the thermodynamics of the gas, the chemical abundances, and the appearance of the galaxy: the gas is typically warmer, has a larger molecular-gas mass fraction, and has a smoother disc. We also conclude that, at relatively high metallicity, the choice of molecular-hydrogen formation rates on dust is not crucial. Moreover, we confirm that a higher initial metallicity produces a colder gas and a larger fraction of molecular gas, with the low-metallicity simulation best matching the observed molecular Kennicutt-Schmidt relation. Finally, our simulations agree quite well with observations that link star formation rate to metal emission lines.

Ab initio molecular crystal structures, spectra, and phase diagrams.

Science.gov (United States)

Hirata, So; Gilliard, Kandis; He, Xiao; Li, Jinjin; Sode, Olaseni

2014-09-16

Conspectus Molecular crystals are chemists' solids in the sense that their structures and properties can be understood in terms of those of the constituent molecules merely perturbed by a crystalline environment. They form a large and important class of solids including ices of atmospheric species, drugs, explosives, and even some organic optoelectronic materials and supramolecular assemblies. Recently, surprisingly simple yet extremely efficient, versatile, easily implemented, and systematically accurate electronic structure methods for molecular crystals have been developed. The methods, collectively referred to as the embedded-fragment scheme, divide a crystal into monomers and overlapping dimers and apply modern molecular electronic structure methods and software to these fragments of the crystal that are embedded in a self-consistently determined crystalline electrostatic field. They enable facile applications of accurate but otherwise prohibitively expensive ab initio molecular orbital theories such as Møller-Plesset perturbation and coupled-cluster theories to a broad range of properties of solids such as internal energies, enthalpies, structures, equation of state, phonon dispersion curves and density of states, infrared and Raman spectra (including band intensities and sometimes anharmonic effects), inelastic neutron scattering spectra, heat capacities, Gibbs energies, and phase diagrams, while accounting for many-body electrostatic (namely, induction or polarization) effects as well as two-body exchange and dispersion interactions from first principles. They can fundamentally alter the role of computing in the studies of molecular crystals in the same way ab initio molecular orbital theories have transformed research practices in gas-phase physical chemistry and synthetic chemistry in the last half century. In this Account, after a brief summary of formalisms and algorithms, we discuss applications of these methods performed in our group as compelling

Crystal and molecular simulation of high-performance polymers.

Science.gov (United States)

Colquhoun, H M; Williams, D J

2000-03-01

Single-crystal X-ray analyses of oligomeric models for high-performance aromatic polymers, interfaced to computer-based molecular modeling and diffraction simulation, have enabled the determination of a range of previously unknown polymer crystal structures from X-ray powder data. Materials which have been successfully analyzed using this approach include aromatic polyesters, polyetherketones, polythioetherketones, polyphenylenes, and polycarboranes. Pure macrocyclic homologues of noncrystalline polyethersulfones afford high-quality single crystals-even at very large ring sizes-and have provided the first examples of a "protein crystallographic" approach to the structures of conventionally amorphous synthetic polymers.

Molecular dynamics simulations of liquid crystals at interfaces

International Nuclear Information System (INIS)

Shield, Mark

2002-01-01

Molecular dynamics simulations of an atomistic model of 4-n-octyl-4'-cyanobiphenyl (8CB) were performed for thin films of 8CB on solid substrates (a pseudopotential representation of the molecular topography of the (100) crystal surface of polyethylene (PE), a highly ordered atomistic model of a pseudo-crystalline PE surface and an atomistic model of a partially orientated film of PE), free standing thin films of 8CB and 8CB droplets in a hexagonal pit. The systems showed strong homeotropic anchoring at the free volume interface and planar anchoring at the solid interface whose strength was dependent upon the surface present. The free volume interface also demonstrated weak signs of smectic wetting of the bulk. Simulations of thin free standing films of liquid crystals showed the ordered nature of the liquid crystals at the two free volume interfaces can be adopted by the region of liquid crystal molecules between the homeotropic layer at each interface only if there is a certain number of liquid crystal molecules present. The perpendicular anchoring imposed by the free volume interface and the solid interface for the thin films on the solid substrates resulted in some evidence for the liquid crystal director undergoing a continual rotation at low temperatures and a definite discontinuous change at higher temperatures. The liquid crystal alignment imparted by these substrates was found to depend upon the topography of the surface and not the direction of the polymer chains in the substrate. The liquid crystal was found to order via an epitaxy-like mechanism. The perpendicular anchoring results in a drop in the order - disorder transition temperature for the molecules in the region between the homeotropic layer at the free volume interface and the planar layers at the solid interface. An increase in the size of this region does not alter the transition temperature. The shape of the liquid crystal molecules is dependent upon the degree of order and thus the nematic

Nonequilibrium Molecular Simulations of New Ionic Lubricants at Metallic Surfaces: Prediction of the Friction.

Science.gov (United States)

Mendonça, Ana C F; Pádua, Agílio A H; Malfreyt, Patrice

2013-03-12

We report nonequilibrium molecular dynamics of ionic liquids interacting with metallic surfaces. A specific set of interaction parameters for ionic liquids composed of alkylammonium cations and alkylsulfonate anions with an iron surface, which has been previously developed (J. Chem. Theory Comput.2012, 8, 3348) is used here. We develop a procedure for a quantitative prediction of the friction coefficient at different loads and shear rates. The simulated friction coefficient agrees very well with the available experimental ones. The dependence of friction on the load, shear velocity, surface topology, and length of alkyl side chains in the ionic liquid is also investigated. The changes in the frictional forces are explained in terms of the specific arrangements and orientations of groups forming the ionic liquid at the vicinity of the surface.

Molecular dynamics of liquid crystals

Science.gov (United States)

Sarman, Sten

1997-02-01

We derive Green-Kubo relations for the viscosities of a nematic liquid crystal. The derivation is based on the application of a Gaussian constraint algorithm that makes the director angular velocity of a liquid crystal a constant of motion. Setting this velocity equal to zero means that a director-based coordinate system becomes an inertial frame and that the constraint torques do not do any work on the system. The system consequently remains in equilibrium. However, one generates a different equilibrium ensemble. The great advantage of this ensemble is that the Green-Kubo relations for the viscosities become linear combinations of time correlation function integrals, whereas they are complicated rational functions in the conventional canonical ensemble. This facilitates the numerical evaluation of the viscosities by molecular dynamics simulations.

Direct Photolithography on Molecular Crystals for High Performance Organic Optoelectronic Devices.

Science.gov (United States)

Yao, Yifan; Zhang, Lei; Leydecker, Tim; Samorì, Paolo

2018-05-23

Organic crystals are generated via the bottom-up self-assembly of molecular building blocks which are held together through weak noncovalent interactions. Although they revealed extraordinary charge transport characteristics, their labile nature represents a major drawback toward their integration in optoelectronic devices when the use of sophisticated patterning techniques is required. Here we have devised a radically new method to enable the use of photolithography directly on molecular crystals, with a spatial resolution below 300 nm, thereby allowing the precise wiring up of multiple crystals on demand. Two archetypal organic crystals, i.e., p-type 2,7-diphenyl[1]benzothieno[3,2- b][1]benzothiophene (Dph-BTBT) nanoflakes and n-type N, N'-dioctyl-3,4,9,10-perylenedicarboximide (PTCDI-C8) nanowires, have been exploited as active materials to realize high-performance top-contact organic field-effect transistors (OFETs), inverter and p-n heterojunction photovoltaic devices supported on plastic substrate. The compatibility of our direct photolithography technique with organic molecular crystals is key for exploiting the full potential of organic electronics for sophisticated large-area devices and logic circuitries, thus paving the way toward novel applications in plastic (opto)electronics.

Time Dependent Hartree Fock Equation: Gateway to Nonequilibrium Plasmas

International Nuclear Information System (INIS)

Dufty, James W.

2007-01-01

This is the Final Technical Report for DE-FG02-2ER54677 award 'Time Dependent Hartree Fock Equation - Gateway to Nonequilibrium Plasmas'. Research has focused on the nonequilibrium dynamics of electrons in the presence of ions, both via basic quantum theory and via semi-classical molecular dynamics (MD) simulation. In addition, fundamental notions of dissipative dynamics have been explored for models of grains and dust, and for scalar fields (temperature) in turbulent edge plasmas. The specific topics addressed were Quantum Kinetic Theory for Metallic Clusters, Semi-classical MD Simulation of Plasmas , and Effects of Dissipative Dynamics.

Revolving supramolecular chiral structures powered by light in nanomotor-doped liquid crystals

Science.gov (United States)

Orlova, Tetiana; Lancia, Federico; Loussert, Charles; Iamsaard, Supitchaya; Katsonis, Nathalie; Brasselet, Etienne

2018-04-01

Molecular machines operated by light have been recently shown to be able to produce oriented motion at the molecular scale1,2 as well as do macroscopic work when embedded in supramolecular structures3-5. However, any supramolecular movement irremediably ceases as soon as the concentration of the interconverting molecular motors or switches reaches a photo-stationary state6,7. To circumvent this limitation, researchers have typically relied on establishing oscillating illumination conditions—either by modulating the source intensity8,9 or by using bespoke illumination arrangements10-13. In contrast, here we report a supramolecular system in which the emergence of oscillating patterns is encoded at the molecular level. Our system comprises chiral liquid crystal structures that revolve continuously when illuminated, under the action of embedded light-driven molecular motors. The rotation at the supramolecular level is sustained by the diffusion of the motors away from a localized illumination area. Above a critical irradiation power, we observe a spontaneous symmetry breaking that dictates the directionality of the supramolecular rotation. The interplay between the twist of the supramolecular structure and the diffusion14 of the chiral molecular motors creates continuous, regular and unidirectional rotation of the liquid crystal structure under non-equilibrium conditions.

Anisotropic frictional heating and defect generation in cyclotrimethylene-trinitramine molecular crystals

Science.gov (United States)

Rajak, Pankaj; Mishra, Ankit; Sheng, Chunyang; Tiwari, Subodh; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya

2018-05-01

Anisotropic frictional response and corresponding heating in cyclotrimethylene-trinitramine molecular crystals are studied using molecular dynamics simulations. The nature of damage and temperature rise due to frictional forces is monitored along different sliding directions on the primary slip plane, (010), and on non-slip planes, (100) and (001). Correlations between the friction coefficient, deformation, and frictional heating are established. We find that the friction coefficients on slip planes are smaller than those on non-slip planes. In response to sliding on a slip plane, the crystal deforms easily via dislocation generation and shows less heating. On non-slip planes, due to the inability of the crystal to deform via dislocation generation, a large damage zone is formed just below the contact area, accompanied by the change in the molecular ring conformation from chair to boat/half-boat. This in turn leads to a large temperature rise below the contact area.

Machine learning for the structure-energy-property landscapes of molecular crystals.

Science.gov (United States)

Musil, Félix; De, Sandip; Yang, Jack; Campbell, Joshua E; Day, Graeme M; Ceriotti, Michele

2018-02-07

Molecular crystals play an important role in several fields of science and technology. They frequently crystallize in different polymorphs with substantially different physical properties. To help guide the synthesis of candidate materials, atomic-scale modelling can be used to enumerate the stable polymorphs and to predict their properties, as well as to propose heuristic rules to rationalize the correlations between crystal structure and materials properties. Here we show how a recently-developed machine-learning (ML) framework can be used to achieve inexpensive and accurate predictions of the stability and properties of polymorphs, and a data-driven classification that is less biased and more flexible than typical heuristic rules. We discuss, as examples, the lattice energy and property landscapes of pentacene and two azapentacene isomers that are of interest as organic semiconductor materials. We show that we can estimate force field or DFT lattice energies with sub-kJ mol -1 accuracy, using only a few hundred reference configurations, and reduce by a factor of ten the computational effort needed to predict charge mobility in the crystal structures. The automatic structural classification of the polymorphs reveals a more detailed picture of molecular packing than that provided by conventional heuristics, and helps disentangle the role of hydrogen bonded and π-stacking interactions in determining molecular self-assembly. This observation demonstrates that ML is not just a black-box scheme to interpolate between reference calculations, but can also be used as a tool to gain intuitive insights into structure-property relations in molecular crystal engineering.

Effect of polar surfaces on organic molecular crystals

Science.gov (United States)

Sharia, Onise; Tsyshevskiy, Roman; Kuklja, Maija; University of Maryland College Park Team

Polar oxide materials reveal intriguing opportunities in the field of electronics, superconductivity and nanotechnology. While behavior of polar surfaces has been widely studied on oxide materials and oxide-oxide interfaces, manifestations and properties of polar surfaces in molecular crystals are still poorly understood. Here we discover that the polar catastrophe phenomenon, known on oxides, also takes place in molecular materials as illustrated with an example of cyclotetramethylene tetranitramine (HMX) crystals. We show that the surface charge separation is a feasible compensation mechanism to counterbalance the macroscopic dipole moment and remove the electrostatic instability. We discuss the role of surface charge on degradation of polar surfaces, electrical conductivity, optical band-gap closure and surface metallization. Research is supported by the US ONR (Grants N00014-16-1-2069 and N00014-16-1-2346) and NSF. We used NERSC, XSEDE and MARCC computational resources.

Crossover from equilibration to aging: Nonequilibrium theory versus simulations.

Science.gov (United States)

Mendoza-Méndez, P; Lázaro-Lázaro, E; Sánchez-Díaz, L E; Ramírez-González, P E; Pérez-Ángel, G; Medina-Noyola, M

2017-08-01

Understanding glasses and the glass transition requires comprehending the nature of the crossover from the ergodic (or equilibrium) regime, in which the stationary properties of the system have no history dependence, to the mysterious glass transition region, where the measured properties are nonstationary and depend on the protocol of preparation. In this work we use nonequilibrium molecular dynamics simulations to test the main features of the crossover predicted by the molecular version of the recently developed multicomponent nonequilibrium self-consistent generalized Langevin equation theory. According to this theory, the glass transition involves the abrupt passage from the ordinary pattern of full equilibration to the aging scenario characteristic of glass-forming liquids. The same theory explains that this abrupt transition will always be observed as a blurred crossover due to the unavoidable finiteness of the time window of any experimental observation. We find that within their finite waiting-time window, the simulations confirm the general trends predicted by the theory.

Nonequilibrium 2-hydroxyoctadecanoic acid monolayers: effect of electrolytes.

Science.gov (United States)

Lendrum, Conrad D; Ingham, Bridget; Lin, Binhua; Meron, Mati; Toney, Michael F; McGrath, Kathryn M

2011-04-19

2-Hydroxyacids display complex monolayer phase behavior due to the additional hydrogen bonding afforded by the presence of the second hydroxy group. The placement of this group at the position α to the carboxylic acid functionality also introduces the possibility of chelation, a utility important in crystallization including biomineralization. Biomineralization, like many biological processes, is inherently a nonequilibrium process. The nonequilibrium monolayer phase behavior of 2-hydroxyoctadecanoic acid was investigated on each of pure water, calcium chloride, sodium bicarbonate and calcium carbonate crystallizing subphases as a precursor study to a model calcium carbonate biomineralizing system, each at a pH of ∼6. The role of the bicarbonate co-ion in manipulating the monolayer structure was determined by comparison with monolayer phase behavior on a sodium chloride subphase. Monolayer phase behavior was probed using surface pressure/area isotherms, surface potential, Brewster angle microscopy, and synchrotron-based grazing incidence X-ray diffraction and X-ray reflectivity. Complex phase behavior was observed for all but the sodium chloride subphase with hydrogen bonding, electrostatic and steric effects defining the symmetry of the monolayer. On a pure water subphase hydrogen bonding dominates with three phases coexisting at low pressures. Introduction of calcium ions into the aqueous subphase ensures strong cation binding to the surfactant head groups through chelation. The monolayer becomes very unstable in the presence of bicarbonate ions within the subphase due to short-range hydrogen bonding interactions between the monolayer and bicarbonate ions facilitated by the sodium cation enhancing surfactant solubility. The combined effects of electrostatics and hydrogen bonding are observed on the calcium carbonate crystallizing subphase. © 2011 American Chemical Society

Determination of the Temperature Dependence of Heat Capacity for Some Molecular Crystals of Nitro Compounds

Science.gov (United States)

Kovalev, Yu. M.; Kuropatenko, V. F.

2018-05-01

An analysis of the existing approximations used for describing the dependence of heat capacity at a constant volume on the temperature of a molecular crystal has been carried out. It is shown that the considered Debye and Einstein approximations do not enable one to adequately describe the dependence of heat capacity at a constant volume on the temperature of the molecular crystals of nitro compounds. This inference requires the development of special approximations that would describe both low-frequency and high-frequency parts of the vibrational spectra of molecular crystals. This work presents a universal dependence allowing one to describe the dependence of heat capacity at a constant volume on temperature for a number of molecular crystals of nitro compounds.

Broken detailed balance and non-equilibrium dynamics in living systems: a review

Science.gov (United States)

Gnesotto, F. S.; Mura, F.; Gladrow, J.; Broedersz, C. P.

2018-06-01

Living systems operate far from thermodynamic equilibrium. Enzymatic activity can induce broken detailed balance at the molecular scale. This molecular scale breaking of detailed balance is crucial to achieve biological functions such as high-fidelity transcription and translation, sensing, adaptation, biochemical patterning, and force generation. While biological systems such as motor enzymes violate detailed balance at the molecular scale, it remains unclear how non-equilibrium dynamics manifests at the mesoscale in systems that are driven through the collective activity of many motors. Indeed, in several cellular systems the presence of non-equilibrium dynamics is not always evident at large scales. For example, in the cytoskeleton or in chromosomes one can observe stationary stochastic processes that appear at first glance thermally driven. This raises the question how non-equilibrium fluctuations can be discerned from thermal noise. We discuss approaches that have recently been developed to address this question, including methods based on measuring the extent to which the system violates the fluctuation-dissipation theorem. We also review applications of this approach to reconstituted cytoskeletal networks, the cytoplasm of living cells, and cell membranes. Furthermore, we discuss a more recent approach to detect actively driven dynamics, which is based on inferring broken detailed balance. This constitutes a non-invasive method that uses time-lapse microscopy data, and can be applied to a broad range of systems in cells and tissue. We discuss the ideas underlying this method and its application to several examples including flagella, primary cilia, and cytoskeletal networks. Finally, we briefly discuss recent developments in stochastic thermodynamics and non-equilibrium statistical mechanics, which offer new perspectives to understand the physics of living systems.

Broken detailed balance and non-equilibrium dynamics in living systems: a review.

Science.gov (United States)

Gnesotto, F S; Mura, F; Gladrow, J; Broedersz, C P

2018-03-05

Living systems operate far from thermodynamic equilibrium. Enzymatic activity can induce broken detailed balance at the molecular scale. This molecular scale breaking of detailed balance is crucial to achieve biological functions such as high-fidelity transcription and translation, sensing, adaptation, biochemical patterning, and force generation. While biological systems such as motor enzymes violate detailed balance at the molecular scale, it remains unclear how non-equilibrium dynamics manifests at the mesoscale in systems that are driven through the collective activity of many motors. Indeed, in several cellular systems the presence of non-equilibrium dynamics is not always evident at large scales. For example, in the cytoskeleton or in chromosomes one can observe stationary stochastic processes that appear at first glance thermally driven. This raises the question how non-equilibrium fluctuations can be discerned from thermal noise. We discuss approaches that have recently been developed to address this question, including methods based on measuring the extent to which the system violates the fluctuation-dissipation theorem. We also review applications of this approach to reconstituted cytoskeletal networks, the cytoplasm of living cells, and cell membranes. Furthermore, we discuss a more recent approach to detect actively driven dynamics, which is based on inferring broken detailed balance. This constitutes a non-invasive method that uses time-lapse microscopy data, and can be applied to a broad range of systems in cells and tissue. We discuss the ideas underlying this method and its application to several examples including flagella, primary cilia, and cytoskeletal networks. Finally, we briefly discuss recent developments in stochastic thermodynamics and non-equilibrium statistical mechanics, which offer new perspectives to understand the physics of living systems.

Use of Nonequilibrium Work Methods to Compute Free Energy Differences Between Molecular Mechanical and Quantum Mechanical Representations of Molecular Systems.

Science.gov (United States)

Hudson, Phillip S; Woodcock, H Lee; Boresch, Stefan

2015-12-03

Carrying out free energy simulations (FES) using quantum mechanical (QM) Hamiltonians remains an attractive, albeit elusive goal. Renewed efforts in this area have focused on using "indirect" thermodynamic cycles to connect "low level" simulation results to "high level" free energies. The main obstacle to computing converged free energy results between molecular mechanical (MM) and QM (ΔA(MM→QM)), as recently demonstrated by us and others, is differences in the so-called "stiff" degrees of freedom (e.g., bond stretching) between the respective energy surfaces. Herein, we demonstrate that this problem can be efficiently circumvented using nonequilibrium work (NEW) techniques, i.e., Jarzynski's and Crooks' equations. Initial applications of computing ΔA(NEW)(MM→QM), for blocked amino acids alanine and serine as well as to generate butane's potentials of mean force via the indirect QM/MM FES method, showed marked improvement over traditional FES approaches.

Quantum dynamics of crystals of molecular magnets inside microwave resonators

Energy Technology Data Exchange (ETDEWEB)

Amigo, R.; Tejada, J.; Chudnovsky, E.M.; Hernandez, J.M.; Garcia-Santiago, A. E-mail: antonio@ubxlab.comtoni@ubxlab.com

2004-05-01

It is shown that crystals of molecular nanomagnets exhibit enhanced magnetic relaxation when placed inside a resonant cavity. Strong dependence of the magnetization curve on the geometry of the cavity has been observed, providing evidence of the coherent microwave radiation by the crystals. These observations open the possibility of building a nanomagnetic microwave laser pumped by the magnetic field.

Quantum dynamics of crystals of molecular magnets inside microwave resonators

International Nuclear Information System (INIS)

Amigo, R.; Tejada, J.; Chudnovsky, E.M.; Hernandez, J.M.; Garcia-Santiago, A.

2004-01-01

It is shown that crystals of molecular nanomagnets exhibit enhanced magnetic relaxation when placed inside a resonant cavity. Strong dependence of the magnetization curve on the geometry of the cavity has been observed, providing evidence of the coherent microwave radiation by the crystals. These observations open the possibility of building a nanomagnetic microwave laser pumped by the magnetic field

Protein surface shielding agents in protein crystallization

International Nuclear Information System (INIS)

Hašek, J.

2011-01-01

The crystallization process can be controlled by protein surface shielding agents blocking undesirable competitive adhesion modes during non-equilibrium processes of deposition of protein molecules on the surface of growing crystalline blocks. The hypothesis is based on a number of experimental proofs from diffraction experiments and also retrieved from the Protein Data Bank. The molecules adhering temporarily on the surface of protein molecules change the propensity of protein molecules to deposit on the crystal surface in a definite position and orientation. The concepts of competitive adhesion modes and protein surface shielding agents acting on the surface of molecules in a non-equilibrium process of protein crystallization provide a useful platform for the control of crystallization. The desirable goal, i.e. a transient preference of a single dominating adhesion mode between protein molecules during crystallization, leads to uniform deposition of proteins in a crystal. This condition is the most important factor for diffraction quality and thus also for the accuracy of protein structure determination. The presented hypothesis is a generalization of the experimentally well proven behaviour of hydrophilic polymers on the surface of protein molecules of other compounds

Rayleigh-Plesset equation of the bubble stable cavitation in water: A nonequilibrium all-atom molecular dynamics simulation study

Science.gov (United States)

Man, Viet Hoang; Li, Mai Suan; Derreumaux, Philippe; Nguyen, Phuong H.

2018-03-01

The Rayleigh-Plesset (RP) equation was derived from the first principles to describe the bubble cavitation in liquids in terms of macroscopic hydrodynamics. A number of nonequilibrium molecular dynamics studies have been carried out to validate this equation in describing the bubble inertial cavitation, but their results are contradictory and the applicability of the RP equation still remains to be examined, especially for the stable cavitation. In this work, we carry out nonequilibrium all-atom simulation to validate the applicability of the RP equation in the description of the stable cavitation of nano-sized bubbles in water. We show that although microscopic effects are not explicitly included, this equation still describes the dynamics of subnano-bubbles quite well as long as the contributions of various terms including inertial, surface tension, and viscosity are correctly taken into account. These terms are directly and inversely proportional to the amplitude and period of the cavitation, respectively. Thus, their contributions to the RP equation depend on these two parameters. This may explain the discrepancy between the current results obtained using different parameters. Finally, the accuracy of the RP equation in the current mathematical modeling studies of the ultrasound-induced blood-brain-barrier experiments is discussed in some detail.

The behavior of matter under nonequilibrium conditions: Fundamental aspects and applications

International Nuclear Information System (INIS)

Prigogine, I.

1989-10-01

As in the previous period, our work has been concerned with the study of the properties of nonequilibrium systems and especially with the mechanism of self-organization. As is well-known, the study of self-organization began with the investigation of hydrodynamical or chemical instabilities studied from the point of view of macroscopic physics. The main outcome is that nonequilibrium generates spatial correlations of macroscopic physics. The main outcome is that nonequilibrium generates spatial correlations of macroscopic range whose characteristics length is an intrinsic property and whose amplitude is determined by nonequilibrium constraints. A survey of the macroscopic approach to nonequilibrium states is given in the paper ''Nonequilibrium States and Long Range Correlations in Chemical Dynamics,'' by G. Nicolis et al. However, over the last few years important progress has been made in the simulation of nonequilibrium situations using mainly molecular dynamics. It appears now that processes corresponding to self-organization as well as the appearance of long-range correlations can be obtained in this way starting from a program involving Newtonian dynamics (generally the laws of interaction correspond to hard spheres or hard disks). Examples of such types of studies leading to Benard instabilities, to chemical clocks, or to spatial structure formation are given in this report. As a result, we may now view self-organization as a direct expression of an appropriate microscopic dynamics. This is the reason why we have devoted much work to the study of large Poincare systems (LPS) involving continuous sets of resonances. These systems have been shown to lead, according to the constraints, either to equilibrium situations or to nonequilibrium states involving long range correlations. We discuss LPS in the frame of classical mechanics

Non-equilibrium assembly of microtubules: from molecules to autonomous chemical robots.

Science.gov (United States)

Hess, H; Ross, Jennifer L

2017-09-18

Biological systems have evolved to harness non-equilibrium processes from the molecular to the macro scale. It is currently a grand challenge of chemistry, materials science, and engineering to understand and mimic biological systems that have the ability to autonomously sense stimuli, process these inputs, and respond by performing mechanical work. New chemical systems are responding to the challenge and form the basis for future responsive, adaptive, and active materials. In this article, we describe a particular biochemical-biomechanical network based on the microtubule cytoskeletal filament - itself a non-equilibrium chemical system. We trace the non-equilibrium aspects of the system from molecules to networks and describe how the cell uses this system to perform active work in essential processes. Finally, we discuss how microtubule-based engineered systems can serve as testbeds for autonomous chemical robots composed of biological and synthetic components.

Crystal structure and pair potentials: A molecular-dynamics study

Energy Technology Data Exchange (ETDEWEB)

Parrinello, M.; Rahman, A.

1980-10-06

With use of a Lagrangian which allows for the variation of the shape and size of the periodically repeating molecular-dynamics cell, it is shown that different pair potentials lead to different crystal structures.

Nonequilibrium statistical physics of small systems: fluctuation relations and beyond (annual reviews of nonlinear dynamics and complexity (vch))

CERN Document Server

2013-01-01

This book offers a comprehensive picture of nonequilibrium phenomena in nanoscale systems. Written by internationally recognized experts in the field, this book strikes a balance between theory and experiment, and includes in-depth introductions to nonequilibrium fluctuation relations, nonlinear dynamics and transport, single molecule experiments, and molecular diffusion in nanopores. The authors explore the application of these concepts to nano- and biosystems by cross-linking key methods and ideas from nonequilibrium statistical physics, thermodynamics, stochastic theory, and dynamical s

Optimal control of transitions between nonequilibrium steady states.

Directory of Open Access Journals (Sweden)

Patrick R Zulkowski

Full Text Available Biological systems fundamentally exist out of equilibrium in order to preserve organized structures and processes. Many changing cellular conditions can be represented as transitions between nonequilibrium steady states, and organisms have an interest in optimizing such transitions. Using the Hatano-Sasa Y-value, we extend a recently developed geometrical framework for determining optimal protocols so that it can be applied to systems driven from nonequilibrium steady states. We calculate and numerically verify optimal protocols for a colloidal particle dragged through solution by a translating optical trap with two controllable parameters. We offer experimental predictions, specifically that optimal protocols are significantly less costly than naive ones. Optimal protocols similar to these may ultimately point to design principles for biological energy transduction systems and guide the design of artificial molecular machines.

Crystallization, X-ray diffraction analysis and SIRAS/molecular-replacenent phasing of three crystal forms of Anabaena sensory rhodopsin transducer

International Nuclear Information System (INIS)

Vogeley, Lutz; Luecke, Hartmut

2006-01-01

Crystals of Anabaena sensory rhodopsin transducer, the transducer for the cyanobacterial photosensor Anabaena sensory rhodopsin, obtained in the space groups P4, C2 and P2 1 2 1 2 1 diffract to 1.8, 2.1 and 2.0 Å, respectively. Phases for these crystal forms were obtained by SIRAS phasing using an iodide quick-soak derivative (P4) and molecular replacement (C2 and P2 1 2 1 2 1 ). Anabaena sensory rhodopsin transducer (ASRT) is a 14.7 kDa soluble signaling protein associated with the membrane-embedded light receptor Anabaena sensory rhodopsin (ASR) from Anabaena sp., a freshwater cyanobacterium. Crystals of ASRT were obtained in three different space groups, P4, C2 and P2 1 2 1 2 1 , which diffract to 1.8, 2.1 and 2.0 Å, respectively. Phases for one of these crystal forms (P4) were obtained by SIRAS phasing using an iodide quick-soak derivative and a partial model was built. Phases for the remaining crystal forms were obtained by molecular replacement using the partial model from the P4 crystal form

Surface-ionization field mass-spectrometry studies of nonequilibrium surface ionization

International Nuclear Information System (INIS)

Blashenkov, Nikolai M; Lavrent'ev, Gennadii Ya

2007-01-01

The ionization of polyatomic molecules on tungsten and tungsten oxide surfaces is considered for quasiequilibrium or essentially nonequilibrium conditions (in the latter case, the term nonequilibrium surface ionization is used for adsorbate ionization). Heterogeneous reactions are supposed to proceed through monomolecular decay of polyatomic molecules or fragments of multimolecular complexes. The nonequilibrium nature of these reactions is established. The dependences of the current density of disordered ions on the surface temperature, electric field strength, and ionized particle energy distribution are obtained in analytical form. Heterogeneous dissociation energies, the ionization potentials of radicals, and the magnitude of reaction departure from equilibrium are determined from experimental data, as are energy exchange times between reaction products and surfaces, the number of molecules in molecular complexes, and the number of effective degrees of freedom in molecules and complexes. In collecting the data a new technique relying on surface-ionization field mass-spectrometry was applied. (instruments and methods of investigation)

Study of molecular movements in some organic crystals by NMR

International Nuclear Information System (INIS)

Alexandre, M.

1971-01-01

After a discussion on molecular crystals (generalities, movements within molecular solids, study of movements, complexes by charge transfer) and some specific ones (molecular complexes of trinitrobenzene or TNB), this research thesis reports the use of nuclear magnetic resonance (NMR) to study molecular movements: generalities on broadband NMR, spin relaxation and strong field network, observation of the absorption signal and measurement of the second moment. The last part reports and discusses experimental results obtained on TNB-naphthalene, on TNB-azulene, on TNB-benzothiophene, and on TNB-indole

Applications of nonequilibrium melting concept to damage-accumulation processes

International Nuclear Information System (INIS)

Lam, N.Q.; Okamoto, P.R.

1998-01-01

The authors recent study of crystalline-to-amorphous transformation led to the successful development of a unified thermodynamic description of disorder-induced amorphization and heat-induced melting, based on a generalized version of the Lindemann melting criterion. The generalized criterion requires that the melting temperature of a defective crystal decreases with increasing static atomic disorder. Hence, any crystal can melt at temperatures below the melting point of its perfect crystalline state when driven far from equilibrium by introducing critical amounts of misfitting solute atoms and lattice imperfections, radiation damage, and/or tensile stresses. This conceptual approach to nonequilibrium melting provides new insight into long-standing materials problems such as brittle fracture, embrittlement, and environmentally-induced cracking, for example irradiation-assisted stress corrosion cracking

Lattice dynamics of a crystal with a molecular impurity

International Nuclear Information System (INIS)

Sahoo, D.; Venkataraman, G.

1975-01-01

The dynamics of a crystal containing a molecular impurity is discussed with allowance for the effects of internal vibrations of the molecule. Cartesian coordinates are used to describe internal vibrations, angular oscillations and centre of mass translations of the impurity, and the displacement of atoms of the host lattice. Next the Hamiltonian is set up and the equations of motion derived. In this process, use is made of Dirac brackets when dealing with vibrational coordinates (of the molecule) which have redundancy and constraints. A method of solution of the normal modes of the system is indicated by using the defect space matrixpartitioning technique. The special case of a rigid molecular impurity is then discussed along with the relevance of the present formalism in the interpretation of a recent neutron scattering experiment. It is also shown how the results of crystal-field approximation model and those of the molecular model approximation are obtained as further special cases of the present formalism. A comparison of the present work with those of others has been made. (author)

NONLINEAR OPTICAL MOLECULAR CRYSTAL BASED ON 2,6-DIAMINOPYRIDINE: SYNTHESIS AND CHARACTERIZATION

Directory of Open Access Journals (Sweden)

I. M. Pavlovetc

2014-05-01

Full Text Available The paper deals with investigation of a new nonlinear optical material based on nonlinear optical chromophore (4-Nitrophenol and aminopyridine (2,6-Diaminopyridine. Calculation results are presented for molecular packing in the crystalline compound, based on the given components. According to these results the finite material must have a noncentrosymmetric lattice, which determines the presence of the second order nonlinear optical response. Investigations carried out in this work confirm these calculations. Results of experiments are given describing the co-crystallization of these components and the following re-crystallization of the obtained material. In order to get a monocrystal form, the optimal conditions for the synthesis of molecular crystals based on these components are determined. Sufficiently large homogeneous crystals are obtained, that gave the possibility to record their spectra in the visible and near infrared parts of the spectrum, to determine their nonlinear optical properties and the level of homogeneity. Their optical (optical transmission and optical laser damage threshold and nonlinear optical properties are presented. For observation and measurement of the nonlinear optical properties an installation was built which implements the comparative method for measurements of nonlinear optical properties. A potassium titanyl oxide phosphate crystal was used as a sample for comparison. Results are given for the conversion efficiency of the primary laser radiation in the second optical harmonic relative to the signal obtained on the potassium titanyl oxide phosphate crystal. Obtained results show that the molecular co-crystal based on 2,6-Diaminopyridine is a promising nonlinear optical material for generating the second optical harmonic on the Nd: YAG laser (532 nm.

NATO Advanced Study Institute on Electronic Structure of Polymers and Molecular Crystals

CERN Document Server

Ladik, János

1975-01-01

The NATO Advanced Study Institute on "Electronic Structure of Polymers and Molecular Crystals" was held at the Facultes Universi­ taires de Namur (F.U.N.) from September 1st till September 14th, 1974. We wish to express our appreciation to the NATO Scientific Affairs Division whose generous support made this Institute possible and to the Facultes Universitaires de Namur and the Societe Chimique de Belgique which provided fellowships and travel grants to a number of students. This volume contains the main lectures about the basic principles of the field and about different recent developments of the theory of the electronic structure of polymers and molecular crystals. The school started with the presentation of the basic SCF-LCAO theory of the electronic structure of periodic polymers and molecular crystals (contributions by Ladik, Andre & Delhalle) showing how a combination of quantum chemical and solid state physical methods can provide band structures for these systems. The numerical aspects of these ...

Molecular type channeling of relativistic electrons in crystals

International Nuclear Information System (INIS)

Vyatkin, E.G.; Filimonov, Yu.M.; Taratin, A.M.; Vorobiev, S.A.

1983-01-01

Channeling of relativistic electrons in direction in a diamond crystal and the channeling radiation spectra are investigated using computer simulation by the binary collision model and using the model of a continuum potential of the atomic rows. In a computer experiment the atomic- and molecular-type states of channeled elcetrons are revealed, and the orientational dependence of the electron trapping probability in these states is obtained. The peculiarities revealed of the angular distributions and radiation spectra of electrons in the molecular-type states allow to discover these states in the experiment. (author)

Adsorption of hydrogen isotopes by metals in non-equilibrium conditions

International Nuclear Information System (INIS)

Livshits, A.I.; Notkin, M.E.; Pustovojt, Yu.M.

1982-01-01

To study the interaction of thermonuclear plasma and additions with metallic walls, nonequilibrium system of thermal atomary hydrogen - ''cold'' (300-1100 K) metal is experimentally investigated. Atomary hydrogen was feeded to samples of Ni and Pd in the shape of atomic beam, coming into vacuum from high-frequency gaseous discharge. It is shown that hydrogen solubility under nonequilibrium conditions increases with surface passivation (contamination); in this case it surpasses equilibrium solubility by value orders. Nickel and iron dissolve more hydrogen than palladium at a certain state of surface ( passivation) and gas (atomary hydrogen). The sign of the temperature dependence of hydrogen solubility in passivated N 1 and Fe changes when alterating molecular hydrogen by atomary hydrogen

14th International Conference on Nonequilibrium Carrier Dynamics in Semiconductors

CERN Document Server

Saraniti, M; Nonequilibrium Carrier Dynamics in Semiconductors

2006-01-01

International experts gather every two years at this established conference to discuss recent developments in theory and experiment in non-equilibrium transport phenomena. These developments have been the driving force behind the spectacular advances in semiconductor physics and devices over the last few decades. Originally known as "Hot Carriers in Semiconductors," the 14th conference in the series covered a wide spectrum of traditional topics dealing with non-equilibrium phenomena, ranging from quantum transport to optical phenomena in mesoscopic and nano-scale structures. Particular attention was given this time to emerging areas of this rapidly evolving field, with many sessions covering terahertz devices, high field transport in nitride semiconductors, spintronics, molecular electronics, and bioelectronics applications.

Crystallization in nano-confinement seeded by a nanocrystal—A molecular dynamics study

KAUST Repository

Pan, Heng; Grigoropoulos, Costas

2014-01-01

Seeded crystallization and solidification in nanoscale confinement volumes have become an important and complex topic. Due to the complexity and limitations in observing nanoscale crystallization, computer simulation can provide valuable details for supporting and interpreting experimental observations. In this article, seeded crystallization from nano-confined liquid, as represented by the crystallization of a suspended gold nano-droplet seeded by a pre-existing gold nanocrystal seed, was investigated using molecular dynamics simulations in canonical (NVT) ensemble. We found that the crystallization temperature depends on nano-confinement volume, crystal orientation, and seed size as explained by classical two-sphere model and Gibbs-Thomson effect. © 2014 AIP Publishing LLC.

Crystallization in nano-confinement seeded by a nanocrystal—A molecular dynamics study

KAUST Repository

Pan, Heng

2014-03-14

Seeded crystallization and solidification in nanoscale confinement volumes have become an important and complex topic. Due to the complexity and limitations in observing nanoscale crystallization, computer simulation can provide valuable details for supporting and interpreting experimental observations. In this article, seeded crystallization from nano-confined liquid, as represented by the crystallization of a suspended gold nano-droplet seeded by a pre-existing gold nanocrystal seed, was investigated using molecular dynamics simulations in canonical (NVT) ensemble. We found that the crystallization temperature depends on nano-confinement volume, crystal orientation, and seed size as explained by classical two-sphere model and Gibbs-Thomson effect. © 2014 AIP Publishing LLC.

Thermochemical nonequilibrium analysis of O2+Ar based on state-resolved kinetics

International Nuclear Information System (INIS)

Kim, Jae Gang; Boyd, Iain D.

2015-01-01

Highlights: • Thermochemical nonequilibrium studies for three lowest lying electronic states of O 2 . • The complete sets of the rovibrational state-to-state transition rates of O 2 +Ar. • Rovibrational relaxations and coupled chemical reactions of O 2 . • Nonequilibrium reaction rates of O 2 derived from the quasi-steady state assumption. - Abstract: The thermochemical nonequilibrium of the three lowest lying electronic states of molecular oxygen, O 2 (X 3 Σ g - ,a 1 Δ g ,b 1 Σ g + ), through interactions with argon is studied in the present work. The multi-body potential energy surfaces of O 2 +Ar are evaluated from the semi-classical RKR potential of O 2 in each electronic state. The rovibrational states and energies of each electronic state are calculated by the quantum mechanical method based on the present inter-nuclear potential of O 2 . Then, the complete sets of the rovibrational state-to-state transition rate coefficients of O 2 +Ar are calculated by the quasi-classical trajectory method including the quasi-bound states. The system of master equations constructed by the present state-to-state transition rate coefficients are solved to analyze the thermochemical nonequilibrium of O 2 +Ar in various heat bath conditions. From these studies, it is concluded that the vibrational relaxation and coupled chemical reactions of each electronic state needs to be treated as a separate nonequilibrium process, and rotational nonequilibrium needs to be considered at translational temperatures above 10,000 K

Advancing non-equilibrium ARPES experiments by a 9.3 eV coherent ultrafast photon source

Energy Technology Data Exchange (ETDEWEB)

Cilento, F., E-mail: federico.cilento@elettra.eu [Elettra – Sincrotrone Trieste S.C.p.A., Strada Statale 14, km 163.5, Trieste 34149 (Italy); C.N.R. – I.O.M., Strada Statale 14, km 163.5, Trieste 34149 (Italy); Crepaldi, A. [Elettra – Sincrotrone Trieste S.C.p.A., Strada Statale 14, km 163.5, Trieste 34149 (Italy); Manzoni, G.; Sterzi, A. [Universitá degli Studi di Trieste, Via A. Valerio 2, Trieste 34127 (Italy); Zacchigna, M. [C.N.R. – I.O.M., Strada Statale 14, km 163.5, Trieste 34149 (Italy); Bugnon, Ph.; Berger, H. [Institute of Condensed Matter Physics, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne (Switzerland); Parmigiani, F. [Elettra – Sincrotrone Trieste S.C.p.A., Strada Statale 14, km 163.5, Trieste 34149 (Italy); Universitá degli Studi di Trieste, Via A. Valerio 2, Trieste 34127 (Italy); International Faculty, University of Köln, 50937 Köln (Germany)

2016-02-15

The quest for investigating the non-equilibrium dynamics of the band structure of strongly-correlated materials over their entire Brillouin zone is a primary objective. However, the actual ultrafast UV light sources are not suitable for addressing several critical questions in the field. Here we report on a novel light source generating sub-250 fs, 9.3 eV photon energy light pulses at 250 kHz repetition rate, obtained via third-harmonic generation in Xe of frequency-doubled 50 fs laser pulses at 1.55 eV. By reporting the measured band dispersion of a Cu(111) crystal and the non-equilibrium dynamics of the Bi{sub 2}Se{sub 3} topological insulator, we prove that this source is suitable for studying the non-equilibrium dynamics of the entire Fermi surface of several complex materials, with high signal statistics and limited space-charge effect.

Simulation and understanding of atomic and molecular quantum crystals

Science.gov (United States)

Cazorla, Claudio; Boronat, Jordi

2017-07-01

Quantum crystals abound in the whole range of solid-state species. Below a certain threshold temperature the physical behavior of rare gases (He 4 and Ne), molecular solids (H2 and CH4 ), and some ionic (LiH), covalent (graphite), and metallic (Li) crystals can be explained only in terms of quantum nuclear effects (QNE). A detailed comprehension of the nature of quantum solids is critical for achieving progress in a number of fundamental and applied scientific fields such as planetary sciences, hydrogen storage, nuclear energy, quantum computing, and nanoelectronics. This review describes the current physical understanding of quantum crystals formed by atoms and small molecules, as well as the wide palette of simulation techniques that are used to investigate them. Relevant aspects in these materials such as phase transformations, structural properties, elasticity, crystalline defects, and the effects of reduced dimensionality are discussed thoroughly. An introduction to quantum Monte Carlo techniques, which in the present context are the simulation methods of choice, and other quantum simulation approaches (e.g., path-integral molecular dynamics and quantum thermal baths) is provided. The overarching objective of this article is twofold: first, to clarify in which crystals and physical situations the disregard of QNE may incur in important bias and erroneous interpretations. And second, to promote the study and appreciation of QNE, a topic that traditionally has been treated in the context of condensed matter physics, within the broad and interdisciplinary areas of materials science.

Nanoscale heterostructures with molecular-scale single-crystal metal wires.

Science.gov (United States)

Kundu, Paromita; Halder, Aditi; Viswanath, B; Kundu, Dipan; Ramanath, Ganpati; Ravishankar, N

2010-01-13

Creating nanoscale heterostructures with molecular-scale (synthesis of nanoscale heterostructures with single-crystal molecular-scale Au nanowires attached to different nanostructure substrates. Our method involves the formation of Au nanoparticle seeds by the reduction of rocksalt AuCl nanocubes heterogeneously nucleated on the substrates and subsequent nanowire growth by oriented attachment of Au nanoparticles from the solution phase. Nanoscale heterostructures fabricated by such site-specific nucleation and growth are attractive for many applications including nanoelectronic device wiring, catalysis, and sensing.

Enhanced configurational sampling with hybrid non-equilibrium molecular dynamics-Monte Carlo propagator

Science.gov (United States)

Suh, Donghyuk; Radak, Brian K.; Chipot, Christophe; Roux, Benoît

2018-01-01

Molecular dynamics (MD) trajectories based on classical equations of motion can be used to sample the configurational space of complex molecular systems. However, brute-force MD often converges slowly due to the ruggedness of the underlying potential energy surface. Several schemes have been proposed to address this problem by effectively smoothing the potential energy surface. However, in order to recover the proper Boltzmann equilibrium probability distribution, these approaches must then rely on statistical reweighting techniques or generate the simulations within a Hamiltonian tempering replica-exchange scheme. The present work puts forth a novel hybrid sampling propagator combining Metropolis-Hastings Monte Carlo (MC) with proposed moves generated by non-equilibrium MD (neMD). This hybrid neMD-MC propagator comprises three elementary elements: (i) an atomic system is dynamically propagated for some period of time using standard equilibrium MD on the correct potential energy surface; (ii) the system is then propagated for a brief period of time during what is referred to as a "boosting phase," via a time-dependent Hamiltonian that is evolved toward the perturbed potential energy surface and then back to the correct potential energy surface; (iii) the resulting configuration at the end of the neMD trajectory is then accepted or rejected according to a Metropolis criterion before returning to step 1. A symmetric two-end momentum reversal prescription is used at the end of the neMD trajectories to guarantee that the hybrid neMD-MC sampling propagator obeys microscopic detailed balance and rigorously yields the equilibrium Boltzmann distribution. The hybrid neMD-MC sampling propagator is designed and implemented to enhance the sampling by relying on the accelerated MD and solute tempering schemes. It is also combined with the adaptive biased force sampling algorithm to examine. Illustrative tests with specific biomolecular systems indicate that the method can yield

Coherence enhanced quantum metrology in a nonequilibrium optical molecule

Science.gov (United States)

Wang, Zhihai; Wu, Wei; Cui, Guodong; Wang, Jin

2018-03-01

We explore the quantum metrology in an optical molecular system coupled to two environments with different temperatures, using a quantum master equation beyond secular approximation. We discover that the steady-state coherence originating from and sustained by the nonequilibrium condition can enhance quantum metrology. We also study the quantitative measures of the nonequilibrium condition in terms of the curl flux, heat current and entropy production at the steady state. They are found to grow with temperature difference. However, an apparent paradox arises considering the contrary behaviors of the steady-state coherence and the nonequilibrium measures in relation to the inter-cavity coupling strength. This paradox is resolved by decomposing the heat current into a population part and a coherence part. Only the latter, the coherence part of the heat current, is tightly connected to the steady-state coherence and behaves similarly with respect to the inter-cavity coupling strength. Interestingly, the coherence part of the heat current flows from the low-temperature reservoir to the high-temperature reservoir, opposite to the direction of the population heat current. Our work offers a viable way to enhance quantum metrology for open quantum systems through steady-state coherence sustained by the nonequilibrium condition, which can be controlled and manipulated to maximize its utility. The potential applications go beyond quantum metrology and extend to areas such as device designing, quantum computation and quantum technology in general.

X-ray scattering studies of non-equilibrium ordering processes

International Nuclear Information System (INIS)

Nagler, S.E.

1991-01-01

We report on the progress of the project entitled ''X-ray Scattering Studies of Non-Equilibrium Ordering Processes.'' The past year has seen continued progress in the study of kinetic effects in metallic binary alloys and polymers. In addition, work has begun on a low dimensional CDW system: blue bronze. A sample chamber has been constructed to perform small angle neutron scattering measurements on a model quantum system with phase separation: solid He3/He4. Work is continuing on magnetic systems. Planned future experiments include an investigation of crystallization in Rubidium

Molecular Weight and Crystallization Temperature Effects on Poly(ethylene terephthalate (PET Homopolymers, an Isothermal Crystallization Analysis

Directory of Open Access Journals (Sweden)

Leonardo A. Baldenegro-Perez

2014-02-01

Full Text Available The isothermal crystallization of poly(ethylene terephthalate (PET homopolymers with different molecular weight was studied in a wide temperature range (140–230 °C using different experimental techniques. Three different morphological regions, labeled r1, r2 and r3, were distinguished as a function of crystallization temperature (Tc. In r1 (low Tc crystallized samples were characterized by a low crystalline degree with a small spherulite texture containing thin crystals. In r2 (intermediate Tc samples showed medium size spherulites composed of two distinct crystalline families (thin and thick crystals. In this temperature range, the crystallization exhibited a maximum value and it was associated with a high content of secondary crystals. In r3 (high Tc, samples presented considerable amorphous zones and regions consisting of oversized spherulites containing only thick crystals. Time-resolved wide-angle X-ray diffraction measurements, using synchrotron radiation, indicated a rapid evolution of the crystalline degree within the second region, in contrast with the quite slow evolution observed in the third region. On the other hand, by small-angle X-ray scattering (SAXS and time-resolved SAXS experiment, it was found that the long period (L as well as the lamellar thickness (lc increase as a function of Tc, corroborating the formation of the thickest crystals in the third region. From all these observations, a morphological model was proposed for each region.

Molecular dynamics studies of the ion beam induced crystallization in silicon

International Nuclear Information System (INIS)

Marques, L.A.; Caturla, M.J.; Huang, H.

1995-01-01

We have studied the ion bombardment induced amorphous-to-crystal transition in silicon using molecular dynamics techniques. The growth of small crystal seeds embedded in the amorphous phase has been monitored for several temperatures in order to get information on the effect of the thermal temperature increase introduced by the incoming ion. The role of ion-induced defects on the growth has been also studied

Open problems in non-equilibrium physics

International Nuclear Information System (INIS)

Kusnezov, D.

1997-01-01

The report contains viewgraphs on the following: approaches to non-equilibrium statistical mechanics; classical and quantum processes in chaotic environments; classical fields in non-equilibrium situations: real time dynamics at finite temperature; and phase transitions in non-equilibrium conditions

Open problems in non-equilibrium physics

Energy Technology Data Exchange (ETDEWEB)

Kusnezov, D.

1997-09-22

The report contains viewgraphs on the following: approaches to non-equilibrium statistical mechanics; classical and quantum processes in chaotic environments; classical fields in non-equilibrium situations: real time dynamics at finite temperature; and phase transitions in non-equilibrium conditions.

Definition of Nonequilibrium Entropy of General Systems

OpenAIRE

Mei, Xiaochun

1999-01-01

The definition of nonequilibrium entropy is provided for the general nonequilibrium processes by connecting thermodynamics with statistical physics, and the principle of entropy increment in the nonequilibrium processes is also proved in the paper. The result shows that the definition of nonequilibrium entropy is not unique.

THE ABUNDANCE OF MOLECULAR HYDROGEN AND ITS CORRELATION WITH MIDPLANE PRESSURE IN GALAXIES: NON-EQUILIBRIUM, TURBULENT, CHEMICAL MODELS

International Nuclear Information System (INIS)

Mac Low, Mordecai-Mark; Glover, Simon C. O.

2012-01-01

Observations of spiral galaxies show a strong linear correlation between the ratio of molecular to atomic hydrogen surface density R mol and midplane pressure. To explain this, we simulate three-dimensional, magnetized turbulence, including simplified treatments of non-equilibrium chemistry and the propagation of dissociating radiation, to follow the formation of H 2 from cold atomic gas. The formation timescale for H 2 is sufficiently long that equilibrium is not reached within the 20-30 Myr lifetimes of molecular clouds. The equilibrium balance between radiative dissociation and H 2 formation on dust grains fails to predict the time-dependent molecular fractions we find. A simple, time-dependent model of H 2 formation can reproduce the gross behavior, although turbulent density perturbations increase molecular fractions by a factor of few above it. In contradiction to equilibrium models, radiative dissociation of molecules plays little role in our model for diffuse radiation fields with strengths less than 10 times that of the solar neighborhood, because of the effective self-shielding of H 2 . The observed correlation of R mol with pressure corresponds to a correlation with local gas density if the effective temperature in the cold neutral medium of galactic disks is roughly constant. We indeed find such a correlation of R mol with density. If we examine the value of R mol in our local models after a free-fall time at their average density, as expected for models of molecular cloud formation by large-scale gravitational instability, our models reproduce the observed correlation over more than an order-of-magnitude range in density.

The Abundance of Molecular Hydrogen and Its Correlation with Midplane Pressure in Galaxies: Non-equilibrium, Turbulent, Chemical Models

Science.gov (United States)

Mac Low, Mordecai-Mark; Glover, Simon C. O.

2012-02-01

Observations of spiral galaxies show a strong linear correlation between the ratio of molecular to atomic hydrogen surface density R mol and midplane pressure. To explain this, we simulate three-dimensional, magnetized turbulence, including simplified treatments of non-equilibrium chemistry and the propagation of dissociating radiation, to follow the formation of H2 from cold atomic gas. The formation timescale for H2 is sufficiently long that equilibrium is not reached within the 20-30 Myr lifetimes of molecular clouds. The equilibrium balance between radiative dissociation and H2 formation on dust grains fails to predict the time-dependent molecular fractions we find. A simple, time-dependent model of H2 formation can reproduce the gross behavior, although turbulent density perturbations increase molecular fractions by a factor of few above it. In contradiction to equilibrium models, radiative dissociation of molecules plays little role in our model for diffuse radiation fields with strengths less than 10 times that of the solar neighborhood, because of the effective self-shielding of H2. The observed correlation of R mol with pressure corresponds to a correlation with local gas density if the effective temperature in the cold neutral medium of galactic disks is roughly constant. We indeed find such a correlation of R mol with density. If we examine the value of R mol in our local models after a free-fall time at their average density, as expected for models of molecular cloud formation by large-scale gravitational instability, our models reproduce the observed correlation over more than an order-of-magnitude range in density.

Non-equilibrium oxidation states of zirconium during early stages of metal oxidation

International Nuclear Information System (INIS)

Ma, Wen; Yildiz, Bilge; Herbert, F. William; Senanayake, Sanjaya D.

2015-01-01

The chemical state of Zr during the initial, self-limiting stage of oxidation on single crystal zirconium (0001), with oxide thickness on the order of 1 nm, was probed by synchrotron x-ray photoelectron spectroscopy. Quantitative analysis of the Zr 3d spectrum by the spectrum reconstruction method demonstrated the formation of Zr 1+ , Zr 2+ , and Zr 3+ as non-equilibrium oxidation states, in addition to Zr 4+ in the stoichiometric ZrO 2 . This finding resolves the long-debated question of whether it is possible to form any valence states between Zr 0 and Zr 4+ at the metal-oxide interface. The presence of local strong electric fields and the minimization of interfacial energy are assessed and demonstrated as mechanisms that can drive the formation of these non-equilibrium valence states of Zr

Path-space variational inference for non-equilibrium coarse-grained systems

International Nuclear Information System (INIS)

Harmandaris, Vagelis; Kalligiannaki, Evangelia; Katsoulakis, Markos; Plecháč, Petr

2016-01-01

In this paper we discuss information-theoretic tools for obtaining optimized coarse-grained molecular models for both equilibrium and non-equilibrium molecular simulations. The latter are ubiquitous in physicochemical and biological applications, where they are typically associated with coupling mechanisms, multi-physics and/or boundary conditions. In general the non-equilibrium steady states are not known explicitly as they do not necessarily have a Gibbs structure. The presented approach can compare microscopic behavior of molecular systems to parametric and non-parametric coarse-grained models using the relative entropy between distributions on the path space and setting up a corresponding path-space variational inference problem. The methods can become entirely data-driven when the microscopic dynamics are replaced with corresponding correlated data in the form of time series. Furthermore, we present connections and generalizations of force matching methods in coarse-graining with path-space information methods. We demonstrate the enhanced transferability of information-based parameterizations to different observables, at a specific thermodynamic point, due to information inequalities. We discuss methodological connections between information-based coarse-graining of molecular systems and variational inference methods primarily developed in the machine learning community. However, we note that the work presented here addresses variational inference for correlated time series due to the focus on dynamics. The applicability of the proposed methods is demonstrated on high-dimensional stochastic processes given by overdamped and driven Langevin dynamics of interacting particles.

Path-space variational inference for non-equilibrium coarse-grained systems

Energy Technology Data Exchange (ETDEWEB)

Harmandaris, Vagelis, E-mail: harman@uoc.gr [Department of Mathematics and Applied Mathematics, University of Crete (Greece); Institute of Applied and Computational Mathematics (IACM), Foundation for Research and Technology Hellas (FORTH), IACM/FORTH, GR-71110 Heraklion (Greece); Kalligiannaki, Evangelia, E-mail: ekalligian@tem.uoc.gr [Department of Mathematics and Applied Mathematics, University of Crete (Greece); Katsoulakis, Markos, E-mail: markos@math.umass.edu [Department of Mathematics and Statistics, University of Massachusetts at Amherst (United States); Plecháč, Petr, E-mail: plechac@math.udel.edu [Department of Mathematical Sciences, University of Delaware, Newark, Delaware (United States)

2016-06-01

In this paper we discuss information-theoretic tools for obtaining optimized coarse-grained molecular models for both equilibrium and non-equilibrium molecular simulations. The latter are ubiquitous in physicochemical and biological applications, where they are typically associated with coupling mechanisms, multi-physics and/or boundary conditions. In general the non-equilibrium steady states are not known explicitly as they do not necessarily have a Gibbs structure. The presented approach can compare microscopic behavior of molecular systems to parametric and non-parametric coarse-grained models using the relative entropy between distributions on the path space and setting up a corresponding path-space variational inference problem. The methods can become entirely data-driven when the microscopic dynamics are replaced with corresponding correlated data in the form of time series. Furthermore, we present connections and generalizations of force matching methods in coarse-graining with path-space information methods. We demonstrate the enhanced transferability of information-based parameterizations to different observables, at a specific thermodynamic point, due to information inequalities. We discuss methodological connections between information-based coarse-graining of molecular systems and variational inference methods primarily developed in the machine learning community. However, we note that the work presented here addresses variational inference for correlated time series due to the focus on dynamics. The applicability of the proposed methods is demonstrated on high-dimensional stochastic processes given by overdamped and driven Langevin dynamics of interacting particles.

Non-equilibrium fluctuation-induced interactions

International Nuclear Information System (INIS)

Dean, David S

2012-01-01

We discuss non-equilibrium aspects of fluctuation-induced interactions. While the equilibrium behavior of such interactions has been extensively studied and is relatively well understood, the study of these interactions out of equilibrium is relatively new. We discuss recent results on the non-equilibrium behavior of systems whose dynamics is of the dissipative stochastic type and identify a number of outstanding problems concerning non-equilibrium fluctuation-induced interactions.

Nonequilibrium Distribution of the Microscopic Thermal Current in Steady Thermal Transport Systems

KAUST Repository

Yukawa, Satoshi; Ogushi, Fumiko; Shimada, Takashi; Ito, Nobuyasu

2010-01-01

Nonequilibrium distribution of the microscopic thermal current is investigated by direct molecular dynamics simulations. The microscopic thermal current in this study is defined by a flow of kinetic energy carried by a single particle. Asymptotic parallel and antiparallel tails of the nonequilibrium distribution to an average thermal current are identical to ones of equilibrium distribution with different temperatures. These temperatures characterizing the tails are dependent on a characteristic length in which a memory of dynamics is completely erased by several particle collisions. This property of the tails of nonequilibrium distribution is confirmed in other thermal transport systems. In addition, statistical properties of a particle trapped by a harmonic potential in a steady thermal conducting state are also studied. This particle feels a finite force parallel to the average thermal current as a consequence of the skewness of the distribution of the current. This force is interpreted as the microscopic origin of thermophoresis.

Determination of the crystal-melt interface kinetic coefficient from molecular dynamics simulations

International Nuclear Information System (INIS)

Monk, J; Mendelev, M I; Yang, Y; Asta, M; Hoyt, J J; Sun, D Y

2010-01-01

The generation and dissipation of latent heat at the moving solid–liquid boundary during non-equilibrium molecular dynamics (MD) simulations of crystallization can lead to significant underestimations of the interface mobility. In this work we examine the heat flow problem in detail for an embedded atom description of pure Ni and offer strategies to obtain an accurate value of the kinetic coefficient, μ. For free-solidification simulations in which the entire system is thermostated using a Nose–Hoover or velocity rescaling algorithm a non-uniform temperature profile is observed and a peak in the temperature is found at the interface position. It is shown that if the actual interface temperature, rather than the thermostat set point temperature, is used to compute the kinetic coefficient then μ is approximately a factor of 2 larger than previous estimates. In addition, we introduce a layered thermostat method in which several sub-regions, aligned normal to the crystallization direction, are indepently thermostated to a desired undercooling. We show that as the number of thermostats increases (i.e., as the width of each independently thermostated layer decreases) the kinetic coefficient converges to a value consistent with that obtained using a single thermostat and the calculated interface temperature. Also, the kinetic coefficient was determined from an analysis of the equilibrium fluctuations of the solid–liquid interface position. We demonstrate that the kinetic coefficient obtained from the relaxation times of the fluctuation spectrum is equivalent to the two values obtained from free-solidification simulations provided a simple correction is made for the contribution of heat flow controlled interface motion. Finally, a one-dimensional phase field model that captures the effect of thermostats has been developed. The mesoscale model reproduces qualitatively the results from MD simulations and thus allows for an a priori estimate of the accuracy of a

Viscosity of nanoconfined polyamide-6,6 oligomers: atomistic reverse nonequilibrium molecular dynamics simulation.

Science.gov (United States)

Eslami, Hossein; Müller-Plathe, Florian

2010-01-14

Our new simulation scheme in isosurface-isothermal-isobaric ensemble [Eslami, H.; Mozaffari, F.; Moghadasi, J.; Müller-Plathe, F. J. Chem. Phys. 2008, 129, 194702], developed to simulate confined fluids in equilibrium with bulk, is applied to simulate polyamide-6,6 oligomers confined between graphite surfaces. The reverse nonequilibrium molecular dynamics simulation technique is employed to shear the graphite surfaces. In this work, six confined systems, with different surface separations, as well as the bulk fluid are simulated. Our results show a viscosity increase with respect to the bulk fluid, with decreasing distance between surfaces. Also, the calculated viscosities of the confined systems show an oscillatory behavior with maxima corresponding to well-formed layers between the surfaces. We observe a substantial slip at the surfaces, with the slip length depending on the shear rate and on the slit width. The slip length and the slip velocity show oscillatory behavior with out-of-phase oscillations with respect to the solvation force oscillations. Moreover, the temperature difference between coldest and hottest parts of the simulation box depends on the shear rate and on the layering effect (solvation force oscillations). An analysis of oligomer deformation under flow shows preferential alignment of oligomers parallel to the surfaces with increasing shear rate.

Stochastic theory of nonequilibrium steady states and its applications. Part I

International Nuclear Information System (INIS)

Zhang Xuejuan; Qian Hong; Qian Min

2012-01-01

The concepts of equilibrium and nonequilibrium steady states are introduced in the present review as mathematical concepts associated with stationary Markov processes. For both discrete stochastic systems with master equations and continuous diffusion processes with Fokker–Planck equations, the nonequilibrium steady state (NESS) is characterized in terms of several key notions which are originated from nonequilibrium physics: time irreversibility, breakdown of detailed balance, free energy dissipation, and positive entropy production rate. After presenting this NESS theory in pedagogically accessible mathematical terms that require only a minimal amount of prerequisites in nonlinear differential equations and the theory of probability, it is applied, in Part I, to two widely studied problems: the stochastic resonance (also known as coherent resonance) and molecular motors (also known as Brownian ratchet). Although both areas have advanced rapidly on their own with a vast amount of literature, the theory of NESS provides them with a unifying mathematical foundation. Part II of this review contains applications of the NESS theory to processes from cellular biochemistry, ranging from enzyme catalyzed reactions, kinetic proofreading, to zeroth-order ultrasensitivity.

Molecular Complex of Lumiflavin and 2-Aminobenzoic Acid : Crystal Structure, Crystal Spectra, and Solution Properties

OpenAIRE

Shieh, Huey-Sheng; Ghisla, Sandro; Hanson, Louise Karle; Ludwig, Martha L.; Nordman, Christer E.

1981-01-01

The molecular complex lumiflavin-2-aminobenzoic acid monohydrate (C13H12N402●C7H7N02●H2O)crystallizes from aqueous solution as red triclinic prisms. The space group is P1 with cell dimensions a = 9.660 A, b = 14.866 Å, c = 7.045 Å, α = 95.44°, β = 95.86°, and γ = 105.66°. The crystal structure was solved by direct methods and refined by block-diagonal least-squares procedures to an R value of 0.050 on the basis of 1338 observed reflections. The structure is composed of stacks of alternating l...

NMR and molecular dynamics of small solutes in liquid crystals

International Nuclear Information System (INIS)

Luyten, P.R.

1984-01-01

NMR relaxation measurements, using a wide variety of modern pulse techniques, can yield valuable information about molecular motions. In this thesis the applicability of theories developed to describe spin relaxation phenomena in partially ordered media is studied for small solutes in liquid crystals. 1 H, 2 H, 13 C and 14 N relaxation measurements are interpreted by means of a model, in which fast anisotropic re-orientational motion in an orienting potential combined with contributions from cooperative fluctuations in the surrounding liquid crystal molecules, induce the observed frequency dependent relaxation behavior. (orig.)

Time-dependent non-equilibrium dielectric response in QM/continuum approaches

Energy Technology Data Exchange (ETDEWEB)

Ding, Feizhi; Lingerfelt, David B.; Li, Xiaosong, E-mail: benedetta.mennucci@unipi.it, E-mail: li@chem.washington.edu [Department of Chemistry, University of Washington, Seattle, Washington 98195 (United States); Mennucci, Benedetta, E-mail: benedetta.mennucci@unipi.it, E-mail: li@chem.washington.edu [Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Risorgimento 35, 56126 Pisa (Italy)

2015-01-21

The Polarizable Continuum Models (PCMs) are some of the most inexpensive yet successful methods for including the effects of solvation in quantum-mechanical calculations of molecular systems. However, when applied to the electronic excitation process, these methods are restricted to dichotomously assuming either that the solvent has completely equilibrated with the excited solute charge density (infinite-time limit), or that it retains the configuration that was in equilibrium with the solute prior to excitation (zero-time limit). This renders the traditional PCMs inappropriate for resolving time-dependent solvent effects on non-equilibrium solute electron dynamics like those implicated in the instants following photoexcitation of a solvated molecular species. To extend the existing methods to this non-equilibrium regime, we herein derive and apply a new formalism for a general time-dependent continuum embedding method designed to be propagated alongside the solute’s electronic degrees of freedom in the time domain. Given the frequency-dependent dielectric constant of the solvent, an equation of motion for the dielectric polarization is derived within the PCM framework and numerically integrated simultaneously with the time-dependent Hartree fock/density functional theory equations. Results for small molecular systems show the anticipated dipole quenching and electronic state dephasing/relaxation resulting from out-of-phase charge fluctuations in the dielectric and embedded quantum system.

Nonequilibrium Phenomena in Plasmas

CERN Document Server

Sharma, A Surjalal

2005-01-01

The complexity of plasmas arises mainly from their inherent nonlinearity and far from equilibrium nature. The nonequilibrium behavior of plasmas is evident in the natural settings, for example, in the Earth's magnetosphere. Similarly, laboratory plasmas such as fusion bottles also have their fair share of complex behavior. Nonequilibrium phenomena are intimately connected with statistical dynamics and form one of the growing research areas in modern nonlinear physics. These studies encompass the ideas of self-organization, phase transition, critical phenomena, self-organized criticality and turbulence. This book presents studies of complexity in the context of nonequilibrium phenomena using theory, modeling, simulations, and experiments, both in the laboratory and in nature.

Statistical mechanics of nonequilibrium liquids

CERN Document Server

Evans, Denis J; Craig, D P; McWeeny, R

1990-01-01

Statistical Mechanics of Nonequilibrium Liquids deals with theoretical rheology. The book discusses nonlinear response of systems and outlines the statistical mechanical theory. In discussing the framework of nonequilibrium statistical mechanics, the book explains the derivation of a nonequilibrium analogue of the Gibbsian basis for equilibrium statistical mechanics. The book reviews the linear irreversible thermodynamics, the Liouville equation, and the Irving-Kirkwood procedure. The text then explains the Green-Kubo relations used in linear transport coefficients, the linear response theory,

Determination of structure and properties of molecular crystals from first principles.

Science.gov (United States)

Szalewicz, Krzysztof

2014-11-18

CONSPECTUS: Until recently, it had been impossible to predict structures of molecular crystals just from the knowledge of the chemical formula for the constituent molecule(s). A solution of this problem has been achieved using intermolecular force fields computed from first principles. These fields were developed by calculating interaction energies of molecular dimers and trimers using an ab initio method called symmetry-adapted perturbation theory (SAPT) based on density-functional theory (DFT) description of monomers [SAPT(DFT)]. For clusters containing up to a dozen or so atoms, interaction energies computed using SAPT(DFT) are comparable in accuracy to the results of the best wave function-based methods, whereas the former approach can be applied to systems an order of magnitude larger than the latter. In fact, for monomers with a couple dozen atoms, SAPT(DFT) is about equally time-consuming as the supermolecular DFT approach. To develop a force field, SAPT(DFT) calculations are performed for a large number of dimer and possibly also trimer configurations (grid points in intermolecular coordinates), and the interaction energies are then fitted by analytic functions. The resulting force fields can be used to determine crystal structures and properties by applying them in molecular packing, lattice energy minimization, and molecular dynamics calculations. In this way, some of the first successful determinations of crystal structures were achieved from first principles, with crystal densities and lattice parameters agreeing with experimental values to within about 1%. Crystal properties obtained using similar procedures but empirical force fields fitted to crystal data have typical errors of several percent due to low sensitivity of empirical fits to interactions beyond those of the nearest neighbors. The first-principles approach has additional advantages over the empirical approach for notional crystals and cocrystals since empirical force fields can only be

Non-dissipative effects in nonequilibrium systems

CERN Document Server

Maes, Christian

2018-01-01

This book introduces and discusses both the fundamental aspects and the measurability of applications of time-symmetric kinetic quantities, outlining the features that constitute the non-dissipative branch of non-equilibrium physics. These specific features of non-equilibrium dynamics have largely been ignored in standard statistical mechanics texts. This introductory-level book offers novel material that does not take the traditional line of extending standard thermodynamics to the irreversible domain. It shows that although stationary dissipation is essentially equivalent with steady non-equilibrium and ubiquitous in complex phenomena, non-equilibrium is not determined solely by the time-antisymmetric sector of energy-entropy considerations. While this should not be very surprising, this book provides timely, simple reminders of the role of time-symmetric and kinetic aspects in the construction of non-equilibrium statistical mechanics.

Non-equilibrium spectroscopy of high-Tc superconductors

International Nuclear Information System (INIS)

Krasnov, V M

2009-01-01

In superconductors, recombination of two non-equilibrium quasiparticles into a Cooper pair results in emission of excitation that mediates superconductivity. This is the basis of the proposed new type of 'non-equilibrium' spectroscopy of high T c superconductors, which may open a possibility for direct and unambiguous determination of the coupling mechanism of high T c superconductivity. In case of low T c superconductors, the feasibility of such the non-equilibrium spectroscopy was demonstrated in classical phonon generation-detection experiments almost four decades ago. Recently it was demonstrated that a similar technique can be used for high T c superconductors, using natural intrinsic Josephson junctions both for injection of non-equilibrium quasiparticles and for detection of the non-equilibrium radiation. Here I analyze theoretically non-equilibrium phenomena in intrinsic Josephson junctions. It is shown that extreme non-equilibrium state can be achieved at bias equal to integer number of the gap voltage, which can lead to laser-like emission from the stack. I argue that identification of the boson type, constituting this non-equilibrium radiation would unambiguously reveal the coupling mechanism of high Tc superconductors.

Molecular reorientation of dye doped nematic liquid crystals in the laser illumination

International Nuclear Information System (INIS)

San, S. E.; Koeysal, O.; Ecevit, F. N.

2002-01-01

In this study it is investigated how dye doped nematic liquid crystals reorient under the illumination of laser beam whose wavelength is appropriate to absorbance characteristics of the doping dye. Nematic liquid crystal E7 is used with anthraquinone dye 1% wt/wt in the preparation of the sample and this material is filled in homegenously aligned measurement cell having 15 μm thickness. Mechanism of molecular reorientation includes the absorbance effects of the energy of laser by doping dye and this reorientation causes the refractive index of the material to be changed. There are potential application possibilities of such molecular reorientation based effects in nonlinear optics such as real time holography whose basis is grating diffraction that is observed and investigated in the frame of fundamentals of molecule light interaction mechanisms. Experimental analyses allowed finding characteristic values of diffraction signals depending on physical parameters of set up for a dye doped liquid crystal system and this system provided a 20 % diffraction efficiency under the optimum circumstances

Extended irreversible thermodynamics and non-equilibrium temperature

Directory of Open Access Journals (Sweden)

Casas-Vazquez, Jose'

2008-02-01

Full Text Available We briefly review the concept of non-equilibrium temperature from the perspectives of extended irreversible thermodynamics, fluctuation theory, and statistical mechanics. The relations between different proposals are explicitly examined in two especially simple systems: an ideal gas in steady shear flow and a forced harmonic oscillator in a thermal bath. We examine with special detail temperatures related to the average molecular kinetic energy along different spatial directions, to the average configurational energy, to the derivative of the entropy with respect to internal energy, to fluctuation-dissipation relation and discuss their measurement.

Physical phenomena in a low-temperature non-equilibrium plasma and in MHD generators with non-equilibrium conductivity

International Nuclear Information System (INIS)

Velikhov, E.P.; Golubev, V.S.; Dykhne, A.M.

1976-01-01

The paper assesses the position in 1975 of theoretical and experimental work on the physics of a magnetohydrodynamic generator with non-equilibrium plasma conductivity. This research started at the beginning of the 1960s; as work on the properties of thermally non-equilibrium plasma in magnetic fields and also in MHD generator ducts progressed, a number of phenomena were discovered and investigated that had either been unknown in plasma physics or had remained uninvestigated until that time: ionization instability and ionization turbulence of plasma in a magnetic field, acoustic instability of a plasma with anisotropic conductivity, the non-equilibrium ionization wave and the energy balance of a non-equilibrium plasma. At the same time, it was discovered what physical requirements an MHD generator with non-equilibrium conductivity must satisfy to achieve high efficiency in converting the thermal or kinetic energy of the gas flow into electric energy. The experiments on MHD power generation with thermally non-equilibrium plasma carried out up to 1975 indicated that it should be possible to achieve conversion efficiencies of up to 20-30%. (author)

Polarizability of acetanilide and RDX in the crystal: effect of molecular geometry

Science.gov (United States)

Tsiaousis, D.; Munn, R. W.; Smith, P. J.; Popelier, P. L. A.

2004-10-01

Density-functional theory with the B3LYP functional at the 6-311++G** level is used to calculate the dipole moment and the static polarizability for acetanilide and 1,3,5-trinitro-1,3,5-triazacyclohexane (RDX) in their in-crystal structures. For acetanilide the dipole moment is 2{1}/{2}% larger than for the gas-phase structure and for RDX (where there is a gross geometry change) it is 15% larger. The polarizability for the in-crystal structure is smaller than for the gas-phase structure by 3% for both species, whereas the in-crystal effective optical polarizability is larger than the gas-phase static polarizability for both crystals. Hence, effects in addition to the molecular geometry change in the crystal must be considered in order to interpret the effective polarizability completely.

DGR, GGR; molecular dynamical codes for simulating radiation damages in diamond and graphite crystals

International Nuclear Information System (INIS)

Taji, Yukichi

1984-06-01

Development has been made of molecular dynamical codes DGR and GGR to simulate radiation damages yielded in the diamond and graphite structure crystals, respectively. Though the usual molecular dynamical codes deal only with the central forces as the mutual interactions between atoms, the present codes can take account of noncentral forces to represent the effect of the covalent bonds characteristic of diamond or graphite crystals. It is shown that lattice defects yielded in these crystals are stable by themselves in the present method without any supports of virtual surface forces set on the crystallite surfaces. By this effect the behavior of lattice defects has become possible to be simulated in a more realistic manner. Some examples of the simulation with these codes are shown. (author)

An optimized intermolecular force field for hydrogen-bonded organic molecular crystals using atomic multipole electrostatics

International Nuclear Information System (INIS)

Pyzer-Knapp, Edward O.; Thompson, Hugh P. G.; Day, Graeme M.

2016-01-01

An empirically parameterized intermolecular force field is developed for crystal structure modelling and prediction. The model is optimized for use with an atomic multipole description of electrostatic interactions. We present a re-parameterization of a popular intermolecular force field for describing intermolecular interactions in the organic solid state. Specifically we optimize the performance of the exp-6 force field when used in conjunction with atomic multipole electrostatics. We also parameterize force fields that are optimized for use with multipoles derived from polarized molecular electron densities, to account for induction effects in molecular crystals. Parameterization is performed against a set of 186 experimentally determined, low-temperature crystal structures and 53 measured sublimation enthalpies of hydrogen-bonding organic molecules. The resulting force fields are tested on a validation set of 129 crystal structures and show improved reproduction of the structures and lattice energies of a range of organic molecular crystals compared with the original force field with atomic partial charge electrostatics. Unit-cell dimensions of the validation set are typically reproduced to within 3% with the re-parameterized force fields. Lattice energies, which were all included during parameterization, are systematically underestimated when compared with measured sublimation enthalpies, with mean absolute errors of between 7.4 and 9.0%

CRYSTAL AND MOLECULAR STRUCTURE OF 5-NITROPIRIDINE PIPERIDINE-SULFENAMIDE

OpenAIRE

Brito, Iván; León, Yasna; Arias, Mauricio; Vargas, Danitza; Carmona, Francisco; Ramírez, Eduardo; Restovic, Ambrosio; Cárdenas, Alejandro; Wittke, Oscar; López-Rodríguez, Matías

2002-01-01

The crystal and molecular structure of 5-nitropiridine piperidine-sulfenamide, C10H13N3O2 S is described and compared with other sulfenamides and with other similar compounds. This structure belongs to a type of divalent sulphur compound and crystallizes in the orthorhombic space group Pnma with a= 27.810(4), b=6.797(1), c=6.110(1)Å, and Dx =1.376 g cm-3 with Z=4. The S-N bond distance of 1.699(4) Å is shorter than a single S-N bond [1.74 Å]. The NO2-(C6H3N)-S-N(C 5H10) molecule lies on a cry...

Molecular-dynamic simulations of the thermophysical properties of hexanitrohexaazaisowurtzitane single crystal at high pressures and temperatures

Science.gov (United States)

Kozlova, S. A.; Gubin, S. A.; Maklashova, I. V.; Selezenev, A. A.

2017-11-01

Molecular dynamic simulations of isothermal compression parameters are performed for a hexanitrohexaazaisowurtzitane single crystal (C6H6O12N12) using a modified ReaxFF-log reactive force field. It is shown that the pressure-compression ratio curve for a single C6H6O12N12 crystal at constant temperature T = 300 K in pressure range P = 0.05-40 GPa is in satisfactory agreement with experimental compression isotherms obtained for a single C6H6O12N12 crystal. Hugoniot molecular-dynamic simulations of the shock-wave hydrostatic compression of a single C6H6O12N12 crystal are performed. Along with Hugoniot temperature-pressure curves, calculated shock-wave pressure-compression ratios for a single C6H6O12N12 crystal are obtained for a wide pressure range of P = 1-40 GPa. It is established that the percussive adiabat obtained for a single C6H6O12N12 crystal is in a good agreement with the experimental data. All calculations are performed using a LAMMPS molecular dynamics simulation software package that provides a ReaxFF-lg reactive force field to support the approach.

Synthesis, crystal growth and characterization of bioactive material: 2- Amino-1H-benzimidazolium pyridine-3-carboxylate single crystal- a proton transfer molecular complex

Science.gov (United States)

Fathima, K. Saiadali; Kavitha, P.; Anitha, K.

2017-09-01

The 1:1 molecular adducts 2- Amino-1H-benzimidazolium pyridine-3-carboxylate (2ABPC) was synthesized and grown as single crystal where 2-aminobenzimidazole (ABI) acts as a donor and nicotinic acid (NA) acts as an acceptor. The presence of proton and carbon were predicted using 1H and 13C NMR spectral analysis. The molecular structure of the crystal was elucidated by subjecting the grown crystals to the single crystal x-ray diffraction analysis and was refined by full matrix least-squares method to R = 0.038 for 2469 reflections. The vibrational modes of functional group have been studied using FTIR and Raman spectroscopic analysis. The UV-Vis spectrum exhibited a visible band at 246 nm for 2ABPC due to the nicotinate anion of the molecule. Further, the antimicrobial activity of 2ABPC complex against B. subtilis, klebsiella pneumonia, Pseudomonas eruginos and E. coli pathogens was investigated. Minimum Inhibitory Concentration (MIC) for this crystal was obtained using UV spectrometer against MRSA pathogen. It was found that the benzimidazole with aminogroup at position 2 increases the general antimicrobial activities of 2ABPC crystal.

Optical Absorption in Molecular Crystals from Time-Dependent Density Functional Theory

Science.gov (United States)

2017-04-23

Our approach represents a full solid-state calculation, allowing for polarization ef- fects while still capable of capturing inter-molecular dis...AFRL-AFOSR-UK-TR-2017-0030 Optical absorption in molecular crystals from time-dependent density functional theory Leeor Kronik WEIZMANN INSTITUTE OF...from time-dependent density functional theory 5a.  CONTRACT NUMBER 5b.  GRANT NUMBER FA9550-15-1-0290 5c.  PROGRAM ELEMENT NUMBER 61102F 6. AUTHOR(S

On nonequilibrium many-body systems. 1: The nonequilibrium statistical operator method

International Nuclear Information System (INIS)

Algarte, A.C.S.; Vasconcellos, A.R.; Luzzi, R.; Sampaio, A.J.C.

1985-01-01

The theoretical aspects involved in the treatment of many-body systems strongly departed from equilibrium are discussed. The nonequilibrium statistical operator (NSO) method is considered in detail. Using Jaynes' maximum entropy formalism complemented with an ad hoc hypothesis a nonequilibrium statistical operator is obtained. This approach introduces irreversibility from the outset and we recover statistical operators like those of Green-Mori and Zubarev as particular cases. The connection with Generalized Thermodynamics and the construction of nonlinear transport equations are briefly described. (Author) [pt

Mass transport thermodynamics in nonisothermal molecular liquid mixtures

Energy Technology Data Exchange (ETDEWEB)

Semenov, Semen N [Institute for Biochemical Physics, Russian Academy of Sciences, Moscow (Russian Federation); Schimpf, M E [Department of Chemistry and Biochemistry, Boise State University, Boise, ID (United States)

2009-10-31

Mass transport in a nonisothermal binary molecular mixture is systematically discussed in terms of nonequilibrium thermodynamics, which for the first time allows a consistent and unambiguous description of the process. The thermodynamic and hydrodynamic approaches are compared, revealing that nonequilibrium thermodynamics and physicochemical hydrodynamics yield essentially the same results for molecular systems. The applicability limits for the proposed version of the thermodynamic approach are determined for large particles. (methodological notes)

Stochastic pumping of non-equilibrium steady-states: how molecules adapt to a fluctuating environment.

Science.gov (United States)

Astumian, R D

2018-01-11

In the absence of input energy, a chemical reaction in a closed system ineluctably relaxes toward an equilibrium state governed by a Boltzmann distribution. The addition of a catalyst to the system provides a way for more rapid equilibration toward this distribution, but the catalyst can never, in and of itself, drive the system away from equilibrium. In the presence of external fluctuations, however, a macromolecular catalyst (e.g., an enzyme) can absorb energy and drive the formation of a steady state between reactant and product that is not determined solely by their relative energies. Due to the ubiquity of non-equilibrium steady states in living systems, the development of a theory for the effects of external fluctuations on chemical systems has been a longstanding focus of non-equilibrium thermodynamics. The theory of stochastic pumping has provided insight into how a non-equilibrium steady-state can be formed and maintained in the presence of dissipation and kinetic asymmetry. This effort has been greatly enhanced by a confluence of experimental and theoretical work on synthetic molecular machines designed explicitly to harness external energy to drive non-equilibrium transport and self-assembly.

Variational cellular model of the molecular and crystal electronic structure

International Nuclear Information System (INIS)

Ferreira, L.G.; Leite, J.R.

1977-12-01

A variational version of the cellular method is developed to calculate the electronic structure of molecules and crystals. Due to the simplicity of the secular equation, the method is easy to be implemented. Preliminary calculations on the hydrogen molecular ion suggest that it is also accurate and of fast convergence [pt

Anomalous doping of a molecular crystal monitored with confocal fluorescence microscopy: Terrylene in a p-terphenyl crystal

Science.gov (United States)

Białkowska, Magda; Deperasińska, Irena; Makarewicz, Artur; Kozankiewicz, Bolesław

2017-09-01

Highly terrylene doped single crystals of p-terphenyl, obtained by co-sublimation of both components, showed bright spots in the confocal fluorescence images. Polarization of the fluorescence excitation spectra, blinking and bleaching, and saturation behavior allowed us to attribute them to single molecules of terrylene anomalously embedded between two neighbor layers of the host crystal, in the (a,b) plane. Such an orientation of terrylene molecules results in much more efficient absorption and collection of the fluorescence photons than in the case of previously investigated molecules embedded in the substitution sites. The above conclusion was supported by quantum chemistry calculations. We postulate that the kind of doping considered in this work should be possible in other molecular crystals where the host molecules are organized in a herringbone pattern.

First principles modeling of hydrocarbons conversion in non-equilibrium plasma

Energy Technology Data Exchange (ETDEWEB)

Deminsky, M.A.; Strelkova, M.I.; Durov, S.G.; Jivotov, V.K.; Rusanov, V.D.; Potapkin, B.V. [Russian Research Centre Kurchatov Inst., Moscow (Russian Federation)

2001-07-01

Theoretical justification of catalytic activity of non-equilibrium plasma in hydrocarbons conversion process is presented in this paper. The detailed model of highest hydrocarbons conversion includes the gas-phase reactions, chemistry of the growth of polycyclic aromatic hydrocarbons (PAHs), precursor of soot particles formation, neutral, charged clusters and soot particle formation, ion-molecular gas-phase and heterogeneous chemistry. The results of theoretical analysis are compared with experimental results. (authors)

Genarris: Random generation of molecular crystal structures and fast screening with a Harris approximation

Science.gov (United States)

Li, Xiayue; Curtis, Farren S.; Rose, Timothy; Schober, Christoph; Vazquez-Mayagoitia, Alvaro; Reuter, Karsten; Oberhofer, Harald; Marom, Noa

2018-06-01

We present Genarris, a Python package that performs configuration space screening for molecular crystals of rigid molecules by random sampling with physical constraints. For fast energy evaluations, Genarris employs a Harris approximation, whereby the total density of a molecular crystal is constructed via superposition of single molecule densities. Dispersion-inclusive density functional theory is then used for the Harris density without performing a self-consistency cycle. Genarris uses machine learning for clustering, based on a relative coordinate descriptor developed specifically for molecular crystals, which is shown to be robust in identifying packing motif similarity. In addition to random structure generation, Genarris offers three workflows based on different sequences of successive clustering and selection steps: the "Rigorous" workflow is an exhaustive exploration of the potential energy landscape, the "Energy" workflow produces a set of low energy structures, and the "Diverse" workflow produces a maximally diverse set of structures. The latter is recommended for generating initial populations for genetic algorithms. Here, the implementation of Genarris is reported and its application is demonstrated for three test cases.

Diffusion of nonequilibrium quasi-particles in a cuprate superconductor

International Nuclear Information System (INIS)

Gedik, N.; Orenstein, J.; Liang, Ruixing; Bonn, D.A.; Hardy, W.N.

2003-01-01

We report a transport study of nonequilibrium quasi-particles in a high-transition-temperature cuprate superconductor using the transient grating technique. Low-intensity laser excitation (at a photon energy of 1.5 electron volts) was used to introduce a spatially periodic density of quasi-particles into a high-quality untwinned single crystal of YBa2Cu3O6.5. Probing the evolution of the initial density through space and time yielded the quasi-particle diffusion coefficient and the inelastic and elastic scattering rates. The technique reported here is potentially applicable to precision measurements of quasi-particle dynamics not only in cuprate superconductors but in other electronic systems as well

Aerospace Applications of Non-Equilibrium Plasma

Science.gov (United States)

Blankson, Isaiah M.

2016-01-01

Nonequilibrium plasma/non-thermal plasma/cold plasmas are being used in a wide range of new applications in aeronautics, active flow control, heat transfer reduction, plasma-assisted ignition and combustion, noise suppression, and power generation. Industrial applications may be found in pollution control, materials surface treatment, and water purification. In order for these plasma processes to become practical, efficient means of ionization are necessary. A primary challenge for these applications is to create a desired non-equilibrium plasma in air by preventing the discharge from transitioning into an arc. Of particular interest is the impact on simulations and experimental data with and without detailed consideration of non-equilibrium effects, and the consequences of neglecting non-equilibrium. This presentation will provide an assessment of the presence and influence of non-equilibrium phenomena for various aerospace needs and applications. Specific examples to be considered will include the forward energy deposition of laser-induced non-equilibrium plasmoids for sonic boom mitigation, weakly ionized flows obtained from pulsed nanosecond discharges for an annular Hall type MHD generator duct for turbojet energy bypass, and fundamental mechanisms affecting the design and operation of novel plasma-assisted reactive systems in dielectric liquids (water purification, in-pipe modification of fuels, etc.).

Nonequilibrium statistical physics

CERN Document Server

Röpke, Gerd

2013-01-01

Authored by one of the top theoretical physicists in Germany, and a well-known authority in the field, this is the only coherent presentation of the subject suitable for masters and PhD students, as well as postdocs in physics and related disciplines.Starting from a general discussion of the nonequilibrium state, different standard approaches such as master equations, and kinetic and linear response theory, are derived after special assumptions. This allows for an insight into the problems of nonequilibrium physics, a discussion of the limits, and suggestions for improvements. Applications

Time-dependent nonequilibrium soft x-ray response during a spin crossover

Energy Technology Data Exchange (ETDEWEB)

van Veenendaal, Michel

2018-03-01

The rapid development of high-brilliance pulsed X-ray sources with femtosecond time resolution has created a need for a better theoretical understanding of the time-dependent soft-X-ray response of dissipative many-body quantum systems. It is demonstrated how soft-X-ray spectroscopies, such as X-ray absorption and resonant inelastic X-ray scattering at transition-metal L-edges, can provide insight into intersystem crossings, such as a spin crossover. The photoinduced doublet-to-quartet spin crossover on cobalt in Fe-Co Prussian blue analogues is used as an example to demonstrate how the X-ray response is affected by the dissipative nonequilibrium dynamics. The time-dependent soft-X-ray spectra provide a wealth of information that reflect the changes in the nonequilibrium initial state via continuously changing spectral lineshapes that cannot be decomposed into initial photoexcited and final metastable spectra, strong broadenings, a collapse of clear selection rules during the intersystem crossing, strong fluctuations in the isotropic branching ratio in X-ray absorption, and crystal-field collapse/oscillations and strongly time-dependent anti-Stokes processes in RIXS.

Charge transport in organic molecular semiconductors from first principles: The bandlike hole mobility in a naphthalene crystal

Science.gov (United States)

Lee, Nien-En; Zhou, Jin-Jian; Agapito, Luis A.; Bernardi, Marco

2018-03-01

Predicting charge transport in organic molecular crystals is notoriously challenging. Carrier mobility calculations in organic semiconductors are dominated by quantum chemistry methods based on charge hopping, which are laborious and only moderately accurate. We compute from first principles the electron-phonon scattering and the phonon-limited hole mobility of naphthalene crystal in the framework of ab initio band theory. Our calculations combine GW electronic bandstructures, ab initio electron-phonon scattering, and the Boltzmann transport equation. The calculated hole mobility is in very good agreement with experiment between 100 -300 K , and we can predict its temperature dependence with high accuracy. We show that scattering between intermolecular phonons and holes regulates the mobility, though intramolecular phonons possess the strongest coupling with holes. We revisit the common belief that only rigid molecular motions affect carrier dynamics in organic molecular crystals. Our paper provides a quantitative and rigorous framework to compute charge transport in organic crystals and is a first step toward reconciling band theory and carrier hopping computational methods.

Non-exponential dynamic relaxation in strongly nonequilibrium nonideal plasmas

International Nuclear Information System (INIS)

Morozov, I V; Norman, G E

2003-01-01

Relaxation of kinetic energy to the equilibrium state is simulated by the molecular dynamics method for nonideal two-component non-degenerate plasmas. Three limiting examples of initial states of strongly nonequilibrium plasma are considered: zero electron velocities, zero ion velocities and zero velocities of both electrons and ions. The initial non-exponential stage, its duration τ nB and subsequent exponential stages of the relaxation process are studied for a wide range of the nonideality parameter and the ion mass

Non-equilibrium supramolecular polymerization.

Science.gov (United States)

Sorrenti, Alessandro; Leira-Iglesias, Jorge; Markvoort, Albert J; de Greef, Tom F A; Hermans, Thomas M

2017-09-18

Supramolecular polymerization has been traditionally focused on the thermodynamic equilibrium state, where one-dimensional assemblies reside at the global minimum of the Gibbs free energy. The pathway and rate to reach the equilibrium state are irrelevant, and the resulting assemblies remain unchanged over time. In the past decade, the focus has shifted to kinetically trapped (non-dissipative non-equilibrium) structures that heavily depend on the method of preparation (i.e., pathway complexity), and where the assembly rates are of key importance. Kinetic models have greatly improved our understanding of competing pathways, and shown how to steer supramolecular polymerization in the desired direction (i.e., pathway selection). The most recent innovation in the field relies on energy or mass input that is dissipated to keep the system away from the thermodynamic equilibrium (or from other non-dissipative states). This tutorial review aims to provide the reader with a set of tools to identify different types of self-assembled states that have been explored so far. In particular, we aim to clarify the often unclear use of the term "non-equilibrium self-assembly" by subdividing systems into dissipative, and non-dissipative non-equilibrium states. Examples are given for each of the states, with a focus on non-dissipative non-equilibrium states found in one-dimensional supramolecular polymerization.

Strong exciton-photon coupling in organic single crystal microcavity with high molecular orientation

Energy Technology Data Exchange (ETDEWEB)

Goto, Kaname [Department of Electronics, Graduate School of Science and Technology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585 (Japan); Yamashita, Kenichi, E-mail: yamasita@kit.ac.jp [Faculty of Electrical Engineering and Electronics, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585 (Japan); Yanagi, Hisao [Graduate School of Materials Science, Nara Institute of Science and Technology (NAIST), 8916-5 Takayama, Ikoma, Nara 630-0192 (Japan); Yamao, Takeshi; Hotta, Shu [Faculty of Materials Science and Technology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585 (Japan)

2016-08-08

Strong exciton-photon coupling has been observed in a highly oriented organic single crystal microcavity. This microcavity consists of a thiophene/phenylene co-oligomer (TPCO) single crystal laminated on a high-reflection distributed Bragg reflector. In the TPCO crystal, molecular transition dipole was strongly polarized along a certain horizontal directions with respect to the main crystal plane. This dipole polarization causes significantly large anisotropies in the exciton transition and optical constants. Especially the anisotropic exciton transition was found to provide the strong enhancement in the coupling with the cavity mode, which was demonstrated by a Rabi splitting energy as large as ∼100 meV even in the “half-vertical cavity surface emitting lasing” microcavity structure.

Strong exciton-photon coupling in organic single crystal microcavity with high molecular orientation

Science.gov (United States)

Goto, Kaname; Yamashita, Kenichi; Yanagi, Hisao; Yamao, Takeshi; Hotta, Shu

2016-08-01

Strong exciton-photon coupling has been observed in a highly oriented organic single crystal microcavity. This microcavity consists of a thiophene/phenylene co-oligomer (TPCO) single crystal laminated on a high-reflection distributed Bragg reflector. In the TPCO crystal, molecular transition dipole was strongly polarized along a certain horizontal directions with respect to the main crystal plane. This dipole polarization causes significantly large anisotropies in the exciton transition and optical constants. Especially the anisotropic exciton transition was found to provide the strong enhancement in the coupling with the cavity mode, which was demonstrated by a Rabi splitting energy as large as ˜100 meV even in the "half-vertical cavity surface emitting lasing" microcavity structure.

Strong exciton-photon coupling in organic single crystal microcavity with high molecular orientation

International Nuclear Information System (INIS)

Goto, Kaname; Yamashita, Kenichi; Yanagi, Hisao; Yamao, Takeshi; Hotta, Shu

2016-01-01

Strong exciton-photon coupling has been observed in a highly oriented organic single crystal microcavity. This microcavity consists of a thiophene/phenylene co-oligomer (TPCO) single crystal laminated on a high-reflection distributed Bragg reflector. In the TPCO crystal, molecular transition dipole was strongly polarized along a certain horizontal directions with respect to the main crystal plane. This dipole polarization causes significantly large anisotropies in the exciton transition and optical constants. Especially the anisotropic exciton transition was found to provide the strong enhancement in the coupling with the cavity mode, which was demonstrated by a Rabi splitting energy as large as ∼100 meV even in the “half-vertical cavity surface emitting lasing” microcavity structure.

Purification, crystallization, preliminary X-ray diffraction and molecular-replacement studies of great cormorant (Phalacrocorax carbo) haemoglobin

International Nuclear Information System (INIS)

Jagadeesan, G.; Malathy, P.; Gunasekaran, K.; Harikrishna Etti, S.; Aravindhan, S.

2014-01-01

The great cormorant hemoglobin has been isolated, purified and crystallized and the three dimensional structure is solved using molecular replacement technique. Haemoglobin is the iron-containing oxygen-transport metalloprotein that is present in the red blood cells of all vertebrates. In recent decades, there has been substantial interest in attempting to understand the structural basis and functional diversity of avian haemoglobins. Towards this end, purification, crystallization, preliminary X-ray diffraction and molecular-replacement studies have been carried out on cormorant (Phalacrocorax carbo) haemoglobin. Crystals were grown by the hanging-drop vapour-diffusion method using PEG 3350, NaCl and glycerol as precipitants. The crystals belonged to the trigonal system P3 1 21, with unit-cell parameters a = b = 55.64, c = 153.38 Å, β = 120.00°; a complete data set was collected to a resolution of 3.5 Å. Matthews coefficient analysis indicated that the crystals contained a half-tetramer in the asymmetric unit

Purification, crystallization, preliminary X-ray diffraction and molecular-replacement studies of great cormorant (Phalacrocorax carbo) haemoglobin

Energy Technology Data Exchange (ETDEWEB)

Jagadeesan, G. [Presidency College, Chennai 600 005 (India); Malathy, P.; Gunasekaran, K. [University of Madras, Chennai 600 025 (India); Harikrishna Etti, S. [GKM College of Engineering and Technology, Kamaraj Salai, Chennai 600 063 (India); Aravindhan, S., E-mail: aravindhanpresidency@gmail.com [Presidency College, Chennai 600 005 (India)

2014-10-25

The great cormorant hemoglobin has been isolated, purified and crystallized and the three dimensional structure is solved using molecular replacement technique. Haemoglobin is the iron-containing oxygen-transport metalloprotein that is present in the red blood cells of all vertebrates. In recent decades, there has been substantial interest in attempting to understand the structural basis and functional diversity of avian haemoglobins. Towards this end, purification, crystallization, preliminary X-ray diffraction and molecular-replacement studies have been carried out on cormorant (Phalacrocorax carbo) haemoglobin. Crystals were grown by the hanging-drop vapour-diffusion method using PEG 3350, NaCl and glycerol as precipitants. The crystals belonged to the trigonal system P3{sub 1}21, with unit-cell parameters a = b = 55.64, c = 153.38 Å, β = 120.00°; a complete data set was collected to a resolution of 3.5 Å. Matthews coefficient analysis indicated that the crystals contained a half-tetramer in the asymmetric unit.

Experiment-scale molecular simulation study of liquid crystal thin films

Science.gov (United States)

Nguyen, Trung Dac; Carrillo, Jan-Michael Y.; Matheson, Michael A.; Brown, W. Michael

2014-03-01

Supercomputers have now reached a performance level adequate for studying thin films with molecular detail at the relevant scales. By exploiting the power of GPU accelerators on Titan, we have been able to perform simulations of characteristic liquid crystal films that provide remarkable qualitative agreement with experimental images. We have demonstrated that key features of spinodal instability can only be observed with sufficiently large system sizes, which were not accessible with previous simulation studies. Our study emphasizes the capability and significance of petascale simulations in providing molecular-level insights in thin film systems as well as other interfacial phenomena.

Influence of pre-strain on thermal stability of non-equilibrium microstructures in a low alloy steel

International Nuclear Information System (INIS)

Sun, Chao; Yang, Shanwu; Wang, Xian; Zhang, Rui; He, Xinlai

2013-01-01

Highlights: ► High pre-strain and low pre-strain influence differently on thermal stability of non-equilibrium microstructures. ► High pre-strain, in which dislocation sources can be actuated and dislocation density is increased excessively, will markedly promote recrystallization. ► Low pre-strain, in which dislocations are induced to redistribute into a low-energy structure, can slow down microstructure evolution. -- Abstract: Non-equilibrium microstructures in steels including martensite and bainite, which are main phases in current high strength steels, possess high strength and hardness. However, these microstructures are metastable due to their high density of crystal defects. In the present investigation, hardness test, optical microscopy and electron microscopy have been carried out to detect microstructure evolution in a low alloy steel, which was reheated and held isothermally at 550 °C. Special emphasis was put on influence of pre-strain on thermal stability of non-equilibrium microstructures. It is found that high pre-strain, in which dislocation sources can be actuated and dislocation density is increased excessively, will markedly promote recrystallization of non-equilibrium microstructures at 550 °C, while low pre-strain, in which only can mono-glide of dislocations can be operated in each grain and dislocations are induced to redistribute into a low-energy structure, can slow down microstructure evolution

Nonequilibrium quantum field theories

International Nuclear Information System (INIS)

Niemi, A.J.

1988-01-01

Combining the Feynman-Vernon influence functional formalism with the real-time formulation of finite-temperature quantum field theories we present a general approach to relativistic quantum field theories out of thermal equilibrium. We clarify the physical meaning of the additional fields encountered in the real-time formulation of quantum statistics and outline diagrammatic rules for perturbative nonequilibrium computations. We derive a generalization of Boltzmann's equation which gives a complete characterization of relativistic nonequilibrium phenomena. (orig.)

Dynamical study of a polydisperse hard-sphere system

KAUST Repository

Nogawa, Tomoaki; Ito, Nobuyasu; Watanabe, Hiroshi

2010-01-01

We study the interplay between the fluid-crystal transition and the glass transition of elastic sphere system with polydispersity using nonequilibrium molecular dynamics simulations. It is found that the end point of the crystal-fluid transition

Studying the Impact of Modified Saccharides on the Molecular Dynamics and Crystallization Tendencies of Model API Nifedipine.

Science.gov (United States)

Kaminska, E; Tarnacka, M; Wlodarczyk, P; Jurkiewicz, K; Kolodziejczyk, K; Dulski, M; Haznar-Garbacz, D; Hawelek, L; Kaminski, K; Wlodarczyk, A; Paluch, M

2015-08-03

Molecular dynamics of pure nifedipine and its solid dispersions with modified carbohydrates as well as the crystallization kinetics of active pharmaceutical ingredient (API) above and below the glass transition temperature were studied in detail by means of broadband dielectric spectroscopy (BDS), differential scanning calorimetry (DSC), and X-ray diffraction method. It was found that the activation barrier of crystallization increases in molecular dispersions composed of acetylated disaccharides, whereas it slightly decreases in those consisting of modified monocarbohydrates for the experiments carried out above the glass transition temperature. As shown by molecular dynamics simulations it can be related to the strength, character, and structure of intermolecular interactions between API and saccharides, which vary dependently on the excipient. Long-term physical stability studies showed that, in solid dispersions consisting of acetylated maltose and acetylated sucrose, the crystallization of nifedipine is dramatically slowed down, although it is still observable for a low concentration of excipients. With increasing content of modified carbohydrates, the crystallization of API becomes completely suppressed. This is most likely due to additional barriers relating to the intermolecular interactions and diffusion of nifedipine that must be overcome to trigger the crystallization process.

Nonequilibrium Statistical Operator Method and Generalized Kinetic Equations

Science.gov (United States)

Kuzemsky, A. L.

2018-01-01

We consider some principal problems of nonequilibrium statistical thermodynamics in the framework of the Zubarev nonequilibrium statistical operator approach. We present a brief comparative analysis of some approaches to describing irreversible processes based on the concept of nonequilibrium Gibbs ensembles and their applicability to describing nonequilibrium processes. We discuss the derivation of generalized kinetic equations for a system in a heat bath. We obtain and analyze a damped Schrödinger-type equation for a dynamical system in a heat bath. We study the dynamical behavior of a particle in a medium taking the dissipation effects into account. We consider the scattering problem for neutrons in a nonequilibrium medium and derive a generalized Van Hove formula. We show that the nonequilibrium statistical operator method is an effective, convenient tool for describing irreversible processes in condensed matter.

Structure and Stability of Molecular Crystals with Many-Body Dispersion-Inclusive Density Functional Tight Binding.

Science.gov (United States)

Mortazavi, Majid; Brandenburg, Jan Gerit; Maurer, Reinhard J; Tkatchenko, Alexandre

2018-01-18

Accurate prediction of structure and stability of molecular crystals is crucial in materials science and requires reliable modeling of long-range dispersion interactions. Semiempirical electronic structure methods are computationally more efficient than their ab initio counterparts, allowing structure sampling with significant speedups. We combine the Tkatchenko-Scheffler van der Waals method (TS) and the many-body dispersion method (MBD) with third-order density functional tight-binding (DFTB3) via a charge population-based method. We find an overall good performance for the X23 benchmark database of molecular crystals, despite an underestimation of crystal volume that can be traced to the DFTB parametrization. We achieve accurate lattice energy predictions with DFT+MBD energetics on top of vdW-inclusive DFTB3 structures, resulting in a speedup of up to 3000 times compared with a full DFT treatment. This suggests that vdW-inclusive DFTB3 can serve as a viable structural prescreening tool in crystal structure prediction.

Interaction of Tenebrio Molitor Antifreeze Protein with Ice Crystal: Insights from Molecular Dynamics Simulations.

Science.gov (United States)

Ramya, L; Ramakrishnan, Vigneshwar

2016-07-01

Antifreeze proteins (AFP) observed in cold-adapting organisms bind to ice crystals and prevent further ice growth. However, the molecular mechanism of AFP-ice binding and AFP-inhibited ice growth remains unclear. Here we report the interaction of the insect antifreeze protein (Tenebrio molitor, TmAFP) with ice crystal by molecular dynamics simulation studies. Two sets of simulations were carried out at 263 K by placing the protein near the primary prism plane (PP) and basal plane (BL) of the ice crystal. To delineate the effect of temperatures, both the PP and BL simulations were carried out at 253 K as well. The analyses revealed that the protein interacts strongly with the ice crystal in BL simulation than in PP simulation both at 263 K and 253 K. Further, it was observed that the interactions are primarily mediated through the interface waters. We also observed that as the temperature decreases, the interaction between the protein and the ice increases which can be attributed to the decreased flexibility and the increased structuring of the protein at low temperature. In essence, our study has shed light on the interaction mechanism between the TmAFP antifreeze protein and the ice crystal. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Formation of the molecular crystal structure during the vacuum sublimation of paracetamol

Science.gov (United States)

Belyaev, A. P.; Rubets, V. P.; Antipov, V. V.; Bordei, N. S.

2015-04-01

The results from structural and thermal studies on the formation of molecular crystals during the vacuum sublimation of paracetamol from its vapor phase are given. It is established that the vapor-crystal phase transition proceeds in a complicated way as the superposition of two phase transitions: a first-order phase transition with a change in density, and a second-order phase transition with a change in ordering. It is shown that the latter is a smeared phase transition that proceeds with the formation of a pretransitional phase that is irreversibly dissipated during phase transformation, leading to the formation of crystals of the rhombic syngony. Data from differential scanning calorimetry and X-ray diffraction analysis are presented along with microphotographs.

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

Science.gov (United States)

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

2016-06-22

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

Melting of superheated molecular crystals

Science.gov (United States)

Cubeta, Ulyana; Bhattacharya, Deepanjan; Sadtchenko, Vlad

2017-07-01

Melting dynamics of micrometer scale, polycrystalline samples of isobutane, dimethyl ether, methyl benzene, and 2-propanol were investigated by fast scanning calorimetry. When films are superheated with rates in excess of 105 K s-1, the melting process follows zero-order, Arrhenius-like kinetics until approximately half of the sample has transformed. Such kinetics strongly imply that melting progresses into the bulk via a rapidly moving solid-liquid interface that is likely to originate at the sample's surface. Remarkably, the apparent activation energies for the phase transformation are large; all exceed the enthalpy of vaporization of each compound and some exceed it by an order of magnitude. In fact, we find that the crystalline melting kinetics are comparable to the kinetics of dielectric α-relaxation in deeply supercooled liquids. Based on these observations, we conclude that the rate of non-isothermal melting for superheated, low-molecular-weight crystals is limited by constituent diffusion into an abnormally dense, glass-like, non-crystalline phase.

Use of X-ray diffraction, molecular simulations, and spectroscopy to determine the molecular packing in a polymer-fullerene bimolecular crystal

KAUST Repository

Miller, Nichole Cates

2012-09-05

The molecular packing in a polymer: fullerene bimolecular crystal is determined using X-ray diffraction (XRD), molecular mechanics (MM) and molecular dynamics (MD) simulations, 2D solid-state NMR spectroscopy, and IR absorption spectroscopy. The conformation of the electron-donating polymer is significantly disrupted by the incorporation of the electron-accepting fullerene molecules, which introduce twists and bends along the polymer backbone and 1D electron-conducting fullerene channels. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Use of X-ray diffraction, molecular simulations, and spectroscopy to determine the molecular packing in a polymer-fullerene bimolecular crystal

KAUST Repository

Miller, Nichole Cates; Cho, Eunkyung; Junk, Matthias J N; Gysel, Roman; Risko, Chad; Kim, Dongwook; Sweetnam, Sean; Miller, Chad E.; Richter, Lee J.; Kline, Regis Joseph; Heeney, Martin J.; McCulloch, Iain A.; Amassian, Aram; Acevedo-Feliz, Daniel; Knox, Christopher; Hansen, Michael Ryan; Dudenko, Dmytro V.; Chmelka, Bradley F.; Toney, Michael F.; Bré das, Jean Luc; McGehee, Michael D.

2012-01-01

The molecular packing in a polymer: fullerene bimolecular crystal is determined using X-ray diffraction (XRD), molecular mechanics (MM) and molecular dynamics (MD) simulations, 2D solid-state NMR spectroscopy, and IR absorption spectroscopy. The conformation of the electron-donating polymer is significantly disrupted by the incorporation of the electron-accepting fullerene molecules, which introduce twists and bends along the polymer backbone and 1D electron-conducting fullerene channels. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Non-equilibrium dog-flea model

Science.gov (United States)

Ackerson, Bruce J.

2017-11-01

We develop the open dog-flea model to serve as a check of proposed non-equilibrium theories of statistical mechanics. The model is developed in detail. Then it is applied to four recent models for non-equilibrium statistical mechanics. Comparison of the dog-flea solution with these different models allows checking claims and giving a concrete example of the theoretical models.

Non-equilibrium phase transitions

CERN Document Server

Henkel, Malte; Lübeck, Sven

2009-01-01

This book describes two main classes of non-equilibrium phase-transitions: (a) static and dynamics of transitions into an absorbing state, and (b) dynamical scaling in far-from-equilibrium relaxation behaviour and ageing. The first volume begins with an introductory chapter which recalls the main concepts of phase-transitions, set for the convenience of the reader in an equilibrium context. The extension to non-equilibrium systems is made by using directed percolation as the main paradigm of absorbing phase transitions and in view of the richness of the known results an entire chapter is devoted to it, including a discussion of recent experimental results. Scaling theories and a large set of both numerical and analytical methods for the study of non-equilibrium phase transitions are thoroughly discussed. The techniques used for directed percolation are then extended to other universality classes and many important results on model parameters are provided for easy reference.

Studies of Phase Transformation in Molecular Crystals Using the Positron Annihilation Technique

DEFF Research Database (Denmark)

Eldrup, Morten Mostgaard; Lightbody, David; Sherwood, John N.

1980-01-01

An examination has been made of the brittle/plastic phase transformation in the molecular crystals cyclohexane, DL-camphene and succinonitrile using the positron annihilation technique. In each material, the transition is characterized by a distinct increase in ortho-positronium lifetime. The inf...

Jacobian elliptic wave solutions in an anharmonic molecular crystal model

International Nuclear Information System (INIS)

Teh, C.G.R.; Lee, B.S.; Koo, W.K.

1997-07-01

Explicit Jacobian elliptic wave solutions are found in the anharmonic molecular crystal model for both the continuum limit and discrete modes. This class of wave solutions include the famous pulse-like and kink-like solitary modes. We would also like to report on the existence of some highly discrete staggered solitary wave modes not found in the continuum limit. (author). 9 refs, 1 fig

Spatially resolved analysis of short-range structure perturbations in a plastically bent molecular crystal

Science.gov (United States)

Panda, Manas K.; Ghosh, Soumyajit; Yasuda, Nobuhiro; Moriwaki, Taro; Mukherjee, Goutam Dev; Reddy, C. Malla; Naumov, Panče

2015-01-01

The exceptional mechanical flexibility observed with certain organic crystals defies the common perception of single crystals as brittle objects. Here, we describe the morphostructural consequences of plastic deformation in crystals of hexachlorobenzene that can be bent mechanically at multiple locations to 360° with retention of macroscopic integrity. This extraordinary plasticity proceeds by segregation of the bent section into flexible layers that slide on top of each other, thereby generating domains with slightly different lattice orientations. Microscopic, spectroscopic and diffraction analyses of the bent crystal showed that the preservation of crystal integrity when stress is applied on the (001) face requires sliding of layers by breaking and re-formation of halogen-halogen interactions. Application of stress on the (100) face, in the direction where π···π interactions dominate the packing, leads to immediate crystal disintegration. Within a broader perspective, this study highlights the yet unrecognized extraordinary malleability of molecular crystals with strongly anisotropic supramolecular interactions.

The Oseen-Frank Limit of Onsager's Molecular Theory for Liquid Crystals

Science.gov (United States)

Liu, Yuning; Wang, Wei

2018-03-01

We study the relationship between Onsager's molecular theory, which involves the effects of nonlocal molecular interactions and the Oseen-Frank theory for nematic liquid crystals. Under the molecular setting, we prove the existence of global minimizers for the generalized Onsager's free energy, subject to a nonlocal boundary condition which prescribes the second moment of the number density function near the boundary. Moreover, when the re-scaled interaction distance tends to zero, the global minimizers will converge to a uniaxial distribution predicted by a minimizing harmonic map. This is achieved through the investigations of the compactness property and the boundary behaviors of the corresponding second moments. A similar result is established for critical points of the free energy that fulfill a natural energy bound.

Exploring Chemical and Thermal Non-equilibrium in Nitrogen Arcs

International Nuclear Information System (INIS)

Ghorui, S; Das, A K

2012-01-01

Plasma torches operating with nitrogen are of special importance as they can operate with usual tungsten based refractory electrodes and offer radical rich non-oxidizing high temperature environment for plasma chemistry. Strong gradients in temperature as well as species densities and huge convective fluxes lead to varying degrees of chemical non-equilibrium in associated regions. An axi-symmetric two-temperature chemical non-equilibrium model of a nitrogen plasma torch has been developed to understand the effects of thermal and chemical non-equilibrium in arcs. A 2-D finite volume CFD code in association with a non-equilibrium property routine enabled extraction of steady state self-consistent distributions of various plasma quantities inside the torch under various thermal and chemical non-equilibrium conditions. Chemical non-equilibrium has been incorporated through computation of diffusive and convective fluxes in each finite volume cell in every iteration and associating corresponding thermodynamic and transport properties through the scheme of 'chemical non-equilibrium parameter' introduced by Ghorui et. al. Recombination coefficient data from Nahar et. al. and radiation data from Krey and Morris have been used in the simulation. Results are presented for distributions of temperature, pressure, velocity, current density, electric potential, species densities and chemical non-equilibrium effects. Obtained results are compared with similar results under LTE.

Dielectric relaxation spectra of liquid crystals in relation to molecular structure

International Nuclear Information System (INIS)

Wrobel, S.

1986-07-01

The dielectric spectra obtained for some members of two homologous series, i.e. for di-alkoxyazoxybenzenes and penthyl-alkoxythiobenzoates, are discussed qualitatively on the basis of the Nordio-Rigatti-Segre diffusion model. It is additionally assumed that the molecular reorientations take place about the principal axes of the inertia tensor. The distribution of correlation times, which is strongly temperature dependent in the vicinity of the clearing point, is interpreted as being caused by fluctuations of the principal axes frame which are due to conformation changes inside the end chains. The Bauer equation is used to describe both principal molecular reorientations, i.e. the reorientations about the long and short axis, observed in liquid crystalline structure by means of dielectric relaxation methods. The energies and entropies of activation have been computed for both principal reorientations. The differences between the high frequency limit of the dielectric permittivity and the refractive index squared of liquid crystals are explained in terms of two librational motions of the molecules observed by other experimental techniques, viz. far infra-red, Raman and inelastic neutron scattering spectroscopies, and found in this work on the basis of dielectrically measured energy barriers. It has been shown qualitatively that intramolecular libratory motions greatly effect the high frequency dielectric spectrum. Finally, molecular motions in liquid crystals are divided into two types: coherent and incoherent. 127 refs., 56 figs., 17 tabs. (author)

Nonequilibrium Green's function theory for nonadiabatic effects in quantum electron transport

Science.gov (United States)

Kershaw, Vincent F.; Kosov, Daniel S.

2017-12-01

We develop nonequilibrium Green's function-based transport theory, which includes effects of nonadiabatic nuclear motion in the calculation of the electric current in molecular junctions. Our approach is based on the separation of slow and fast time scales in the equations of motion for Green's functions by means of the Wigner representation. Time derivatives with respect to central time serve as a small parameter in the perturbative expansion enabling the computation of nonadiabatic corrections to molecular Green's functions. Consequently, we produce a series of analytic expressions for non-adiabatic electronic Green's functions (up to the second order in the central time derivatives), which depend not solely on the instantaneous molecular geometry but likewise on nuclear velocities and accelerations. An extended formula for electric current is derived which accounts for the non-adiabatic corrections. This theory is concisely illustrated by the calculations on a model molecular junction.

Non-equilibrium synergistic effects in atmospheric pressure plasmas.

Science.gov (United States)

Guo, Heng; Zhang, Xiao-Ning; Chen, Jian; Li, He-Ping; Ostrikov, Kostya Ken

2018-03-19

Non-equilibrium is one of the important features of an atmospheric gas discharge plasma. It involves complicated physical-chemical processes and plays a key role in various actual plasma processing. In this report, a novel complete non-equilibrium model is developed to reveal the non-equilibrium synergistic effects for the atmospheric-pressure low-temperature plasmas (AP-LTPs). It combines a thermal-chemical non-equilibrium fluid model for the quasi-neutral plasma region and a simplified sheath model for the electrode sheath region. The free-burning argon arc is selected as a model system because both the electrical-thermal-chemical equilibrium and non-equilibrium regions are involved simultaneously in this arc plasma system. The modeling results indicate for the first time that it is the strong and synergistic interactions among the mass, momentum and energy transfer processes that determine the self-consistent non-equilibrium characteristics of the AP-LTPs. An energy transfer process related to the non-uniform spatial distributions of the electron-to-heavy-particle temperature ratio has also been discovered for the first time. It has a significant influence for self-consistently predicting the transition region between the "hot" and "cold" equilibrium regions of an AP-LTP system. The modeling results would provide an instructive guidance for predicting and possibly controlling the non-equilibrium particle-energy transportation process in various AP-LTPs in future.

Molecular and crystal structure of 3,4-dihydroxy-2-oxo-1-methyl-4-phenylpiperidine

International Nuclear Information System (INIS)

Kuleshova, L.N.; Khrustalev, V.N.; Struchkov, Yu.T.; Soldatenkov, A.T.; Bekro, I.A.; Mamyrbekova, Zh.A.; Soldatova, S.A.

1996-01-01

The molecular and crystal structure of 3,4-dihydroxy-2-oxo-1-methyl-4-phenylpiperidine was determined. The crystal is orthorhombic: sp. gr. Pca21; a=15.764, b=5.635, and c=25.536 A; and Z=8. The structure was solved by direct methods; R1=0.051, for 2643 unique refections. Symmetry-independent molecules are related by a pseudocenter of symmetry. The piperidine cycle has an asymmetric half-chair conformation. The orientation of substituents is determined. In the crystal, intermolecular OH...O hydrogen bonds link the molecules into chains parallel to the Y-axis

Non-Equilibrium Thermodynamics of Self-Replicating Protocells

DEFF Research Database (Denmark)

Fellermann, Harold; Corominas-Murtra, Bernat; Hansen, Per Lyngs

2018-01-01

We provide a non-equilibrium thermodynamic description of the life-cycle of a droplet based, chemically feasible, system of protocells. By coupling the protocells metabolic kinetics with its thermodynamics, we demonstrate how the system can be driven out of equilibrium to ensure protocell growth...... and replication. This coupling allows us to derive the equations of evolution and to rigorously demonstrate how growth and replication life-cycle can be understood as a non-equilibrium thermodynamic cycle. The process does not appeal to genetic information or inheritance, and is based only on non......-equilibrium physics considerations. Our non-equilibrium thermodynamic description of simple, yet realistic, processes of protocell growth and replication, represents an advance in our physical understanding of a central biological phenomenon both in connection to the origin of life and for modern biology....

Link prediction based on nonequilibrium cooperation effect

Science.gov (United States)

Li, Lanxi; Zhu, Xuzhen; Tian, Hui

2018-04-01

Link prediction in complex networks has become a common focus of many researchers. But most existing methods concentrate on neighbors, and rarely consider degree heterogeneity of two endpoints. Node degree represents the importance or status of endpoints. We describe the large-degree heterogeneity as the nonequilibrium between nodes. This nonequilibrium facilitates a stable cooperation between endpoints, so that two endpoints with large-degree heterogeneity tend to connect stably. We name such a phenomenon as the nonequilibrium cooperation effect. Therefore, this paper proposes a link prediction method based on the nonequilibrium cooperation effect to improve accuracy. Theoretical analysis will be processed in advance, and at the end, experiments will be performed in 12 real-world networks to compare the mainstream methods with our indices in the network through numerical analysis.

Microscopic Rate Constants of Crystal Growth from Molecular Dynamic Simulations Combined with Metadynamics

Directory of Open Access Journals (Sweden)

Dániel Kozma

2012-01-01

Full Text Available Atomistic simulation of crystal growth can be decomposed into two steps: the determination of the microscopic rate constants and a mesoscopic kinetic Monte Carlo simulation. We proposed a method to determine kinetic rate constants of crystal growth. We performed classical molecular dynamics on the equilibrium liquid/crystal interface of argon. Metadynamics was used to explore the free energy surface of crystal growth. A crystalline atom was selected at the interface, and it was displaced to the liquid phase by adding repulsive Gaussian potentials. The activation free energy of this process was calculated as the maximal potential energy density of the Gaussian potentials. We calculated the rate constants at different interfacial structures using the transition state theory. In order to mimic real crystallization, we applied a temperature difference in the calculations of the two opposite rate constants, and they were applied in kinetic Monte Carlo simulation. The novelty of our technique is that it can be used for slow crystallization processes, while the simple following of trajectories can be applied only for fast reactions. Our method is a possibility for determination of elementary rate constants of crystal growth that seems to be necessary for the long-time goal of computer-aided crystal design.

Photoluminescence characteristics of Pb-doped, molecular-beam-epitaxy grown ZnSe crystal layers

International Nuclear Information System (INIS)

Mita, Yoh; Kuronuma, Ryoichi; Inoue, Masanori; Sasaki, Shoichiro; Miyamoto, Yoshinobu

2004-01-01

The characteristic green photoluminescence emission and related phenomena in Pb-doped, molecular-beam-epitaxy (MBE)-grown ZnSe crystal layers were investigated to explore the nature of the center responsible for the green emission. The intensity of the green emission showed a distinct nonlinear dependence on excitation intensity. Pb-diffused polycrystalline ZnSe was similarly examined for comparison. The characteristic green emission has been observed only in MBE-grown ZnSe crystal layers with moderate Pb doping. The results of the investigations on the growth conditions, luminescence, and related properties of the ZnSe crystal layers suggest that the green emission is due to isolated Pb replacing Zn and surrounded with regular ZnSe lattice with a high perfection

Characterization of nonequilibrium states of trapped Bose–Einstein condensates

Science.gov (United States)

Yukalov, V. I.; Novikov, A. N.; Bagnato, V. S.

2018-06-01

The generation of different nonequilibrium states in trapped Bose–Einstein condensates is studied by numerically solving the nonlinear Schrödinger equation. Inducing nonequilibrium states by shaking a trap creates the following states: weak nonequilibrium, the state of vortex germs, the state of vortex rings, the state of straight vortex lines, the state of deformed vortices, vortex turbulence, grain turbulence, and wave turbulence. A characterization of nonequilibrium states is advanced by introducing effective temperature, Fresnel number, and Mach number.

A nonequilibrium simulation method for calculating tracer diffusion coefficients of small solutes in n-alkane liquids and polymers

NARCIS (Netherlands)

van der Vegt, N.F.A.; Briels, Willem J.; Wessling, Matthias; Strathmann, H.

1998-01-01

The tracer diffusion coefficients of methane in n-alkane liquids of increasing chain length were calculated by measuring the friction from short time nonequilibrium molecular dynamics simulations. The frictional constant was calculated from the exponentially decaying distance between two methane

Comparison of Green-Kubo and nonequilibrium calculations of the self-diffusion constant of a Lennard-Jones fluid

International Nuclear Information System (INIS)

Erpenbeck, J.J.

1987-01-01

We apply the so-called ''synthetic'' nonequilibrium molecular-dynamics method to the calculation of the self-diffusion constant of a Lennard-Jones fluid at a number density of 0.85/σ 3 and a temperature of 1.08 epsilon-c/k/sub B/ (where epsilon-c and σ are the energy and length parameters of the potential and k/sub B/ is the Boltzmann constant). By comparing with the Green-Kubo calculation for the same state of the system and for the same number of particles, N, we find the latter calculation to yield more precise values of the self-diffusion constant for a given number of molecular-dynamics time steps. Even at small values of the diffusion current, a nontrivial time is needed for the nonequilibrium calculation to reach the steady state. For larger values of the driving force, the steady-state flow appears to become unstable and evidence of a secondary flow pattern is presented. The presence of these instabilities acts as a limit to the range of the driving force for which the steady-state method can be applied. With increasing N the range of stable values of the diffusion current density decreases. For the Green-Kubo calculations, the N dependence of the self-diffusion constant is found to be anomalous for N = 108, with the 1/N dependence only exhibited for at least 500 particles. The nonequilibrium results, while approximately independent of N for 108 and 500 particles, are found to have a similar anomalous N dependence when we extend the calculations to 1372 particles, thereby bringing the Green-Kubo and nonequilibrium results into agreement in the large-system limit

Molecular crystals of 2-amino-1,3,4-thiadiazole with inorganic oxyacids – crystal engineering, phase transformations and NLO properties

Czech Academy of Sciences Publication Activity Database

Matulková, Irena; Cihelka, J.; Pojarová, Michaela; Fejfarová, Karla; Dušek, Michal; Císařová, I.; Vaněk, Přemysl; Kroupa, Jan; Němec, P.; Tesařová, N.; Němec, I.

2014-01-01

Roč. 16, č. 9 (2014), s. 1763-1776 ISSN 1466-8033 Grant - others:AVČR(CZ) Praemium Academiae Institutional support: RVO:68378271 Keywords : molecular crystals * inorganic salts * structure determination * second harmonic generation Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 4.034, year: 2014

Picosecond Transient Photoconductivity in Functionalized Pentacene Molecular Crystals Probed by Terahertz Pulse Spectroscopy

Science.gov (United States)

Hegmann, F. A.; Tykwinski, R. R.; Lui, K. P.; Bullock, J. E.; Anthony, J. E.

2002-11-01

We have measured transient photoconductivity in functionalized pentacene molecular crystals using ultrafast optical pump-terahertz probe techniques. The single crystal samples were excited using 800nm, 100fs pulses, and the change in transmission of time-delayed, subpicosecond terahertz pulses was used to probe the photoconducting state over a temperature range from 10 to 300K. A subpicosecond rise in photoconductivity is observed, suggesting that mobile carriers are a primary photoexcitation. At times longer than 4ps, a power-law decay is observed consistent with dispersive transport.

Molecular complex of lumiflavin and 2-aminobenzoic acid: crystal structure, crystal spectra, and solution properties.

Science.gov (United States)

Shieh, H S; Ghisla, S; Hanson, L K; Ludwig, M L; Nordman, C E

1981-08-04

The molecular complex lumiflavin-2-aminobenzoic acid monohydrate (C13H12N4O2.C7H7NO2.H2O) crystallizes from from aqueous solution as red triclinic prisms. The space group is P1 with cell dimensions a = 9.660 A, b = 14.866 A, c = 7.045 A, alpha = 95.44 degrees , beta = 95.86 degrees, and gamma = 105.66 degrees . The crystal structure was solved by direct methods and refined by block-diagonal least-squares procedures to an R value of 0.050 on the basis of 1338 observed reflections. The structure is composed of stacks of alternating lumiflavin adn un-ionized (neutral) 2-aminobenzoic acid molecules. Two different modes of stacking interaction are observed. In one, 2-aminobenzoic acid overlaps all three of the isoalloxazine rings, at a mean distance of 3.36 A; in the other, 2-aminobenzoic acid interacts distance of 3.36 A; in the other, 2-aminobenzoic acid interacts with the pyrazine and dimethylbenzene moieties, at a distance of 3.42 A. Perpendicular to the stacking direction, the molecules form a continuous sheet. Each flavin is hydrogen bonded via O(2) and NH(3) to two symmetrically related aminobenzoates; the water of crystallization forms three hydrogen bonds, bridging two flavins, via O(4) and N(5), and one aminobenzoic acid. The red color of the crystals results from a charge-transfer transition involving stacked flavin and 2-aminobenzoic acid. The red color of the crystals results from a charge-transfer transition involving stacked flavin and 2-aminobenzoic acid molecules. Measurements of the polarized optical absorption spectra of crystals show that the transition moment direction for the long wavelength absorbance (beyond 530 nm) contains an out-of-plane component which can only arise from a charge-transfer interaction. Since the amino N does not make exceptionally close interactions with isoalloxazine atoms in either stacking mode (minimum interatomic distance 3.52 A), the charge transfer is presumed to involve pi orbitals of the 2-aminobenzoic acid donor.

Equilibrium and nonequilibrium solvation and solute electronic structure

International Nuclear Information System (INIS)

Kim, H.J.; Hynes, J.T.

1990-01-01

When a molecular solute is immersed in a polar and polarizable solvent, the electronic wave function of the solute system is altered compared to its vacuum value; the solute electronic structure is thus solvent-dependent. Further, the wave function will be altered depending upon whether the polarization of the solvent is or is not in equilibrium with the solute charge distribution. More precisely, while the solvent electronic polarization should be in equilibrium with the solute electronic wave function, the much more sluggish solvent orientational polarization need not be. We call this last situation non-equilibrium solvation. We outline a nonlinear Schroedinger equation approach to these issues

Interface Engineering for Organic Electronics; Manufacturing of Hybrid Inorganic-Organic Molecular Crystal Devices

NARCIS (Netherlands)

de Veen, P.J.

2011-01-01

Organic semiconductors are at the basis of Organic Electronics. Objective of this dissertation is “to fabricate high-quality organic molecular single-crystal devices”, to explore the intrinsic properties of organic semiconductors. To achieve this, the in situ fabrication of complete field-effect

Statistical thermodynamics of nonequilibrium processes

CERN Document Server

Keizer, Joel

1987-01-01

The structure of the theory ofthermodynamics has changed enormously since its inception in the middle of the nineteenth century. Shortly after Thomson and Clausius enunciated their versions of the Second Law, Clausius, Maxwell, and Boltzmann began actively pursuing the molecular basis of thermo­ dynamics, work that culminated in the Boltzmann equation and the theory of transport processes in dilute gases. Much later, Onsager undertook the elucidation of the symmetry oftransport coefficients and, thereby, established himself as the father of the theory of nonequilibrium thermodynamics. Com­ bining the statistical ideas of Gibbs and Langevin with the phenomenological transport equations, Onsager and others went on to develop a consistent statistical theory of irreversible processes. The power of that theory is in its ability to relate measurable quantities, such as transport coefficients and thermodynamic derivatives, to the results of experimental measurements. As powerful as that theory is, it is linear and...

The molecular ordering phenomenon in dye-doped nematic liquid crystals

International Nuclear Information System (INIS)

Prakash Yadav, Satya; Pandey, Kamal Kumar; Kumar Misra, Abhishek; Kumar Tripathi, Pankaj; Manohar, Rajiv

2011-01-01

The experimental results of this work point out the role of the guest dye molecules in the molecular ordering of nematic liquid crystals. We have discussed the changes in the energies of interactions between rod-like nematic molecules and anthraquinone dye by considering the presence of steric and dipole-dipole interactions in the dye-doped system. The concentration of the dye plays an important role in the determination of molecular ordering in such dye-doped systems. Below a certain concentration of dye (known as the critical concentration), where the interaction between the dye molecules can be neglected, the addition of dye molecules introduces some disorder into the system in the form of domain formation. Above this critical concentration, this disorder is small.

The molecular ordering phenomenon in dye-doped nematic liquid crystals

Energy Technology Data Exchange (ETDEWEB)

Prakash Yadav, Satya; Pandey, Kamal Kumar; Kumar Misra, Abhishek; Kumar Tripathi, Pankaj; Manohar, Rajiv, E-mail: rajiv.manohar@gmail.com [Liquid Crystal Research Laboratory, Physics Department, University of Lucknow, Lucknow-226007 (India)

2011-03-15

The experimental results of this work point out the role of the guest dye molecules in the molecular ordering of nematic liquid crystals. We have discussed the changes in the energies of interactions between rod-like nematic molecules and anthraquinone dye by considering the presence of steric and dipole-dipole interactions in the dye-doped system. The concentration of the dye plays an important role in the determination of molecular ordering in such dye-doped systems. Below a certain concentration of dye (known as the critical concentration), where the interaction between the dye molecules can be neglected, the addition of dye molecules introduces some disorder into the system in the form of domain formation. Above this critical concentration, this disorder is small.

Molecular rotation-vibration dynamics of low-symmetric hydrate crystal in the terahertz region.

Science.gov (United States)

Fu, Xiaojian; Wu, Hongya; Xi, Xiaoqing; Zhou, Ji

2014-01-16

The rotational and vibrational dynamics of molecules in copper sulfate pentahydrate crystal are investigated with terahertz dielectric spectra. It is shown that the relaxation-like dielectric dispersion in the low frequency region is related to the reorientation of water molecules under the driving of terahertz electric field, whereas the resonant dispersion can be ascribed to lattice vibration. It is also found that, due to the hydrogen-bond effect, the vibrational mode at about 1.83 THz along [-111] direction softens with decreasing temperature, that is, the crystal expands in this direction when cooled. On the contrary, the mode hardens in the direction perpendicular to [-111] during the cooling process. This contributes to the further understanding of the molecular structure and bonding features of hydrate crystals.

Foundations of atmospheric pressure non-equilibrium plasmas

Science.gov (United States)

Bruggeman, Peter J.; Iza, Felipe; Brandenburg, Ronny

2017-12-01

Non-equilibrium plasmas have been intensively studied over the past century in the context of material processing, environmental remediation, ozone generation, excimer lamps and plasma display panels. Research on atmospheric pressure non-equilibrium plasmas intensified over the last two decades leading to a large variety of plasma sources that have been developed for an extended application range including chemical conversion, medicine, chemical analysis and disinfection. The fundamental understanding of these discharges is emerging but there remain a lot of unexplained phenomena in these intrinsically complex plasmas. The properties of non-equilibrium plasmas at atmospheric pressure span over a huge range of electron densities as well as heavy particle and electron temperatures. This paper provides an overview of the key underlying processes that are important for the generation and stabilization of atmospheric pressure non-equilibrium plasmas. The unique physical and chemical properties of theses discharges are also summarized.

Relation between photochromic properties and molecular structures in salicylideneaniline crystals.

Science.gov (United States)

Johmoto, Kohei; Ishida, Takashi; Sekine, Akiko; Uekusa, Hidehiro; Ohashi, Yuji

2012-06-01

The crystal structures of the salicylideneaniline derivatives N-salicylidene-4-tert-butyl-aniline (1), N-3,5-di-tert-butyl-salicylidene-3-methoxyaniline (2), N-3,5-di-tert-butyl-salicylidene-3-bromoaniline (3), N-3,5-di-tert-butyl-salicylidene-3-chloroaniline (4), N-3,5-di-tert-butyl-salicylidene-4-bromoaniline (5), N-3,5-di-tert-butyl-salicylidene-aniline (6), N-3,5-di-tert-butyl-salicylidene-4-carboxyaniline (7) and N-salicylidene-2-chloroaniline (8) were analyzed by X-ray diffraction analysis at ambient temperature to investigate the relationship between their photochromic properties and molecular structures. A clear correlation between photochromism and the dihedral angle of the two benzene rings in the salicylideneaniline derivatives was observed. Crystals with dihedral angles less than 20° were non-photochromic, whereas those with dihedral angles greater than 30° were photochromic. Crystals with dihedral angles between 20 and 30° could be either photochromic or non-photochromic. Inhibition of the pedal motion by intra- or intermolecular steric hindrance, however, can result in non-photochromic behaviour even if the dihedral angle is larger than 30°.

I. Dissociation free energies of drug-receptor systems via non-equilibrium alchemical simulations: a theoretical framework.

Science.gov (United States)

Procacci, Piero

2016-06-01

In this contribution I critically revise the alchemical reversible approach in the context of the statistical mechanics theory of non-covalent bonding in drug-receptor systems. I show that most of the pitfalls and entanglements for the binding free energy evaluation in computer simulations are rooted in the equilibrium assumption that is implicit in the reversible method. These critical issues can be resolved by using a non-equilibrium variant of the alchemical method in molecular dynamics simulations, relying on the production of many independent trajectories with a continuous dynamical evolution of an externally driven alchemical coordinate, completing the decoupling of the ligand in a matter of a few tens of picoseconds rather than nanoseconds. The absolute binding free energy can be recovered from the annihilation work distributions by applying an unbiased unidirectional free energy estimate, on the assumption that any observed work distribution is given by a mixture of normal distributions, whose components are identical in either direction of the non-equilibrium process, with weights regulated by the Crooks theorem. I finally show that the inherent reliability and accuracy of the unidirectional estimate of the decoupling free energies, based on the production of a few hundreds of non-equilibrium independent sub-nanosecond unrestrained alchemical annihilation processes, is a direct consequence of the funnel-like shape of the free energy surface in molecular recognition. An application of the technique to a real drug-receptor system is presented in the companion paper.

Molecular nucleation mechanisms and control strategies for crystal polymorph selection

Science.gov (United States)

van Driessche, Alexander E. S.; van Gerven, Nani; Bomans, Paul H. H.; Joosten, Rick R. M.; Friedrich, Heiner; Gil-Carton, David; Sommerdijk, Nico A. J. M.; Sleutel, Mike

2018-04-01

The formation of condensed (compacted) protein phases is associated with a wide range of human disorders, such as eye cataracts, amyotrophic lateral sclerosis, sickle cell anaemia and Alzheimer’s disease. However, condensed protein phases have their uses: as crystals, they are harnessed by structural biologists to elucidate protein structures, or are used as delivery vehicles for pharmaceutical applications. The physiochemical properties of crystals can vary substantially between different forms or structures (‘polymorphs’) of the same macromolecule, and dictate their usability in a scientific or industrial context. To gain control over an emerging polymorph, one needs a molecular-level understanding of the pathways that lead to the various macroscopic states and of the mechanisms that govern pathway selection. However, it is still not clear how the embryonic seeds of a macromolecular phase are formed, or how these nuclei affect polymorph selection. Here we use time-resolved cryo-transmission electron microscopy to image the nucleation of crystals of the protein glucose isomerase, and to uncover at molecular resolution the nucleation pathways that lead to two crystalline states and one gelled state. We show that polymorph selection takes place at the earliest stages of structure formation and is based on specific building blocks for each space group. Moreover, we demonstrate control over the system by selectively forming desired polymorphs through site-directed mutagenesis, specifically tuning intermolecular bonding or gel seeding. Our results differ from the present picture of protein nucleation, in that we do not identify a metastable dense liquid as the precursor to the crystalline state. Rather, we observe nucleation events that are driven by oriented attachments between subcritical clusters that already exhibit a degree of crystallinity. These insights suggest ways of controlling macromolecular phase transitions, aiding the development of protein

Designs of Plasmonic Metamasks for Photopatterning Molecular Orientations in Liquid Crystals

Directory of Open Access Journals (Sweden)

Yubing Guo

2016-12-01

Full Text Available Aligning liquid crystal (LC molecules into spatially non-uniform orientation patterns is central to the functionalities of many emerging LC devices. Recently, we developed a new projection photopatterning technique by using plasmonic metamasks (PMMs, and demonstrated high-resolution and high-throughput patterning of molecular orientations into arbitrary patterns. Here we present comparisons between two different types of metamask designs: one based on curvilinear nanoslits in metal films; the other based on rectangular nanoapertures in metal films. By using numerical simulations and experimental studies, we show that the PMMs based on curvilinear nanoslits exhibit advantages in their broadband and high optical transmission, while face challenges in mask designing for arbitrary molecular orientations. In contrast, the PMMs based on nanoapertures, though limited in optical transmission, present the great advantage of allowing for patterning arbitrary molecular orientation fields.

Nonequilibrium constitutive models for RELAP5/MOD2

International Nuclear Information System (INIS)

Lin, J.C.; Trapp, J.A.; Riemke, R.A.; Ransom, V.H.

1983-01-01

RELAP5/MOD2 is a new version of RELAP5 containing improved modeling features that provide a generic pressurized-water transient simulation capability. In particular, the nonequilibrium modeling capability has been generalized to include conditions that occur in operational transients including repressurization and emergency-feed-water injection with loss-of-coolant accidents. The improvements include addition of a second energy equation to the hydrodynamic model, addition of nonequilibrium heat-transfer models, and the associated nonequilibrium vapor-generation models. The objective of this paper is to describe these models and to report the developmental assessment results obtained from similar of several separate effects experiments. The assessment shows that RELAP5 calculated results are in good agreement with data and the nonequilibrium phenomena are properly modeled

Laserlike Vibrational Instability in Rectifying Molecular Conductors

DEFF Research Database (Denmark)

Lu, Jing Tao; Hedegård, Per; Brandbyge, Mads

2011-01-01

We study the damping of molecular vibrations due to electron-hole pair excitations in donor-acceptor (D-A) type molecular rectifiers. At finite voltage additional nonequilibrium electron-hole pair excitations involving both electrodes become possible, and contribute to the stimulated emission....... We investigate the effect in realistic molecular rectifier structures using first-principles calculations....

Introduction to the nonequilibrium functional renormalization group

International Nuclear Information System (INIS)

Berges, J.; Mesterházy, D.

2012-01-01

In these lectures we introduce the functional renormalization group out of equilibrium. While in thermal equilibrium typically a Euclidean formulation is adequate, nonequilibrium properties require real-time descriptions. For quantum systems specified by a given density matrix at initial time, a generating functional for real-time correlation functions can be written down using the Schwinger-Keldysh closed time path. This can be used to construct a nonequilibrium functional renormalization group along similar lines as for Euclidean field theories in thermal equilibrium. Important differences include the absence of a fluctuation-dissipation relation for general out-of-equilibrium situations. The nonequilibrium renormalization group takes on a particularly simple form at a fixed point, where the corresponding scale-invariant system becomes independent of the details of the initial density matrix. We discuss some basic examples, for which we derive a hierarchy of fixed point solutions with increasing complexity from vacuum and thermal equilibrium to nonequilibrium. The latter solutions are then associated to the phenomenon of turbulence in quantum field theory.

Model non-equilibrium molecular dynamics simulations of heat transfer from a hot gold surface to an alkylthiolate self-assembled monolayer.

Science.gov (United States)

Zhang, Yue; Barnes, George L; Yan, Tianying; Hase, William L

2010-05-07

Model non-equilibrium molecular dynamics (MD) simulations are presented of heat transfer from a hot Au {111} substrate to an alkylthiolate self-assembled monolayer (H-SAM) to assist in obtaining an atomic-level understanding of experiments by Wang et al. (Z. Wang, J. A. Carter, A. Lagutchev, Y. K. Koh, N.-H. Seong, D. G. Cahill, and D. D. Dlott, Science, 2007, 317, 787). Different models are considered to determine how they affect the heat transfer dynamics. They include temperature equilibrated (TE) and temperature gradient (TG) thermostat models for the Au(s) surface, and soft and stiff S/Au(s) models for bonding of the S-atoms to the Au(s) surface. A detailed analysis of the non-equilibrium heat transfer at the heterogeneous interface is presented. There is a short time temperature gradient within the top layers of the Au(s) surface. The S-atoms heat rapidly, much faster than do the C-atoms in the alkylthiolate chains. A high thermal conductivity in the H-SAM, perpendicular to the interface, results in nearly identical temperatures for the CH(2) and CH(3) groups versus time. Thermal-induced disorder is analyzed for the Au(s) substrate, the S/Au(s) interface and the H-SAM. Before heat transfer occurs from the hot Au(s) substrate to the H-SAM, there is disorder at the S/Au(s) interface and within the alkylthiolate chains arising from heat-induced disorder near the surface of hot Au(s). The short-time rapid heating of the S-atoms enhances this disorder. The increasing disorder of H-SAM chains with time results from both disorder at the Au/S interface and heat transfer to the H-SAM chains.

Molecular Imprinting Technology in Quartz Crystal Microbalance (QCM) Sensors

Science.gov (United States)

Emir Diltemiz, Sibel; Keçili, Rüstem; Ersöz, Arzu; Say, Rıdvan

2017-01-01

Molecularly imprinted polymers (MIPs) as artificial antibodies have received considerable scientific attention in the past years in the field of (bio)sensors since they have unique features that distinguish them from natural antibodies such as robustness, multiple binding sites, low cost, facile preparation and high stability under extreme operation conditions (higher pH and temperature values, etc.). On the other hand, the Quartz Crystal Microbalance (QCM) is an analytical tool based on the measurement of small mass changes on the sensor surface. QCM sensors are practical and convenient monitoring tools because of their specificity, sensitivity, high accuracy, stability and reproducibility. QCM devices are highly suitable for converting the recognition process achieved using MIP-based memories into a sensor signal. Therefore, the combination of a QCM and MIPs as synthetic receptors enhances the sensitivity through MIP process-based multiplexed binding sites using size, 3D-shape and chemical function having molecular memories of the prepared sensor system toward the target compound to be detected. This review aims to highlight and summarize the recent progress and studies in the field of (bio)sensor systems based on QCMs combined with molecular imprinting technology. PMID:28245588

Molecular Imprinting Technology in Quartz Crystal Microbalance (QCM Sensors

Directory of Open Access Journals (Sweden)

Sibel Emir Diltemiz

2017-02-01

Full Text Available Molecularly imprinted polymers (MIPs as artificial antibodies have received considerable scientific attention in the past years in the field of (biosensors since they have unique features that distinguish them from natural antibodies such as robustness, multiple binding sites, low cost, facile preparation and high stability under extreme operation conditions (higher pH and temperature values, etc.. On the other hand, the Quartz Crystal Microbalance (QCM is an analytical tool based on the measurement of small mass changes on the sensor surface. QCM sensors are practical and convenient monitoring tools because of their specificity, sensitivity, high accuracy, stability and reproducibility. QCM devices are highly suitable for converting the recognition process achieved using MIP-based memories into a sensor signal. Therefore, the combination of a QCM and MIPs as synthetic receptors enhances the sensitivity through MIP process-based multiplexed binding sites using size, 3D-shape and chemical function having molecular memories of the prepared sensor system toward the target compound to be detected. This review aims to highlight and summarize the recent progress and studies in the field of (biosensor systems based on QCMs combined with molecular imprinting technology.

Small angle neutron scattering (SANS) under non-equilibrium conditions

International Nuclear Information System (INIS)

Oberthur, R.C.

1984-01-01

The use of small angle neutron scattering (SANS) for the study of systems under non-equilibrium conditions is illustrated by three types of experiments in the field of polymer research: - the relaxation of a system from an initial non-equilibrium state towards equilibrium, - the cyclic or repetitive installation of a series of non-equilibrium states in a system, - the steady non-equilibrium state maintained by a constant dissipation of energy within the system. Characteristic times obtained in these experiments with SANS are compared with the times obtained from quasi-elastic neutron and light scattering, which yield information about the equilibrium dynamics of the system. The limits of SANS applied to non-equilibrium systems for the measurement of relaxation times at different length scales are shown and compared to the limits of quasielastic neutron and light scattering

Deuteron NMR resolved mesogen vs. crosslinker molecular order and reorientational exchange in liquid single crystal elastomers

Czech Academy of Sciences Publication Activity Database

Milavec, J.; Domenici, V.; Zupančič, B.; Rešetič, A.; Bubnov, Alexej; Zalar, B.

2016-01-01

Roč. 18, č. 5 (2016), s. 4071-4077 ISSN 1463-9076 R&D Projects: GA ČR GA15-02843S; GA MŠk(CZ) LD14007 Grant - others:EU - ICT(XE) COST Action IC1208 Institutional support: RVO:68378271 Keywords : liquid single crystal elastomer * NMR * liquid crystal * molecular order * monomers Subject RIV: JJ - Other Materials Impact factor: 4.123, year: 2016

A novel model for smectic liquid crystals: Elastic anisotropy and response to a steady-state flow.

Science.gov (United States)

Püschel-Schlotthauer, Sergej; Meiwes Turrión, Victor; Stieger, Tillmann; Grotjahn, Robin; Hall, Carol K; Mazza, Marco G; Schoen, Martin

2016-10-28

By means of a combination of equilibrium Monte Carlo and molecular dynamics simulations and nonequilibrium molecular dynamics we investigate the ordered, uniaxial phases (i.e., nematic and smectic A) of a model liquid crystal. We characterize equilibrium behavior through their diffusive behavior and elastic properties. As one approaches the equilibrium isotropic-nematic phase transition, diffusion becomes anisotropic in that self-diffusion D ⊥ in the direction orthogonal to a molecule's long axis is more hindered than self-diffusion D ∥ in the direction parallel to that axis. Close to nematic-smectic A phase transition the opposite is true, D ∥ flow depending on whether the convective velocity is parallel or orthogonal to the plane of smectic layers. We find that in Poiseuille-like flow the viscosity of the smectic A phase is higher than in plug flow. This can be rationalized via the velocity-field component in the direction of the flow. In a sufficiently strong flow these smectic layers are not destroyed but significantly bent.

Shape Changing Nonlocal Molecular Deformations in a Nematic Liquid Crystal

International Nuclear Information System (INIS)

Kavitha, L.; Venkatesh, M.; Gopi, D.

2010-07-01

The nature of nonlinear molecular deformations in a homeotropically aligned nematic liquid crystal (NLC) is presented. We start from the basic dynamical equation for the director axis of a NLC with elastic deformation mapped onto an integro-differential perturbed Nonlinear Schroedinger equation which includes the nonlocal term. By invoking the modified extended tangent hyperbolic function method aided with symbolic computation, we obtain a series of solitary wave solutions. Under the influence of the nonlocality induced by the reorientation nonlinearity due to fluctuations in the molecular orientation, the solitary wave exhibits shape changing property for different choices of parameters. This intriguing property, as a result of the relation between the coherence of the solitary deformation and the nonlocality, reveals a strong need for deeper understanding in the theory of self-localization in NLC systems. (author)

Study on Properties of Energy Spectra of the Molecular Crystals

Science.gov (United States)

Pang, Xiao-Feng; Chen, Xiang-Rong

The energy-spectra of nonlinear vibration of molecular crystals such as acetanilide have been calculated by using discrete nonlinear Schrödinger equation appropriate to the systems, containing various interactions. The energy levels including higher excited states are basically consistent with experimental values obtained by infrared absorption and Raman scattering in acetanilide. We further give the features of distribution of the energy-spectra for the acetanilide. Using the energy spectra we also explained well experimental results obtained by Careri et al..

Nonequilibrium statistical physics a modern perspective

CERN Document Server

Livi, Roberto

2017-01-01

Statistical mechanics has been proven to be successful at describing physical systems at thermodynamic equilibrium. Since most natural phenomena occur in nonequilibrium conditions, the present challenge is to find suitable physical approaches for such conditions: this book provides a pedagogical pathway that explores various perspectives. The use of clear language, and explanatory figures and diagrams to describe models, simulations and experimental findings makes the book a valuable resource for undergraduate and graduate students, and also for lecturers organizing teaching at varying levels of experience in the field. Written in three parts, it covers basic and traditional concepts of nonequilibrium physics, modern aspects concerning nonequilibrium phase transitions, and application-orientated topics from a modern perspective. A broad range of topics is covered, including Langevin equations, Levy processes, directed percolation, kinetic roughening and pattern formation.

Equivalence of the equilibrium and the nonequilibrium molecular dynamics methods for thermal conductivity calculations: From bulk to nanowire silicon

Science.gov (United States)

Dong, Haikuan; Fan, Zheyong; Shi, Libin; Harju, Ari; Ala-Nissila, Tapio

2018-03-01

Molecular dynamics (MD) simulations play an important role in studying heat transport in complex materials. The lattice thermal conductivity can be computed either using the Green-Kubo formula in equilibrium MD (EMD) simulations or using Fourier's law in nonequilibrium MD (NEMD) simulations. These two methods have not been systematically compared for materials with different dimensions and inconsistencies between them have been occasionally reported in the literature. Here we give an in-depth comparison of them in terms of heat transport in three allotropes of Si: three-dimensional bulk silicon, two-dimensional silicene, and quasi-one-dimensional silicon nanowire. By multiplying the correlation time in the Green-Kubo formula with an appropriate effective group velocity, we can express the running thermal conductivity in the EMD method as a function of an effective length and directly compare it to the length-dependent thermal conductivity in the NEMD method. We find that the two methods quantitatively agree with each other for all the systems studied, firmly establishing their equivalence in computing thermal conductivity.

Crystal nucleation and dendrite growth of metastable phases in undercooled melts

International Nuclear Information System (INIS)

Herlach, Dieter

2011-01-01

Research highlights: → Homogenous nucleation. → Effects of convection on dendrite growth kinetics. → Description of disorder trapping validated by experiment. - Abstract: An undercooled melt possesses an enhanced free enthalpy that opens up the possibility to crystallize metastable crystalline solids in competition with their stable counterparts. Crystal nucleation selects the crystallographic phase whereas the growth dynamics controls microstructure evolution. We apply containerless processing techniques such as electromagnetic and electrostatic levitation to containerlesss undercool and solidify metallic melts. Owing to the complete avoidance of heterogeneous nucleation on container-walls a large undercooling range becomes accessible with the extra benefit that the freely suspended drop is direct accessible for in situ observation of crystallization far away from equilibrium. Results of investigations of maximum undercoolability on pure zirconium are presented showing the limit of maximum undercoolability set by the onset of homogeneous nucleation. Rapid dendrite growth is measured as a function of undercooling by a high-speed camera and analysed within extended theories of non-equilibrium solidification. In such both supersaturated solid solutions and disordered superlattice structure of intermetallics are formed at high growth velocities. A sharp interface theory of dendrite growth is capable to describe the non-equilibrium solidification phenomena during rapid crystallization of deeply undercooled melts. Eventually, anomalous growth behaviour of Al-rich Al-Ni alloys is presented, which may be caused by forced convection.

Crystal water as the mol-ecular glue for obtaining different co-crystal ratios: the case of gallic acid tris-caffeine hexa-hydrate.

Science.gov (United States)

Vella-Zarb, L; Baisch, U

2018-04-01

The crystal structure of the hexa-hydrate co-crystal of gallic acid and caffeine, C 7 H 6 O 5 ·3C 8 H 10 N 4 O 2 ·6H 2 O or GAL3CAF·6H 2 O , is a remarkable example of the importance of hydrate water acting as structural glue to facilitate the crystallization of two components of different stoichiometries and thus to compensate an imbalance of hydrogen-bond donors and acceptors. The water mol-ecules provide the additional hydrogen bonds required to form a crystalline solid. Whereas the majority of hydrogen bonds forming the inter-molecular network between gallic acid and caffeine are formed by crystal water, only one direct classical hydrogen bond between two mol-ecules is formed between the carb-oxy-lic oxygen of gallic acid and the carbonyl oxygen of caffeine with d ( D ⋯ A ) = 2.672 (2) Å. All other hydrogen bonds either involve crystal water or utilize protonated carbon atoms as donors.

Coherent anti-Stokes Raman scattering and spontaneous Raman scattering diagnostics of nonequilibrium plasmas and flows

Science.gov (United States)

Lempert, Walter R.; Adamovich, Igor V.

2014-10-01

The paper provides an overview of the use of coherent anti-Stokes Raman scattering (CARS) and spontaneous Raman scattering for diagnostics of low-temperature nonequilibrium plasmas and nonequilibrium high-enthalpy flows. A brief review of the theoretical background of CARS, four-wave mixing and Raman scattering, as well as a discussion of experimental techniques and data reduction, are included. The experimental results reviewed include measurements of vibrational level populations, rotational/translational temperature, electric fields in a quasi-steady-state and transient molecular plasmas and afterglow, in nonequilibrium expansion flows, and behind strong shock waves. Insight into the kinetics of vibrational energy transfer, energy thermalization mechanisms and dynamics of the pulse discharge development, provided by these experiments, is discussed. Availability of short pulse duration, high peak power lasers, as well as broadband dye lasers, makes possible the use of these diagnostics at relatively low pressures, potentially with a sub-nanosecond time resolution, as well as obtaining single laser shot, high signal-to-noise spectra at higher pressures. Possibilities for the development of single-shot 2D CARS imaging and spectroscopy, using picosecond and femtosecond lasers, as well as novel phase matching and detection techniques, are discussed.

The crystal structures of three pyrazine-2,5-dicarb-oxamides: three-dimensional supra-molecular structures.

Science.gov (United States)

Cati, Dilovan S; Stoeckli-Evans, Helen

2017-05-01

The complete mol-ecules of the title compounds, N 2 , N 5 -bis-(pyridin-2-ylmeth-yl)pyrazine-2,5-dicarboxamide, C 18 H 16 N 6 O 2 (I), 3,6-dimethyl- N 2 , N 5 -bis-(pyridin-2-yl-meth-yl)pyrazine-2,5-dicarboxamide, C 20 H 20 N 6 O 2 (II), and N 2 , N 5 -bis-(pyridin-4-ylmeth-yl)pyrazine-2,5-dicarboxamide, C 18 H 16 N 6 O 2 (III), are generated by inversion symmetry, with the pyrazine rings being located about centres of inversion. Each mol-ecule has an extended conformation with the pyridine rings inclined to the pyrazine ring by 89.17 (7)° in (I), 75.83 (8)° in (II) and by 82.71 (6)° in (III). In the crystal of (I), mol-ecules are linked by N-H⋯N hydrogen bonds, forming layers lying parallel to the bc plane. The layers are linked by C-H⋯O hydrogen bonds, forming a three-dimensional supra-molecular structure. In the crystal of (II), mol-ecules are also linked by N-H⋯N hydrogen bonds, forming layers lying parallel to the (10-1) plane. As in (I), the layers are linked by C-H⋯O hydrogen bonds, forming a three-dimensional supra-molecular structure. In the crystal of (III), mol-ecules are again linked by N-H⋯N hydrogen bonds, but here form corrugated sheets lying parallel to the bc plane. Within the sheets, neighbouring pyridine rings are linked by offset π-π inter-actions [inter-centroid distance = 3.739 (1) Å]. The sheets are linked by C-H⋯O hydrogen bonds, forming a three-dimensional supra-molecular structure. Compound (I) crystallizes in the monoclinic space group P 2 1 / c . Another monoclinic polymorph, space group C 2/ c , has been reported on by Cockriel et al. [ Inorg. Chem. Commun. (2008), 11 , 1-4]. The mol-ecular structures of the two polymorphs are compared.

Pressure-induced organic topological nodal-line semimetal in the three-dimensional molecular crystal Pd (dddt) 2

Science.gov (United States)

Liu, Zhao; Wang, Haidi; Wang, Z. F.; Yang, Jinlong; Liu, Feng

2018-04-01

The nodal-line semimetal represents a class of topological materials characterized with highest band degeneracy. It is usually found in inorganic materials of high crystal symmetry or a minimum symmetry of inversion aided with accidental band degeneracy [Phys. Rev. Lett. 118, 176402 (2017), 10.1103/PhysRevLett.118.176402]. Based on first-principles band structure, Wannier charge center, and topological surface state calculations, here we predict a pressure-induced topological nodal-line semimetal in the absence of spin-orbit coupling (SOC) in the synthesized single-component 3D molecular crystal Pd (dddt) 2 . We show a Γ -centered single nodal line undulating within a narrow energy window across the Fermi level. This intriguing nodal line is generated by pressure-induced accidental band degeneracy, without protection from any crystal symmetry. When SOC is included, the fourfold degenerated nodal line is gapped and Pd (dddt) 2 becomes a strong 3D topological metal with an Z2 index of (1;000). However, the tiny SOC gap makes it still possible to detect the nodal-line properties experimentally. Our findings afford an attractive route for designing and realizing topological states in 3D molecular crystals, as they are weakly bonded through van der Waals forces with a low crystal symmetry so that their electronic structures can be easily tuned by pressure.

The rotational temperature of polar molecular ions in Coulomb crystals

International Nuclear Information System (INIS)

Bertelsen, Anders; Joergensen, Solvejg; Drewsen, Michael

2006-01-01

With MgH + ions as a test case, we investigate to what extent the rotational motion of smaller polar molecular ions sympathetically cooled into Coulomb crystals in linear Paul traps couples to the translational motions of the ion ensemble. By comparing the results obtained from rotational resonance-enhanced multiphoton photo-dissociation experiments with data from theoretical simulations, we conclude that the effective rotational temperature exceeds the translational temperature (<100 mK) by more than two orders of magnitude, indicating a very weak coupling. (letter to the editor)

Rate of tunneling nonequilibrium quasiparticles in superconducting qubits

International Nuclear Information System (INIS)

Ansari, Mohammad H

2015-01-01

In superconducting qubits the lifetime of quantum states cannot be prolonged arbitrarily by decreasing temperature. At low temperature quasiparticles tunneling between the electromagnetic environment and superconducting islands takes the condensate state out of equilibrium due to charge imbalance. We obtain the tunneling rate from a phenomenological model of non-equilibrium, where nonequilibrium quasiparticle tunnelling stimulates a temperature-dependent chemical potential shift in the superconductor. As a result we obtain a non-monotonic behavior for relaxation rate as a function of temperature. Depending on the fabrication parameters for some qubits, the lowest tunneling rate of nonequilibrium quasiparticles can take place only near the onset temperature below which nonequilibrium quasiparticles dominate over equilibrium one. Our theory also indicates that such tunnelings can influence the probability of transitions in qubits through a coupling to the zero-point energy of phase fluctuations. (paper)

Capillary crystallization and molecular-replacement solution of haemoglobin II from the clam Lucina pectinata

International Nuclear Information System (INIS)

Gavira, José A.; Jesus, Walleska de; Camara-Artigas, Ana; López-Garriga, Juan; García-Ruiz, Juan M.

2006-01-01

The haemoglobin II from the clam L. pectinata has been crystallized using counter-diffusion in single capillary in the presence of agarose to improve crystal quality. Initial phases have been obtained by molecular replacement. Haemoglobin II is one of three haemoglobins present in the cytoplasm of the Lucina pectinata mollusc that inhabits the Caribbean coast. Using HBII purified from its natural source, crystallization screening was performed using the counter-diffusion method with capillaries of 0.2 mm inner diameter. Crystals of HbII suitable for data collection and structure determination were grown in the presence of agarose at 0.1%(w/v) in order to improve their quality. The crystals belong to the tetragonal space group P4 2 2 1 2, with unit-cell parameters a = b = 73.92, c = 152.35 Å, and diffracted X-rays to a resolution of better than 2.0 Å. The asymmetric unit is a homodimer with a corresponding Matthews coefficient (V M ) of 3.15 Å 3 Da −1 and a solvent content of 61% by volume

Quantum simulation and quantum information processing with molecular dipolar crystals

International Nuclear Information System (INIS)

Ortner, M.

2011-01-01

In this thesis interactions between dipolar crystals and neutral atoms or separated molecules have been investigated. They were motivated to realize new kinds of lattice models in mixtures of atoms and polar molecules where an MDC functions as an underlying periodic lattice structure for the second species. Such models bring out the peculiar features of MDC's, that include a controllable, potentially sub-optical wavelength periodicity and strong particle phonon interactions. Only stable collisional configurations have been investigated, excluding chemical reactions between the substituents, and crystal distortions beyond the scope of perturbation theory. The system was treated in the polaron picture where particles of the second species are dressed by surrounding crystal phonons. To describe the competition between coherent and incoherent dynamics of the polarons, a master equation in the Brownian motion limit was used with phonons treated as a thermal heat bath. It was shown analytically that in a wide range of realistic parameters the corrections to the coherent time evolution are small, and that the dynamics of the dressed particles can be described by an effective extended Hubbard model with controllable system parameters. The last chapter of this thesis contains a proposal for QIP with cold polar molecules that, in contrast to previous works, uses an MDC as a quantum register. It was motivated by the unique features of dipolar molecules and to exploit the peculiar physical conditions in dipolar crystals. In this proposal the molecular dipole moments were tailored by non-local fields to include a small, switchable, state-dependent dipole moment in addition to the large internal state independent moment that stabilizes the crystal. It was shown analytically that a controllable, non-trivial phonon-mediated interaction can be generated that exceeds non-trivial, direct dipole-dipole couplings. The addressability problem due to high crystal densities was overcome by

Transport processes and sound velocity in vibrationally non-equilibrium gas of anharmonic oscillators

Science.gov (United States)

Rydalevskaya, Maria A.; Voroshilova, Yulia N.

2018-05-01

Vibrationally non-equilibrium flows of chemically homogeneous diatomic gases are considered under the conditions that the distribution of the molecules over vibrational levels differs significantly from the Boltzmann distribution. In such flows, molecular collisions can be divided into two groups: the first group corresponds to "rapid" microscopic processes whereas the second one corresponds to "slow" microscopic processes (their rate is comparable to or larger than that of gasdynamic parameters variation). The collisions of the first group form quasi-stationary vibrationally non-equilibrium distribution functions. The model kinetic equations are used to study the transport processes under these conditions. In these equations, the BGK-type approximation is used to model only the collision operators of the first group. It allows us to simplify derivation of the transport fluxes and calculation of the kinetic coefficients. Special attention is given to the connection between the formulae for the bulk viscosity coefficient and the sound velocity square.

Achieving Radiation Tolerance through Non-Equilibrium Grain Boundary Structures.

Science.gov (United States)

Vetterick, Gregory A; Gruber, Jacob; Suri, Pranav K; Baldwin, Jon K; Kirk, Marquis A; Baldo, Pete; Wang, Yong Q; Misra, Amit; Tucker, Garritt J; Taheri, Mitra L

2017-09-25

Many methods used to produce nanocrystalline (NC) materials leave behind non-equilibrium grain boundaries (GBs) containing excess free volume and higher energy than their equilibrium counterparts with identical 5 degrees of freedom. Since non-equilibrium GBs have increased amounts of both strain and free volume, these boundaries may act as more efficient sinks for the excess interstitials and vacancies produced in a material under irradiation as compared to equilibrium GBs. The relative sink strengths of equilibrium and non-equilibrium GBs were explored by comparing the behavior of annealed (equilibrium) and as-deposited (non-equilibrium) NC iron films on irradiation. These results were coupled with atomistic simulations to better reveal the underlying processes occurring on timescales too short to capture using in situ TEM. After irradiation, NC iron with non-equilibrium GBs contains both a smaller number density of defect clusters and a smaller average defect cluster size. Simulations showed that excess free volume contribute to a decreased survival rate of point defects in cascades occurring adjacent to the GB and that these boundaries undergo less dramatic changes in structure upon irradiation. These results suggest that non-equilibrium GBs act as more efficient sinks for defects and could be utilized to create more radiation tolerant materials in future.

Influence of Frenkel Excitons and Charge Transfer States on the Spectroscopic Properties of Organic Molecular Crystals

OpenAIRE

Gisslén, Linus Mathias

2010-01-01

Perylene derivatives are robust organic dyes absorbing and emitting light in the visible range and in the near infrared. They display a strong tendency to self-assemble into molecular aggregates, liquid crystals, or even crystals. In this thesis, we have demonstrated a successful realization of a theoretical approach describing the fundamental interactions influencing on exciton transfer in crystalline perylenes pigments. Furthermore, the microscopic parameter set obtained has allowed to calc...

Non-equilibrium thermodynamics, maximum entropy production and Earth-system evolution.

Science.gov (United States)

Kleidon, Axel

2010-01-13

The present-day atmosphere is in a unique state far from thermodynamic equilibrium. This uniqueness is for instance reflected in the high concentration of molecular oxygen and the low relative humidity in the atmosphere. Given that the concentration of atmospheric oxygen has likely increased throughout Earth-system history, we can ask whether this trend can be generalized to a trend of Earth-system evolution that is directed away from thermodynamic equilibrium, why we would expect such a trend to take place and what it would imply for Earth-system evolution as a whole. The justification for such a trend could be found in the proposed general principle of maximum entropy production (MEP), which states that non-equilibrium thermodynamic systems maintain steady states at which entropy production is maximized. Here, I justify and demonstrate this application of MEP to the Earth at the planetary scale. I first describe the non-equilibrium thermodynamic nature of Earth-system processes and distinguish processes that drive the system's state away from equilibrium from those that are directed towards equilibrium. I formulate the interactions among these processes from a thermodynamic perspective and then connect them to a holistic view of the planetary thermodynamic state of the Earth system. In conclusion, non-equilibrium thermodynamics and MEP have the potential to provide a simple and holistic theory of Earth-system functioning. This theory can be used to derive overall evolutionary trends of the Earth's past, identify the role that life plays in driving thermodynamic states far from equilibrium, identify habitability in other planetary environments and evaluate human impacts on Earth-system functioning. This journal is © 2010 The Royal Society

Plasma wave instabilities in nonequilibrium graphene

DEFF Research Database (Denmark)

Aryal, Chinta M.; Hu, Ben Yu-Kuang; Jauho, Antti-Pekka

2016-01-01

We study two-stream instabilities in a nonequilibrium system in which a stream of electrons is injected into doped graphene. As with equivalent nonequilibrium parabolic band systems, we find that the graphene systems can support unstable charge-density waves whose amplitudes grow with time. We...... of the injected electrons that maximizes the growth rate increases with increasing | q |. We compare the range and strength of the instability in graphene to that of two- and three-dimensional parabolic band systems....

A computer program for external modes in complex ionic crystals (the rigid molecular-ion model)

International Nuclear Information System (INIS)

Chaplot, S.L.

1978-01-01

A computer program DISPR has been developed to calculate the external mode phonon dispersion relation in the harmonic approximation for complex ionic crystals using the rigid molecular ion model. A description of the program, the flow diagram and the required input information are given. A sample calculation for α-KNO 3 is presented. The program can handle any type of crystal lattice with any number of atoms and molecules per unit cell with suitable changes in dimension statements. (M.G.B.)

First-principles studies of PETN molecular crystal vibrational frequencies under high pressure

Science.gov (United States)

Perger, Warren; Zhao, Jijun

2005-07-01

The vibrational frequencies of the PETN molecular crystal were calculated using the first-principles CRYSTAL03 program which employs an all-electron LCAO approach and calculates analytic first derivatives of the total energy with respect to atomic displacements. Numerical second derivatives were used to enable calculation of the vibrational frequencies at ambient pressure and under various states of compression. Three different density functionals, B3LYP, PW91, and X3LYP were used to examine the effect of the exchange-correlation functional on the vibrational frequencies. The pressure-induced shift of the vibrational frequencies will be presented and compared with experiment. The average deviation with experimental results is shown to be on the order of 2-3%, depending on the functional used.

Molecular-crystal approach to accounting of correlation corrections in the chemical bond theory in crystals: electronic structure of Ti2O3 crystal

International Nuclear Information System (INIS)

Ehvarestov, R.A.; Panin, A.I.

2000-01-01

The problem on the possibility of partial accounting for the electron correlation effects within the frames of the Hartree-Fock unlimited method (HF). The local characteristic of the electron structure of the molecular systems for the case of the multi-determinant wave functions, configurational interaction methods and multiconfigurational self-consistent field (MCSCF) are determined. The molecular-crystalline approach is applied to studies on the electron correlation effects in the Ti 2 O 3 crystal. It is shown on the basis of the [Ti 2 O 9 ] 12- cluster electron structure calculation, that the Hartree-Fock unlimited method accounts in a number of cases for an essential part of statistical correlation effects. The energy values and local characteristics of the [Ti 2 O 9 ] 12- cluster, calculated through the HF and MCSCF methods, are presented [ru

Gas flow parameter determination by molecular beam method

International Nuclear Information System (INIS)

Zarvin, A.E.; Sharafutdinov, R.G.

1977-01-01

This paper describes a molecular-beam system intended for studying nonequilibrium processes in supersonic rarefied gas flows. The system represented is a small molecular beam source placed inside the low intensity wind tunnel of the Institute of Thermophysics, Siberian Branch of the USSR Academy of Sciences. The time-of-flight method is used for measuring molecular velocity distribution functions on molecular beam axis. (Auth.)

A multifluid model extended for strong temperature nonequilibrium

Energy Technology Data Exchange (ETDEWEB)

Chang, Chong [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

2016-08-08

We present a multifluid model in which the material temperature is strongly affected by the degree of segregation of each material. In order to track temperatures of segregated form and mixed form of the same material, they are defined as different materials with their own energy. This extension makes it necessary to extend multifluid models to the case in which each form is defined as a separate material. Statistical variations associated with the morphology of the mixture have to be simplified. Simplifications introduced include combining all molecularly mixed species into a single composite material, which is treated as another segregated material. Relative motion within the composite material, diffusion, is represented by material velocity of each component in the composite material. Compression work, momentum and energy exchange, virtual mass forces, and dissipation of the unresolved kinetic energy have been generalized to the heterogeneous mixture in temperature nonequilibrium. The present model can be further simplified by combining all mixed forms of materials into a composite material. Molecular diffusion in this case is modeled by the Stefan-Maxwell equations.

Electron transport in doped fullerene molecular junctions

Science.gov (United States)

Kaur, Milanpreet; Sawhney, Ravinder Singh; Engles, Derick

The effect of doping on the electron transport of molecular junctions is analyzed in this paper. The doped fullerene molecules are stringed to two semi-infinite gold electrodes and analyzed at equilibrium and nonequilibrium conditions of these device configurations. The contemplation is done using nonequilibrium Green’s function (NEGF)-density functional theory (DFT) to evaluate its density of states (DOS), transmission coefficient, molecular orbitals, electron density, charge transfer, current, and conductance. We conclude from the elucidated results that Au-C16Li4-Au and Au-C16Ne4-Au devices behave as an ordinary p-n junction diode and a Zener diode, respectively. Moreover, these doped fullerene molecules do not lose their metallic nature when sandwiched between the pair of gold electrodes.

Non-Equilibrium Thermodynamics in Multiphase Flows

CERN Document Server

Mauri, Roberto

2013-01-01

Non-equilibrium thermodynamics is a general framework that allows the macroscopic description of irreversible processes. This book introduces non-equilibrium thermodynamics and its applications to the rheology of multiphase flows. The subject is relevant to graduate students in chemical and mechanical engineering, physics and material science. This book is divided into two parts. The first part presents the theory of non-equilibrium thermodynamics, reviewing its essential features and showing, when possible, some applications. The second part of this book deals with how the general theory can be applied to model multiphase flows and, in particular, how to determine their constitutive relations. Each chapter contains problems at the end, the solutions of which are given at the end of the book. No prior knowledge of statistical mechanics is required; the necessary prerequisites are elements of transport phenomena and on thermodynamics. “The style of the book is mathematical, but nonetheless it remains very re...

Nonequilibrium thermodynamics of restricted Boltzmann machines

Science.gov (United States)

Salazar, Domingos S. P.

2017-08-01

In this work, we analyze the nonequilibrium thermodynamics of a class of neural networks known as restricted Boltzmann machines (RBMs) in the context of unsupervised learning. We show how the network is described as a discrete Markov process and how the detailed balance condition and the Maxwell-Boltzmann equilibrium distribution are sufficient conditions for a complete thermodynamics description, including nonequilibrium fluctuation theorems. Numerical simulations in a fully trained RBM are performed and the heat exchange fluctuation theorem is verified with excellent agreement to the theory. We observe how the contrastive divergence functional, mostly used in unsupervised learning of RBMs, is closely related to nonequilibrium thermodynamic quantities. We also use the framework to interpret the estimation of the partition function of RBMs with the annealed importance sampling method from a thermodynamics standpoint. Finally, we argue that unsupervised learning of RBMs is equivalent to a work protocol in a system driven by the laws of thermodynamics in the absence of labeled data.

Nonequilibrium thermodynamics of restricted Boltzmann machines.

Science.gov (United States)

Salazar, Domingos S P

2017-08-01

In this work, we analyze the nonequilibrium thermodynamics of a class of neural networks known as restricted Boltzmann machines (RBMs) in the context of unsupervised learning. We show how the network is described as a discrete Markov process and how the detailed balance condition and the Maxwell-Boltzmann equilibrium distribution are sufficient conditions for a complete thermodynamics description, including nonequilibrium fluctuation theorems. Numerical simulations in a fully trained RBM are performed and the heat exchange fluctuation theorem is verified with excellent agreement to the theory. We observe how the contrastive divergence functional, mostly used in unsupervised learning of RBMs, is closely related to nonequilibrium thermodynamic quantities. We also use the framework to interpret the estimation of the partition function of RBMs with the annealed importance sampling method from a thermodynamics standpoint. Finally, we argue that unsupervised learning of RBMs is equivalent to a work protocol in a system driven by the laws of thermodynamics in the absence of labeled data.

Nonequilibrium chemistry in shocked molecular clouds

International Nuclear Information System (INIS)

Iglesias, E.R.; Silk, J.

1978-01-01

The gas phase chemistry is studied behind a 10 km s -1 shock propagating into a dense molecular cloud. Our principal conclusions are that the concentrations of certain molecules (CO, NH 3 , HCN, N 2 ) are unperturbed by the shock; other molecules (H 2 CO, CN, HCO + ) are greatly decreased in abundance; and substantial amounts of H 2 O, HCO, and CH 4 are produced. Approximately 10 6 yr (independent of the density) must elapse after shock passage before chemical equilibrium is attained

Nonequilibrium steady state of biochemical cycle kinetics under non-isothermal conditions

Science.gov (United States)

Jin, Xiao; Ge, Hao

2018-04-01

The nonequilibrium steady state of isothermal biochemical cycle kinetics has been extensively studied, but that under non-isothermal conditions has been much less extensively investigated. When the heat exchange between subsystems is slow, the isothermal assumption of the whole system breaks down, as is true for many types of living organisms. Here, starting with a four-state model of molecular transporter across the cell membrane, we generalize the nonequilibrium steady-state theory of isothermal biochemical cycle kinetics to the circumstances with non-uniform temperatures of subsystems in terms of general master equation models. We obtain a new thermodynamic relationship between the chemical reaction rates and thermodynamic potentials in non-isothermal circumstances, based on the overdamped dynamics along the continuous reaction coordinate. We show that the entropy production can vary up to 3% in real cells, even when the temperature difference across the cell membrane is only approximately 1 K. We then decompose the total thermodynamic driving force into its thermal and chemical components and predict that the net flux of molecules transported by the molecular transporter can potentially go against the temperature gradient in the absence of a chemical driving force. Furthermore, we demonstrate that the simple application of the isothermal transition-state rate formula for each chemical reaction in terms of only the reactant’ temperature is not thermodynamically consistent. Therefore, we mathematically derive several revised reaction rate formulas that are not only consistent with the new thermodynamic relationship but also approximate the exact reaction rate better than Kramers’ rate formula under isothermal conditions.

Preparation and crystal and molecular structure of mer-trichlorotris(dimethylphenylphosphine)technetium(III)

Energy Technology Data Exchange (ETDEWEB)

Bandoli, G; Clemente, D A; Mazzi, U [Consiglio Nazionale delle Ricerche, Padua (Italy). Lab. di Chimica e Tecnologia dei Radioelementi

1976-01-01

The crystal and molecular structure of the title compound has been determined from single-crystal X-ray diffractometer data by Fourier methods and refined by anisotropic block-diagonal least-squares to R 0.054 for 4 065 independent observed reflections. Crystals are monoclinic, space group P2/sub 1//n, with cell parameters a = 10.935(9), b = 39.191(11), c = 13.738(7) A, ..beta.. = 107.33(7)/sup 0/, and Z = 8. The two crystallographically independent molecules are stereochemically equivalent (there is only a small difference in the orientation of a benzene ring) and the metal atom has a somewhat distorted octahedral co-ordination, with two pairs of like ligands mutually trans. Technetium-ligand bond distances are: Tc-Cl(trans to P) 2.46(1), Tc-Cl(trans to Cl) both 2.33(1), Tc-P(trans to Cl) 2.42(1) and Tc-P(trans to P) both 2.47(1) A. The noticeable trans-influence of the phosphine ligands on Tc-Cl bonds is discussed.

Inorganic bromine in organic molecular crystals: Database survey and four case studies

Science.gov (United States)

Nemec, Vinko; Lisac, Katarina; Stilinović, Vladimir; Cinčić, Dominik

2017-01-01

We present a Cambridge Structural Database and experimental study of multicomponent molecular crystals containing bromine. The CSD study covers supramolecular behaviour of bromide and tribromide anions as well as halogen bonded dibromine molecules in crystal structures of organic salts and cocrystals, and a study of the geometries and complexities in polybromide anion systems. In addition, we present four case studies of organic structures with bromide, tribromide and polybromide anions as well as the neutral dibromine molecule. These include the first observed crystal with diprotonated phenazine, a double salt of phenazinium bromide and tribromide, a cocrystal of 4-methoxypyridine with the neutral dibromine molecule as a halogen bond donor, as well as bis(4-methoxypyridine)bromonium polybromide. Structural features of the four case studies are in the most part consistent with the statistically prevalent behaviour indicated by the CSD study for given bromine species, although they do exhibit some unorthodox structural features and in that indicate possible supramolecular causes for aberrations from the statistically most abundant (and presumably most favourable) geometries.

Radiationless decay, fission and fusion of excitons in irradiated molecular crystals

International Nuclear Information System (INIS)

Klein, Gerard.

1977-01-01

The creation and evolution of excited states in ionizing particle tracks were investigated. The passage of high energy ionizing particles in molecular crystals results in the formation of highly excited states which energy is generally above the molecular ionization potential. The theory of non radiative transitions, which describes the transitions from the highly excited states to the lowest singlet and triplet excitons S 1 and T 1 is developed. Among these non radiative transitions, the fission of singlet excitons into two singlet or triplet excitons of lower energies is studied experimentally. These results and a kinematics study of the S 1 and T 1 excitons in ionizing particle tracks were used to get a complete description of the scintillation. These results are in good agreement with the experimental measurements on the scintillation [fr

Canonical operator formulation of nonequilibrium thermodynamics

International Nuclear Information System (INIS)

Mehrafarin, M.

1992-09-01

A novel formulation of nonequilibrium thermodynamics is proposed which emphasises the fundamental role played by the Boltzmann constant k in fluctuations. The equivalence of this and the stochastic formulation is demonstrated. The k → 0 limit of this theory yields the classical deterministic description of nonequilibrium thermodynamics. The new formulation possesses unique features which bear two important results namely the thermodynamic uncertainty principle and the quantisation of entropy production rate. Such a theory becomes indispensable whenever fluctuations play a significant role. (author). 7 refs

Realization of hydrodynamic experiments on quasi-2D liquid crystal films in microgravity

Science.gov (United States)

Clark, Noel A.; Eremin, Alexey; Glaser, Matthew A.; Hall, Nancy; Harth, Kirsten; Klopp, Christoph; Maclennan, Joseph E.; Park, Cheol S.; Stannarius, Ralf; Tin, Padetha; Thurmes, William N.; Trittel, Torsten

2017-08-01

Freely suspended films of smectic liquid crystals are unique examples of quasi two-dimensional fluids. Mechanically stable and with quantized thickness of the order of only a few molecular layers, smectic films are ideal systems for studying fundamental fluid physics, such as collective molecular ordering, defect and fluctuation phenomena, hydrodynamics, and nonequilibrium behavior in two dimensions (2D), including serving as models of complex biological membranes. Smectic films can be drawn across openings in planar supports resulting in thin, meniscus-bounded membranes, and can also be prepared as bubbles, either supported on an inflation tube or floating freely. The quantized layering renders smectic films uniquely useful in 2D fluid physics. The OASIS team has pursued a variety of ground-based and microgravity applications of thin liquid crystal films to fluid structure and hydrodynamic problems in 2D and quasi-2D systems. Parabolic flights and sounding rocket experiments were carried out in order to explore the shape evolution of free floating smectic bubbles, and to probe Marangoni effects in flat films. The dynamics of emulsions of smectic islands (thicker regions on thin background films) and of microdroplet inclusions in spherical films, as well as thermocapillary effects, were studied over extended periods within the OASIS (Observation and Analysis of Smectic Islands in Space) project on the International Space Station. We summarize the technical details of the OASIS hardware and give preliminary examples of key observations.

Non-equilibrium phase transitions in complex plasma

International Nuclear Information System (INIS)

Suetterlin, K R; Raeth, C; Ivlev, A V; Thomas, H M; Khrapak, S; Zhdanov, S; Rubin-Zuzic, M; Morfill, G E; Wysocki, A; Loewen, H; Goedheer, W J; Fortov, V E; Lipaev, A M; Molotkov, V I; Petrov, O F

2010-01-01

Complex plasma being the 'plasma state of soft matter' is especially suitable for investigations of non-equilibrium phase transitions. Non-equilibrium phase transitions can manifest in dissipative structures or self-organization. Two specific examples are lane formation and phase separation. Using the permanent microgravity laboratory PK-3 Plus, operating onboard the International Space Station, we performed unique experiments with binary mixtures of complex plasmas that showed both lane formation and phase separation. These observations have been augmented by comprehensive numerical and theoretical studies. In this paper we present an overview of our most important results. In addition we put our results in context with research of complex plasmas, binary systems and non-equilibrium phase transitions. Necessary and promising future complex plasma experiments on phase separation and lane formation are briefly discussed.

Toward a Multi-scale Phase Transition Kinetics Methodology: From Non-Equilibrium Statistical Mechanics to Hydrodynamics

Science.gov (United States)

Belof, Jonathan; Orlikowski, Daniel; Wu, Christine; McLaughlin, Keith

2013-06-01

Shock and ramp compression experiments are allowing us to probe condensed matter under extreme conditions where phase transitions and other non-equilibrium aspects can now be directly observed, but first principles simulation of kinetics remains a challenge. A multi-scale approach is presented here, with non-equilibrium statistical mechanical quantities calculated by molecular dynamics (MD) and then leveraged to inform a classical nucleation and growth kinetics model at the hydrodynamic scale. Of central interest is the free energy barrier for the formation of a critical nucleus, with direct NEMD presenting the challenge of relatively long timescales necessary to resolve nucleation. Rather than attempt to resolve the time-dependent nucleation sequence directly, the methodology derived here is built upon the non-equilibrium work theorem in order to bias the formation of a critical nucleus and thus construct the nucleation and growth rates. Having determined these kinetic terms from MD, a hydrodynamics implementation of Kolmogorov-Johnson-Mehl-Avrami (KJMA) kinetics and metastabilty is applied to the dynamic compressive freezing of water and compared with recent ramp compression experiments [Dolan et al., Nature (2007)] Lawrence Livermore National Laboratory is operated by Lawrence Livermore National Security, LLC, for the U.S. Department of Energy, National Nuclear Security Administration under Contract DE-AC52-07NA27344.

Dissipation, generalized free energy, and a self-consistent nonequilibrium thermodynamics of chemically driven open subsystems.

Science.gov (United States)

Ge, Hao; Qian, Hong

2013-06-01

Nonequilibrium thermodynamics of a system situated in a sustained environment with influx and efflux is usually treated as a subsystem in a larger, closed "universe." A question remains with regard to what the minimally required description for the surrounding of such an open driven system is so that its nonequilibrium thermodynamics can be established solely based on the internal stochastic kinetics. We provide a solution to this problem using insights from studies of molecular motors in a chemical nonequilibrium steady state (NESS) with sustained external drive through a regenerating system or in a quasisteady state (QSS) with an excess amount of adenosine triphosphate (ATP), adenosine diphosphate (ADP), and inorganic phosphate (Pi). We introduce the key notion of minimal work that is needed, W(min), for the external regenerating system to sustain a NESS (e.g., maintaining constant concentrations of ATP, ADP and Pi for a molecular motor). Using a Markov (master-equation) description of a motor protein, we illustrate that the NESS and QSS have identical kinetics as well as the second law in terms of the same positive entropy production rate. The heat dissipation of a NESS without mechanical output is exactly the W(min). This provides a justification for introducing an ideal external regenerating system and yields a free-energy balance equation between the net free-energy input F(in) and total dissipation F(dis) in an NESS: F(in) consists of chemical input minus mechanical output; F(dis) consists of dissipative heat, i.e. the amount of useful energy becoming heat, which also equals the NESS entropy production. Furthermore, we show that for nonstationary systems, the F(dis) and F(in) correspond to the entropy production rate and housekeeping heat in stochastic thermodynamics and identify a relative entropy H as a generalized free energy. We reach a new formulation of Markovian nonequilibrium thermodynamics based on only the internal kinetic equation without further

An Exact Solution for the Assessment of Nonequilibrium Sorption of Radionuclides in the Vadose Zone

International Nuclear Information System (INIS)

Drake, R. L.; Chen, J-S.

2002-01-01

In a report on model evaluation, the authors ran the HYDRUS Code, among other transport codes, to evaluate the impacts of nonequilibrium sorption sites on the time-evolution of 99Tc and 90Sr through the vadose zone. Since our evaluation was based on a rather low, annual recharge rate, many of the numerical results derived from HYDRUS indicated that the nonequilibrium sorption sites, in essence, acted as equilibrium sorption sites. To help explain these results, we considered a ''stripped-down'' version of the HYDRUS system. This ''stripped-down'' version possesses two dependent variables, one for the radionuclides in solution and the other for the radionuclides adsorbed to the nonequilibrium sites; and it possesses constant physical parameters. The resultant governing equation for the radionuclides in solution is a linear, advection-dispersion-reaction (i.e., radioactive decay) partial differential equation containing a history integral term accounting for the nonequilibrium sorption sites. It is this ''stripped-down'' version, which is the subject of this paper. We found an exact solution to this new version of the model. The exact solution is given in terms of a single definite integral of terms involving elementary functions of the independent variables and the system parameters. This integral possesses adequate convergence properties and is easy to evaluate, both in a quantitative matter and in a qualitative manner. The parameters that are considered in the system are as follows: the radionuclide's equilibrium partition coefficient between water and soil, the bulk density of the soil, the fractions of equilibrium/nonequilibrium sorption sites, the volumetric water content, the first order equilibrium adsorption rate constant, the first order radioactive decay rate constant, the liquid water soil tortuosity factor, the molecular diffusion coefficient in water, the longitudinal dispersivity factor, and the Darcian fluid flux density. In addition, the system

Nonequilibrium Langevin dynamics: A demonstration study of shear flow fluctuations in a simple fluid

Science.gov (United States)

Belousov, Roman; Cohen, E. G. D.; Rondoni, Lamberto

2017-08-01

The present paper is based on a recent success of the second-order stochastic fluctuation theory in describing time autocorrelations of equilibrium and nonequilibrium physical systems. In particular, it was shown to yield values of the related deterministic parameters of the Langevin equation for a Couette flow in a microscopic molecular dynamics model of a simple fluid. In this paper we find all the remaining constants of the stochastic dynamics, which then is simulated numerically and compared directly with the original physical system. By using these data, we study in detail the accuracy and precision of a second-order Langevin model for nonequilibrium physical systems theoretically and computationally. We find an intriguing relation between an applied external force and cumulants of the resulting flow fluctuations. This is characterized by a linear dependence of an athermal cumulant ratio, an apposite quantity introduced here. In addition, we discuss how the order of a given Langevin dynamics can be raised systematically by introducing colored noise.

Molecular dynamics studies and quantification of the effect of chirality on the formation of liquid crystal mesophases

International Nuclear Information System (INIS)

Solymosi, Miklos

2002-01-01

Results are presented from theoretical studies and from a series of molecular dynamics simulations undertaken to quantify the effect of chirality on the formation of liquid crystal mesophases. In the theoretical studies we have proposed a scaled chiral index with a formulation which allows comparison to be made between molecules comprising different numbers of atoms. We have undertaken chirality calculations utilizing the proposed scaled chiral index, G 0S , for one optimized static molecular geometry for a range of liquid crystal chiral dopants and ferroelectric liquid crystal molecules. The scaled chiral index, G 0S , allows a rapid calculation to be made of a pseudoscalar quantity which shows a good correlation with the helical twisting power of liquid crystal chiral dopants in a nematic liquid crystal solvent. This could prove a powerful aid in the design of novel dopant molecules where the dopant is rigid and the helical twisting is predominantly a steric effect. The same scaled chirality index, G 0S , calculation for ferroelectric liquid crystal molecules hints at an inverse correlation with spontaneous polarization agreeing with some experimental results. The scaled chiral index is a chemically useful index that can also be decomposed into atomic or functional group contributions, thereby creating a new measure of the asymmetric potential of functional groups and their different possible substitution positions. In the molecular dynamics simulation studies we have investigated two three-site Gay-Berne models, one chiral and the other achiral, each with a rotated central site forming a zigzag shape. In the chiral model one of the end site was additionally rotated out of the plane of the other two sites by a chiral angle θ c . Results from the achiral phase simulations support the theory that steric molecular shape can be associated with a driving force that leads to the smectic A - smectic C phase transition since such a transition was observed in the achiral

Density-functional method for nonequilibrium electron transport

DEFF Research Database (Denmark)

Brandbyge, Mads; Mozos, J.L.; Ordejon, P.

2002-01-01

the contact and the electrodes on the same footing. The effect of the finite bias (including self-consistency and the solution of the electrostatic problem) is taken into account using nonequilibrium Green's functions. We relate the nonequilibrium Green's function expressions to the more transparent scheme...... wires connected to aluminum electrodes with extended or finite cross section, (ii) single atom gold wires, and finally (iii) large carbon nanotube systems with point defects....

Teaching at the edge of knowledge: Non-equilibrium statistical physics

Science.gov (United States)

Schmittmann, Beate

2007-03-01

As physicists become increasingly interested in biological problems, we frequently find ourselves confronted with complex open systems, involving many interacting constituents and characterized by non-vanishing fluxes of mass or energy. Faced with the task of predicting macroscopic behaviors from microscopic information for these non-equilibrium systems, the familiar Gibbs-Boltzmann framework fails. The development of a comprehensive theoretical characterization of non-equilibrium behavior is one of the key challenges of modern condensed matter physics. In its absence, several approaches have been developed, from master equations to thermostatted molecular dynamics, which provide key insights into the rich and often surprising phenomenology of systems far from equilibrium. In my talk, I will address some of these methods, selecting those that are most relevant for a broad range of interdisciplinary problems from biology to traffic, finance, and sociology. The ``portability'' of these methods makes them valuable for graduate students from a variety of disciplines. To illustrate how different methods can complement each other when probing a problem from, e.g., the life sciences, I will discuss some recent attempts at modeling translation, i.e., the process by which the genetic information encoded on an mRNA is translated into the corresponding protein.

Orientation Dependence in Molecular Dynamics Simulations of Shocked Single Crystals

International Nuclear Information System (INIS)

Germann, Timothy C.; Holian, Brad Lee; Lomdahl, Peter S.; Ravelo, Ramon

2000-01-01

We use multimillion-atom molecular dynamics simulations to study shock wave propagation in fcc crystals. As shown recently, shock waves along the direction form intersecting stacking faults by slippage along {111} close-packed planes at sufficiently high shock strengths. We find even more interesting behavior of shocks propagating in other low-index directions: for the case, an elastic precursor separates the shock front from the slipped (plastic) region. Shock waves along the direction generate a leading solitary wave train, followed (at sufficiently high shock speeds) by an elastic precursor, and then a region of complex plastic deformation. (c) 2000 The American Physical Society

The efficiency of driving chemical reactions by a physical non-equilibrium is kinetically controlled.

Science.gov (United States)

Göppel, Tobias; Palyulin, Vladimir V; Gerland, Ulrich

2016-07-27

An out-of-equilibrium physical environment can drive chemical reactions into thermodynamically unfavorable regimes. Under prebiotic conditions such a coupling between physical and chemical non-equilibria may have enabled the spontaneous emergence of primitive evolutionary processes. Here, we study the coupling efficiency within a theoretical model that is inspired by recent laboratory experiments, but focuses on generic effects arising whenever reactant and product molecules have different transport coefficients in a flow-through system. In our model, the physical non-equilibrium is represented by a drift-diffusion process, which is a valid coarse-grained description for the interplay between thermophoresis and convection, as well as for many other molecular transport processes. As a simple chemical reaction, we consider a reversible dimerization process, which is coupled to the transport process by different drift velocities for monomers and dimers. Within this minimal model, the coupling efficiency between the non-equilibrium transport process and the chemical reaction can be analyzed in all parameter regimes. The analysis shows that the efficiency depends strongly on the Damköhler number, a parameter that measures the relative timescales associated with the transport and reaction kinetics. Our model and results will be useful for a better understanding of the conditions for which non-equilibrium environments can provide a significant driving force for chemical reactions in a prebiotic setting.

Contributions of different degrees of freedom to thermal transport in the C60 molecular crystal

Science.gov (United States)

Kumar, Sushant; Shao, Cheng; Lu, Simon; McGaughey, Alan J. H.

2018-03-01

Three models of the C60 molecular crystal are studied using molecular dynamics simulations to resolve the roles played by intermolecular and intramolecular degrees of freedom (DOF) in its structural, mechanical, and thermal properties at temperatures between 35 and 400 K. In the full DOF model, all DOF are active. In the rigid body model, the intramolecular DOF are frozen, such that only center of mass (COM) translations and molecular rotations/librations are active. In the point mass model, the molecule is replaced by a point mass, such that only COM translations are active. The zero-pressure lattice constants and bulk moduli predicted from the three models fall within ranges of 0.15 and 20%. The thermal conductivity of the point mass model is the largest across the temperature range, showing a crystal-like temperature dependence (i.e., it decreases with increasing temperature) due to the presence of phonon modes associated with the COM translations. The rigid body model thermal conductivity is the smallest and follows two distinct regimes. It is crystal-like at low temperatures and becomes temperature invariant at high temperatures. The latter is typical of the behavior of an amorphous material. By calculating the rotational diffusion coefficient, the transition between the two regimes is found to occur at the temperature where the molecules begin to rotate freely. Above this temperature, phonons related to COM translations are scattered by the rotational DOF. The full DOF model thermal conductivity is larger than that of the rigid body model, indicating that intramolecular DOF contribute to thermal transport.

"Non-equilibrium" block copolymer micelles with glassy cores: a predictive approach based on theory of equilibrium micelles.

Science.gov (United States)

Nagarajan, Ramanathan

2015-07-01

Micelles generated in water from most amphiphilic block copolymers are widely recognized to be non-equilibrium structures. Typically, the micelles are prepared by a kinetic process, first allowing molecular scale dissolution of the block copolymer in a common solvent that likes both the blocks and then gradually replacing the common solvent by water to promote the hydrophobic blocks to aggregate and create the micelles. The non-equilibrium nature of the micelle originates from the fact that dynamic exchange between the block copolymer molecules in the micelle and the singly dispersed block copolymer molecules in water is suppressed, because of the glassy nature of the core forming polymer block and/or its very large hydrophobicity. Although most amphiphilic block copolymers generate such non-equilibrium micelles, no theoretical approach to a priori predict the micelle characteristics currently exists. In this work, we propose a predictive approach for non-equilibrium micelles with glassy cores by applying the equilibrium theory of micelles in two steps. In the first, we calculate the properties of micelles formed in the mixed solvent while true equilibrium prevails, until the micelle core becomes glassy. In the second step, we freeze the micelle aggregation number at this glassy state and calculate the corona dimension from the equilibrium theory of micelles. The condition when the micelle core becomes glassy is independently determined from a statistical thermodynamic treatment of diluent effect on polymer glass transition temperature. The predictions based on this "non-equilibrium" model compare reasonably well with experimental data for polystyrene-polyethylene oxide diblock copolymer, which is the most extensively studied system in the literature. In contrast, the application of the equilibrium model to describe such a system significantly overpredicts the micelle core and corona dimensions and the aggregation number. The non-equilibrium model suggests ways to

Nonequilibrium Enhances Adaptation Efficiency of Stochastic Biochemical Systems.

Directory of Open Access Journals (Sweden)

Chen Jia

Full Text Available Adaptation is a crucial biological function possessed by many sensory systems. Early work has shown that some influential equilibrium models can achieve accurate adaptation. However, recent studies indicate that there are close relationships between adaptation and nonequilibrium. In this paper, we provide an explanation of these two seemingly contradictory results based on Markov models with relatively simple networks. We show that as the nonequilibrium driving becomes stronger, the system under consideration will undergo a phase transition along a fixed direction: from non-adaptation to simple adaptation then to oscillatory adaptation, while the transition in the opposite direction is forbidden. This indicates that although adaptation may be observed in equilibrium systems, it tends to occur in systems far away from equilibrium. In addition, we find that nonequilibrium will improve the performance of adaptation by enhancing the adaptation efficiency. All these results provide a deeper insight into the connection between adaptation and nonequilibrium. Finally, we use a more complicated network model of bacterial chemotaxis to validate the main results of this paper.

Nonequilibrium dynamics in an interacting Fe-C nanoparticle system

DEFF Research Database (Denmark)

Jönsson, P.; Hansen, Mikkel Fougt; Nordblad, P.

2000-01-01

Nonequilibrium dynamics in an interacting Fe-C nanoparticle sample, exhibiting a low-temperature spin-glass-like phase, has been studied by low-frequency ac susceptibility and magnetic relaxation experiments. The nonequilibrium behavior shows characteristic spin-glass features, but some qualitative...

Linking Equilibrium and Nonequilibrium Dynamics in Glass-Forming Systems

DEFF Research Database (Denmark)

Mauro, John C.; Guo, Xiaoju; Smedskjær, Morten Mattrup

, we show that the nonequilibrium glassy dynamics are intimately connected with the equilibrium liquid dynamics. This is accomplished by deriving a new functional form for the thermal history dependence of nonequilibrium viscosity, which is validated against experimental measurements of industrial...

Nonequilibrium mesoscopic transport: a genealogy

International Nuclear Information System (INIS)

Das, Mukunda P; Green, Frederick

2012-01-01

Models of nonequilibrium quantum transport underpin all modern electronic devices, from the largest scales to the smallest. Past simplifications such as coarse graining and bulk self-averaging served well to understand electronic materials. Such particular notions become inapplicable at mesoscopic dimensions, edging towards the truly quantum regime. Nevertheless a unifying thread continues to run through transport physics, animating the design of small-scale electronic technology: microscopic conservation and nonequilibrium dissipation. These fundamentals are inherent in quantum transport and gain even greater and more explicit experimental meaning in the passage to atomic-sized devices. We review their genesis, their theoretical context, and their governing role in the electronic response of meso- and nanoscopic systems. (topical review)

Nonequilibrium thermodynamics of nucleation

NARCIS (Netherlands)

Schweizer, M.; Sagis, L.M.C.

2014-01-01

We present a novel approach to nucleation processes based on the GENERIC framework (general equation for the nonequilibrium reversible-irreversible coupling). Solely based on the GENERIC structure of time-evolution equations and thermodynamic consistency arguments of exchange processes between a

Stochastic thermodynamics, fluctuation theorems and molecular machines

International Nuclear Information System (INIS)

Seifert, Udo

2012-01-01

Stochastic thermodynamics as reviewed here systematically provides a framework for extending the notions of classical thermodynamics such as work, heat and entropy production to the level of individual trajectories of well-defined non-equilibrium ensembles. It applies whenever a non-equilibrium process is still coupled to one (or several) heat bath(s) of constant temperature. Paradigmatic systems are single colloidal particles in time-dependent laser traps, polymers in external flow, enzymes and molecular motors in single molecule assays, small biochemical networks and thermoelectric devices involving single electron transport. For such systems, a first-law like energy balance can be identified along fluctuating trajectories. For a basic Markovian dynamics implemented either on the continuum level with Langevin equations or on a discrete set of states as a master equation, thermodynamic consistency imposes a local-detailed balance constraint on noise and rates, respectively. Various integral and detailed fluctuation theorems, which are derived here in a unifying approach from one master theorem, constrain the probability distributions for work, heat and entropy production depending on the nature of the system and the choice of non-equilibrium conditions. For non-equilibrium steady states, particularly strong results hold like a generalized fluctuation–dissipation theorem involving entropy production. Ramifications and applications of these concepts include optimal driving between specified states in finite time, the role of measurement-based feedback processes and the relation between dissipation and irreversibility. Efficiency and, in particular, efficiency at maximum power can be discussed systematically beyond the linear response regime for two classes of molecular machines, isothermal ones such as molecular motors, and heat engines such as thermoelectric devices, using a common framework based on a cycle decomposition of entropy production. (review article)

Information theory explanation of the fluctuation theorem, maximum entropy production and self-organized criticality in non-equilibrium stationary states

CERN Document Server

Dewar, R

2003-01-01

Jaynes' information theory formalism of statistical mechanics is applied to the stationary states of open, non-equilibrium systems. First, it is shown that the probability distribution p subGAMMA of the underlying microscopic phase space trajectories GAMMA over a time interval of length tau satisfies p subGAMMA propor to exp(tau sigma subGAMMA/2k sub B) where sigma subGAMMA is the time-averaged rate of entropy production of GAMMA. Three consequences of this result are then derived: (1) the fluctuation theorem, which describes the exponentially declining probability of deviations from the second law of thermodynamics as tau -> infinity; (2) the selection principle of maximum entropy production for non-equilibrium stationary states, empirical support for which has been found in studies of phenomena as diverse as the Earth's climate and crystal growth morphology; and (3) the emergence of self-organized criticality for flux-driven systems in the slowly-driven limit. The explanation of these results on general inf...

Efficiency bounds for nonequilibrium heat engines

International Nuclear Information System (INIS)

Mehta, Pankaj; Polkovnikov, Anatoli

2013-01-01

We analyze the efficiency of thermal engines (either quantum or classical) working with a single heat reservoir like an atmosphere. The engine first gets an energy intake, which can be done in an arbitrary nonequilibrium way e.g. combustion of fuel. Then the engine performs the work and returns to the initial state. We distinguish two general classes of engines where the working body first equilibrates within itself and then performs the work (ergodic engine) or when it performs the work before equilibrating (non-ergodic engine). We show that in both cases the second law of thermodynamics limits their efficiency. For ergodic engines we find a rigorous upper bound for the efficiency, which is strictly smaller than the equivalent Carnot efficiency. I.e. the Carnot efficiency can be never achieved in single reservoir heat engines. For non-ergodic engines the efficiency can be higher and can exceed the equilibrium Carnot bound. By extending the fundamental thermodynamic relation to nonequilibrium processes, we find a rigorous thermodynamic bound for the efficiency of both ergodic and non-ergodic engines and show that it is given by the relative entropy of the nonequilibrium and initial equilibrium distributions. These results suggest a new general strategy for designing more efficient engines. We illustrate our ideas by using simple examples. -- Highlights: ► Derived efficiency bounds for heat engines working with a single reservoir. ► Analyzed both ergodic and non-ergodic engines. ► Showed that non-ergodic engines can be more efficient. ► Extended fundamental thermodynamic relation to arbitrary nonequilibrium processes

Efficient hybrid non-equilibrium molecular dynamics--Monte Carlo simulations with symmetric momentum reversal.

Science.gov (United States)

Chen, Yunjie; Roux, Benoît

2014-09-21

Hybrid schemes combining the strength of molecular dynamics (MD) and Metropolis Monte Carlo (MC) offer a promising avenue to improve the sampling efficiency of computer simulations of complex systems. A number of recently proposed hybrid methods consider new configurations generated by driving the system via a non-equilibrium MD (neMD) trajectory, which are subsequently treated as putative candidates for Metropolis MC acceptance or rejection. To obey microscopic detailed balance, it is necessary to alter the momentum of the system at the beginning and/or the end of the neMD trajectory. This strict rule then guarantees that the random walk in configurational space generated by such hybrid neMD-MC algorithm will yield the proper equilibrium Boltzmann distribution. While a number of different constructs are possible, the most commonly used prescription has been to simply reverse the momenta of all the particles at the end of the neMD trajectory ("one-end momentum reversal"). Surprisingly, it is shown here that the choice of momentum reversal prescription can have a considerable effect on the rate of convergence of the hybrid neMD-MC algorithm, with the simple one-end momentum reversal encountering particularly acute problems. In these neMD-MC simulations, different regions of configurational space end up being essentially isolated from one another due to a very small transition rate between regions. In the worst-case scenario, it is almost as if the configurational space does not constitute a single communicating class that can be sampled efficiently by the algorithm, and extremely long neMD-MC simulations are needed to obtain proper equilibrium probability distributions. To address this issue, a novel momentum reversal prescription, symmetrized with respect to both the beginning and the end of the neMD trajectory ("symmetric two-ends momentum reversal"), is introduced. Illustrative simulations demonstrate that the hybrid neMD-MC algorithm robustly yields a correct

Efficient hybrid non-equilibrium molecular dynamics - Monte Carlo simulations with symmetric momentum reversal

Science.gov (United States)

Chen, Yunjie; Roux, Benoît

2014-09-01

Hybrid schemes combining the strength of molecular dynamics (MD) and Metropolis Monte Carlo (MC) offer a promising avenue to improve the sampling efficiency of computer simulations of complex systems. A number of recently proposed hybrid methods consider new configurations generated by driving the system via a non-equilibrium MD (neMD) trajectory, which are subsequently treated as putative candidates for Metropolis MC acceptance or rejection. To obey microscopic detailed balance, it is necessary to alter the momentum of the system at the beginning and/or the end of the neMD trajectory. This strict rule then guarantees that the random walk in configurational space generated by such hybrid neMD-MC algorithm will yield the proper equilibrium Boltzmann distribution. While a number of different constructs are possible, the most commonly used prescription has been to simply reverse the momenta of all the particles at the end of the neMD trajectory ("one-end momentum reversal"). Surprisingly, it is shown here that the choice of momentum reversal prescription can have a considerable effect on the rate of convergence of the hybrid neMD-MC algorithm, with the simple one-end momentum reversal encountering particularly acute problems. In these neMD-MC simulations, different regions of configurational space end up being essentially isolated from one another due to a very small transition rate between regions. In the worst-case scenario, it is almost as if the configurational space does not constitute a single communicating class that can be sampled efficiently by the algorithm, and extremely long neMD-MC simulations are needed to obtain proper equilibrium probability distributions. To address this issue, a novel momentum reversal prescription, symmetrized with respect to both the beginning and the end of the neMD trajectory ("symmetric two-ends momentum reversal"), is introduced. Illustrative simulations demonstrate that the hybrid neMD-MC algorithm robustly yields a correct

Quantum thermodynamics: a nonequilibrium Green's function approach.

Science.gov (United States)

Esposito, Massimiliano; Ochoa, Maicol A; Galperin, Michael

2015-02-27

We establish the foundations of a nonequilibrium theory of quantum thermodynamics for noninteracting open quantum systems strongly coupled to their reservoirs within the framework of the nonequilibrium Green's functions. The energy of the system and its coupling to the reservoirs are controlled by a slow external time-dependent force treated to first order beyond the quasistatic limit. We derive the four basic laws of thermodynamics and characterize reversible transformations. Stochastic thermodynamics is recovered in the weak coupling limit.

Molecular dynamics on diffusive time scales from the phase-field-crystal equation.

Science.gov (United States)

Chan, Pak Yuen; Goldenfeld, Nigel; Dantzig, Jon

2009-03-01

We extend the phase-field-crystal model to accommodate exact atomic configurations and vacancies by requiring the order parameter to be non-negative. The resulting theory dictates the number of atoms and describes the motion of each of them. By solving the dynamical equation of the model, which is a partial differential equation, we are essentially performing molecular dynamics simulations on diffusive time scales. To illustrate this approach, we calculate the two-point correlation function of a fluid.

Pressure-induced phase transitions in organic molecular crystals: a combination of x-ray single-crystal and powder diffraction, raman and IR-spectroscopy

International Nuclear Information System (INIS)

Boldyreva, E V; Goryainov, S V; Seryotkin, Y V; Kolesnik, E N; Shakhtshneider, T P; Ivashevskaya, S N; Drebushchak, T N; Sowa, H; Ahsbahs, H; Chernyshev, V V; Dmitriev, V P

2008-01-01

The contribution summarizes the results of recent studies of phase transitions induced by high pressure in a number of molecular organic crystals, such as polymorphs of paracetamol, chlorpropamide, polymorphs of glycine, L- and DL-serine, β-alanine. The main attention is paid to the following topics: (1) Reversible / irreversible transformations; (2) Different behavior of single crystals / powders; (3) The role of pressure-transmitting liquid; (4) The role of the kinetic factors: phase transitions on decompression, or after a long storage at a selected pressure; (5) Isosymmetric phase transitions; (6) The role of the changes in the hydrogen bond networks / intramolecular conformational changes in the phase transitions; (7) Superstructures / nanostructures formed as a result of pressure-induced phase transitions

Pressure-induced phase transitions in organic molecular crystals: a combination of x-ray single-crystal and powder diffraction, raman and IR-spectroscopy

Energy Technology Data Exchange (ETDEWEB)

Boldyreva, E V; Goryainov, S V; Seryotkin, Y V; Kolesnik, E N; Shakhtshneider, T P; Ivashevskaya, S N; Drebushchak, T N [Research and Education Center ' Molecular Design and Ecologically Safe Technologies' , REC-008, Novosibirsk State University (Russian Federation); Sowa, H [Goettingen University (Germany); Ahsbahs, H; Chernyshev, V V [Marburg University (Germany); Dmitriev, V P [Swiss-Norwegian Beamline ESRF, Grenoble (France)], E-mail: boldyrev@nsu.ru

2008-07-15

The contribution summarizes the results of recent studies of phase transitions induced by high pressure in a number of molecular organic crystals, such as polymorphs of paracetamol, chlorpropamide, polymorphs of glycine, L- and DL-serine, {beta}-alanine. The main attention is paid to the following topics: (1) Reversible / irreversible transformations; (2) Different behavior of single crystals / powders; (3) The role of pressure-transmitting liquid; (4) The role of the kinetic factors: phase transitions on decompression, or after a long storage at a selected pressure; (5) Isosymmetric phase transitions; (6) The role of the changes in the hydrogen bond networks / intramolecular conformational changes in the phase transitions; (7) Superstructures / nanostructures formed as a result of pressure-induced phase transitions.

On the fundamental equation of nonequilibrium statistical physics—Nonequilibrium entropy evolution equation and the formula for entropy production rate

Institute of Scientific and Technical Information of China (English)

无

2010-01-01

In this paper the author presents an overview on his own research works. More than ten years ago, we proposed a new fundamental equation of nonequilibrium statistical physics in place of the present Liouville equation. That is the stochastic velocity type’s Langevin equation in 6N dimensional phase space or its equivalent Liouville diffusion equation. This equation is time-reversed asymmetrical. It shows that the form of motion of particles in statistical thermodynamic systems has the drift-diffusion duality, and the law of motion of statistical thermodynamics is expressed by a superposition of both the law of dynamics and the stochastic velocity and possesses both determinism and probability. Hence it is different from the law of motion of particles in dynamical systems. The stochastic diffusion motion of the particles is the microscopic origin of macroscopic irreversibility. Starting from this fundamental equation the BBGKY diffusion equation hierarchy, the Boltzmann collision diffusion equation, the hydrodynamic equations such as the mass drift-diffusion equation, the Navier-Stokes equation and the thermal conductivity equation have been derived and presented here. What is more important, we first constructed a nonlinear evolution equation of nonequilibrium entropy density in 6N, 6 and 3 dimensional phase space, predicted the existence of entropy diffusion. This entropy evolution equation plays a leading role in nonequilibrium entropy theory, it reveals that the time rate of change of nonequilibrium entropy density originates together from its drift, diffusion and production in space. From this evolution equation, we presented a formula for entropy production rate (i.e. the law of entropy increase) in 6N and 6 dimensional phase space, proved that internal attractive force in nonequilibrium system can result in entropy decrease while internal repulsive force leads to another entropy increase, and derived a common expression for this entropy decrease rate or

Nonequilibrium statistical mechanics ensemble method

CERN Document Server

Eu, Byung Chan

1998-01-01

In this monograph, nonequilibrium statistical mechanics is developed by means of ensemble methods on the basis of the Boltzmann equation, the generic Boltzmann equations for classical and quantum dilute gases, and a generalised Boltzmann equation for dense simple fluids The theories are developed in forms parallel with the equilibrium Gibbs ensemble theory in a way fully consistent with the laws of thermodynamics The generalised hydrodynamics equations are the integral part of the theory and describe the evolution of macroscopic processes in accordance with the laws of thermodynamics of systems far removed from equilibrium Audience This book will be of interest to researchers in the fields of statistical mechanics, condensed matter physics, gas dynamics, fluid dynamics, rheology, irreversible thermodynamics and nonequilibrium phenomena

Characterization of molecular associations involving L-ornithine and α-ketoglutaric acid: crystal structure of L-ornithinium α-ketoglutarate.

Science.gov (United States)

Allouchi, H; Céolin, R; Berthon, L; Tombret, F; Rietveld, I B

2014-07-01

The crystal structure of L-ornithinium α-ketoglutarate (C5H13N2O2, C5H5O5) has been solved by direct methods using single crystal X-ray diffraction data. It crystallizes in the monoclinic system, space group P21, unit cell parameters a=15.4326(3), b=5.2015(1), c=16.2067(3) Å and β=91.986(1)°, containing two independent pairs of molecular ions in the asymmetric unit. An extensive hydrogen-bond network and electrostatic charges due to proton transfer provide an important part of the cohesive energy of the crystal. The conformational versatility of L-ornithine and α-ketoglutaric acid is illustrated by the present results and crystal structures available from the Cambridge Structural Database. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

Density functional/molecular dynamics simulations of nucleus-driven crystallization of amorphous Ge2Sb2Te5

Energy Technology Data Exchange (ETDEWEB)

Akola, Jaakko [Department of Physics, Tampere University of Technology (Finland); COMP Centre of Excellence, Department of Applied Physics, Aalto University (Finland); GRSS and PGI-1, Forschungszentrum Juelich (Germany); Kalikka, Janne; Larrucea, Julen [Nanoscience Center, Department of Physics, University of Jyvaeskylae (Finland); Jones, Robert O. [GRSS and PGI-1, Forschungszentrum Juelich (Germany)

2013-07-01

Early stages of nucleus-driven crystallization of the prototype phase change material Ge{sub 2}Sb{sub 2}Te{sub 5} have been studied by massively-parallel density functional/molecular dynamics simulations for amorphous samples (460 and 648 atoms) at 500, 600, and 700 K. All systems assumed a fixed cubic seed of 58 atoms and 6 vacancies in order to achieve sub-nanosecond phase transition. Crystallization occurs within 600 ps for the 460-atom system at 600 and 700 K, and signs of crystallization (nucleus growth, percolation) are present in the others. Crystallization is accompanied by an increase in the number of ABAB squares (A: Ge,Sb, B: Te), and atoms of all elements move significantly. The evolution of cavities/vacancies is closely monitored. The existence of Te-Te, Ge-Ge, Ge-Sb, and Sb-Sb (wrong) bonds is an inevitable consequence of rapid crystallization.

Quantum Transport Through Tunable Molecular Diodes

KAUST Repository

Obodo, Tobechukwu Joshua

2017-07-31

Employing self-interaction corrected density functional theory combined with the non-equilibrium Green\\'s function method, we study the quantum transport through molecules with different numbers of phenyl (donor) and pyrimidinyl (acceptor) rings in order to evaluate the effects of the molecular composition on the transport properties. Excellent agreement with the results of recent experiments addressing the rectification behavior of molecular junctions is obtained, which demonstrates the potential of quantum transport simulations for designing high performance junctions by tuning the molecular specifications.

Nonequilibrium entropies

International Nuclear Information System (INIS)

Maes, Christian

2012-01-01

In contrast to the quite unique entropy concept useful for systems in (local) thermodynamic equilibrium, there is a variety of quite distinct nonequilibrium entropies, reflecting different physical points. We disentangle these entropies as they relate to heat, fluctuations, response, time asymmetry, variational principles, monotonicity, volume contraction or statistical forces. However, not all of those extensions yield state quantities as understood thermodynamically. At the end we sketch how aspects of dynamical activity can take over for obtaining an extended Clausius relation.

Non-equilibrium dynamics due to moving deflagration front at RDX/HTPB interface

Science.gov (United States)

Chaudhuri, Santanu; Joshi, Kaushik; Lacevic, Naida

Reactive dissipative particle dynamics (DPD-RX), a promising tool in characterizing the sensitivity and performance of heterogeneous solid propellants like polymer bonded explosives (PSXs), requires further testing for non-equilibrium dynamics. It is important to understand detailed atomistic chemistry for developing coarse grain reactive models needed for the DPD-RX. In order to obtain insights into combustion chemistry of RDX/HTPB binder, we used reactive molecular dynamics (RMD) to obtain energy up-pumping and reaction mechanisms at RDX/HTPB interface when exposed to a self-sustaining deflagration front. Hot spots are ignited near and away from the heterogeneous interface using the thermal pulse. The results show that the hot spot near interface significantly delays the transition from ignition to deflagration. We will present the mechanical response and the combustion chemistry of HTPB when the propagating deflagration front hits the polymer binder. We will discuss our efforts to incorporate this RMD based chemistry into the DPD-RX which will enable us to perform such non-equilibrium dynamics simulations on large-length scale with microstructural heterogeneities. Funding from DTRA Grant Number HDTRA1-15-1-0034 is acknowledged.

Spectral non-equilibrium property in homogeneous isotropic turbulence and its implication in subgrid-scale modeling

Energy Technology Data Exchange (ETDEWEB)

Fang, Le [Laboratory of Mathematics and Physics, Ecole Centrale de Pékin, Beihang University, Beijing 100191 (China); Zhu, Ying [Laboratory of Mathematics and Physics, Ecole Centrale de Pékin, Beihang University, Beijing 100191 (China); National Key Laboratory of Science and Technology on Aero-Engine Aero-Thermodynamics, School of Energy and Power Engineering, Beihang University, Beijing 100191 (China); Liu, Yangwei, E-mail: liuyangwei@126.com [National Key Laboratory of Science and Technology on Aero-Engine Aero-Thermodynamics, School of Energy and Power Engineering, Beihang University, Beijing 100191 (China); Lu, Lipeng [National Key Laboratory of Science and Technology on Aero-Engine Aero-Thermodynamics, School of Energy and Power Engineering, Beihang University, Beijing 100191 (China)

2015-10-09

The non-equilibrium property in turbulence is a non-negligible problem in large-eddy simulation but has not yet been systematically considered. The generalization from equilibrium turbulence to non-equilibrium turbulence requires a clear recognition of the non-equilibrium property. As a preliminary step of this recognition, the present letter defines a typical non-equilibrium process, that is, the spectral non-equilibrium process, in homogeneous isotropic turbulence. It is then theoretically investigated by employing the skewness of grid-scale velocity gradient, which permits the decomposition of resolved velocity field into an equilibrium one and a time-reversed one. Based on this decomposition, an improved Smagorinsky model is proposed to correct the non-equilibrium behavior of the traditional Smagorinsky model. The present study is expected to shed light on the future studies of more generalized non-equilibrium turbulent flows. - Highlights: • A spectral non-equilibrium process in isotropic turbulence is defined theoretically. • A decomposition method is proposed to divide a non-equilibrium turbulence field. • An improved Smagorinsky model is proposed to correct the non-equilibrium behavior.

Time step rescaling recovers continuous-time dynamical properties for discrete-time Langevin integration of nonequilibrium systems.

Science.gov (United States)

Sivak, David A; Chodera, John D; Crooks, Gavin E

2014-06-19

When simulating molecular systems using deterministic equations of motion (e.g., Newtonian dynamics), such equations are generally numerically integrated according to a well-developed set of algorithms that share commonly agreed-upon desirable properties. However, for stochastic equations of motion (e.g., Langevin dynamics), there is still broad disagreement over which integration algorithms are most appropriate. While multiple desiderata have been proposed throughout the literature, consensus on which criteria are important is absent, and no published integration scheme satisfies all desiderata simultaneously. Additional nontrivial complications stem from simulating systems driven out of equilibrium using existing stochastic integration schemes in conjunction with recently developed nonequilibrium fluctuation theorems. Here, we examine a family of discrete time integration schemes for Langevin dynamics, assessing how each member satisfies a variety of desiderata that have been enumerated in prior efforts to construct suitable Langevin integrators. We show that the incorporation of a novel time step rescaling in the deterministic updates of position and velocity can correct a number of dynamical defects in these integrators. Finally, we identify a particular splitting (related to the velocity Verlet discretization) that has essentially universally appropriate properties for the simulation of Langevin dynamics for molecular systems in equilibrium, nonequilibrium, and path sampling contexts.

High pressure 129I Moessbauer studies of GeI4 molecular crystals

International Nuclear Information System (INIS)

Pasternak, M.P.; Taylor, R.D.

1989-01-01

The Moessbauer effect in 129 I in conjunction with Diamond-Anvil-Cell high pressure techniques was applied to investigate the high pressure phase(s) of the molecular crystal GeI 4 . The 129 I Quadrupole Interaction was the main probe for characterizing the intermolecular structural transformation with pressure. With increasing pressure, at about 15 GPAa, the onset of a partial molecular-association phase (HP1) is first observed. In HP1 two out of the four iodines strongly overlap to form linear chains of GeI 4 . The HP1 phase coexists with the low pressure (LP) molecular phase, but its population increases with increasing pressure. At P ∼20 GPa a second high pressure phase (HP2) is identified where all four iodines strongly overlap to form a three dimensional, fully molecular-associated structure. With increasing pressure and at P > 20 GPa, HP2 is the only phase up to P = 34 GPa, the highest pressure used. A significant hysteresis of the relative abundances with pressure is observed. The isomer shift of the HP2 and HP1 structures is considerably larger than that of the LP one. 11 refs., 3 figs

High pressure 129I Moessbauer studies of GeI4 molecular crystals

International Nuclear Information System (INIS)

Pasternak, M.P.; Los Alamos National Lab.; Taylor, R.D.

1990-01-01

The Moessbauer effect in 129 I in cunjunction with Diamond-Anvil-Cell high pressure techniques was applied to investigate the high pressure phase(s) of the molecular crystal GeI 4 . The 129 I Quadrupole Interaction was the main probe for characterizing the intermolecular structural transformation with pressure. With increasing pressure, at about 15 GPa, the onset of a partial molecular-association phase (HP1) is first observed. In HP1 two out of the four iodines strongly overlap to form linear chains of GeI 4 . The HP1 phase coexists with the low pressure (LP) molecular phase, but its population increases with increasing pressure. At P≅20 GPa a second high pressure phase (HP2) is identified where all four iodines strongly overlap to form a three dimensional, fully molecular-associated structure. With increasing pressure and at P>20 GPa, HP2 is the only phase up to P=34 GPa, the highest pressure used. A significant hysteresis of the relative abundances with pressure is observed. The isomer shift of the HP2 and HP1 structures is considerably larger than that of the LP one. (orig.)

Gas-kinetic unified algorithm for hypersonic flows covering various flow regimes solving Boltzmann model equation in nonequilibrium effect

International Nuclear Information System (INIS)

Li, Zhihui; Ma, Qiang; Wu, Junlin; Jiang, Xinyu; Zhang, Hanxin

2014-01-01

Based on the Gas-Kinetic Unified Algorithm (GKUA) directly solving the Boltzmann model equation, the effect of rotational non-equilibrium is investigated recurring to the kinetic Rykov model with relaxation property of rotational degrees of freedom. The spin movement of diatomic molecule is described by moment of inertia, and the conservation of total angle momentum is taken as a new Boltzmann collision invariant. The molecular velocity distribution function is integrated by the weight factor on the internal energy, and the closed system of two kinetic controlling equations is obtained with inelastic and elastic collisions. The optimization selection technique of discrete velocity ordinate points and numerical quadrature rules for macroscopic flow variables with dynamic updating evolvement are developed to simulate hypersonic flows, and the gas-kinetic numerical scheme is constructed to capture the time evolution of the discretized velocity distribution functions. The gas-kinetic boundary conditions in thermodynamic non-equilibrium and numerical procedures are studied and implemented by directly acting on the velocity distribution function, and then the unified algorithm of Boltzmann model equation involving non-equilibrium effect is presented for the whole range of flow regimes. The hypersonic flows involving non-equilibrium effect are numerically simulated including the inner flows of shock wave structures in nitrogen with different Mach numbers of 1.5-Ma-25, the planar ramp flow with the whole range of Knudsen numbers of 0.0009-Kn-10 and the three-dimensional re-entering flows around tine double-cone body

Thermal force approach to molecular evolution.

Science.gov (United States)

Braun, Dieter; Libchaber, Albert

2004-06-01

Recent experiments are discussed where temperature gradients across mesoscopic pores are shown to provide essential mechanisms for autonomous molecular evolution. On the one hand, laminar thermal convection can drive DNA replication as the molecules are continuously cycled between hot and cold regions of a chamber. On the other hand, thermophoresis can accumulate charged biopolymers in similar convection settings. The experiments show that temperature differences analogous to those across porous rocks present a robust nonequilibrium boundary condition to feed the replication and accumulation of evolving molecules. It is speculated that similar nonequilibrium conditions near porous submarine hydrothermal mounds could have triggered the origin of life. In such a scenario, the encapsulation of cells with membranes would be a later development. It is expected that detailed studies of mesoscopic boundary conditions under nonequilibrium conditions will reveal new connecting pieces in the fascinating puzzle of the origins of life.

Introduction to nonequilibrium statistical mechanics with quantum field theory

International Nuclear Information System (INIS)

Kita, Takafumi

2010-01-01

In this article, we present a concise and self-contained introduction to nonequilibrium statistical mechanics with quantum field theory by considering an ensemble of interacting identical bosons or fermions as an example. Readers are assumed to be familiar with the Matsubara formalism of equilibrium statistical mechanics such as Feynman diagrams, the proper self-energy, and Dyson's equation. The aims are threefold: (1) to explain the fundamentals of nonequilibrium quantum field theory as simple as possible on the basis of the knowledge of the equilibrium counterpart; (2) to elucidate the hierarchy in describing nonequilibrium systems from Dyson's equation on the Keldysh contour to the Navier-Stokes equation in fluid mechanics via quantum transport equations and the Boltzmann equation; (3) to derive an expression of nonequilibrium entropy that evolves with time. In stage (1), we introduce nonequilibrium Green's function and the self-energy uniquely on the round-trip Keldysh contour, thereby avoiding possible confusions that may arise from defining multiple Green's functions at the very beginning. We try to present the Feynman rules for the perturbation expansion as simple as possible. In particular, we focus on the self-consistent perturbation expansion with the Luttinger-Ward thermodynamic functional, i.e., Baym's Φ-derivable approximation, which has a crucial property for nonequilibrium systems of obeying various conservation laws automatically. We also show how the two-particle correlations can be calculated within the Φ-derivable approximation, i.e., an issue of how to handle the 'Bogoliubov-Born-Green-Kirkwood-Yvons (BBGKY) hierarchy'. Aim (2) is performed through successive reductions of relevant variables with the Wigner transformation, the gradient expansion based on the Groenewold-Moyal product, and Enskog's expansion from local equilibrium. This part may be helpful for convincing readers that nonequilibrium systems can be handled microscopically with

FT-IR, FT-Raman, and DFT computational studies of melaminium nitrate molecular-ionic crystal

Science.gov (United States)

Tanak, Hasan; Marchewka, Mariusz K.

2013-02-01

The experimental and theoretical vibrational spectra of melaminium nitrate were studied. The Raman and infrared (FT-IR) spectra of the melaminium nitrate and its deuterated analogue were recorded in the solid phase. Molecular geometry and vibrational frequency values of melaminium nitrate in the electronic ground state were calculated using the density functional method (B3LYP) with the 6-31++G(d,p) basis set. The calculated results show that the optimized geometry can well reproduce the crystal structure, and the theoretical vibrational frequency values show good agreement with experimental values. The NBO analysis reveals that the N-H···O and N-H···N intermolecular interactions significantly influence crystal packing in this molecule.

Non-equilibrium phase transition

International Nuclear Information System (INIS)

Mottola, E.; Cooper, F.M.; Bishop, A.R.; Habib, S.; Kluger, Y.; Jensen, N.G.

1998-01-01

This is the final report of a one-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). Non-equilibrium phase transitions play a central role in a very broad range of scientific areas, ranging from nuclear, particle, and astrophysics to condensed matter physics and the material and biological sciences. The aim of this project was to explore the path to a deeper and more fundamental understanding of the common physical principles underlying the complex real time dynamics of phase transitions. The main emphasis was on the development of general theoretical tools to deal with non-equilibrium processes, and of numerical methods robust enough to capture the time-evolving structures that occur in actual experimental situations. Specific applications to Laboratory multidivisional efforts in relativistic heavy-ion physics (transition to a new phase of nuclear matter consisting of a quark-gluon plasma) and layered high-temperature superconductors (critical currents and flux flow at the National High Magnetic Field Laboratory) were undertaken

Investigation of Non-Equilibrium Radiation for Earth Entry

Science.gov (United States)

Brandis, A. M.; Johnston, C. O.; Cruden, B. A.

2016-01-01

For Earth re-entry at velocities between 8 and 11.5 km/s, the accuracy of NASA's computational uid dynamic and radiative simulations of non-equilibrium shock layer radiation is assessed through comparisons with measurements. These measurements were obtained in the NASA Ames Research Center's Electric Arc Shock Tube (EAST) facility. The experiments were aimed at measuring the spatially and spectrally resolved radiance at relevant entry conditions for both an approximate Earth atmosphere (79% N2 : 21% O2 by mole) as well as a more accurate composition featuring the trace species Ar and CO2 (78.08% N2 : 20.95% O2 : 0.04% CO2 : 0.93% Ar by mole). The experiments were configured to target a wide range of conditions, of which shots from 8 to 11.5 km/s at 0.2 Torr (26.7 Pa) are examined in this paper. The non-equilibrium component was chosen to be the focus of this study as it can account for a significant percentage of the emitted radiation for Earth re-entry, and more importantly, non-equilibrium has traditionally been assigned a large uncertainty for vehicle design. The main goals of this study are to present the shock tube data in the form of a non-equilibrium metric, evaluate the level of agreement between the experiment and simulations, identify key discrepancies and to examine critical aspects of modeling non-equilibrium radiating flows. Radiance pro les integrated over discreet wavelength regions, ranging from the Vacuum Ultra Violet (VUV) through to the Near Infra-Red (NIR), were compared in order to maximize both the spectral coverage and the number of experiments that could be used in the analysis. A previously defined non-equilibrium metric has been used to allow comparisons with several shots and reveal trends in the data. Overall, LAURA/HARA is shown to under-predict EAST by as much as 40% and over-predict by as much as 12% depending on the shock speed. DPLR/NEQAIR is shown to under-predict EAST by as much as 50% and over-predict by as much as 20% depending

Synthesis, crystal growth and characterization of bioactive material: 2-amino-1H-benzo[d]imidazol-3-ium salicylate single crystal-a proton transfer molecular complex

Science.gov (United States)

Fathima, K. Saiadali; Anitha, K.

2017-05-01

The 1:1 molecular adducts 2-aminobenzimidazolium salicylate (ABIS) single crystal was synthesized and grown from 2-aminobenzimidazole (ABI) as a donor and salicylic acid (SA) as an acceptor. The cell parameter was determined using single crystal X-Ray diffraction method and the complex ABIS belongs to monoclinic system. The spectroscopic studies showed that ABIS crystal was an ion pair complex. The FTIR and Raman spectra showed that the presence of O-H, C=N, C=O vibration which confirms the proton transfer from SA to ABI. The UV-Vis spectrum exhibited a visible band at 359nm for ABIS due to the salicylate anion of the molecule. Further the antimicrobial activity of ABIS complex against Staphylococcus aureus, klebsiella pneumonia, Pseudomonas eruginos and E.coli pathogens was investigated. So the complex molecule inhibits both Gram positive and Gram negative bacterial. It is found that benzimidazole with aminogroup at position 2 increases the general antimicrobial activities of ABIS crystal.

Non-equilibrium Quasi-Chemical Nucleation Model

Science.gov (United States)

Gorbachev, Yuriy E.

2018-04-01

Quasi-chemical model, which is widely used for nucleation description, is revised on the basis of recent results in studying of non-equilibrium effects in reacting gas mixtures (Kolesnichenko and Gorbachev in Appl Math Model 34:3778-3790, 2010; Shock Waves 23:635-648, 2013; Shock Waves 27:333-374, 2017). Non-equilibrium effects in chemical reactions are caused by the chemical reactions themselves and therefore these contributions should be taken into account in the corresponding expressions for reaction rates. Corrections to quasi-equilibrium reaction rates are of two types: (a) spatially homogeneous (caused by physical-chemical processes) and (b) spatially inhomogeneous (caused by gas expansion/compression processes and proportional to the velocity divergency). Both of these processes play an important role during the nucleation and are included into the proposed model. The method developed for solving the generalized Boltzmann equation for chemically reactive gases is applied for solving the set of equations of the revised quasi-chemical model. It is shown that non-equilibrium processes lead to essential deviation of the quasi-stationary distribution and therefore the nucleation rate from its traditional form.

Non-equilibrium concentration fluctuations in binary liquids with realistic boundary conditions.

Science.gov (United States)

Ortiz de Zárate, J M; Kirkpatrick, T R; Sengers, J V

2015-09-01

Because of the spatially long-ranged nature of spontaneous fluctuations in thermal non-equilibrium systems, they are affected by boundary conditions for the fluctuating hydrodynamic variables. In this paper we consider a liquid mixture between two rigid and impervious plates with a stationary concentration gradient resulting from a temperature gradient through the Soret effect. For liquid mixtures with large Lewis and Schmidt numbers, we are able to obtain explicit analytical expressions for the intensity of the non-equilibrium concentration fluctuations as a function of the frequency ω and the wave number q of the fluctuations. In addition we elucidate the spatial dependence of the intensity of the non-equilibrium fluctuations responsible for a non-equilibrium Casimir effect.

Ab initio electronic structure and correlations in pristine and potassium-doped molecular crystals of copper phthalocyanine

NARCIS (Netherlands)

Giovannetti, G.; Brocks, G.; van den Brink, J.

2008-01-01

We investigate the effect that potassium intercalation has on the electronic structure of copper phthalocyanine (CuPc) molecular crystals by means of ab initio density functional calculations. Pristine CuPc (in its alpha and beta structures) is found to be an insulator containing local magnetic

Comparative sequence and structural analyses of G-protein-coupled receptor crystal structures and implications for molecular models.

Directory of Open Access Journals (Sweden)

Catherine L Worth

Full Text Available BACKGROUND: Up until recently the only available experimental (high resolution structure of a G-protein-coupled receptor (GPCR was that of bovine rhodopsin. In the past few years the determination of GPCR structures has accelerated with three new receptors, as well as squid rhodopsin, being successfully crystallized. All share a common molecular architecture of seven transmembrane helices and can therefore serve as templates for building molecular models of homologous GPCRs. However, despite the common general architecture of these structures key differences do exist between them. The choice of which experimental GPCR structure(s to use for building a comparative model of a particular GPCR is unclear and without detailed structural and sequence analyses, could be arbitrary. The aim of this study is therefore to perform a systematic and detailed analysis of sequence-structure relationships of known GPCR structures. METHODOLOGY: We analyzed in detail conserved and unique sequence motifs and structural features in experimentally-determined GPCR structures. Deeper insight into specific and important structural features of GPCRs as well as valuable information for template selection has been gained. Using key features a workflow has been formulated for identifying the most appropriate template(s for building homology models of GPCRs of unknown structure. This workflow was applied to a set of 14 human family A GPCRs suggesting for each the most appropriate template(s for building a comparative molecular model. CONCLUSIONS: The available crystal structures represent only a subset of all possible structural variation in family A GPCRs. Some GPCRs have structural features that are distributed over different crystal structures or which are not present in the templates suggesting that homology models should be built using multiple templates. This study provides a systematic analysis of GPCR crystal structures and a consistent method for identifying

Comparative sequence and structural analyses of G-protein-coupled receptor crystal structures and implications for molecular models.

Science.gov (United States)

Worth, Catherine L; Kleinau, Gunnar; Krause, Gerd

2009-09-16

Up until recently the only available experimental (high resolution) structure of a G-protein-coupled receptor (GPCR) was that of bovine rhodopsin. In the past few years the determination of GPCR structures has accelerated with three new receptors, as well as squid rhodopsin, being successfully crystallized. All share a common molecular architecture of seven transmembrane helices and can therefore serve as templates for building molecular models of homologous GPCRs. However, despite the common general architecture of these structures key differences do exist between them. The choice of which experimental GPCR structure(s) to use for building a comparative model of a particular GPCR is unclear and without detailed structural and sequence analyses, could be arbitrary. The aim of this study is therefore to perform a systematic and detailed analysis of sequence-structure relationships of known GPCR structures. We analyzed in detail conserved and unique sequence motifs and structural features in experimentally-determined GPCR structures. Deeper insight into specific and important structural features of GPCRs as well as valuable information for template selection has been gained. Using key features a workflow has been formulated for identifying the most appropriate template(s) for building homology models of GPCRs of unknown structure. This workflow was applied to a set of 14 human family A GPCRs suggesting for each the most appropriate template(s) for building a comparative molecular model. The available crystal structures represent only a subset of all possible structural variation in family A GPCRs. Some GPCRs have structural features that are distributed over different crystal structures or which are not present in the templates suggesting that homology models should be built using multiple templates. This study provides a systematic analysis of GPCR crystal structures and a consistent method for identifying suitable templates for GPCR homology modelling that will

Breakdown of Bose-Einstein distribution in photonic crystals.

Science.gov (United States)

Lo, Ping-Yuan; Xiong, Heng-Na; Zhang, Wei-Min

2015-03-30

In the last two decades, considerable advances have been made in the investigation of nano-photonics in photonic crystals. Previous theoretical investigations of photon dynamics were carried out at zero temperature. Here, we investigate micro/nano cavity photonics in photonic crystals at finite temperature. Due to photonic-band-gap-induced localized long-lived photon dynamics, we discover that cavity photons in photonic crystals do not obey Bose-Einstein statistical distribution. Within the photonic band gap and in the vicinity of the band edge, cavity photons combine the long-lived non-Markovain dynamics with thermal fluctuations together to form photon states that memorize the initial cavity state information. As a result, Bose-Einstein distribution is completely broken down in these regimes, even if the thermal energy is larger or much larger than the cavity detuning energy. In this investigation, a crossover phenomenon from equilibrium to nonequilibrium steady states is also revealed.

Molecular assembly and electro polymerization of 3,4-ethylenedioxy thiophene on Au(100) single crystal electrode using in-situ electrochemical scanning tunneling microscopy

International Nuclear Information System (INIS)

Garcia, Jonyl L.; Tongol, Bernard John V.; ShuehLin Yau

2012-01-01

Electrochemical scanning tunneling microscopy (Ec-STM) is a powerful technique that can provide molecular-level information regarding electrode surface processes in-situ in electrolyte solvent under ambient conditions. In this study, the adsorption and electro polymerization of an industrially important conducting polymer precursor, 3,4-ethylenedioxy thiophene (EDOT), on Au (100) single crystal was probed using Ec-STM. The Au (100) single crystal electrode substrate used for this study was fabricated using the well-known Clavilier's flame melting procedure. Cyclic voltammetry (CV) was used along with Ec-STM to characterize the bare, EDOT-modified, and poly(EDOT)-modified Au (100) single crystal electrode. Time-dependent Ec-STM imaging at 0.550 V showed the formation of an EDOT self-assembled monolayer through 2-D surface dillusion. The resulting EDOT molecular assembly on Au (100) single crystal electrode was found to fit in a 4√2χ3√2 unit cell. Difference in apparent corrugation between molecular rows was attributed to different angular orientation with respect to the substrate. The electro polymerization of EDOT on Au (100) single crystal electrode was done by potentiostatic and potentiodynamic methods. Both methods suggested a solution-process mechanism for EDOT electro polymerization. (author)

X-ray scattering studies of non-equilibrium ordering processes: Progress report, November 1, 1988--October 31, 1989

International Nuclear Information System (INIS)

Nagler, S.E.

1989-01-01

We report on the progress of our project entitled ''X-ray Scattering Studies of Non-Equilibrium Ordering Processes.'' In-house time-resolved x-ray scattering has been used to investigate ordering kinetics in single crystal thin films of Cu 3 Au. Scaling analysis of the results shows that two dimensional kinetic behavior is observed in 260 /angstrom/ thick films. Significant improvements have been made in the local capabilities for fast time resolved measurements and data analysis. Measurements of microphase separation and ordering kinetics have been made in block-co-polymers, and experiments on Au-Cd martensitic material are continuing. 15 refs., 7 figs

Molecular Dynamics Modeling of PPTA Crystals in Aramid Fibers

Energy Technology Data Exchange (ETDEWEB)

Mercer, Brian Scott [Univ. of California, Berkeley, CA (United States)

2016-05-19

In this work, molecular dynamics modeling is used to study the mechanical properties of PPTA crystallites, which are the fundamental microstructural building blocks of polymer aramid bers such as Kevlar. Particular focus is given to constant strain rate axial loading simulations of PPTA crystallites, which is motivated by the rate-dependent mechanical properties observed in some experiments with aramid bers. In order to accommodate the covalent bond rupture that occurs in loading a crystallite to failure, the reactive bond order force eld ReaxFF is employed to conduct the simulations. Two major topics are addressed: The rst is the general behavior of PPTA crystallites under strain rate loading. Constant strain rate loading simulations of crystalline PPTA reveal that the crystal failure strain increases with increasing strain rate, while the modulus is not a ected by the strain rate. Increasing temperature lowers both the modulus and the failure strain. The simulations also identify the C N bond connecting the aromatic rings as weakest primary bond along the backbone of the PPTA chain. The e ect of chain-end defects on PPTA micromechanics is explored, and it is found that the presence of a chain-end defect transfers load to the adjacent chains in the hydrogen-bonded sheet in which the defect resides, but does not in uence the behavior of any other chains in the crystal. Chain-end defects are found to lower the strength of the crystal when clustered together, inducing bond failure via stress concentrations arising from the load transfer to bonds in adjacent chains near the defect site. The second topic addressed is the nature of primary and secondary bond failure in crystalline PPTA. Failure of both types of bonds is found to be stochastic in nature and driven by thermal uctuations of the bonds within the crystal. A model is proposed which uses reliability theory to model bonds under constant strain rate loading as components with time-dependent failure rate

Properties of Energy Spectra of Molecular Crystals Investigated by Nonlinear Theory

Science.gov (United States)

Pang, Xiao-Feng; Zhang, Huai-Wu

We calculate the quantum energy spectra of molecular crystals, such as acetanilide, by using discrete nonlinear Schrodinger equation, containing various interactions, appropriate to the systems. The energy spectra consist of many energy bands, in each energy band there are a lot of energy levels including some higher excited states. The result of energy spectrum is basically consistent with experimental values obtained by infrared absorption and Raman scattering in acetanilide and can also explain some experimental results obtained by Careri et al. Finally, we further discuss the influences of variously characteristic parameters on the energy spectra of the systems.

Post-irradiation chemical reactions during devitrification of molecular matrices (review)

International Nuclear Information System (INIS)

Barkalov, I.M.; Kiryukhin, D.P.

1993-01-01

At temperatures above the melting point (mp) a material is in a thermodynamic equilibrium state, in which any thermodynamic function of state (specific volume, enthalpy, and entrophy) is governed unambiguously by the temperature, pressure, etc. At temperatures below the mp, the material is converted to another equilibrium state, i.e., a crystal. However, during rapid cooling, a state of a nonequilibrium supercooled liquid can be obtained. Further cooling of this state below the glass-transition temperature, T g1 , leads to the additional formation of a nonequilibrium solid amorphous state, often simply called glass. In the vitreous state, species are capable of only vibrational and small-scale rotational motions. The translational mobility that is characteristic of the liquid state is completely lost. Very important for what follows is the fact that the transition from a supercooled liquid to the vitreous state or the reverse transition (devitrification) is accompanied by a sharp change of properties: the viscosity changes by 10-15 orders of magnitude, the modulus of elasticity changes 10-1000 fold, the coefficient of thermal expansion changes 10-100 fold, etc. Most impressive is the gigantic viscosity jump in the narrow temperature-dependent glass-transition region. This means that the molecular mobility governing the chemical-transformation dynamics undergoes a sharp change in this region. The nature of the chemical process during passage through the glass-softening region should change because of a sharp change of the mobility of the reactants, with a huge change of molecular mobility being attained by a temperature change of only a few degrees. During radiolysis of vitreous matrices, active species of radical and ionic nature are formed. This review discusses the recombination reactions of radiolysis products during heating to the supercooled state

Nonequilibrium two-dimensional Ising model with stationary uphill diffusion

Science.gov (United States)

Colangeli, Matteo; Giardinà, Cristian; Giberti, Claudio; Vernia, Cecilia

2018-03-01

Usually, in a nonequilibrium setting, a current brings mass from the highest density regions to the lowest density ones. Although rare, the opposite phenomenon (known as "uphill diffusion") has also been observed in multicomponent systems, where it appears as an artificial effect of the interaction among components. We show here that uphill diffusion can be a substantial effect, i.e., it may occur even in single component systems as a consequence of some external work. To this aim we consider the two-dimensional ferromagnetic Ising model in contact with two reservoirs that fix, at the left and the right boundaries, magnetizations of the same magnitude but of opposite signs.We provide numerical evidence that a class of nonequilibrium steady states exists in which, by tuning the reservoir magnetizations, the current in the system changes from "downhill" to "uphill". Moreover, we also show that, in such nonequilibrium setup, the current vanishes when the reservoir magnetization attains a value approaching, in the large volume limit, the magnetization of the equilibrium dynamics, thus establishing a relation between equilibrium and nonequilibrium properties.

Deterministic thermostats, theories of nonequilibrium systems and parallels with the ergodic condition

International Nuclear Information System (INIS)

Jepps, Owen G; Rondoni, Lamberto

2010-01-01

Deterministic 'thermostats' are mathematical tools used to model nonequilibrium steady states of fluids. The resulting dynamical systems correctly represent the transport properties of these fluids and are easily simulated on modern computers. More recently, the connection between such thermostats and entropy production has been exploited in the development of nonequilibrium fluid theories. The purpose and limitations of deterministic thermostats are discussed in the context of irreversible thermodynamics and the development of theories of nonequilibrium phenomena. We draw parallels between the development of such nonequilibrium theories and the development of notions of ergodicity in equilibrium theories. (topical review)

On microscopic stress nonequilibrium: Application to the magnetopause

International Nuclear Information System (INIS)

Wu, Z.J.

1986-01-01

The main purpose of this paper is to propose the concept of microscopic stress nonequilibrium (or simply micro-nonequilibrium) in plasma physics. This concept arises as a consequence of the insolubility of the steady-state Vlasov-Maxwell equations (or the kinetic-field equations in general) under certain conditions. In what follows: (1) A general stress equilibrium condition for tangential plasma discontinuities is derived from the Maxwell tensor and the plasma stress tensor. (2) An equivalent equilibrium condition, which takes the form of equations of motion of a ''fictitious particle'', is also derived from the above condition. (3) A general solution of the distribution functions is derived according to Jeans's theorem or Liouville's theorem for the solar wind particles in a tangential magnetopause. (4) This solution is applied to the equilibrium condition to investigate the equilibrium state of the tangential magnetopause. Both Parker's tail-region and Wu's dawn-side ''nonequilibria''are confirmed to be micro-nonequilibria because of the violation of the above equilibrium condition. (5) The effects of various factors in micro-nonequilibria are discussed. It is found that randomly trapped particles and inwards electric field in the magnetopause layer generally cannot relieve the dawn-side or tail-region micro-nonequilibria; and that a northward magnetic field in the solar wind generally can suppress the dawn-side nonequilibrium, while a southward field can jeopardize a dusk-side Vlasov equilibrium. (6) Discussion: The concept of ''micro-nonequilibrium'' may become of importance in basic plasma dynamics. It is also possible that the micro-nonequilibrium may play a fundamental role in solar wind particles entering the magnetopause and in magnetospheric substorms

Study of alloy crystallization in systems undergoing peritectic transformations

International Nuclear Information System (INIS)

Psarev, V.I.; Kirij, V.G.; Kuznetsov, A.V.; Psareva, I.V.; Ivanov, A.L.

1982-01-01

Studies into Ge-Te, In-Te, Al-Mn, Sb-Zn, Sn-Au systems are carried out at melt cooling rates from 50 deg/h to 10 5 deg/h to establish regularities in stable and metastable crystallization of alloys undergoing peritectic transformations. Methods of metallographic, X-ray phase and X-ray diffraction analyses are used. Differentiation in types of peritectic transformations is made through their mechanisms under equilibrium and non-equilibrium crystallization conditions for various alloy systems. It is found out that ability to supercooling even at low or moderate cooling rates for Te-Ge and Te-In system melts can be one of the main indication of the possibility of amorphous alloy formation [ru

On the excess energy of nonequilibrium plasma

International Nuclear Information System (INIS)

Timofeev, A. V.

2012-01-01

The energy that can be released in plasma due to the onset of instability (the excess plasma energy) is estimated. Three potentially unstable plasma states are considered, namely, plasma with an anisotropic Maxwellian velocity distribution of plasma particles, plasma with a two-beam velocity distribution, and an inhomogeneous plasma in a magnetic field with a local Maxwellian velocity distribution. The excess energy can serve as a measure of the degree to which plasma is nonequilibrium. In particular, this quantity can be used to compare plasmas in different nonequilibrium states.

Nonequilibrium thermodynamics and fluctuation relations for small systems

International Nuclear Information System (INIS)

Cao Liang; Ke Pu; Qiao Li-Yan; Zheng Zhi-Gang

2014-01-01

In this review, we give a retrospect of the recent progress in nonequilibrium statistical mechanics and thermodynamics in small dynamical systems. For systems with only a few number of particles, fluctuations and nonlinearity become significant and contribute to the nonequilibrium behaviors of the systems, hence the statistical properties and thermodynamics should be carefully studied. We review recent developments of this topic by starting from the Gallavotti—Cohen fluctuation theorem, and then to the Evans—Searles transient fluctuation theorem, Jarzynski free-energy equality, and the Crooks fluctuation relation. We also investigate the nonequilibrium free energy theorem for trajectories involving changes of the heat bath temperature and propose a generalized free-energy relation. It should be noticed that the non-Markovian property of the heat bath may lead to the violation of the free-energy relation. (topical review - statistical physics and complex systems)

Experimental study of nonequilibrium post-chf heat transfer in rod bundles

International Nuclear Information System (INIS)

Unal, C.; Tuzla, K.; Badr, O.; Neti, S.; Chen, J.

1986-01-01

Verifications and improvements of nonequilibrium heat transfer models, for post-critical-heat-flux convective boiling, has been greatly affected by the lack of experimental data regarding the degree of thermodynamic nonequilibrium. Recent studies had been successful in measuring vapor superheats in a vertical single tube. This paper extends the nonequilibrium convective boiling data to a rod bundle geometry. Vapor superheat measurements were obtained in a rod bundle with nine heated rods and a heated shroud. Tests were carried out with water at low mass fluxes with a wide range of dryout conditions. Significant nonequilibrium was observed, with vapor superheats of up to 600 0 C. Parametric effects of mass flux, heat flux and inlet conditions on vapor superheat are presented

The dynamics of single protein molecules is non-equilibrium and self-similar over thirteen decades in time

Science.gov (United States)

Hu, Xiaohu; Hong, Liang; Dean Smith, Micholas; Neusius, Thomas; Cheng, Xiaolin; Smith, Jeremy C.

2016-02-01

Internal motions of proteins are essential to their function. The time dependence of protein structural fluctuations is highly complex, manifesting subdiffusive, non-exponential behaviour with effective relaxation times existing over many decades in time, from ps up to ~102 s (refs ,,,). Here, using molecular dynamics simulations, we show that, on timescales from 10-12 to 10-5 s, motions in single proteins are self-similar, non-equilibrium and exhibit ageing. The characteristic relaxation time for a distance fluctuation, such as inter-domain motion, is observation-time-dependent, increasing in a simple, power-law fashion, arising from the fractal nature of the topology and geometry of the energy landscape explored. Diffusion over the energy landscape follows a non-ergodic continuous time random walk. Comparison with single-molecule experiments suggests that the non-equilibrium self-similar dynamical behaviour persists up to timescales approaching the in vivo lifespan of individual protein molecules.

A two-temperature chemical non-equilibrium modeling of DC arc plasma

International Nuclear Information System (INIS)

Qian Haiyang; Wu Bin

2011-01-01

To a better understanding of non-equilibrium characteristics of DC arc plasma,a two-dimensional axisymmetric two-temperature chemical non-equilibrium (2T-NCE) model is applied for direct current arc argon plasma generator with water-cooled constrictor at atmospheric pressure. The results show that the electron temperature and heavy particle temperature has a relationship under different working parameters, indicating that DC arc plasma has a strong non-equilibrium characteristic, and the variation is obvious. (authors)

Nonequilibrium states of high tc YBCO superconductors under tunnel injection of quasiparticles

International Nuclear Information System (INIS)

Iguchi, I.; Wang, Q.; Lee, K.; Yoshida, K.

1995-01-01

The nonequilibrium states of high Tc superconductors are investigated by means of tunnel injection of quasiparticles using Pb(or Au)/MgO/YBCO tunnel junctions. The effective critical-current reduction due to tunnel injection is observed, whose behaviour is different from simple heating. The observed results suggest that the resultant nonequilibrium states may also differ from those described by conventional nonequilibrium models

Molecular Dynamic Simulation of Space and Earth-Grown Crystal Structures of Thermostable T1 Lipase Geobacillus zalihae Revealed a Better Structure.

Science.gov (United States)

Ishak, Siti Nor Hasmah; Aris, Sayangku Nor Ariati Mohamad; Halim, Khairul Bariyyah Abd; Ali, Mohd Shukuri Mohamad; Leow, Thean Chor; Kamarudin, Nor Hafizah Ahmad; Masomian, Malihe; Rahman, Raja Noor Zaliha Raja Abd

2017-09-25

Less sedimentation and convection in a microgravity environment has become a well-suited condition for growing high quality protein crystals. Thermostable T1 lipase derived from bacterium Geobacillus zalihae has been crystallized using the counter diffusion method under space and earth conditions. Preliminary study using YASARA molecular modeling structure program for both structures showed differences in number of hydrogen bond, ionic interaction, and conformation. The space-grown crystal structure contains more hydrogen bonds as compared with the earth-grown crystal structure. A molecular dynamics simulation study was used to provide insight on the fluctuations and conformational changes of both T1 lipase structures. The analysis of root mean square deviation (RMSD), radius of gyration, and root mean square fluctuation (RMSF) showed that space-grown structure is more stable than the earth-grown structure. Space-structure also showed more hydrogen bonds and ion interactions compared to the earth-grown structure. Further analysis also revealed that the space-grown structure has long-lived interactions, hence it is considered as the more stable structure. This study provides the conformational dynamics of T1 lipase crystal structure grown in space and earth condition.

Nonequilibrium quantum fluctuations of work.

Science.gov (United States)

Allahverdyan, A E

2014-09-01

The concept of work is basic for statistical thermodynamics. To gain a fuller understanding of work and its (quantum) features, it needs to be represented as an average of a fluctuating quantity. Here I focus on the work done between two moments of time for a thermally isolated quantum system driven by a time-dependent Hamiltonian. I formulate two natural conditions needed for the fluctuating work to be physically meaningful for a system that starts its evolution from a nonequilibrium state. The existing definitions do not satisfy these conditions due to issues that are traced back to noncommutativity. I propose a definition of fluctuating work that is free of previous drawbacks and that applies for a wide class of nonequilibrium initial states. It allows the deduction of a generalized work-fluctuation theorem that applies for an arbitrary (out-of-equilibrium) initial state.

Structure of fault stackings of molecular layers X-M-X in CdI2 polytypic crystals

International Nuclear Information System (INIS)

Palosz, B.; Przedmojski, J.

1984-01-01

The arrangements of molecular layers I-Cd-I, which may be regarded as 'faulted' for CdI 2 polytypic crystals, are analyzed. Tentative classification of faults into those which are intermediate structure between the basic polytypes 2H and 4H and faults occurring between different blocks of pure structure 4 H is proposed. The connection between some growth parameters and the structure of faults in CdI 2 crystals grown from solutions is discussed. It is shown that the geometrical classification of stacking faults used for layered inorganic crystals is not appropriate for the description of the faults existing in polytypic crystals of MX 2 type. The effect of weak external electric and magnetic fields on the polytypic structure of CdI 2 is analyzed. The experiments performed for several hundred of polytypes of CdI 2 showed that the external fields may, in some conditions, affect the organization of the polytypic structure of crystals very strongly. In particular, it was found that the external fields may change the period of polytype cells and that the relative number of hexagonal and rhombohedral polytypes differ very strongly for crystals grown in the absence and in the presence of external electric and magnetic fields. (author)

Generation and extinction of crystal nuclei in an extremely non-equilibrium glassy state of salol

CERN Document Server

Paladi, F

2003-01-01

Strange generation and subsequent extinction of crystal nuclei were observed in the glassy state of salol (phenyl salicylate) during the course of ageing at very low constant-temperatures. The presence/absence of crystal nuclei within the glass were judged, by using a differential scanning calorimeter (DSC), from whether the crystal growth and fusion phenomena were observed in the following heating process or not. The liquid sample was cooled rapidly at 200 K min sup - sup 1 from 333 K above the fusion temperature down to a desired ageing temperature (T sub a) below the glass transition temperature (T sub g = 220 K), aged there for different periods (t sub a), and then heated up to 213 K at 200 K min sup - sup 1. The DSC measurement was carried out at 10 K min sup - sup 1 from 213 to 333 K. The ageing periods were taken in a range between 30 s and 316 min. At T sub a = 213 K, crystal nucleation was found to proceed for ageing longer than 100 min. No crystal nucleation was found at T sub a in between 123 and 1...

Nonequilibrium statistical Zubarev's operator and Green's functions for an inhomogeneous electron gas

Directory of Open Access Journals (Sweden)

P.Kostrobii

2006-01-01

Full Text Available Nonequilibrium properties of an inhomogeneous electron gas are studied using the method of the nonequilibrium statistical operator by D.N. Zubarev. Generalized transport equations for the mean values of inhomogeneous operators of the electron number density, momentum density, and total energy density for weakly and strongly nonequilibrium states are obtained. We derive a chain of equations for the Green's functions, which connects commutative time-dependent Green's functions "density-density", "momentum-momentum", "enthalpy-enthalpy" with reduced Green's functions of the generalized transport coefficients and with Green's functions for higher order memory kernels in the case of a weakly nonequilibrium spatially inhomogeneous electron gas.

Wall ablation of heated compound-materials into non-equilibrium discharge plasmas

Science.gov (United States)

Wang, Weizong; Kong, Linghan; Geng, Jinyue; Wei, Fuzhi; Xia, Guangqing

2017-02-01

The discharge properties of the plasma bulk flow near the surface of heated compound-materials strongly affects the kinetic layer parameters modeled and manifested in the Knudsen layer. This paper extends the widely used two-layer kinetic ablation model to the ablation controlled non-equilibrium discharge due to the fact that the local thermodynamic equilibrium (LTE) approximation is often violated as a result of the interaction between the plasma and solid walls. Modifications to the governing set of equations, to account for this effect, are derived and presented by assuming that the temperature of the electrons deviates from that of the heavy particles. The ablation characteristics of one typical material, polytetrafluoroethylene (PTFE) are calculated with this improved model. The internal degrees of freedom as well as the average particle mass and specific heat ratio of the polyatomic vapor, which strongly depends on the temperature, pressure and plasma non-equilibrium degree and plays a crucial role in the accurate determination of the ablation behavior by this model, are also taken into account. Our assessment showed the significance of including such modifications related to the non-equilibrium effect in the study of vaporization of heated compound materials in ablation controlled arcs. Additionally, a two-temperature magneto-hydrodynamic (MHD) model accounting for the thermal non-equilibrium occurring near the wall surface is developed and applied into an ablation-dominated discharge for an electro-thermal chemical launch device. Special attention is paid to the interaction between the non-equilibrium plasma and the solid propellant surface. Both the mass exchange process caused by the wall ablation and plasma species deposition as well as the associated momentum and energy exchange processes are taken into account. A detailed comparison of the results of the non-equilibrium model with those of an equilibrium model is presented. The non-equilibrium results

A phase-field model for non-equilibrium solidification of intermetallics

International Nuclear Information System (INIS)

Assadi, H.

2007-01-01

Intermetallics may exhibit unique solidification behaviour-including slow growth kinetics, anomalous partitioning and formation of unusual growth morphologies-because of departure from local equilibrium. A phase-field model is developed and used to illustrate these non-equilibrium effects in solidification of a prototype B2 intermetallic phase. The model takes sublattice compositions as primary field variables, from which chemical long-range order is derived. The diffusive reactions between the two sublattices, and those between each sublattice and the liquid phase are taken as 'internal' kinetic processes, which take place within control volumes of the system. The model can thus capture solute and disorder trapping effects, which are consistent-over a wide range of the solid/liquid interface thickness-with the predictions of the sharp-interface theory of solute and disorder trapping. The present model can also take account of solid-state ordering and thus illustrate the effects of chemical ordering on microstructure formation and crystal growth kinetics

Non-Equilibrium Chemistry of O-Rich AGB Stars as Revealed by ALMA

Science.gov (United States)

Wong, Ka Tat

2018-04-01

Chemical models suggest that pulsation driven shocks propagating from the stellar surfaces of oxygen-rich evolved stars to the dust formation zone trigger non-equilibrium chemistry in the shocked gas near the star, including the formation of carbon-bearing molecules in the stellar winds dominated by oxygen-rich chemistry. Recent long-baseline ALMA observations are able to give us a detailed view of the molecular line emission and absorption at an angular resolution of a few stellar radii. I am going to present the latest results from the ALMA observations of IK Tau and o Cet in late 2017, with a particular focus on HCN.

[Structure of crambin in solution, crystal and in the trajectories of molecular dynamics simulations].

Science.gov (United States)

Abaturov, L V; Nosova, N G

2013-01-01

The mechanisms of the three-dimensional crambin structure alterations in the crystalline environments and in the trajectories of the molecular dynamics simulations in the vacuum and crystal surroundings have been analyzed. In the crystalline state and in the solution the partial regrouping of remote intramolecular packing contacts, involved in the formation and stabilization of the tertiary structure of the crambin molecule, occurs in NMR structures. In the crystalline state it is initiated by the formation of the intermolecular contacts, the conformational influence of its appearance is distributed over the structure. The changes of the conformations and positions of the residues of the loop segments, where the intermolecular contacts of the crystal surroundings are preferably concentrated, are most observable. Under the influence of these contacts the principal change of the regular secondary structure of crambin is taking place: extension of the two-strand beta structure to the three-strand structure with the participation of the single last residue N46 of the C-terminal loop. In comparison with the C-terminal loop the more profound changes are observed in the conformation and the atomic positions of the backbone atoms and in the solvent accessibility of the residues of the interhelical loop. In the solution of the ensemble of the 8 NMR structures relative accessibility to the solvent differs more noticeably also in the region of the loop segments and rather markedly in the interhelical loop. In the crambin cryogenic crystal structures the positions of the atoms of the backbone and/or side chain of 14-18 of 46 residues are discretely disordered. The disorganizations of at least 8 of 14 residues occur directly in the regions of the intermolecular contacts and another 5 residues are disordered indirectly through the intramolecular contacts with the residues of the intermolecular contacts. Upon the molecular dynamics simulation in the vacuum surrounding as in the

Crystallization of glass-forming liquids: Specific surface energy

International Nuclear Information System (INIS)

Schmelzer, Jürn W. P.; Abyzov, Alexander S.

2016-01-01

A generalization of the Stefan-Skapski-Turnbull relation for the melt-crystal specific interfacial energy is developed in terms of the generalized Gibbs approach extending its standard formulation to thermodynamic non-equilibrium states. With respect to crystal nucleation, this relation is required in order to determine the parameters of the critical crystal clusters being a prerequisite for the computation of the work of critical cluster formation. As one of its consequences, a relation for the dependence of the specific surface energy of critical clusters on temperature and pressure is derived applicable for small and moderate deviations from liquid-crystal macroscopic equilibrium states. Employing the Stefan-Skapski-Turnbull relation, general expressions for the size and the work of formation of critical crystal clusters are formulated. The resulting expressions are much more complex as compared to the respective relations obtained via the classical Gibbs theory. Latter relations are retained as limiting cases of these more general expressions for moderate undercoolings. By this reason, the formulated, here, general relations for the specification of the critical cluster size and the work of critical cluster formation give a key for an appropriate interpretation of a variety of crystallization phenomena occurring at large undercoolings which cannot be understood in terms of the Gibbs’ classical treatment.

Evidence from mixed hydrate nucleation for a funnel model of crystallization

Science.gov (United States)

Hall, Kyle Wm.; Carpendale, Sheelagh; Kusalik, Peter G.

2016-01-01

The molecular-level details of crystallization remain unclear for many systems. Previous work has speculated on the phenomenological similarities between molecular crystallization and protein folding. Here we demonstrate that molecular crystallization can involve funnel-shaped potential energy landscapes through a detailed analysis of mixed gas hydrate nucleation, a prototypical multicomponent crystallization process. Through this, we contribute both: (i) a powerful conceptual framework for exploring and rationalizing molecular crystallization, and (ii) an explanation of phenomenological similarities between protein folding and crystallization. Such funnel-shaped potential energy landscapes may be typical of broad classes of molecular ordering processes, and can provide a new perspective for both studying and understanding these processes. PMID:27790987

Time-dependent nonequilibrium soft x-ray response during a spin crossover

Science.gov (United States)

van Veenendaal, Michel

2018-03-01

A theoretical framework is developed for better understanding the time-dependent soft-x-ray response of dissipative quantum many-body systems. It is shown how x-ray absorption and resonant inelastic x-ray scattering (RIXS) at transition-metal L edges can provide insight into ultrafast intersystem crossings of importance for energy conversion, ultrafast magnetism, and catalysis. The photoinduced doublet-to-quartet spin crossover on cobalt in Fe-Co Prussian blue analogs is used as a model system to demonstrate how the x-ray response is affected by the nonequilibrium dynamics on a femtosecond time scale. Changes in local spin and symmetry and the underlying mechanism are reflected in strong broadenings, a collapse of clear selection rules during the intersystem crossing, fluctuations in the isotropic branching ratio in x-ray absorption, crystal-field collapse and/or oscillations, and time-dependent anti-Stokes processes in RIXS.

INTRODUCTION: Nonequilibrium Processes in Plasmas

Science.gov (United States)

Petrović, Zoran; Marić, Dragana; Malović, Gordana

2009-07-01

lead to new fundamental understanding is illustrated well in the paper by Uwe Czarnetzki which describes a new method for separate control of flux and energy of ions reaching the surface of electrodes. Deborah O'Connell from Belfast has shown space and phase resolved mode transitions in rf inductively coupled plasmas obtained by optical emission measurements. At the same time an application of a similar rf discharge for the treatment of paper was presented by Irina Filatova from Belarus. Many applications of non-equilibrium plasmas depend on the development of plasma sources operating at atmospheric pressure and one such source that promises to be prominent in medicine is described by Timo Gans. In a similar way, practical considerations require studies of the injection of liquids into plasmas and progress on the development of one such source is described by Mathew Goeckner and his colleagues from Dallas. From the Institute Jožef Štefan in Slovenia and the group of Miran Mozetič we have a detailed review of their work on functionalization of organic materials by oxygen plasmas. Even higher density plasmas, where the collective phenomena dominate, show different degrees of non-equilibrium and one example presented here by Zoltan Donko deals with two dimensional plasma dust crystals and liquids, while the lecture by Jovo Vranješ from Belgium deals with the treatment of collisions in multicomponent plasmas. Finally we have papers on the transport of pollutants. The association of the two fields started initially through joint interest in some of the methods for removal of NOx and SOx, from electrostatic precipitation of industrial dust to dielectric barrier discharges. The joint work continued on the application of flowing afterglow plasma combined with a hollow cathode discharge in order to achieve a proton transfer mass analysis of organic volatile compounds and also on the possibilities of applying similar methods for solving transport equations. In this volume we

Nonequilibrium quantum solvation with a time-dependent Onsager cavity

Science.gov (United States)

Kirchberg, H.; Nalbach, P.; Thorwart, M.

2018-04-01

We formulate a theory of nonequilibrium quantum solvation in which parameters of the solvent are explicitly depending on time. We assume in a simplest approach a spherical molecular Onsager cavity with a time-dependent radius. We analyze the relaxation properties of a test molecular point dipole in a dielectric solvent and consider two cases: (i) a shrinking Onsager sphere and (ii) a breathing Onsager sphere. Due to the time-dependent solvent, the frequency-dependent response function of the dipole becomes time-dependent. For a shrinking Onsager sphere, the dipole relaxation is in general enhanced. This is reflected in a temporally increasing linewidth of the absorptive part of the response. Furthermore, the effective frequency-dependent response function shows two peaks in the absorptive part which are symmetrically shifted around the eigenfrequency. By contrast, a breathing sphere reduces damping as compared to the static sphere. Interestingly, we find a non-monotonous dependence of the relaxation rate on the breathing rate and a resonant suppression of damping when both rates are comparable. Moreover, the linewidth of the absorptive part of the response function is strongly reduced for times when the breathing sphere reaches its maximal extension.

Modelling Thomson scattering for systems with non-equilibrium electron distributions

Directory of Open Access Journals (Sweden)

Chapman D.A.

2013-11-01

Full Text Available We investigate the effect of non-equilibrium electron distributions in the analysis of Thomson scattering for a range of conditions of interest to inertial confinement fusion experiments. Firstly, a generalised one-component model based on quantum statistical theory is given in the random phase approximation (RPA. The Chihara expression for electron-ion plasmas is then adapted to include the new non-equilibrium electron physics. The theoretical scattering spectra for both diffuse and dense plasmas in which non-equilibrium electron distributions are expected to arise are considered. We find that such distributions strongly influence the spectra and are hence an important consideration for accurately determining the plasma conditions.

Non-equilibrium plasma chemistry at high pressure and its applications

International Nuclear Information System (INIS)

Bai Xiyao; Zhang Zhitao; Bai Mindong; Zhu Qiaoying

2000-01-01

A review is presented of research and development of gas discharge and non-equilibrium plasma including, new ideas of non-equilibrium plasma at high gas pressure. With special technology, strong electric fields (>400 Td) can be achieved by which electrons are accelerated suddenly, becoming high energy electrons (> 10 eV) at high pressure. On impact with the electrons, the gas molecules dissociate into ions, atomic ions, atoms and free radicals, and new substances or molecules can be synthesized through custom design. Chemical reaction difficult to achieve by conventional method can be realized or accelerated. Non-equilibrium plasma chemistry at high pressure has wide application prospects

Evolution and non-equilibrium physics

DEFF Research Database (Denmark)

Becker, Nikolaj; Sibani, Paolo

2014-01-01

We argue that the stochastic dynamics of interacting agents which replicate, mutate and die constitutes a non-equilibrium physical process akin to aging in complex materials. Specifically, our study uses extensive computer simulations of the Tangled Nature Model (TNM) of biological evolution...

Overcoming the Time Limitation in Molecular Dynamics Simulation of Crystal Nucleation: A Persistent-Embryo Approach

Science.gov (United States)

Sun, Yang; Song, Huajing; Zhang, Feng; Yang, Lin; Ye, Zhuo; Mendelev, Mikhail I.; Wang, Cai-Zhuang; Ho, Kai-Ming

2018-02-01

The crystal nucleation from liquid in most cases is too rare to be accessed within the limited time scales of the conventional molecular dynamics (MD) simulation. Here, we developed a "persistent embryo" method to facilitate crystal nucleation in MD simulations by preventing small crystal embryos from melting using external spring forces. We applied this method to the pure Ni case for a moderate undercooling where no nucleation can be observed in the conventional MD simulation, and obtained nucleation rate in good agreement with the experimental data. Moreover, the method is applied to simulate an even more sluggish event: the nucleation of the B 2 phase in a strong glass-forming Cu-Zr alloy. The nucleation rate was found to be 8 orders of magnitude smaller than Ni at the same undercooling, which well explains the good glass formability of the alloy. Thus, our work opens a new avenue to study solidification under realistic experimental conditions via atomistic computer simulation.

Overcoming the Time Limitation in Molecular Dynamics Simulation of Crystal Nucleation: A Persistent-Embryo Approach.

Science.gov (United States)

Sun, Yang; Song, Huajing; Zhang, Feng; Yang, Lin; Ye, Zhuo; Mendelev, Mikhail I; Wang, Cai-Zhuang; Ho, Kai-Ming

2018-02-23

The crystal nucleation from liquid in most cases is too rare to be accessed within the limited time scales of the conventional molecular dynamics (MD) simulation. Here, we developed a "persistent embryo" method to facilitate crystal nucleation in MD simulations by preventing small crystal embryos from melting using external spring forces. We applied this method to the pure Ni case for a moderate undercooling where no nucleation can be observed in the conventional MD simulation, and obtained nucleation rate in good agreement with the experimental data. Moreover, the method is applied to simulate an even more sluggish event: the nucleation of the B2 phase in a strong glass-forming Cu-Zr alloy. The nucleation rate was found to be 8 orders of magnitude smaller than Ni at the same undercooling, which well explains the good glass formability of the alloy. Thus, our work opens a new avenue to study solidification under realistic experimental conditions via atomistic computer simulation.

Limiting processes in non-equilibrium classical statistical mechanics

International Nuclear Information System (INIS)

Jancel, R.

1983-01-01

After a recall of the basic principles of the statistical mechanics, the results of ergodic theory, the transient at the thermodynamic limit and his link with the transport theory near the equilibrium are analyzed. The fundamental problems put by the description of non-equilibrium macroscopic systems are investigated and the kinetic methods are stated. The problems of the non-equilibrium statistical mechanics are analyzed: irreversibility and coarse-graining, macroscopic variables and kinetic description, autonomous reduced descriptions, limit processes, BBGKY hierarchy, limit theorems [fr

Understanding water: Molecular dynamics simulations of solubilized and crystallized myoglobin

Energy Technology Data Exchange (ETDEWEB)

Wei Gu; Garcia, A.E.; Schoenborn, B.P. [Los Alamos National Laboratory, NM (United States)

1994-12-31

Molecular dynamics simulations were performed on CO myoglobin to evaluate the stability of the bound water molecules as determined in a neutron diffraction analysis. The myoglobin structure derived from the neutron analysis provided the starting coordinate set used in the simulations. The simulations show that only a few water molecules are tightly bound to protein atoms, while most solvent molecules are labile, breaking and reforming hydrogen bonds. Comparison between myoglobin in solution and in a single crystal highlighted some of the packing effects on the solvent structure and shows that water solvent plays an indispensable role in protein dynamics and structural stability. The described observations explain some of the differences in the experimental results of protein hydration as observed in NMR, neutron and X-ray diffraction studies.

Understanding water: Molecular dynamics simulations of solubilized and crystallized myoglobin

International Nuclear Information System (INIS)

Wei Gu; Garcia, A.E.; Schoenborn, B.P.

1994-01-01

Molecular dynamics simulations were performed on CO myoglobin to evaluate the stability of the bound water molecules as determined in a neutron diffraction analysis. The myoglobin structure derived from the neutron analysis provided the starting coordinate set used in the simulations. The simulations show that only a few water molecules are tightly bound to protein atoms, while most solvent molecules are labile, breaking and reforming hydrogen bonds. Comparison between myoglobin in solution and in a single crystal highlighted some of the packing effects on the solvent structure and shows that water solvent plays an indispensable role in protein dynamics and structural stability. The described observations explain some of the differences in the experimental results of protein hydration as observed in NMR, neutron and X-ray diffraction studies

Nonequilibrium temperatures and second-sound propagation along nanowires and thin layers

International Nuclear Information System (INIS)

Jou, D.; Cimmelli, V.A.; Sellitto, A.

2009-01-01

It is shown that the dispersion relation of heat waves along nanowires or thin layers could allow to compare two different definitions of nonequilibrium temperature, since thermal waves are predicted to propagate with different phase speed depending on the definition of nonequilibrium temperature being used. The difference is small, but it could be in principle measurable in nanosystems, as for instance nanowires and thin layers, in a given frequency range. Such an experiment could provide a deeper view on the problem of the definition of temperature in nonequilibrium situations.

Inviscid flux-splitting algorithms for real gases with non-equilibrium chemistry

Science.gov (United States)

Shuen, Jian-Shun; Liou, Meng-Sing; Van Leer, Bram

1990-01-01

Formulations of inviscid flux splitting algorithms for chemical nonequilibrium gases are presented. A chemical system for air dissociation and recombination is described. Numerical results for one-dimensional shock tube and nozzle flows of air in chemical nonequilibrium are examined.

Monte Carlo Optimization of Crystal Configuration for Pixelated Molecular SPECT Scanners

Energy Technology Data Exchange (ETDEWEB)

Mahani, Hojjat [Radiation Application Research School, Nuclear Science and Technology Research Institute, Tehran (Iran, Islamic Republic of); Research Center for Molecular and Cellular Imaging, Tehran University of Medical Science, Tehran (Iran, Islamic Republic of); Raisali, Gholamreza [Radiation Application Research School, Nuclear Science and Technology Research Institute, Tehran (Iran, Islamic Republic of); Kamali-Asl, Alireza [Radiation Medicine Department, Shahid Beheshti University, Tehran (Iran, Islamic Republic of); Ay, Mohammad Reza, E-mail: mohammadreza_ay@sina.tums.ac.ir [Research Center for Molecular and Cellular Imaging, Tehran University of Medical Science, Tehran (Iran, Islamic Republic of); Department of Medical Physics and Biomedical Engineering, Tehran University of Medical Science, Tehran (Iran, Islamic Republic of)

2017-02-01

Resolution-sensitivity-PDA tradeoff is the most challenging problem in design and optimization of pixelated preclinical SPECT scanners. In this work, we addressed such a challenge from a crystal point-of-view by looking for an optimal pixelated scintillator using GATE Monte Carlo simulation. Various crystal configurations have been investigated and the influence of different pixel sizes, pixel gaps, and three scintillators on tomographic resolution, sensitivity, and PDA of the camera were evaluated. The crystal configuration was then optimized using two objective functions: the weighted-sum and the figure-of-merit methods. The CsI(Na) reveals the highest sensitivity of the order of 43.47 cps/MBq in comparison to the NaI(Tl) and the YAP(Ce), for a 1.5×1.5 mm{sup 2} pixel size and 0.1 mm gap. The results show that the spatial resolution, in terms of FWHM, improves from 3.38 to 2.21 mm while the sensitivity simultaneously deteriorates from 42.39 cps/MBq to 27.81 cps/MBq when pixel size varies from 2×2 mm{sup 2} to 0.5×0.5 mm{sup 2} for a 0.2 mm gap, respectively. The PDA worsens from 0.91 to 0.42 when pixel size decreases from 0.5×0.5 mm{sup 2} to 1×1 mm{sup 2} for a 0.2 mm gap at 15° incident-angle. The two objective functions agree that the 1.5×1.5 mm{sup 2} pixel size and 0.1 mm Epoxy gap CsI(Na) configuration provides the best compromise for small-animal imaging, using the HiReSPECT scanner. Our study highlights that crystal configuration can significantly affect the performance of the camera, and thereby Monte Carlo optimization of pixelated detectors is mandatory in order to achieve an optimal quality tomogram. - Highlights: • We optimized pixelated crystal configuration for the purpose of molecular SPECT imaging. • The weighted-sum and the figure-of-merit methods were used in order to search for an optimal crystal configuration. • The higher the pixel size, the poorer the resolution and simultaneously the higher the sensitivity and the PDA. • The

Monte Carlo Optimization of Crystal Configuration for Pixelated Molecular SPECT Scanners

International Nuclear Information System (INIS)

Mahani, Hojjat; Raisali, Gholamreza; Kamali-Asl, Alireza; Ay, Mohammad Reza

2017-01-01

Resolution-sensitivity-PDA tradeoff is the most challenging problem in design and optimization of pixelated preclinical SPECT scanners. In this work, we addressed such a challenge from a crystal point-of-view by looking for an optimal pixelated scintillator using GATE Monte Carlo simulation. Various crystal configurations have been investigated and the influence of different pixel sizes, pixel gaps, and three scintillators on tomographic resolution, sensitivity, and PDA of the camera were evaluated. The crystal configuration was then optimized using two objective functions: the weighted-sum and the figure-of-merit methods. The CsI(Na) reveals the highest sensitivity of the order of 43.47 cps/MBq in comparison to the NaI(Tl) and the YAP(Ce), for a 1.5×1.5 mm"2 pixel size and 0.1 mm gap. The results show that the spatial resolution, in terms of FWHM, improves from 3.38 to 2.21 mm while the sensitivity simultaneously deteriorates from 42.39 cps/MBq to 27.81 cps/MBq when pixel size varies from 2×2 mm"2 to 0.5×0.5 mm"2 for a 0.2 mm gap, respectively. The PDA worsens from 0.91 to 0.42 when pixel size decreases from 0.5×0.5 mm"2 to 1×1 mm"2 for a 0.2 mm gap at 15° incident-angle. The two objective functions agree that the 1.5×1.5 mm"2 pixel size and 0.1 mm Epoxy gap CsI(Na) configuration provides the best compromise for small-animal imaging, using the HiReSPECT scanner. Our study highlights that crystal configuration can significantly affect the performance of the camera, and thereby Monte Carlo optimization of pixelated detectors is mandatory in order to achieve an optimal quality tomogram. - Highlights: • We optimized pixelated crystal configuration for the purpose of molecular SPECT imaging. • The weighted-sum and the figure-of-merit methods were used in order to search for an optimal crystal configuration. • The higher the pixel size, the poorer the resolution and simultaneously the higher the sensitivity and the PDA. • The higher the pixel gap, the

Crucial role of molecular planarity on the second order nonlinear optical property of pyridine based chalcone single crystals

Science.gov (United States)

Menezes, Anthoni Praveen; Jayarama, A.; Ng, Seik Weng

2015-05-01

An efficient nonlinear optical material 2E-3-(4-bromophenyl)-1-(pyridin-3-yl) prop-2-en-1-one (BPP) was synthesized and single crystals were grown using slow evaporation solution growth technique at room temperature. Grown crystal had prismatic morphology and its structure was confirmed by various spectroscopic studies, elemental analysis, and single crystal X-ray diffraction (XRD) technique. The single crystal XRD of the crystal showed that BPP crystallizes in monoclinic system with noncentrosymmetric space group P21 and the cell parameters are a = 5.6428(7) Å, b = 3.8637(6) Å, c = 26.411(2) Å, β = 97.568(11) deg and v = 575.82(12) Å3. The UV-Visible spectrum reveals that the crystal is optically transparent and has high optical energy band gap of 3.1 eV. The powder second harmonic generation efficiency (SHG) of BPP is 6.8 times that of KDP. From thermal analysis it is found that the crystal melts at 139 °C and decomposes at 264 °C. High optical transparency down to blue region, higher powder SHG efficiency and better thermal stability than that of urea makes this chalcone derivative a promising candidate for SHG applications. Furthermore, effect of molecular planarity on SHG efficiency and role of pyridine ring adjacent to carbonyl group in forming noncentrosymmetric crystal systems of chalcone family is also discussed.

X-ray scattering studies of non-equilibrium ordering processes

International Nuclear Information System (INIS)

Nagler, S.E.

1990-01-01

We report on the progress of our project entitled ''X-ray Scattering of Non-Equilibrium Ordering Processes.'' During the past year we have made the first synchrotron measurements of ordering in Cu 3 Au have revealed the presence of an intermediate, non-equilibrium ordered state. Preliminary work involving x-ray magnetic scattering has been carried out. Work is continuing in these areas as well as on related problems. 5 refs

Advances in nonlinear polymers and inorganic crystals, liquid crystals, and laser media

International Nuclear Information System (INIS)

Musikant, S.

1987-01-01

These proceedings collect papers on laser materials. Topics include: solid state lasers, fracture mechanics in laser materials, optical second harmonic generation, nonlinear optics, molecular crystals, crystal-phase transformation, and materials for laser fusion reactors

Zubarev's Nonequilibrium Statistical Operator Method in the Generalized Statistics of Multiparticle Systems

Science.gov (United States)

Glushak, P. A.; Markiv, B. B.; Tokarchuk, M. V.

2018-01-01

We present a generalization of Zubarev's nonequilibrium statistical operator method based on the principle of maximum Renyi entropy. In the framework of this approach, we obtain transport equations for the basic set of parameters of the reduced description of nonequilibrium processes in a classical system of interacting particles using Liouville equations with fractional derivatives. For a classical systems of particles in a medium with a fractal structure, we obtain a non-Markovian diffusion equation with fractional spatial derivatives. For a concrete model of the frequency dependence of a memory function, we obtain generalized Kettano-type diffusion equation with the spatial and temporal fractality taken into account. We present a generalization of nonequilibrium thermofield dynamics in Zubarev's nonequilibrium statistical operator method in the framework of Renyi statistics.

Fragmentation function in non-equilibrium QCD using closed-time path integral formalism

International Nuclear Information System (INIS)

Nayak, Gouranga C.

2009-01-01

In this paper we implement the Schwinger-Keldysh closed-time path integral formalism in non-equilibrium QCD in accordance to the definition of the Collins-Soper fragmentation function. We consider a high-p T parton in QCD medium at initial time τ 0 with an arbitrary non-equilibrium (non-isotropic) distribution function f(vector (p)) fragmenting to a hadron. We formulate the parton-to-hadron fragmentation function in non-equilibrium QCD in the light-cone quantization formalism. It may be possible to include final-state interactions with the medium via a modification of the Wilson lines in this definition of the non-equilibrium fragmentation function. This may be relevant to the study of hadron production from a quark-gluon plasma at RHIC and LHC. (orig.)

Temperature-mediated polymorphism in molecular crystals: The impact on crystal packing and charge transport

KAUST Repository

Stevens, Loah A.; Goetz, Katelyn P.; Fonari, Alexandr; Shu, Ying; Williamson, Rachel M.; Bredas, Jean-Luc; Coropceanu, Veaceslav P.; Jurchescu, Oana D.; Collis, Gavin E.

2015-01-01

We report a novel synthesis to ultra high purity 7,14-bis((trimethylsilyl)ethynyl)dibenzo[b,def]-chrysene (TMS-DBC) and the use of this material in the growth of single crystals by solution and vapor deposition techniques. We observe that the substrate temperature has a dramatic impact on the crystal growth, producing two distinct polymorphs of TMS-DBC; low temperature (LT) fine red needles and high temperature (HT) large yellow platelets. Single crystal X-ray crystallography confirms packing structures where the LT crystals form a 1D slipped-stack structure, while the HT crystals adopt a 2D brickwork motif. These polymorphs also represent a rare example where both are extremely stable and do not interconvert to the other crystal structure upon solvent or thermal annealing. Single crystal organic field-effect transistors of the LT and HT crystals show that the HT 2D brickwork motif produces hole mobilities as high as 2.1 cm2 V-1 s-1, while the mobility of the 1D structure is significantly lower, at 0.028 cm2 V-1 s-1. Electronic-structure calculations indicate that the superior charge transport in the brickwork polymorph in comparison to the slipped-stack polymorph is due to the presence of an increased dimensionality of the charge migration pathways.

Temperature-mediated polymorphism in molecular crystals: The impact on crystal packing and charge transport

KAUST Repository

Stevens, Loah A.

2015-01-13

We report a novel synthesis to ultra high purity 7,14-bis((trimethylsilyl)ethynyl)dibenzo[b,def]-chrysene (TMS-DBC) and the use of this material in the growth of single crystals by solution and vapor deposition techniques. We observe that the substrate temperature has a dramatic impact on the crystal growth, producing two distinct polymorphs of TMS-DBC; low temperature (LT) fine red needles and high temperature (HT) large yellow platelets. Single crystal X-ray crystallography confirms packing structures where the LT crystals form a 1D slipped-stack structure, while the HT crystals adopt a 2D brickwork motif. These polymorphs also represent a rare example where both are extremely stable and do not interconvert to the other crystal structure upon solvent or thermal annealing. Single crystal organic field-effect transistors of the LT and HT crystals show that the HT 2D brickwork motif produces hole mobilities as high as 2.1 cm2 V-1 s-1, while the mobility of the 1D structure is significantly lower, at 0.028 cm2 V-1 s-1. Electronic-structure calculations indicate that the superior charge transport in the brickwork polymorph in comparison to the slipped-stack polymorph is due to the presence of an increased dimensionality of the charge migration pathways.

Non-equilibrium modelling of distillation

NARCIS (Netherlands)

Wesselingh, JA; Darton, R

1997-01-01

There are nasty conceptual problems in the classical way of describing distillation columns via equilibrium stages, and efficiencies or HETP's. We can nowadays avoid these problems by simulating the behaviour of a complete column in one go using a non-equilibrium model. Such a model has phase

Scattering of atomic and molecular ions from single crystal surfaces of Cu, Ag and Fe

International Nuclear Information System (INIS)

Zoest, J.M. van.

1986-01-01

This thesis deals with analysis of crystal surfaces of Cu, Ag and Fe with Low Energy Ion scattering Spectroscopy (LEIS). Different atomic and molecular ions with fixed energies below 7 keV are scattered by a metal single crystal (with adsorbates). The energy and direction of the scattered particles are analysed for different selected charge states. In that way information can be obtained concerning the composition and atomic and electronic structure of the single crystal surface. Energy spectra contain information on the composition of the surface, while structural atomic information is obtained by direction measurements (photograms). In Ch.1 a description is given of the experimental equipment, in Ch.2 a characterization of the LEIS method. Ch.3 deals with the neutralization of keV-ions in surface scattering. Two different ways of data interpretation are presented. First a model is treated in which the observed directional dependence of neutralization action of the first atom layer of the surface is presented by a laterally varying thickness of the neutralizing layer. Secondly it is shown that the data can be reproduced by a more realistic, physical model based on atomic transition matrix elements. In Ch.4 the low energy hydrogen scattering is described. The study of the dissociation of H 2 + at an Ag surface r0230ted in a model based on electronic dissociation, initialized by electron capture into a repulsive (molecular) state. In Ch.5 finally the method is applied to the investigation of the surface structure of oxidized Fe. (Auth.)

Dynamical study of a polydisperse hard-sphere system

KAUST Repository

Nogawa, Tomoaki

2010-08-10

We study the interplay between the fluid-crystal transition and the glass transition of elastic sphere system with polydispersity using nonequilibrium molecular dynamics simulations. It is found that the end point of the crystal-fluid transition line, which corresponds to the critical polydispersity above which the crystal state is unstable, is on the glass transition line. This means that crystal and fluid states at the melting point becomes less distinguishable as polydispersity increases and finally they become identical state, i.e., marginal glass state, at critical polydispersity. © 2010 The American Physical Society.

Non-Equilibrium Liouville and Wigner Equations: Moment Methods and Long-Time Approximations

Directory of Open Access Journals (Sweden)

Ramon F. Álvarez-Estrada

2014-03-01

Full Text Available We treat the non-equilibrium evolution of an open one-particle statistical system, subject to a potential and to an external “heat bath” (hb with negligible dissipation. For the classical equilibrium Boltzmann distribution, Wc,eq, a non-equilibrium three-term hierarchy for moments fulfills Hermiticity, which allows one to justify an approximate long-time thermalization. That gives partial dynamical support to Boltzmann’s Wc,eq, out of the set of classical stationary distributions, Wc;st, also investigated here, for which neither Hermiticity nor that thermalization hold, in general. For closed classical many-particle systems without hb (by using Wc,eq, the long-time approximate thermalization for three-term hierarchies is justified and yields an approximate Lyapunov function and an arrow of time. The largest part of the work treats an open quantum one-particle system through the non-equilibrium Wigner function, W. Weq for a repulsive finite square well is reported. W’s (< 0 in various cases are assumed to be quasi-definite functionals regarding their dependences on momentum (q. That yields orthogonal polynomials, HQ,n(q, for Weq (and for stationary Wst, non-equilibrium moments, Wn, of W and hierarchies. For the first excited state of the harmonic oscillator, its stationary Wst is a quasi-definite functional, and the orthogonal polynomials and three-term hierarchy are studied. In general, the non-equilibrium quantum hierarchies (associated with Weq for the Wn’s are not three-term ones. As an illustration, we outline a non-equilibrium four-term hierarchy and its solution in terms of generalized operator continued fractions. Such structures also allow one to formulate long-time approximations, but make it more difficult to justify thermalization. For large thermal and de Broglie wavelengths, the dominant Weq and a non-equilibrium equation for W are reported: the non-equilibrium hierarchy could plausibly be a three-term one and possibly not

Synthesis and properties of large crystal of aluminum-deficient ultrasil molecular sieve materials

International Nuclear Information System (INIS)

Durrani, J.; Akhtar, J.; Chughtai, N.A.; Arif, M.; Saeed, K.; Ahmed, M.; Siddique, M.

2003-01-01

Large crystals of aluminum-deficient and silica rich molecular sieve materials such as Silicalite-I, Silicalite-II ZSM11-B and ZSM11-Fe have been synthesized hydro thermally from the aqueous silicate gel of (R/sub 2/O -SiO/sub 2/- B/sub 2/O/sub 3/ -Fe/sub 2/O/ sub 3/ -H/sub 2/O) using PTFE-lined stainless digestion bomb. The term R is a alkyl group. The synthesized materials were identified for crystallinity, thermal stability, phase, crystal structure, morphology and unit cell dimensions using thermogravimetry (TG/DTA), differential scanning calorimetric(DSC), X-ray diffraction (XRD), scanning electron microscopy (SEM) and other analytical techniques. All product materials were found to be white crystalline and crysto-graphically pure. Surface area and particle size distribution of materials were also ascertained. /sup 57/Fe Mossbauer spectroscopic studies on as-synthesized and calcined samples have confirmed the uniform dispersion of Fe/sup 3+/ ions in the tetrahedral framework of ZSM11-Fe material. (author)

Transient magnetic tunneling mediated by a molecular bridge

Czech Academy of Sciences Publication Activity Database

Kalvová, Anděla; Špička, Václav; Velický, B.

2015-01-01

Roč. 28, č. 3 (2015), 1087-1091 ISSN 1557-1939 R&D Projects: GA ČR GAP204/12/0897 Institutional support: RVO:68378271 Keywords : non-equilibrium * initial conditions * transient currents * molecular islands Subject RIV: BE - Theoretical Physics Impact factor: 1.100, year: 2015

Unsolved problems of crystallization and melting of flexible macromolecules

International Nuclear Information System (INIS)

Wunderlich, B.

1992-01-01

The thermodynamics, kinetics, and computer simulations of crystallization and melting is discussed. The thermodynamics is shown to be well understood, although for many specific crystals not enough details for full description are available. Experiments on the crystallization kinetics of poly(ethylene) and poly(oxyethylene) in the presence of crystal nuclei as a function of molecular mass revealed that with increasing mass, the crystallization behavior deviates increasingly from that of small, rigid molecules. Instead of showing a continuously changing, linear crystallization rate with temperature through the equilibrium melting temperature, T m 0 , these flexible macromolecules show a region of practically zero crystallization rate between T m 0 and about (T m 0 - 15) K, creating a temperature region of metastability in the melt that cannot be broken by nucleation with pregrown crystals. Molecular Nucleation was proposed as a cooperative process to be of overriding importance for the description of polymer crystallization, and to be at the center of segregation of molecules of lower molecular mass by growing crystal fronts. Initial efforts to model sufficiently large crystals using Monte Carlo and molecular dynamics methods are presented. Some of the short-time intermediates in the melting, crystallization, and annealing processes seem to have little similarity to commonly assumed models of crystallization and melting and are presented as discussion topics

Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of chlorite dismutase: a detoxifying enzyme producing molecular oxygen

Energy Technology Data Exchange (ETDEWEB)

Geus, Daniël C. de, E-mail: d.de.geus@chem.leidenuniv.nl; Thomassen, Ellen A. J.; Feltz, Clarisse L. van der; Abrahams, Jan Pieter [Biophysical Structural Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden (Netherlands)

2008-08-01

Preliminary X-ray data collection and analysis for crystals of chlorite dismutase, a haem-based enzyme that very effectively reduces chlorite to chloride while producing molecular oxygen, is reported to 2.1 Å resolution. Chlorite dismutase, a homotetrameric haem-based protein, is one of the key enzymes of (per)chlorate-reducing bacteria. It is highly active (< 2 kU mg{sup −1}) in reducing the toxic compound chlorite to the innocuous chloride anion and molecular oxygen. Chlorite itself is produced as the intermediate product of (per)chlorate reduction. The chlorite dismutase gene in Azospira oryzae strain GR-1 employing degenerate primers has been identified and the active enzyme was subsequently overexpressed in Escherichia coli. Chlorite dismutase was purified, proven to be active and crystallized using sitting drops with PEG 2000 MME, KSCN and ammonium sulfate as precipitants. The crystals belonged to space group P2{sub 1}2{sub 1}2 and were most likely to contain six subunits in the asymmetric unit. The refined unit-cell parameters were a = 164.46, b = 169.34, c = 60.79 Å. The crystals diffracted X-rays to 2.1 Å resolution on a synchrotron-radiation source and a three-wavelength MAD data set has been collected. Determination of the chlorite dismutase structure will provide insights into the active site of the enzyme, for which no structures are currently available.

Equilibrium and nonequilibrium dynamics of soft sphere fluids.

Science.gov (United States)

Ding, Yajun; Mittal, Jeetain

2015-07-14

We use computer simulations to test the freezing-point scaling relationship between equilibrium transport coefficients (self-diffusivity, viscosity) and thermodynamic parameters for soft sphere fluids. The fluid particles interact via the inverse-power potential (IPP), and the particle softness is changed by modifying the exponent of the distance-dependent potential term. In the case of IPP fluids, density and temperature are not independent variables and can be combined to obtain a coupling parameter to define the thermodynamic state of the system. We find that the rescaled coupling parameter, based on its value at the freezing point, can approximately collapse the diffusivity and viscosity data for IPP fluids over a wide range of particle softness. Even though the collapse is far from perfect, the freezing-point scaling relationship provides a convenient and effective way to compare the structure and dynamics of fluid systems with different particle softness. We further show that an alternate scaling relationship based on two-body excess entropy can provide an almost perfect collapse of the diffusivity and viscosity data below the freezing transition. Next, we perform nonequilibrium molecular dynamics simulations to calculate the shear-dependent viscosity and to identify the distinct role of particle softness in underlying structural changes associated with rheological properties. Qualitatively, we find a similar shear-thinning behavior for IPP fluids with different particle softness, though softer particles exhibit stronger shear-thinning tendency. By investigating the distance and angle-dependent pair correlation functions in these systems, we find different structural features in the case of IPP fluids with hard-sphere like and softer particle interactions. Interestingly, shear-thinning in hard-sphere like fluids is accompanied by enhanced translational order, whereas softer fluids exhibit loss of order with shear. Our results provide a systematic evaluation

The nonextensive parameter for nonequilibrium electron gas in an electromagnetic field

International Nuclear Information System (INIS)

Yu, Haining; Du, Jiulin

2014-01-01

The nonextensive parameter for nonequilibrium electron gas of the plasma in an electromagnetic field is studied. We exactly obtained an expression of the q-parameter based on Boltzmann kinetic theories for plasmas, where Coulombian interactions and Lorentz forces play dominant roles. We show that the q-parameter different from unity is related by an equation to temperature gradient, electric field strength, magnetic induction as well as overall bulk velocity of the gas. The effect of the magnetic field on the q-parameter depends on the overall bulk velocity. Thus the q-parameter for the electron gas in an electromagnetic field represents the nonequilibrium nature or nonisothermal configurations of the plasma with electromagnetic interactions. - Highlights: • An expression of the q-parameter is obtained for nonequilibrium plasma with electromagnetic interactions. • The q-parameter is related to temperature gradient, electric field strength, magnetic induction as well as overall bulk velocity of the plasma. • The q-parameter represents the nonequilibrium nature of the complex plasma with electromagnetic interactions

The nonextensive parameter for nonequilibrium electron gas in an electromagnetic field

Energy Technology Data Exchange (ETDEWEB)

Yu, Haining; Du, Jiulin, E-mail: jldu@tju.edu.cn

2014-11-15

The nonextensive parameter for nonequilibrium electron gas of the plasma in an electromagnetic field is studied. We exactly obtained an expression of the q-parameter based on Boltzmann kinetic theories for plasmas, where Coulombian interactions and Lorentz forces play dominant roles. We show that the q-parameter different from unity is related by an equation to temperature gradient, electric field strength, magnetic induction as well as overall bulk velocity of the gas. The effect of the magnetic field on the q-parameter depends on the overall bulk velocity. Thus the q-parameter for the electron gas in an electromagnetic field represents the nonequilibrium nature or nonisothermal configurations of the plasma with electromagnetic interactions. - Highlights: • An expression of the q-parameter is obtained for nonequilibrium plasma with electromagnetic interactions. • The q-parameter is related to temperature gradient, electric field strength, magnetic induction as well as overall bulk velocity of the plasma. • The q-parameter represents the nonequilibrium nature of the complex plasma with electromagnetic interactions.

Non-equilibrium transport in the quantum dot: quench dynamics and non-equilibrium steady state

Science.gov (United States)

Culver, Adrian; Andrei, Natan

We present an exact method of calculating the non-equilibrium current driven by a voltage drop across a quantum dot. The system is described by the two lead Anderson model at zero temperature with on-site Coulomb repulsion and non-interacting, linearized leads. We prepare the system in an initial state consisting of a free Fermi sea in each lead with the voltage drop given as the difference between the two Fermi levels. We quench the system by coupling the dot to the leads at t = 0 and following the time evolution of the wavefunction. In the long time limit a new type of Bethe Ansatz wavefunction emerges, which satisfies the Lippmann-Schwinger equation with the two Fermi seas serving as the boundary conditions. This exact, non-perturbative solution describes the non-equilibrium steady state of the system. We describe how to use this solution to compute the infinite time limit of the expectation value of the current operator at a given voltage, which would yield the I-V characteristic of the dot. Research supported by NSF Grant DMR 1410583.

On non-equilibrium states in QFT model with boundary interaction

International Nuclear Information System (INIS)

Bazhanov, Vladimir V.; Lukyanov, Sergei L.; Zamolodchikov, Alexander B.

1999-01-01

We prove that certain non-equilibrium expectation values in the boundary sine-Gordon model coincide with associated equilibrium-state expectation values in the systems which differ from the boundary sine-Gordon in that certain extra boundary degrees of freedom (q-oscillators) are added. Applications of this result to actual calculation of non-equilibrium characteristics of the boundary sine-Gordon model are also discussed

Interaction Heterogeneity can Favorably Impact Colloidal Crystal Nucleation

Science.gov (United States)

Jenkins, Ian C.; Crocker, John C.; Sinno, Talid

2017-10-01

Colloidal particles with short-ranged attractions, e.g., micron-scale spheres functionalized with single-stranded DNA oligomers, are susceptible to becoming trapped in disordered configurations even when a crystalline arrangement is the ground state. Moreover, for reasons that are not well understood, seemingly minor variations in the particle formulation can lead to dramatic changes in the crystallization outcome. We demonstrate, using a combination of equilibrium and nonequilibrium computer simulations, that interaction heterogeneity—variations in the energetic interactions among different particle pairs in the population—may favorably impact crystal nucleation. Specifically, interaction heterogeneity is found to lower the free energy barrier to nucleation via the formation of clusters comprised preferentially of strong-binding particle pairs. Moreover, gelation is inhibited by "spreading out over time" the nucleation process, resulting in a reduced density of stable nuclei, allowing each to grow unhindered and larger. Our results suggest a simple and robust approach for enhancing colloidal crystallization near the "sticky sphere" limit, and support the notion that differing extents of interaction heterogeneity arising from various particle functionalization protocols may contribute to the otherwise unexplained variations in crystallization outcomes reported in the literature.

Nonequilibrium thermodynamics of dilute polymer solutions in flow.

Science.gov (United States)

Latinwo, Folarin; Hsiao, Kai-Wen; Schroeder, Charles M

2014-11-07

Modern materials processing applications and technologies often occur far from equilibrium. To this end, the processing of complex materials such as polymer melts and nanocomposites generally occurs under strong deformations and flows, conditions under which equilibrium thermodynamics does not apply. As a result, the ability to determine the nonequilibrium thermodynamic properties of polymeric materials from measurable quantities such as heat and work is a major challenge in the field. Here, we use work relations to show that nonequilibrium thermodynamic quantities such as free energy and entropy can be determined for dilute polymer solutions in flow. In this way, we determine the thermodynamic properties of DNA molecules in strong flows using a combination of simulations, kinetic theory, and single molecule experiments. We show that it is possible to calculate polymer relaxation timescales purely from polymer stretching dynamics in flow. We further observe a thermodynamic equivalence between nonequilibrium and equilibrium steady-states for polymeric systems. In this way, our results provide an improved understanding of the energetics of flowing polymer solutions.

Initial conditions of non-equilibrium quark-gluon plasma evolution

International Nuclear Information System (INIS)

Shmatov, S.V.

2002-01-01

In accordance with the hydrodynamic Bjorken limit, the initial energy density and temperature for a chemical non-equilibrium quark-gluon system formed in the heavy ion collisions at the LHC are computed. The dependence of this value on the type of colliding nuclei and the collision impact parameter is studied. The principle possibility of the non-equilibrium quark-gluon plasma (QGP) formation in the light nuclei collisions is shown. The life time of QGP is calculated. (author)

Non-equilibrium thermodynamics

CERN Document Server

De Groot, Sybren Ruurds

1984-01-01

The study of thermodynamics is especially timely today, as its concepts are being applied to problems in biology, biochemistry, electrochemistry, and engineering. This book treats irreversible processes and phenomena - non-equilibrium thermodynamics.S. R. de Groot and P. Mazur, Professors of Theoretical Physics, present a comprehensive and insightful survey of the foundations of the field, providing the only complete discussion of the fluctuating linear theory of irreversible thermodynamics. The application covers a wide range of topics: the theory of diffusion and heat conduction, fluid dyn

Non-equilibrium Dynamics, Thermalization and Entropy Production

International Nuclear Information System (INIS)

Hinrichsen, Haye; Janotta, Peter; Gogolin, Christian

2011-01-01

This paper addresses fundamental aspects of statistical mechanics such as the motivation of a classical state space with spontaneous transitions, the meaning of non-equilibrium in the context of thermalization, and the justification of these concepts from the quantum-mechanical point of view. After an introductory part we focus on the problem of entropy production in non-equilibrium systems. In particular, the generally accepted formula for entropy production in the environment is analyzed from a critical perspective. It is shown that this formula is only valid in the limit of separated time scales of the system's and the environmental degrees of freedom. Finally, we present an alternative simple proof of the fluctuation theorem.

Modelling non-equilibrium thermodynamic systems from the speed-gradient principle.

Science.gov (United States)

Khantuleva, Tatiana A; Shalymov, Dmitry S

2017-03-06

The application of the speed-gradient (SG) principle to the non-equilibrium distribution systems far away from thermodynamic equilibrium is investigated. The options for applying the SG principle to describe the non-equilibrium transport processes in real-world environments are discussed. Investigation of a non-equilibrium system's evolution at different scale levels via the SG principle allows for a fresh look at the thermodynamics problems associated with the behaviour of the system entropy. Generalized dynamic equations for finite and infinite number of constraints are proposed. It is shown that the stationary solution to the equations, resulting from the SG principle, entirely coincides with the locally equilibrium distribution function obtained by Zubarev. A new approach to describe time evolution of systems far from equilibrium is proposed based on application of the SG principle at the intermediate scale level of the system's internal structure. The problem of the high-rate shear flow of viscous fluid near the rigid plane plate is discussed. It is shown that the SG principle allows closed mathematical models of non-equilibrium processes to be constructed.This article is part of the themed issue 'Horizons of cybernetical physics'. © 2017 The Author(s).

Modeling inelastic phonon scattering in atomic- and molecular-wire junctions

DEFF Research Database (Denmark)

Paulsson, Magnus; Frederiksen, Thomas; Brandbyge, Mads

2005-01-01

Computationally inexpensive approximations describing electron-phonon scattering in molecular-scale conductors are derived from the nonequilibrium Green's function method. The accuracy is demonstrated with a first-principles calculation on an atomic gold wire. Quantitative agreement between the f...

Modeling of two-phase flow with thermal and mechanical non-equilibrium

International Nuclear Information System (INIS)

Houdayer, G.; Pinet, B.; Le Coq, G.; Reocreux, M.; Rousseau, J.C.

1977-01-01

To improve two-phase flow modeling by taking into account thermal and mechanical non-equilibrium a joint effort on analytical experiment and physical modeling has been undertaken. A model describing thermal non-equilibrium effects is first presented. A correlation of mass transfer has been developed using steam water critical flow tests. This model has been used to predict in a satisfactory manner blowdown tests. It has been incorporated in CLYSTERE system code. To take into account mechanical non-equilibrium, a six equations model is written. To get information on the momentum transfers special nitrogen-water tests have been undertaken. The first results of these studies are presented

Nonequilibrium excitations and transport of Dirac electrons in electric-field-driven graphene

Science.gov (United States)

Li, Jiajun; Han, Jong E.

2018-05-01

We investigate nonequilibrium excitations and charge transport in charge-neutral graphene driven with dc electric field by using the nonequilibrium Green's-function technique. Due to the vanishing Fermi surface, electrons are subject to nontrivial nonequilibrium excitations such as highly anisotropic momentum distribution of electron-hole pairs, an analog of the Schwinger effect. We show that the electron-hole excitations, initiated by the Landau-Zener tunneling with a superlinear I V relation I ∝E3 /2 , reaches a steady state dominated by the dissipation due to optical phonons, resulting in a marginally sublinear I V with I ∝E , in agreement with recent experiments. The linear I V starts to show the sign of current saturation as the graphene is doped away from the Dirac point, and recovers the semiclassical relation for the saturated velocity. We give a detailed discussion on the nonequilibrium charge creation and the relation between the electron-phonon scattering rate and the electric field in the steady-state limit. We explain how the apparent Ohmic I V is recovered near the Dirac point. We propose a mechanism where the peculiar nonequilibrium electron-hole creation can be utilized in a infrared device.

Dynamics and Thermodynamics of Molecular Machines

DEFF Research Database (Denmark)

Golubeva, Natalia

2014-01-01

to their microscopic size, molecular motors are governed by principles fundamentally different from those describing the operation of man-made motors such as car engines. In this dissertation the dynamic and thermodynamic properties of molecular machines are studied using the tools of nonequilibrium statistical......Molecular machines, or molecular motors, are small biophysical devices that perform a variety of essential metabolic processes such as DNA replication, protein synthesis and intracellular transport. Typically, these machines operate by converting chemical energy into motion and mechanical work. Due...... mechanics. The first part focuses on noninteracting molecular machines described by a paradigmatic continuum model with the aim of comparing and contrasting such a description to the one offered by the widely used discrete models. Many molecular motors, for example, kinesin involved in cellular cargo...

Point defects and atomic transport in crystals

International Nuclear Information System (INIS)

Lidiard, A.B.

1981-02-01

There are two principle aspects to the theory of atomic transport in crystals as caused by the action of point defects, namely (1) the calculation of relevant properties of the point defects (energies and other thermodynamic characteristics of the different possible defects, activation energies and other mobility parameters) and (2) the statistical mechanics of assemblies of defects, both equilibrium and non-equilibrium assemblies. In the five lectures given here both these aspects are touched on. The first two lectures are concerned with the calculation of relevant point defect properties, particularly in ionic crystals. The first lecture is more general, the second is concerned particularly with some recent calculations of the free volumes of formation of defects in various ionic solids; these solve a rather long-standing problem in this area. The remaining three lectures are concerned with the kinetic theory of defects mainly in relaxation, drift and diffusion situations

Flux-split algorithms for flows with non-equilibrium chemistry and vibrational relaxation

Science.gov (United States)

Grossman, B.; Cinnella, P.

1990-01-01

The present consideration of numerical computation methods for gas flows with nonequilibrium chemistry thermodynamics gives attention to an equilibrium model, a general nonequilibrium model, and a simplified model based on vibrational relaxation. Flux-splitting procedures are developed for the fully-coupled inviscid equations encompassing fluid dynamics and both chemical and internal energy-relaxation processes. A fully coupled and implicit large-block structure is presented which embodies novel forms of flux-vector split and flux-difference split algorithms valid for nonequilibrium flow; illustrative high-temperature shock tube and nozzle flow examples are given.

Optical orientation of the homogeneous nonequilibrium Bose-Einstein condensate of exciton polaritons

Science.gov (United States)

Korenev, V. L.

2012-07-01

A simple model, describing the steady state of the nonequilibrium polarization of a homogeneous Bose-Einstein condensate of exciton polaritons, is considered. It explains the suppression of spin splitting of a nonequilibrium polariton condensate in an external magnetic field, the linear polarization, the linear-to-circular polarization conversion, and the unexpected sign of the circular polarization of the condensate all on equal footing. It is shown that inverse effects are possible, to wit, spontaneous circular polarization and the enhancement of spin splitting of a nonequilibrium condensate of polaritons.

On the definition of equilibrium and non-equilibrium states in dynamical systems

OpenAIRE

Akimoto, Takuma

2008-01-01

We propose a definition of equilibrium and non-equilibrium states in dynamical systems on the basis of the time average. We show numerically that there exists a non-equilibrium non-stationary state in the coupled modified Bernoulli map lattice.

Investigation on non-equilibrium performance of composite adsorbent for resorption refrigeration

International Nuclear Information System (INIS)

Jiang, L.; Wang, L.W.; Zhou, Z.S.; Zhu, F.Q.; Wang, R.Z.

2016-01-01

Highlights: • Performance of resorption refrigeration is analyzed based on non-equilibrium reaction process. • The porous matrix improves the heat and mass performance of composite adsorbent. • The actual desorption process has the significant hysteresis phenomenon. • The highest energy efficiency of Manganese and Calcium chloride working pair is 0.272. - Abstract: The aims of this paper is to indicate that the non-equilibrium adsorption testing results is more suitable for prediction of real refrigeration performance than equilibrium data. Therefore, a test unit is constructed to test the non-equilibrium performance of different composite adsorbents. The adsorption and desorption quantity are measured and calculated by smart differential pressure transmitter. The non-equilibrium adsorption performances of working pair of Manganese chloride–ammonia, Calcium chloride–ammonia and Ammonium chloride–ammonia are investigated respectively. Results show that hysteresis phenomena happens obviously in non-equilibrium desorption process, which is related with dual variables rather than single variable. Based on the testing results, resorption refrigeration performance is analyzed, in which Manganese chloride is used as high temperature salt (HTS), and Calcium chloride, Ammonium chloride are selected as low temperature salt (LTS) for comparison. Results show that the highest COP and SCP for resorption refrigeration are about 0.272 and 45.6 W/kg, respectively. Performance of Manganese chloride–Calcium chloride and Manganese chloride–Ammonium chloride working pairs are much lower when compared with theoretical data.

Nanoparticles in liquid crystals, and liquid crystals in nanoparticles

Science.gov (United States)

de Pablo, Juan

2015-03-01

Liquid crystals are remarkably sensitive to interfacial interactions. Small perturbations at a liquid crystal interface, for example, can be propagated over relatively long length scales, thereby providing the basis for a wide range of applications that rely on amplification of molecular events into macroscopic observables. Our recent research efforts have focused on the reverse phenomenon; that is, we have sought to manipulate the interfacial assembly of nanoparticles or the organization of surface active molecules by controlling the structure of a liquid crystal. This presentation will consist of a review of the basic principles that are responsible for liquid crystal-mediated interactions, followed by demonstrations of those principles in the context of two types of systems. In the first, a liquid crystal is used to direct the assembly of nanoparticles; through a combination of molecular and continuum models, it is found that minute changes in interfacial energy and particle size lead to liquid-crystal induced attractions that can span multiple orders of magnitude. Theoretical predictions are confirmed by experimental observations, which also suggest that LC-mediated assembly provides an effective means for fabrication of plasmonic devices. In the second type of system, the structure of a liquid crystal is controlled by confinement in submicron droplets. The morphology of the liquid crystal in a drop depends on a delicate balance between bulk and interfacial contributions to the free energy; that balance can be easily perturbed by adsorption of analytes or nanoparticles at the interface, thereby providing the basis for development of hierarchical assembly of responsive, anisotropic materials. Theoretical predictions also indicate that the three-dimensional order of a liquid crystal can be projected onto a two-dimensional interface, and give rise to novel nanostructures that are not found in simple isotropic fluids.

Step-wise pulling protocols for non-equilibrium dynamics

Science.gov (United States)

Ngo, Van Anh

-from-equilibrium ensembles, which can be used to characterize non-equilibrium dynamics. Furthermore, we have applied the stepwise pulling protocols and Jarzynski's Equality to investigate the ion selectivity of potassium channels via molecular dynamics simulations. The mechanism of the potassium ion selectivity has remained poorly understood for over fifty years, although a Nobel Prize was awarded to the discovery of the molecular structure of a potassium-selective channel in 2003. In one year of performing simulations, we were able to reproduce the major results of ion selectivity accumulated in fifty years. We have been even boldly going further to propose a new model for ion selectivity based on the structural rearrangement of the selectivity filter of potassium-selective KcsA channels. This structural rearrangement has never been shown to play such a pivotal role in selecting and conducting potassium ions, but effectively rejecting sodium ions. Using the stepwise pulling protocols, we are also able to estimate conductance for ion channels, which remains elusive by using other methods. In the light of ion channels, we have also investigated how a synthetic channel of telemeric G-quadruplex conducts different types of ions. These two studies on ion selectivity not only constitute an interesting part of this dissertation, but also will enable us to further explore a new set of ion-selectivity principles. Beside the focus of my dissertation, I used million-atom molecular dynamics simulations to investigate the mechanical properties of body-centered-cubic (BCCS) and face-centered-cubic (FCCS) supercrystals of DNA-functionalized gold nanoparticles. These properties are valuable for examining whether these supercrystals can be used in gene delivery and gene therapy. The formation of such ordered supercrystals is useful to protect DNAs or RNAs from being attacked and destroyed by enzymes in cells. I also performed all-atom molecular dynamics simulations to study a pure oleic acid (OA) membrane

Non-equilibrium work distribution for interacting colloidal particles under friction

International Nuclear Information System (INIS)

Gomez-Solano, Juan Ruben; July, Christoph; Mehl, Jakob; Bechinger, Clemens

2015-01-01

We experimentally investigate the non-equilibrium steady-state distribution of the work done by an external force on a mesoscopic system with many coupled degrees of freedom: a colloidal crystal mechanically driven across a commensurate periodic light field. Since this system mimics the spatiotemporal dynamics of a crystalline surface moving on a corrugated substrate, our results show general properties of the work distribution for atomically flat surfaces undergoing friction. We address the role of several parameters which can influence the shape of the work distribution, e.g. the number of particles used to locally probe the properties of the system and the time interval to measure the work. We find that, when tuning the control parameters to induce particle depinning from the substrate, there is an abrupt change of the shape of the work distribution. While in the completely static and sliding friction regimes the work distribution is Gaussian, non-Gaussian tails show up due to the spatiotemporal heterogeneity of the particle dynamics during the transition between these two regimes. (paper)

Temperature sensitivity of void nucleation and growth parameters for single crystal copper: a molecular dynamics study

International Nuclear Information System (INIS)

Rawat, S; Chavan, V M; Warrier, M; Chaturvedi, S

2011-01-01

The effect of temperature on the void nucleation and growth is studied using the molecular dynamics (MD) code LAMMPS (Large-Scale Atomic/Molecular Massively Parallel Simulator). Single crystal copper is triaxially expanded at 5 × 10 9  s −1 strain rate keeping the temperature constant. It is shown that the nucleation and growth of voids at these atomistic scales follows a macroscopic nucleation and growth (NAG) model. As the temperature increases there is a steady decrease in the nucleation and growth thresholds. As the melting point of copper is approached, a double-dip in the pressure–time profile is observed. Analysis of this double-dip shows that the first minimum corresponds to the disappearance of the long-range order due to the creation of stacking faults and the system no longer has a FCC structure. There is no nucleation of voids at this juncture. The second minimum corresponds to the nucleation and incipient growth of voids. We present the sensitivity of NAG parameters to temperature and the analysis of double-dip in the pressure–time profile for single crystal copper at 1250 K

Effect of Molecular Flexibility on the Nematic-to-Isotropic Phase Transition for Highly Biaxial Molecular Non-Symmetric Liquid Crystal Dimers

Science.gov (United States)

Sebastián, Nerea; López, David Orencio; Diez-Berart, Sergio; de la Fuente, María Rosario; Salud, Josep; Pérez-Jubindo, Miguel Angel; Ros, María Blanca

2011-01-01

In this work, a study of the nematic (N)–isotropic (I) phase transition has been made in a series of odd non-symmetric liquid crystal dimers, the α-(4-cyanobiphenyl-4’-yloxy)-ω-(1-pyrenimine-benzylidene-4’-oxy) alkanes, by means of accurate calorimetric and dielectric measurements. These materials are potential candidates to present the elusive biaxial nematic (NB) phase, as they exhibit both molecular biaxiality and flexibility. According to the theory, the uniaxial nematic (NU)–isotropic (I) phase transition is first-order in nature, whereas the NB–I phase transition is second-order. Thus, a fine analysis of the critical behavior of the N–I phase transition would allow us to determine the presence or not of the biaxial nematic phase and understand how the molecular biaxiality and flexibility of these compounds influences the critical behavior of the N–I phase transition. PMID:28824100

Non-equilibrium many body dynamics

International Nuclear Information System (INIS)

Creutz, M.; Gyulassy, M.

1997-01-01

This Riken BNL Research Center Symposium on Non-Equilibrium Many Body Physics was held on September 23-25, 1997 as part of the official opening ceremony of the Center at Brookhaven National Lab. A major objective of theoretical work at the center is to elaborate on the full spectrum of strong interaction physics based on QCD, including the physics of confinement and chiral symmetry breaking, the parton structure of hadrons and nuclei, and the phenomenology of ultra-relativistic nuclear collisions related to the up-coming experiments at RHIC. The opportunities and challenges of nuclear and particle physics in this area naturally involve aspects of the many body problem common to many other fields. The aim of this symposium was to find common theoretical threads in the area of non-equilibrium physics and modern transport theories. The program consisted of invited talks on a variety topics from the fields of atomic, condensed matter, plasma, astrophysics, cosmology, and chemistry, in addition to nuclear and particle physics. Separate abstracts have been indexed into the database for contributions to this workshop

Nonequilibrium dynamical mean-field theory

Energy Technology Data Exchange (ETDEWEB)

Eckstein, Martin

2009-12-21

The aim of this thesis is the investigation of strongly interacting quantum many-particle systems in nonequilibrium by means of the dynamical mean-field theory (DMFT). An efficient numerical implementation of the nonequilibrium DMFT equations within the Keldysh formalism is provided, as well a discussion of several approaches to solve effective single-site problem to which lattice models such as the Hubbard-model are mapped within DMFT. DMFT is then used to study the relaxation of the thermodynamic state after a sudden increase of the interaction parameter in two different models: the Hubbard model and the Falicov-Kimball model. In the latter case an exact solution can be given, which shows that the state does not even thermalize after infinite waiting times. For a slow change of the interaction, a transition to adiabatic behavior is found. The Hubbard model, on the other hand, shows a very sensitive dependence of the relaxation on the interaction, which may be called a dynamical phase transition. Rapid thermalization only occurs at the interaction parameter which corresponds to this transition. (orig.)

Nonequilibrium dynamical mean-field theory

International Nuclear Information System (INIS)

Eckstein, Martin

2009-01-01

The aim of this thesis is the investigation of strongly interacting quantum many-particle systems in nonequilibrium by means of the dynamical mean-field theory (DMFT). An efficient numerical implementation of the nonequilibrium DMFT equations within the Keldysh formalism is provided, as well a discussion of several approaches to solve effective single-site problem to which lattice models such as the Hubbard-model are mapped within DMFT. DMFT is then used to study the relaxation of the thermodynamic state after a sudden increase of the interaction parameter in two different models: the Hubbard model and the Falicov-Kimball model. In the latter case an exact solution can be given, which shows that the state does not even thermalize after infinite waiting times. For a slow change of the interaction, a transition to adiabatic behavior is found. The Hubbard model, on the other hand, shows a very sensitive dependence of the relaxation on the interaction, which may be called a dynamical phase transition. Rapid thermalization only occurs at the interaction parameter which corresponds to this transition. (orig.)

Non-equilibrium many body dynamics

Energy Technology Data Exchange (ETDEWEB)

Creutz, M.; Gyulassy, M.

1997-09-22

This Riken BNL Research Center Symposium on Non-Equilibrium Many Body Physics was held on September 23-25, 1997 as part of the official opening ceremony of the Center at Brookhaven National Lab. A major objective of theoretical work at the center is to elaborate on the full spectrum of strong interaction physics based on QCD, including the physics of confinement and chiral symmetry breaking, the parton structure of hadrons and nuclei, and the phenomenology of ultra-relativistic nuclear collisions related to the up-coming experiments at RHIC. The opportunities and challenges of nuclear and particle physics in this area naturally involve aspects of the many body problem common to many other fields. The aim of this symposium was to find common theoretical threads in the area of non-equilibrium physics and modern transport theories. The program consisted of invited talks on a variety topics from the fields of atomic, condensed matter, plasma, astrophysics, cosmology, and chemistry, in addition to nuclear and particle physics. Separate abstracts have been indexed into the database for contributions to this workshop.

Continuum model of non-equilibrium solvation and solvent effect on ultra-fast processes

International Nuclear Information System (INIS)

Li Xiangyuan; Fu Kexiang; Zhu Quan

2006-01-01

In the past 50 years, non-equilibrium solvation theory for ultra-fast processes such as electron transfer and light absorption/emission has attracted particular interest. A great deal of research efforts was made in this area and various models which give reasonable qualitative descriptions for such as solvent reorganization energy in electron transfer and spectral shift in solution, were developed within the framework of continuous medium theory. In a series of publications by the authors, we clarified that the expression of the non-equilibrium electrostatic free energy that is at the dominant position of non-equilibrium solvation and serves as the basis of various models, however, was incorrectly formulated. In this work, the authors argue that reversible charging work integration was inappropriately applied in the past to an irreversible path linking the equilibrium or the non-equilibrium state. Because the step from the equilibrium state to the nonequilibrium state is factually thermodynamically irreversible, the conventional expression for non-equilibrium free energy that was deduced in different ways is unreasonable. Here the authors derive the non-equilibrium free energy to a quite different form according to Jackson integral formula. Such a difference throws doubts to the models including the famous Marcus two-sphere model for solvent reorganization energy of electron transfer and the Lippert-Mataga equation for spectral shift. By introducing the concept of 'spring energy' arising from medium polarizations, the energy constitution of the non-equilibrium state is highlighted. For a solute-solvent system, the authors separate the total electrostatic energy into different components: the self-energies of solute charge and polarized charge, the interaction energy between them and the 'spring energy' of the solvent polarization. With detailed reasoning and derivation, our formula for non-equilibrium free energy can be reached through different ways. Based on the

Electrolytes: transport properties and non-equilibrium thermodynamics

International Nuclear Information System (INIS)

Miller, D.G.

1980-12-01

This paper presents a review on the application of non-equilibrium thermodynamics to transport in electrolyte solutions, and some recent experimental work and results for mutual diffusion in electrolyte solutions

Black hole evaporation in a heat bath as a nonequilibrium process and its final fate

International Nuclear Information System (INIS)

Saida, Hiromi

2007-01-01

We consider a black hole in a heat bath, and the whole system which consists of the black hole and the heat bath is isolated from outside environments. When the black hole evaporates, the Hawking radiation causes an energy flow from the black hole to the heat bath. Therefore, since no energy flow arises in an equilibrium state, the thermodynamic state of the whole system is not in equilibrium. That is, in a region around the black hole, the matter field of Hawking radiation and that of heat bath should be in a nonequilibrium state due to the energy flow. Using a simple model which reflects the nonequilibrium nature of energy flow, we find the nonequilibrium effect on a black hole evaporation as follows: if the nonequilibrium region around a black hole is not so large, the evaporation time scale of a black hole in a heat bath becomes longer than that in an empty space (a situation without heat bath), because of the incoming energy flow from the heat bath to the black hole. However, if the nonequilibrium region around a black hole is sufficiently large, the evaporation time scale in a heat bath becomes shorter than that in an empty space, because a nonequilibrium effect of the temperature difference between the black hole and heat bath appears as a strong energy extraction from the black hole by the heat bath. Further, a specific nonequilibrium phenomenon is found: a quasi-equilibrium evaporation stage under the nonequilibrium effect proceeds abruptly to a quantum evaporation stage at a semi-classical level (at black hole radius R g > Planck length) within a very short time scale with a strong burst of energy. (Contrarily, when the nonequilibrium effect is not taken into account, a quasi-equilibrium stage proceeds smoothly to a quantum stage at R g < Planck length without so strong an energy burst.) That is, the nonequilibrium effect of energy flow tends to make a black hole evaporation process more dynamical and to accelerate that process. Finally, on the final fate

Phase transitions, nonequilibrium dynamics, and critical behavior of strongly interacting systems

International Nuclear Information System (INIS)

Mottola, E.; Bhattacharya, T.; Cooper, F.

1998-01-01

This is the final report of a three-year, Laboratory Directed Research and Development project at Los Alamos National Laboratory. In this effort, large-scale simulations of strongly interacting systems were performed and a variety of approaches to the nonequilibrium dynamics of phase transitions and critical behavior were investigated. Focus areas included (1) the finite-temperature quantum chromodynamics phase transition and nonequilibrium dynamics of a new phase of matter (the quark-gluon plasma) above the critical temperature, (2) nonequilibrium dynamics of a quantum fields using mean field theory, and (3) stochastic classical field theoretic models with applications to spinodal decomposition and structural phase transitions in a variety of systems, such as spin chains and shape memory alloys

Phase transitions, nonequilibrium dynamics, and critical behavior of strongly interacting systems

Energy Technology Data Exchange (ETDEWEB)

Mottola, E.; Bhattacharya, T.; Cooper, F. [and others

1998-12-31

This is the final report of a three-year, Laboratory Directed Research and Development project at Los Alamos National Laboratory. In this effort, large-scale simulations of strongly interacting systems were performed and a variety of approaches to the nonequilibrium dynamics of phase transitions and critical behavior were investigated. Focus areas included (1) the finite-temperature quantum chromodynamics phase transition and nonequilibrium dynamics of a new phase of matter (the quark-gluon plasma) above the critical temperature, (2) nonequilibrium dynamics of a quantum fields using mean field theory, and (3) stochastic classical field theoretic models with applications to spinodal decomposition and structural phase transitions in a variety of systems, such as spin chains and shape memory alloys.

Generators of nonequilibrium low-temperature plasma

International Nuclear Information System (INIS)

Dautov, G.Yu.

1988-01-01

Results are described of a study and of the characteristics of sources of a non-equilibrium gas-discharge plasma. The plasma generators considered include glow, high frequency, and arc discharge generators. Thermodynamic, ionic, and electronic processes occurring in the plasmas are evaluated

Non-equilibrium mean-field theories on scale-free networks

International Nuclear Information System (INIS)

Caccioli, Fabio; Dall'Asta, Luca

2009-01-01

Many non-equilibrium processes on scale-free networks present anomalous critical behavior that is not explained by standard mean-field theories. We propose a systematic method to derive stochastic equations for mean-field order parameters that implicitly account for the degree heterogeneity. The method is used to correctly predict the dynamical critical behavior of some binary spin models and reaction–diffusion processes. The validity of our non-equilibrium theory is further supported by showing its relation with the generalized Landau theory of equilibrium critical phenomena on networks

Structural, vibrational and theoretical studies of anilinium trichloroacetate: New hydrogen bonded molecular crystal with nonlinear optical properties

Science.gov (United States)

Tanak, H.; Pawlus, K.; Marchewka, M. K.; Pietraszko, A.

2014-01-01

In this work, we report a combined experimental and theoretical study on molecular structure, vibrational spectra and NBO analysis of the potential nonlinear optical (NLO) material anilinium trichloroacetate. The FT-IR and FT-Raman spectra of the compound have been recorded together between 4000-80 cm-1 and 3600-80 cm-1 regions, respectively. The compound crystallizes in the noncentrosymmetric space group of monoclinic system. The optimized molecular structure, vibrational wavenumbers, IR intensities and Raman activities have been calculated by using density functional method (B3LYP) with 6-311++G(d,p) as higher basis set. The obtained vibrational wavenumbers and optimized geometric parameters were seen to be in good agreement with the experimental data. DSC measurements on powder samples do not indicate clearly on the occurrence of phase transitions in the temperature 113-293 K. The Kurtz and Perry powder reflection technique appeared to be very effective in studies of second-order nonlinear optical properties of the molecule. The non-linear optical properties are also addressed theoretically. The predicted NLO properties of the title compound are much greater than ones of urea. In addition, DFT calculations of the title compound, molecular electrostatic potential, frontier orbitals and thermodynamic properties were also performed at 6-311++G(d,p) level of theory. For title crystal the SHG efficiency was estimated by Kurtz-Perry method to be deff = 0.70 deff (KDP).

GaN Schottky diodes with single-crystal aluminum barriers grown by plasma-assisted molecular beam epitaxy

Energy Technology Data Exchange (ETDEWEB)

Tseng, H. Y.; Yang, W. C.; Lee, P. Y.; Lin, C. W.; Cheng, Kai-Yuan; Hsieh, K. C.; Cheng, K. Y., E-mail: kycheng@ee.nthu.edu.tw [Department of Electrical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan (China); Hsu, C.-H. [Division of Scientific Research, National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan (China)

2016-08-22

GaN-based Schottky barrier diodes (SBDs) with single-crystal Al barriers grown by plasma-assisted molecular beam epitaxy are fabricated. Examined using in-situ reflection high-energy electron diffractions, ex-situ high-resolution x-ray diffractions, and high-resolution transmission electron microscopy, it is determined that epitaxial Al grows with its [111] axis coincident with the [0001] axis of the GaN substrate without rotation. In fabricated SBDs, a 0.2 V barrier height enhancement and 2 orders of magnitude reduction in leakage current are observed in single crystal Al/GaN SBDs compared to conventional thermal deposited Al/GaN SBDs. The strain induced piezoelectric field is determined to be the major source of the observed device performance enhancements.

Effect of Chain Conformation on the Single-Molecule Melting Force in Polymer Single Crystals: Steered Molecular Dynamics Simulations Study.

Science.gov (United States)

Feng, Wei; Wang, Zhigang; Zhang, Wenke

2017-02-28

Understanding the relationship between polymer chain conformation as well as the chain composition within the single crystal and the mechanical properties of the corresponding single polymer chain will facilitate the rational design of high performance polymer materials. Here three model systems of polymer single crystals, namely poly(ethylene oxide) (PEO), polyethylene (PE), and nylon-66 (PA66) have been chosen to study the effects of chain conformation, helical (PEO) versus planar zigzag conformation (PE, PA66), and chain composition (PE versus PA66) on the mechanical properties of a single polymer chain. To do that, steered molecular dynamics simulations were performed on those polymer single crystals by pulling individual polymer chains out of the crystals. Our results show that the patterns of force-extension curve as well as the chain moving mode are closely related to the conformation of the polymer chain in the single crystal. In addition, hydrogen bonds can enhance greatly the force required to stretch the polymer chain out of the single crystal. The dynamic breaking and reformation of multivalent hydrogen bonds have been observed for the first time in PA66 at the single molecule level.

Inulin crystal initiation via a glucose-fructose cross-link of adjacent polymer chains: atomic force microscopy and static molecular modelling.

Science.gov (United States)

Cooper, Peter D; Rajapaksha, K Harinda; Barclay, Thomas G; Ginic-Markovic, Milena; Gerson, Andrea R; Petrovsky, Nikolai

2015-03-06

Semi-crystalline microparticles of inulin (MPI) have clinical utility as potent human vaccine adjuvants but their relevant surface structure and crystal assembly remain undefined. We show inulin crystal surfaces to resemble multi-layered, discoid radial spherulites resulting from very rapid formation of complex tertiary structures, implying directed crystal initiation. Physical and in silico molecular modelling of unit cells confirm steric feasibility of initiation by hydrogen-bonded cross-linking of terminal glucose to a fructose of another chain, mimicking bonding in sucrose crystals. A strong, chelate-like dual H-bond is proposed to compel the known antiparallel alignment of inulin chains. Such cross-linking would require one extra fructose per chain in the native inulin crystal, as observed. Completion of five H-bonded internal ring-domains would 'lock in' each new 6-fructose structural unit of each antiparallel helix pair to create a new isoform. All known properties of inulin isoforms follow readily from these concepts. Copyright © 2014 Elsevier Ltd. All rights reserved.

Variation in the defect structure of p-CdTe single crystals at the passage of the laser shock wave

International Nuclear Information System (INIS)

Baidullaeva, A.; Vlasenko, A.I.; Gorkovenko, B.L.; Lomovtsev, A.V.; Mozol', P.E.

2000-01-01

Variations in the minority-carrier lifetime, photoluminescence spectra, dark current and photocurrent temperature dependences of high-resistivity p-CdTe crystals under the action of the laser shock wave are investigated. It is shown that the variations in the aforementioned characteristics during the passage of the shock wave are defined by the generation of the nonequilibrium carriers from deep centers, and, after that, the variations are defined by the formation of intrinsic defects and their subsequent interaction with the defects existing in the initial crystals

Coherent application of a contact structure to formulate Classical Non-Equilibrium Thermodynamics

NARCIS (Netherlands)

Knobbe, E; Roekaerts, D.J.E.M.

2017-01-01

This contribution presents an outline of a new mathematical formulation for
Classical Non-Equilibrium Thermodynamics (CNET) based on a contact
structure in differential geometry. First a non-equilibrium state space is introduced as the third key element besides the first and second law of

Non-equilibrium properties of Josephson critical current in Nb-based three terminal superconducting tunnel devices

International Nuclear Information System (INIS)

Ammendola, G.; Parlato, L.; Peluso, G.; Pepe, G.

1998-01-01

Tunnel quasi-particle injection into a superconducting film provides useful information on the non-equilibrium state inside the perturbed superconductor as well as on the potential application to electronic devices. Three terminal injector-detector superconducting devices have a long history in non-equilibrium superconductivity. In the recent past non-equilibrium phenomena have attracted again considerable attention because of many superconducting based detectors involve processes substantially non-equilibrium in nature. The possibility of using a stacked double tunnel junction to study the influence of non-equilibrium superconductivity on the Josephson critical current is now considered. An experimental study of the effect of quasi-particle injection on the Josephson current both in steady-state and pulsed experiments down to T=1.2 K is presented using 3 terminal Nb-based stacked double tunnel devices. The feasibility of a new class of particle detectors based on the direct measurement of the change in the Josephson current following the absorption of a X-ray quantum is also discussed in terms of non-equilibrium theories. (orig.)

Molecular Dynamics Study on Nucleation Behavior and Lamellar Mergence of Polyethylene Globule Crystallization

Science.gov (United States)

Yang, Xiaozhen; Wang, Simiao

2012-02-01

The site order parameter (SOP) has been adopted to analyze various order structure formation and distribution during the crystallization of a multi-chain polyethylene globule simulated by molecular dynamics. We found that the nucleation relies on crystallinity fluctuation with increase of amplitude, and the baby nucleus in the fluctuation suddenly appears with different shape and increasing size. In the growth stage, a number of lamellar mergence was observed and their selective behaviors were suggested to be related to the orientation difference between the merging lamellae. We obtained that SOP distribution of all atoms in the system during crystallization appears with two peaks: one for the amorphous phase and the other for the crystalline phase. Mesomorphic structures with medium orders locate between the two peaks as an order promotion pathway. Obtained data show that the medium order structure fluctuates at the growth front and does not always be available; the medium order structure existing at the front is not always good for developing. It is possibly caused by chain entanglement.

Numerical fluid dynamics calculations of nonequilibrium steam-water flows with entrained droplets

International Nuclear Information System (INIS)

Williams, K.A.

1984-01-01

The present work has developed a computational fluid dynamics formulation that efficiently solves the conservation laws for a vapor field, a continuous liquid field, and two dispersed droplet fields. The thermal-hydraulic effects resulting from the exchange of mass, momentum and energy between the vapor and the dispersed droplet phases has been accurately modeled. This work is an advancement of the state-of-the-art for engineering analyses of nonequilibrium steam-water-droplet flows in heated channels. It is particularly applicable for boiling steam-water flows in which it is important to represent the effects of significant thermal nonequilibrium between the vapor and the liquid phases. This work was shown to be in good agreement with unique experimental measurements of significant thermal nonequilibrium between the vapor and dispersed droplets. The tests analyzed covered a range of mass fluxes and wall heating rates, and were all at low pressures where nonequilibrium effects are most pronounced

Non-equilibrium dynamics of 2D liquid crystals driven by transmembrane gas flow.

Science.gov (United States)

Seki, Kazuyoshi; Ueda, Ken; Okumura, Yu-ichi; Tabe, Yuka

2011-07-20

Free-standing films composed of several layers of chiral smectic liquid crystals (SmC*) exhibited unidirectional director precession under various vapor transfers across the films. When the transferred vapors were general organic solvents, the precession speed linearly depended on the momentum of the transmembrane vapors, where the proportional constant was independent of the kind of vapor. In contrast, the same SmC* films under water transfer exhibited precession in the opposite direction. As a possible reason for the rotational inversion, we suggest the competition of two origins for the torques, one of which is microscopic and the other macroscopic. Next, we tried to move an external object by making use of the liquid crystal (LC) motion. When a solid or a liquid particle was set on a film under vapor transfer, the particle was rotated in the same direction as the LC molecules. Using home-made laser tweezers, we measured the force transmitted from the film to the particle, which we found to be several pN.

Forces and energy dissipation in inhomogeneous non-equilibrium superconductors

International Nuclear Information System (INIS)

Poluehktov, Yu.M.; Slezov, V.V.

1987-01-01

The phenomenological theory of volume forces and dissipation processes in inhomogeneous non-equilibrium superconductors near temperature transition from the normal to superconducting state is constructed. The approach is based on application of dynamic equations of superconductivity formulated on the basis of the Lagrangian formalism. These equations are generalized the Ginzburg-Landau theory in the nonstationary non-equilibrium case for ''foul'' superconductors. The value estimations of volume forces arising in inhomogeneities during relaxation of an order parameter and when the electrical field is penetrated into the superconductor, are given

Crystal structure and vibrational spectra of piperazinium bis(4-hydroxybenzenesulphonate) molecular-ionic crystal

Science.gov (United States)

Marchewka, M. K.; Pietraszko, A.

2008-02-01

The piperazinium bis(4-hydroxybenzenesulphonate) crystallizes from water solution at room temperature in P2 1/ c space group of monoclinic system. The crystals are built up of doubly protonated piperazinium cations and ionized 4-hydroxybenzenesulphonate anions that interact through weak hydrogen bonds of O-H⋯O and N-H⋯O type. Mutual orientation of anions is determined by non-conventional hydrogen bonds of C-H⋯π type. Room temperature powder FT IR and FT Raman measurements were carried out. The vibrational spectra are in full agreement with the structure obtained from X-ray crystallography. The big single crystals of the title salt can be grown.

Crystal and Molecular Structure of Bis(2,2-diphenyl-N-(di-n-propylcarbamothioyl acetamidocopper(II Complex

Directory of Open Access Journals (Sweden)

Hakan Arslan

2011-01-01

Full Text Available Bis(2,2-diphenyl-N-(di-n-propylcarbamothioyl acetamidocopper(II complex has been synthesized and characterized by elemental analysis and FT-IR spectroscopy. The crystal and molecular structure of the title compound has been determined from single crystal X-ray diffraction data. It crystallizes in the triclinic space group P-1, with a = 13.046(2 Å, b = 13.135(2 Å, c = 13.179(2 Å, α= 67.083(4°, β= 67.968(4°, γ = 84.756(4° and Dcalc =1.330 g/cm3 for Z = 2. The crystal structure confirms that the complex is a mononuclear copper(II complex and the 2,2-diphenyl-N-(di-n-propyl-carbamothioylacetamide ligand is a bidentate chelating ligand, coordinating to the copper atom through the thiocarbonyl and carbonyl groups. This coordination has a slightly distorted square-planar geometry (O1-Cu1-O2: 86.48(11°, O1-Cu1-S1: 93.85(9°, O2-Cu1-S2: 94.20(9° and S1-Cu1-S2: 91.21(4°. The title molecule shows a cis-arrangement and C–O, C–S and C–N bond lengths of the complex suggest considerable electronic delocalization in the chelate rings.

Transition voltages of vacuum-spaced and molecular junctions with Ag and Pt electrodes

KAUST Repository

Wu, Kunlin; Bai, Meilin; Sanvito, Stefano; Hou, Shimin

2014-01-01

The transition voltage of vacuum-spaced and molecular junctions constructed with Ag and Pt electrodes is investigated by non-equilibrium Green's function formalism combined with density functional theory. Our calculations show that, similarly

Crystallization and preliminary characterization of three different crystal forms of human saposin C heterologously expressed in Pichia pastoris

International Nuclear Information System (INIS)

Schultz-Heienbrok, Robert; Remmel, Natascha; Klingenstein, R.; Rossocha, Maksim; Sandhoff, Konrad; Saenger, Wolfram; Maier, Timm

2006-01-01

Three different crystal forms were obtained of human saposin C. The structures could not be determined by molecular replacement using known solution structures of the protein as search models, supporting the notion of a highly flexible protein. The amphiphilic saposin proteins (A, B, C and D) act at the lipid–water interface in lysosomes, mediating the hydrolysis of membrane building blocks by water-soluble exohydrolases. Human saposin C activates glucocerebrosidase and β-galactosylceramidase. The protein has been expressed in Pichia pastoris, purified and crystallized in three different crystal forms, diffracting to a maximum resolution of 2.5 Å. Hexagonal crystals grew from 2-propanol-containing solution and contain a single molecule in the asymmetric unit according to the Matthews coefficient. Orthorhombic and tetragonal crystals were both obtained with pentaerythritol ethoxylate and are predicted to contain two molecules in the asymmetric unit. Attempts to determine the respective crystal structures by molecular replacement using either the known NMR structure of human saposin C or a related crystal structure as search models have so far failed. The failure of the molecular-replacement method is attributed to conformational changes of the protein, which are known to be required for its biological activity. Crystal structures of human saposin C therefore might be the key to mapping out the conformational trajectory of saposin-like proteins

Phase transitions in nonequilibrium traffic theory

Energy Technology Data Exchange (ETDEWEB)

Zhang, H.M.

2000-02-01

This paper uses the center difference scheme of Lax-Friedrichs to numerically solve a newly developed continuum traffic flow theory and the kinematic theory of Lighthill and Whitham, and Richards, and it studies the flow-concentration phase transitions in flow containing both shock and rarefaction waves. A homogeneous road with finite length was modeled by both theories. Numerical simulations show that both theories yield nearly identical results for two representative Riemann problems--one has a shock solution and the other a rarefaction wave solution. Their phase transition curves, however, are different: those derived from the new theory have two branches--one for acceleration flow and one for deceleration flow, whereas those derived from the LWR theory comprise a single curve--the equilibrium curve. The phase transition curves in the shock case agree well with certain experimental observations but disagree with others. This disagreement may be resolved by studying transitions among nonequilibrium states, which awaits further development of a more accurate finite difference approximation of the nonequilibrium theory.

Nonequilibrium thermodynamic models and applications to hydrogen plasma

International Nuclear Information System (INIS)

Cho, K.Y.

1988-01-01

A generalized multithermal equilibrium (GMTE) thermodynamic model is developed and presented with applications to hydrogen. A new chemical equilibrium equation for GMTE is obtained without the ensemble temperature concept, used by a previous MTE model. The effects of the GMTE model on the derivation and calculation of the thermodynamic, transport, and radiative properties are presented and significant differences from local thermal equilibrium (LTE) and two temperature model are discussed. When the electron translational temperature (T e ) is higher than the translational temperature of the heavy particles, the effects of hydrogen molecular species to the properties are significant at high T e compared with LTE results. The density variations of minor species are orders of magnitude with kinetic nonequilibrium at a constant electron temperature. A collisional-radiative model is also developed with the GMTE chemical equilibrium equation to study the effects of radiative transfer and the ambipolar diffusion on the population distribution of the excited atoms. The nonlocal radiative transfer effect is parameterized by an absorption factor, which is defined as a ratio of the absorbed intensity to the spontaneous emission coefficient

Non-equilibrium thermodynamical description of rhythmic motion patterns of active systems: a canonical-dissipative approach.

Science.gov (United States)

Dotov, D G; Kim, S; Frank, T D

2015-02-01

We derive explicit expressions for the non-equilibrium thermodynamical variables of a canonical-dissipative limit cycle oscillator describing rhythmic motion patterns of active systems. These variables are statistical entropy, non-equilibrium internal energy, and non-equilibrium free energy. In particular, the expression for the non-equilibrium free energy is derived as a function of a suitable control parameter. The control parameter determines the Hopf bifurcation point of the deterministic active system and describes the effective pumping of the oscillator. In analogy to the equilibrium free energy of the Landau theory, it is shown that the non-equilibrium free energy decays as a function of the control parameter. In doing so, a similarity between certain equilibrium and non-equilibrium phase transitions is pointed out. Data from an experiment on human rhythmic movements is presented. Estimates for pumping intensity as well as the thermodynamical variables are reported. It is shown that in the experiment the non-equilibrium free energy decayed when pumping intensity was increased, which is consistent with the theory. Moreover, pumping intensities close to zero could be observed at relatively slow intended rhythmic movements. In view of the Hopf bifurcation underlying the limit cycle oscillator model, this observation suggests that the intended limit cycle movements were actually more similar to trajectories of a randomly perturbed stable focus. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Non-Equilibrium Thermodynamic Chemistry and the Composition of the Atmosphere of Mars

Science.gov (United States)

Levine, J. S.; Summers, M. E.

2003-01-01

A high priority objective of the Mars Exploration Program is to Determine if life exists today (MEPAG Goal I, Objective A). The measurement of gases of biogenic origin may be an approach to detect the presence of microbial life on the surface or subsurface of Mars. Chemical thermodynamic calculations indicate that on both Earth and Mars, certain gases should exist in extremely low concentrations, if at all. Microbial metabolic activity is an important non-equilibrium chemistry process on Earth, and if microbial life exists on Mars, may be an important nonequilibrium chemistry process on Mars. The non-equilibrium chemistry of the atmosphere of Mars is discussed in this paper.

Demonstration of Hybrid DSMC-CFD Capability for Nonequilibrium Reacting Flow

Science.gov (United States)

2018-02-09

AFRL-RV-PS- TR-2018-0056 AFRL-RV-PS- TR-2018-0056 DEMONSTRATION OF HYBRID DSMC-CFD CAPABILITY FOR NONEQUILIBRIUM REACTING FLOW Thomas E...4. TITLE AND SUBTITLE Demonstration of Hybrid DSMC-CFD Capability for Nonequilibrium Reacting Flow 5a. CONTRACT NUMBER 5b. GRANT NUMBER FA9453-17-1...simulation codes. The models are based on new ab-intio rate data obtained using state -of-the-art potential energy surfaces for air species. A probability

Nonequilibrium candidate Monte Carlo is an efficient tool for equilibrium simulation

Energy Technology Data Exchange (ETDEWEB)

Nilmeier, J. P.; Crooks, G. E.; Minh, D. D. L.; Chodera, J. D.

2011-10-24

Metropolis Monte Carlo simulation is a powerful tool for studying the equilibrium properties of matter. In complex condensed-phase systems, however, it is difficult to design Monte Carlo moves with high acceptance probabilities that also rapidly sample uncorrelated configurations. Here, we introduce a new class of moves based on nonequilibrium dynamics: candidate configurations are generated through a finite-time process in which a system is actively driven out of equilibrium, and accepted with criteria that preserve the equilibrium distribution. The acceptance rule is similar to the Metropolis acceptance probability, but related to the nonequilibrium work rather than the instantaneous energy difference. Our method is applicable to sampling from both a single thermodynamic state or a mixture of thermodynamic states, and allows both coordinates and thermodynamic parameters to be driven in nonequilibrium proposals. While generating finite-time switching trajectories incurs an additional cost, driving some degrees of freedom while allowing others to evolve naturally can lead to large enhancements in acceptance probabilities, greatly reducing structural correlation times. Using nonequilibrium driven processes vastly expands the repertoire of useful Monte Carlo proposals in simulations of dense solvated systems.

Replacing leads by self-energies using non-equilibrium Green's functions

International Nuclear Information System (INIS)

Michael, Fredrick; Johnson, M.D.

2003-01-01

Open quantum systems consist of semi-infinite leads which transport electrons to and from the device of interest. We show here that within the non-equilibrium Green's function technique for continuum systems, the leads can be replaced by simple c-number self-energies. Our starting point is an approach for continuum systems developed by Feuchtwang. The reformulation developed here is simpler to understand and carry out than the somewhat unwieldly manipulations typical in the Feuchtwang method. The self-energies turn out to have a limited variability: the retarded self-energy Σ r depends on the arbitrary choice of internal boundary conditions, but the non-equilibrium self-energy or scattering function Σ which determines transport is invariant for a broad class of boundary conditions. Expressed in terms of these self-energies, continuum non-equilibrium transport calculations take a particularly simple form similar to that developed for discrete systems

Analysis of non-equilibrium phenomena in inductively coupled plasma generators

Energy Technology Data Exchange (ETDEWEB)

Zhang, W.; Panesi, M., E-mail: mpanesi@illinois.edu [University of Illinois at Urbana-Champaign, Urbana, Illinois 61822 (United States); Lani, A. [Von Karman Institute for Fluid Dynamics, Rhode-Saint-Genèse (Belgium)

2016-07-15

This work addresses the modeling of non-equilibrium phenomena in inductively coupled plasma discharges. In the proposed computational model, the electromagnetic induction equation is solved together with the set of Navier-Stokes equations in order to compute the electromagnetic and flow fields, accounting for their mutual interaction. Semi-classical statistical thermodynamics is used to determine the plasma thermodynamic properties, while transport properties are obtained from kinetic principles, with the method of Chapman and Enskog. Particle ambipolar diffusive fluxes are found by solving the Stefan-Maxwell equations with a simple iterative method. Two physico-mathematical formulations are used to model the chemical reaction processes: (1) A Local Thermodynamics Equilibrium (LTE) formulation and (2) a thermo-chemical non-equilibrium (TCNEQ) formulation. In the TCNEQ model, thermal non-equilibrium between the translational energy mode of the gas and the vibrational energy mode of individual molecules is accounted for. The electronic states of the chemical species are assumed in equilibrium with the vibrational temperature, whereas the rotational energy mode is assumed to be equilibrated with translation. Three different physical models are used to account for the coupling of chemistry and energy transfer processes. Numerical simulations obtained with the LTE and TCNEQ formulations are used to characterize the extent of non-equilibrium of the flow inside the Plasmatron facility at the von Karman Institute. Each model was tested using different kinetic mechanisms to assess the sensitivity of the results to variations in the reaction parameters. A comparison of temperatures and composition profiles at the outlet of the torch demonstrates that the flow is in non-equilibrium for operating conditions characterized by pressures below 30 000 Pa, frequency 0.37 MHz, input power 80 kW, and mass flow 8 g/s.

Post-CHF heat transfer: a non-equilibrium, relaxation model

International Nuclear Information System (INIS)

Jones, O.C. Jr.; Zuber, N.

1977-01-01

Existing phenomenological models of heat transfer in the non-equilibrium, liquid-deficient, dispersed flow regime can sometimes predict the thermal behavior fairly well but are quite complex, requiring coupled simultaneous differential equations to describe the axial gradients of mass and energy along with those of droplet acceleration and size. In addition, empirical relations are required to express the droplet breakup and increased effective heat transfer due to holdup. This report describes the development of a different approach to the problem. It is shown that the non-equilibrium component of the total energy can be expressed as a first order, inhomogeneous relaxation equation in terms of one variable coefficient termed the Superheat Relaxation number. A demonstration is provided to show that this relaxation number can be correlated using local variables in such a manner to allow the single non-equilibrium equation to accurately calculate the effects of mass velocity and heat flux along with tube length, diameter, and critical quality for equilibrium qualities from 0.13 to over 3.0

NON-EQUILIBRIUM HELIUM IONIZATION IN AN MHD SIMULATION OF THE SOLAR ATMOSPHERE

International Nuclear Information System (INIS)

Golding, Thomas Peter; Carlsson, Mats; Leenaarts, Jorrit

2016-01-01

The ionization state of the gas in the dynamic solar chromosphere can depart strongly from the instantaneous statistical equilibrium commonly assumed in numerical modeling. We improve on earlier simulations of the solar atmosphere that only included non-equilibrium hydrogen ionization by performing a 2D radiation-magnetohydrodynamics simulation featuring non-equilibrium ionization of both hydrogen and helium. The simulation includes the effect of hydrogen Lyα and the EUV radiation from the corona on the ionization and heating of the atmosphere. Details on code implementation are given. We obtain helium ion fractions that are far from their equilibrium values. Comparison with models with local thermodynamic equilibrium (LTE) ionization shows that non-equilibrium helium ionization leads to higher temperatures in wavefronts and lower temperatures in the gas between shocks. Assuming LTE ionization results in a thermostat-like behavior with matter accumulating around the temperatures where the LTE ionization fractions change rapidly. Comparison of DEM curves computed from our models shows that non-equilibrium ionization leads to more radiating material in the temperature range 11–18 kK, compared to models with LTE helium ionization. We conclude that non-equilibrium helium ionization is important for the dynamics and thermal structure of the upper chromosphere and transition region. It might also help resolve the problem that intensities of chromospheric lines computed from current models are smaller than those observed

Ionization Energies, Electron Affinities, and Polarization Energies of Organic Molecular Crystals: Quantitative Estimations from a Polarizable Continuum Model (PCM)–Tuned Range-Separated Density Functional Approach

KAUST Repository

Sun, Haitao

2016-05-16

We propose a new methodology for the first-principles description of the electronic properties relevant for charge transport in organic molecular crystals. This methodology, which is based on the combination of a non-empirical, optimally tuned range-separated hybrid functional with the polarizable continuum model, is applied to a series of eight representative molecular semiconductor crystals. We show that it provides ionization energies, electron affinities, and transport gaps in very good agreement with experimental values as well as with the results of many-body perturbation theory within the GW approximation at a fraction of the computational costs. Hence, this approach represents an easily applicable and computationally efficient tool to estimate the gas-to-crystal-phase shifts of the frontier-orbital quasiparticle energies in organic electronic materials.

Laser synthesis of a copper–single-walled carbon nanotube nanocomposite via molecular-level mixing and non-equilibrium solidification

International Nuclear Information System (INIS)

Tu, Jay F; Rajule, Nilesh; Molian, Pal; Liu, Yi

2016-01-01

A copper–single-walled carbon nanotube (Cu–SWCNT) metal nanocomposite could be an ideal material if it can substantially improve the strength of copper while preserving the metal’s excellent thermal and electrical properties. However, synthesis of such a nanocomposite is highly challenging, because copper and SWCNTs do not form intermetallic compounds and are insoluble; as a result, there are serious issues regarding wettability and fine dispersion of SWCNTs within the copper matrix. In this paper we present a novel wet process, called the laser surface implantation process (LSI), to synthesize Cu–SWCNT nanocomposites by mixing SWCNTs into molten copper. The LSI process includes drilling several microholes on a copper substrate, filling the microholes with SWCNTs suspended in solution, and melting the copper substrate to create a micro-well of molten copper. The molten copper advances radially outward to engulf the microholes with pre-deposited SWCNTs to form the Cu–SWCNT implant upon solidification. Rapid and non-equilibrium solidification is achieved due to copper’s excellent heat conductivity, so that SWCNTs are locked in position within the copper matrix without agglomerating into large clusters. This wet process is very different from the typical dry processes used in powder metallurgy. Very high hardness improvement, up to 527% over pure copper, was achieved, confirmed by micro-indentation tests, with only a 0.23% SWCNT volume fraction. The nanostructure of the nanocomposite was characterized by TEM imaging, energy-dispersive x-ray spectroscopy mapping and spectroscopy measurements. The SWCNTs were found to be finely dispersed within the copper matrix with cluster sizes in the range of nanometers, achieving the goal of molecular-level mixing. (paper)

Crystallization and preliminary X-ray characterization of a thermostable low-molecular-weight 1,4-β-d-glucan glucohydrolase from an alkalothermophilic Thermomonospora sp

Energy Technology Data Exchange (ETDEWEB)

Manikandan, K. [Department of Physics, Indian Institute of Science, Bangalore 560 012 (India); Jagtap, S.; Rao, M. [Division of Biochemical Sciences, National Chemical Laboratory, Pune 411 008 (India); Ramakumar, S., E-mail: ramak@physics.iisc.ernet.in [Department of Physics, Indian Institute of Science, Bangalore 560 012 (India); Bioinformatics Centre, Indian Institute of Science, Bangalore 560 012 (India)

2006-04-01

A low-molecular-weight cellulase from an alkalothermophilic Thermomonospora sp. has been crystallized. A diffraction data set has been collected to 2.3 Å resolution. Cellulases catalyze the hydrolysis of β-1,4-glycosidic linkages within cellulose, the most abundant organic polymer on earth. The cellulase (TSC; EC 3.2.1.4) from an alkalothermophilic Thermomonospora sp. has a low molecular weight of 14.2 kDa. It is optimally active at 323 K and stable over the wide pH range of 5–9. Moreover, it has bifunctional activity against cellulose and xylan polymers. In this study, TSC was purified from the native source and crystallized by the hanging-drop vapour-diffusion method. The crystals belong to the orthorhombic space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 49.9, b = 79.5, c = 99.7 Å, and diffract to better than 2.3 Å resolution.

Crystallization and preliminary X-ray characterization of a thermostable low-molecular-weight 1,4-β-d-glucan glucohydrolase from an alkalothermophilic Thermomonospora sp

International Nuclear Information System (INIS)

Manikandan, K.; Jagtap, S.; Rao, M.; Ramakumar, S.

2006-01-01

A low-molecular-weight cellulase from an alkalothermophilic Thermomonospora sp. has been crystallized. A diffraction data set has been collected to 2.3 Å resolution. Cellulases catalyze the hydrolysis of β-1,4-glycosidic linkages within cellulose, the most abundant organic polymer on earth. The cellulase (TSC; EC 3.2.1.4) from an alkalothermophilic Thermomonospora sp. has a low molecular weight of 14.2 kDa. It is optimally active at 323 K and stable over the wide pH range of 5–9. Moreover, it has bifunctional activity against cellulose and xylan polymers. In this study, TSC was purified from the native source and crystallized by the hanging-drop vapour-diffusion method. The crystals belong to the orthorhombic space group P2 1 2 1 2 1 , with unit-cell parameters a = 49.9, b = 79.5, c = 99.7 Å, and diffract to better than 2.3 Å resolution

Non-equilibrium plasma reactor for natrual gas processing

International Nuclear Information System (INIS)

Shair, F.H.; Ravimohan, A.L.

1974-01-01

A non-equilibrium plasma reactor for natural gas processing into ethane and ethylene comprising means of producing a non-equilibrium chemical plasma wherein selective conversion of the methane in natural gas to desired products of ethane and ethylene at a pre-determined ethane/ethylene ratio in the chemical process may be intimately controlled and optimized at a high electrical power efficiency rate by mixing with a recycling gas inert to the chemical process such as argon, helium, or hydrogen, reducing the residence time of the methane in the chemical plasma, selecting the gas pressure in the chemical plasma from a wide range of pressures, and utilizing pulsed electrical discharge producing the chemical plasma. (author)

Redistribution of erbium during the crystallization of buried amorphous silicon layers

International Nuclear Information System (INIS)

Aleksandrov, O.V.; Nikolaev, Yu.A.; Sobolev, N.A.; Sakharov, V.I.; Serenkov, I.T.; Kudryavtsev, Yu.A.

1999-01-01

The redistribution of Er during its implantation in silicon at doses close to the amorphization threshold and its subsequent solid-phase epitaxial (SPE) crystallization is investigated. The formation of a buried amorphous (a) layer is discovered at Er doses equal to 5x10 13 and 1x10 14 cm -2 using Rutherford backscattering. The segregation of Er in this case takes place inwardly from the two directions corresponding to the upper and lower boundaries of the buried αlayer and leads to the formation of a concentration peak at the meeting place of the two crystallization fronts. A method for calculating the coordinate dependence of the segregation coefficient k from the distribution profiles of the erbium impurity before and after annealing is proposed. The k(x) curve exhibits a drop, whose width increases with decreasing Er implantation dose. Its appearance is attributed to the nonequilibrium nature of the segregation process at the beginning of SPE crystallization

Nonequilibrium molecular dynamics study of ring polymer melts under shear and elongation flows: A comparison with their linear analogs

Energy Technology Data Exchange (ETDEWEB)

Yoon, Jeongha; Kim, Jinseong; Baig, Chunggi, E-mail: cbaig@unist.ac.kr [Department of Chemical Engineering, School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 689-798 (Korea, Republic of)

2016-07-15

We present detailed results for the structural and rheological properties of unknotted and unconcatenated ring polyethylene (PE) melts under shear and elongation flows via direct atomistic nonequilibrium molecular dynamics simulations. Short (C{sub 78}H{sub 156}) and long (C{sub 400}H{sub 800}) ring PE melts were subjected to planar Couette flow (PCF) and planar elongational flow (PEF) across a wide range of strain rates from linear to highly nonlinear flow regimes. The results are analyzed in detail through a direct comparison with those of the corresponding linear polymers. We found that, in comparison to their linear analogs, ring melts possess rather compact chain structures at or near the equilibrium state and exhibit a considerably lesser degree of structural deformation with respect to the applied flow strength under both PCF and PEF. The large structural resistance of ring polymers against an external flow field is attributed to the intrinsic closed-loop configuration of the ring and the topological constraint of nonconcatenation between ring chains in the melt. As a result, there appears to be a substantial discrepancy between ring and linear systems in terms of their structural and rheological properties such as chain orientation, the distribution of chain dimensions, viscosity, flow birefringence, hydrostatic pressure, the pair correlation function, and potential interaction energies. The findings and conclusions drawn in this work would be a useful guide in future exploration of the characteristic dynamical and relaxation mechanisms of ring polymers in bulk or confined systems under flowing conditions.

Non-equilibrium versus equilibrium emission of complex fragments from hot nuclei

International Nuclear Information System (INIS)

Viola, V.E.; Kwiatkowski, K.; Yennello, S.; Fields, D.E.

1989-01-01

The relative contributions of equilibrium and non-equilibrium mechanisms for intermediate-mass fragment emission have been deduced for Z=3-14 fragments formed in 3 He- and 14 N-induced reactions on Ag and Au targets. Complete inclusive excitation function measurements have been performed for 3 He projectiles from E/A=67 to 1,200 MeV and for 14 N from E/A=20 to 50 MeV. The data are consistent with a picture in which equilibrated emission is important at the lowest energies, but with increasing bombarding energy the cross sections are increasingly dominated by non-equilibrium processes. Non-equilibrium emission is also shown to be favored for light fragments relative to heavy fragments. These results are supported by coincidence studies of intermediate-mass fragments tagged by linear momentum transfer measurements

Convection with local thermal non-equilibrium and microfluidic effects

CERN Document Server

Straughan, Brian

2015-01-01

This book is one of the first devoted to an account of theories of thermal convection which involve local thermal non-equilibrium effects, including a concentration on microfluidic effects. The text introduces convection with local thermal non-equilibrium effects in extraordinary detail, making it easy for readers newer to the subject area to understand. This book is unique in the fact that it addresses a large number of convection theories and provides many new results which are not available elsewhere. This book will be useful to researchers from engineering, fluid mechanics, and applied mathematics, particularly those interested in microfluidics and porous media.

Crystallization and molecular-replacement studies of the monoclonal antibody mAbR310 specific for the (R)-HNE-modified protein

International Nuclear Information System (INIS)

Ito, Sohei; Tatsuda, Emi; Ishino, Kousuke; Suzuki, Kenichiro; Sakai, Hiroshi; Uchida, Koji

2006-01-01

Antigen-free Fab fragment of mAbR310, which recognizes (R)-HNE modified protein, has been crystallized. Initial phases have been obtained by molecular replacement. 4-Hydroxy-2-nonenal (HNE), a major racemic product of lipid peroxidation, reacts with histidine to form a stable HNE–histidine Michael addition-type adduct possessing three chiral centres in the cyclic hemiacetal structure. Monoclonal antibodies against HNE-modified protein have been widely used for assessing oxidative stress in vitro and in vivo. Here, the purification, crystallization and preliminary crystallographic analysis of a Fab fragment of novel monoclonal antibody R310 (mAbR310), which recognizes (R)-HNE-modified protein, are reported. The Fab fragment of mAbR310 was obtained by digestion with papain, purified and crystallized. Using hanging-drop vapour-diffusion crystallization techniques, crystals of mAbR310 Fab were obtained. The crystal belongs to the monoclinic space group C2 (unit-cell parameters a = 127.04, b = 65.31, c = 64.29 Å, β = 118.88°) and diffracted X-rays to a resolution of 1.84 Å. The asymmetric unit contains one molecule of mAbR310, with a corresponding crystal volume per protein weight of 2.51 Å 3 Da −1 and a solvent content of 51.0%

Non-equilibrium thermodynamics and physical kinetics

CERN Document Server

Bikkin, Halid

2014-01-01

This graduate textbook covers contemporary directions of non-equilibrium statistical mechanics as well as classical methods of kinetics. With one of the main propositions being to avoid terms such as "obviously" and "it is easy to show", this treatise is an easy-to-read introduction into this traditional, yet vibrant field.

Exploring the nonequilibrium dynamics of ultracold quantum gases by using numerical tools

Science.gov (United States)

Heidrich-Meisner, Fabian

Numerical tools such as exact diagonalization or the density matrix renormalization group method have been vital for the study of the nonequilibrium dynamics of strongly correlated many-body systems. Moreover, they provided unique insight for the interpretation of quantum gas experiments, whenever a direct comparison with theory is possible. By considering the example of the experiment by Ronzheimer et al., in which both an interaction quench and the release of bosons from a trap into an empty optical lattice (sudden expansion) was realized, I discuss several nonequilibrium effects of strongly interacting quantum gases. These include the thermalization of a closed quantum system and its connection to the eigenstate thermalization hypothesis, nonequilibrium mass transport, dynamical fermionization, and transient phenomena such as quantum distillation or dynamical quasicondensation. I highlight the role of integrability in giving rise to ballistic transport in strongly interacting 1D systems and in determining the asymptotic state after a quantum quench. The talk concludes with a perspective on open questions concerning 2D systems and the numerical simulation of their nonequilibrium dynamics. Supported by Deutsche Forschungsgemeinschaft (DFG) via FOR 801.

Comparing two non-equilibrium approaches to modelling of a free-burning arc

International Nuclear Information System (INIS)

Baeva, M; Uhrlandt, D; Benilov, M S; Cunha, M D

2013-01-01

Two models of high-pressure arc discharges are compared with each other and with experimental data for an atmospheric-pressure free-burning arc in argon for arc currents of 20–200 A. The models account for space-charge effects and thermal and ionization non-equilibrium in somewhat different ways. One model considers space-charge effects, thermal and ionization non-equilibrium in the near-cathode region and thermal non-equilibrium in the bulk plasma. The other model considers thermal and ionization non-equilibrium in the entire arc plasma and space-charge effects in the near-cathode region. Both models are capable of predicting the arc voltage in fair agreement with experimental data. Differences are observed in the arc attachment to the cathode, which do not strongly affect the near-cathode voltage drop and the total arc voltage for arc currents exceeding 75 A. For lower arc currents the difference is significant but the arc column structure is quite similar and the predicted bulk plasma characteristics are relatively close to each other. (paper)

Generation, detection and spectroscopic studies of high-frequency nonequilibrium phonons in crystals

International Nuclear Information System (INIS)

Dennis, W.M.; Yen, W.M.

2007-01-01

In this article we will review studies conducted in the past two decades on the dynamic properties of high-frequency (THz) phonons generated monochromatically with high power far infrared (FIR) laser pulses using defect-induced phonon absorption and detected using a vibronic sideband spectrometer fashioned after that devised by Kaplyanskii, the honoree of this special issue. The temporal and spectral evolution of the phonon signature provides information on the mechanisms that dominate the relaxation of high-frequency phonons in real crystals

Thermal non-equilibrium in porous medium adjacent to vertical plate: ANN approach

Science.gov (United States)

Ahmed, N. J. Salman; Ahamed, K. S. Nazim; Al-Rashed, Abdullah A. A. A.; Kamangar, Sarfaraz; Athani, Abdulgaphur

2018-05-01

Thermal non-equilibrium in porous medium is a condition that refers to temperature discrepancy in solid matrix and fluid of porous medium. This type of flow is complex flow requiring complex set of partial differential equations that govern the flow behavior. The current work is undertaken to predict the thermal non-equilibrium behavior of porous medium adjacent to vertical plate using artificial neural network. A set of neurons in 3 layers are trained to predict the heat transfer characteristics. It is found that the thermal non-equilibrium heat transfer behavior in terms of Nusselt number of fluid as well as solid phase can be predicted accurately by using well-trained neural network.

The impact of episodic nonequilibrium fracture-matrix flow on geological repository performance

International Nuclear Information System (INIS)

Buscheck, T.A.; Nitao, J.J.; Chestnut, D.A.

1991-01-01

Adequate representation of fracture-matrix interaction during episodic infiltration events is crucial in making valid hydrological predictions of repository performance at Yucca Mountain. Various approximations have been applied to represent fracture-matrix flow interaction, including the Equivalent Continuum Model (ECM), which assumes capillary equilibrium between fractures and matrix, and the Fracture-Matrix Model (FMM), which accounts for nonequilibrium fracture-matrix flow. We analyze the relative impact of matrix imbibition on episodic nonequilibrium fracture-matrix flow for the eight major hydrostratigraphic units in the unsaturated zone at Yucca Mountain. Comparisons are made between ECM and FMM predictions to determine the applicability of the ECM. The implications of nonequilibrium fracture-matrix flow on radionuclide transport are also discussed

Generic finite size scaling for discontinuous nonequilibrium phase transitions into absorbing states

Science.gov (United States)

de Oliveira, M. M.; da Luz, M. G. E.; Fiore, C. E.

2015-12-01

Based on quasistationary distribution ideas, a general finite size scaling theory is proposed for discontinuous nonequilibrium phase transitions into absorbing states. Analogously to the equilibrium case, we show that quantities such as response functions, cumulants, and equal area probability distributions all scale with the volume, thus allowing proper estimates for the thermodynamic limit. To illustrate these results, five very distinct lattice models displaying nonequilibrium transitions—to single and infinitely many absorbing states—are investigated. The innate difficulties in analyzing absorbing phase transitions are circumvented through quasistationary simulation methods. Our findings (allied to numerical studies in the literature) strongly point to a unifying discontinuous phase transition scaling behavior for equilibrium and this important class of nonequilibrium systems.

Modeling, Measurements, and Fundamental Database Development for Nonequilibrium Hypersonic Aerothermodynamics

Science.gov (United States)

Bose, Deepak

2012-01-01

The design of entry vehicles requires predictions of aerothermal environment during the hypersonic phase of their flight trajectories. These predictions are made using computational fluid dynamics (CFD) codes that often rely on physics and chemistry models of nonequilibrium processes. The primary processes of interest are gas phase chemistry, internal energy relaxation, electronic excitation, nonequilibrium emission and absorption of radiation, and gas-surface interaction leading to surface recession and catalytic recombination. NASAs Hypersonics Project is advancing the state-of-the-art in modeling of nonequilibrium phenomena by making detailed spectroscopic measurements in shock tube and arcjets, using ab-initio quantum mechanical techniques develop fundamental chemistry and spectroscopic databases, making fundamental measurements of finite-rate gas surface interactions, implementing of detailed mechanisms in the state-of-the-art CFD codes, The development of new models is based on validation with relevant experiments. We will present the latest developments and a roadmap for the technical areas mentioned above

Picosecond dissociation of amyloid fibrils with infrared laser: A nonequilibrium simulation study

Energy Technology Data Exchange (ETDEWEB)

Hoang Viet, Man; Roland, Christopher, E-mail: cmroland@ncsu.edu; Sagui, Celeste, E-mail: sagui@ncsu.edu [Department of Physics, North Carolina State University, Raleigh, North Carolina 27695-8202 (United States); Derreumaux, Philippe; Nguyen, Phuong H., E-mail: phuong.nguyen@ibpc.fr [Laboratoire de Biochimie Théorique, UPR 9080, CNRS Université Denis Diderot, Sorbonne Paris Cité IBPC, 13 rue Pierre et Marie Curie, 75005 Paris (France); Li, Mai Suan [Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw (Poland); Institute for Computational Science and Technology, SBI Building, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City (Viet Nam)

2015-10-21

Recently, mid-infrared free-electron laser technology has been developed to dissociate amyloid fibrils. Here, we present a theoretical framework for this type of experiment based on laser-induced nonequilibrium all-atom molecular dynamics simulations. We show that the fibril is destroyed due to the strong resonance between its amide I vibrational modes and the laser field. The effects of laser irradiation are determined by a balance between fibril formation and dissociation. While the overall rearrangements of the fibril finish over short time scales, the interaction between the peptides and the solvent continues over much longer times indicating that the waters play an important role in the dissociation process. Our results thus provide new insights into amyloid fibril dissociation by laser techniques and open up new venues to investigate the complex phenomena associated with amyloidogenesis.

Separating NaCl and AlCl3·6H2O Crystals from Acidic Solution Assisted by the Non-Equilibrium Phase Diagram of AlCl3-NaCl-H2O(-HCl Salt-Water System at 353.15 K

Directory of Open Access Journals (Sweden)

Huaigang Cheng

2017-08-01

Full Text Available Extracting AlCl3·6H2O from acid leaching solution through crystallization is one of the key processes to extracting aluminum from fly ash, coal gangue and other industrial solid wastes. However, the obtained products usually have low purity and a key problem is the lack of accurate data for phase equilibrium. This paper presented the non-equilibrium phase diagrams of AlCl3-NaCl-H2O (HCl salt-water systems under continuous heating and evaporation conditions, which were the main components of the acid leaching solution obtained through a sodium-assisted activation hydrochloric acid leaching process. The ternary system was of a simple eutonic type under different acidities. There were three crystalline regions; the crystalline regions of AlCl3·6H2O, NaCl and the mixture AlCl3·6H2O/NaCl, respectively. The phase diagram was used to optimize the crystallization process of AlCl3·6H2O and NaCl. A process was designed to evaporate and remove NaCl at the first stage of the evaporation process, and then continue to evaporate and crystallize AlCl3·6H2O after solid-liquid separation. The purities of the final salt products were 99.12% for NaCl and up to 97.35% for AlCl3·6H2O, respectively.

Predicting Crystallization of Amorphous Drugs with Terahertz Spectroscopy

DEFF Research Database (Denmark)

Sibik, Juraj; Löbmann, Korbinian; Rades, Thomas

2015-01-01

of the crystallization. We determine the onset temperature Tβ above which the JG relaxation contributes to the fast molecular dynamics and analytically quantify the level of this contribution. We then show there is a strong correlation between the increase in the fast molecular dynamics and onset of crystallization...

Analysis of Time Reversible Born-Oppenheimer Molecular Dynamics

Directory of Open Access Journals (Sweden)

Lin Lin

2013-12-01

Full Text Available We analyze the time reversible Born-Oppenheimer molecular dynamics (TRBOMD scheme, which preserves the time reversibility of the Born-Oppenheimer molecular dynamics even with non-convergent self-consistent field iteration. In the linear response regime, we derive the stability condition, as well as the accuracy of TRBOMD for computing physical properties, such as the phonon frequency obtained from the molecular dynamics simulation. We connect and compare TRBOMD with Car-Parrinello molecular dynamics in terms of accuracy and stability. We further discuss the accuracy of TRBOMD beyond the linear response regime for non-equilibrium dynamics of nuclei. Our results are demonstrated through numerical experiments using a simplified one-dimensional model for Kohn-Sham density functional theory.

Characterization of ion Coulomb crystals in a linear Paul trap

International Nuclear Information System (INIS)

Okada, K.; Takayanagi, T.; Wada, M.; Ohtani, S.; Schuessler, H. A.

2010-01-01

We describe a simple and fast method for simulating observed images of ion Coulomb crystals. In doing so, cold elastic collisions between Coulomb crystals and virtual very light atoms are implemented in a molecular dynamics (MD) simulation code. Such an approach reproduces the observed images of Coulomb crystals by obtaining density plots of the statistics of existence of each ion. The simple method has the advantage of short computing time in comparison with previous calculation methods. As a demonstration of the simulation, the formation of a planar Coulomb crystal with a small number of ions has been investigated in detail in a linear ion trap both experimentally and by simulation. However, also large Coulomb crystals including up to 1400 ions have been photographed and simulated to extract the secular temperature and the number of ions. For medium-sized crystals, a comparison between experiments and calculations has been performed. Moreover, an MD simulation of the sympathetic cooling of small molecular ions was performed in order to test the possibility of extracting the temperature and the number of refrigerated molecular ions from crystal images of laser-cooled ions. Such information is basic to studying ultracold ion-molecule reactions using ion Coulomb crystals including sympathetically cooled molecular ions.

Localization and orientation of heavy-atom cluster compounds in protein crystals using molecular replacement

International Nuclear Information System (INIS)

Dahms, Sven O.; Kuester, Miriam; Streb, Carsten; Roth, Christian; Sträter, Norbert; Than, Manuel E.

2013-01-01

A new approach is presented that allows the efficient localization and orientation of heavy-atom cluster compounds used in experimental phasing by a molecular replacement procedure. This permits the calculation of meaningful phases up to the highest resolution of the diffraction data. Heavy-atom clusters (HA clusters) containing a large number of specifically arranged electron-dense scatterers are especially useful for experimental phase determination of large complex structures, weakly diffracting crystals or structures with large unit cells. Often, the determination of the exact orientation of the HA cluster and hence of the individual heavy-atom positions proves to be the critical step in successful phasing and subsequent structure solution. Here, it is demonstrated that molecular replacement (MR) with either anomalous or isomorphous differences is a useful strategy for the correct placement of HA cluster compounds. The polyoxometallate cluster hexasodium α-metatungstate (HMT) was applied in phasing the structure of death receptor 6. Even though the HA cluster is bound in alternate partially occupied orientations and is located at a special position, its correct localization and orientation could be determined at resolutions as low as 4.9 Å. The broad applicability of this approach was demonstrated for five different derivative crystals that included the compounds tantalum tetradecabromide and trisodium phosphotungstate in addition to HMT. The correct placement of the HA cluster depends on the length of the intramolecular vectors chosen for MR, such that both a larger cluster size and the optimal choice of the wavelength used for anomalous data collection strongly affect the outcome

Non-equilibrium reactive flux: A unified framework for slow and fast reaction kinetics.

Science.gov (United States)

Bose, Amartya; Makri, Nancy

2017-10-21

The flux formulation of reaction rate theory is recast in terms of the expectation value of the reactive flux with an initial condition that corresponds to a non-equilibrium, factorized reactant density. In the common case of slow reactive processes, the non-equilibrium expression reaches the plateau regime only slightly slower than the equilibrium flux form. When the reactants are described by a single quantum state, as in the case of electron transfer reactions, the factorized reactant density describes the true initial condition of the reactive process. In such cases, the time integral of the non-equilibrium flux expression yields the reactant population as a function of time, allowing characterization of the dynamics in cases where there is no clear separation of time scales and thus a plateau regime cannot be identified. The non-equilibrium flux offers a unified approach to the kinetics of slow and fast chemical reactions and is ideally suited to mixed quantum-classical methods.

Effects of nonequilibrium adsorption on nuclide transport in a porous rock

International Nuclear Information System (INIS)

Shi-Ping Teng; Ching-Hor Lee

1994-01-01

An analytical solution covering the entire range of adsorption properties of rock has been derived for the migration of radionuclide in a porous rock matrix. The analysis takes into account the advective transport, hydrodynamic dispersion, adsorption between solid phase and liquid phase, and the radioactive decay. For adsorption of nuclide within the rock, the effects of no adsorption, linear nonequilibrium adsorption, and linear equilibrium adsorption are integrated into a generic transient analytical solution. The results indicate that the assumption of equilibrium adsorption can result in underestimation of the concentration profile in the early stages of migration. However, both the equilibrium and nonequilibrium profiles eventually approach the same value. It is also noted that for the case of nonequilibrium adsorption, plateaus appear in the concentration profile of the breakthrough curves. The effects of different adsorption rates are also analyzed

Electron and phonon drag in thermoelectric transport through coherent molecular conductors

DEFF Research Database (Denmark)

Lü, Jing-Tao; Wang, Jian-Sheng; Hedegård, Per

2016-01-01

We study thermoelectric transport through a coherent molecular conductor connected to two electron and two phonon baths using the nonequilibrium Green's function method. We focus on the mutual drag between electron and phonon transport as a result of ‘momentum’ transfer, which happens only when...

On Equivalence of Nonequilibrium Thermodynamic and Statistical Entropies

Directory of Open Access Journals (Sweden)

Purushottam D. Gujrati

2015-02-01

Full Text Available We review the concept of nonequilibrium thermodynamic entropy and observables and internal variables as state variables, introduced recently by us, and provide a simple first principle derivation of additive statistical entropy, applicable to all nonequilibrium states by treating thermodynamics as an experimental science. We establish their numerical equivalence in several cases, which includes the most important case when the thermodynamic entropy is a state function. We discuss various interesting aspects of the two entropies and show that the number of microstates in the Boltzmann entropy includes all possible microstates of non-zero probabilities even if the system is trapped in a disjoint component of the microstate space. We show that negative thermodynamic entropy can appear from nonnegative statistical entropy.

Linear response in the nonequilibrium zero range process

International Nuclear Information System (INIS)

Maes, Christian; Salazar, Alberto

2014-01-01

We explore a number of explicit response formulæ around the boundary driven zero range process to changes in the exit and entrance rates. In such a nonequilibrium regime kinetic (and not only thermodynamic) aspects make a difference in the response. Apart from a number of formal approaches, we illustrate a general decomposition of the linear response into entropic and frenetic contributions, the latter being realized from changes in the dynamical activity at the boundaries. In particular in this way one obtains nonlinear modifications to the Green–Kubo relation. We end by bringing some general remarks about the situation where that nonequilibrium response remains given by the (equilibrium) Kubo formula such as for the density profile in the boundary driven Lorentz gas

Crystallization of carbohydrate oxidase from Microdochium nivale

International Nuclear Information System (INIS)

Dušková, Jarmila; Dohnálek, Jan; Skálová, Tereza; Østergaard, Lars Henrik; Fuglsang, Claus Crone; Kolenko, Petr; Štěpánková, Andrea; Hašek, Jindřich

2009-01-01

Industrially used carbohydrate oxidase was successfully crystallized in several forms, diffraction data suitable for structural analysis were collected. Microdochium nivale carbohydrate oxidase was produced by heterologous recombinant expression in Aspergillus oryzae, purified and crystallized. The enzyme crystallizes with varying crystal morphologies depending on the crystallization conditions. Several different crystal forms were obtained using the hanging-drop vapour-diffusion method, two of which were used for diffraction measurements. Hexagon-shaped crystals (form I) diffracted to 2.66 Å resolution, with unit-cell parameters a = b = 55.7, c = 610.4 Å and apparent space group P6 2 22. Analysis of the data quality showed almost perfect twinning of the crystals. Attempts to solve the structure by molecular replacement did not give satisfactory results. Recently, clusters of rod-shaped crystals (form II) were grown in a solution containing PEG MME 550. These crystals belonged to the monoclinic system C2, with unit-cell parameters a = 132.9, b = 56.6, c = 86.5 Å, β = 95.7°. Data sets were collected to a resolution of 2.4 Å. The structure was solved by the molecular-replacement method. Model refinement is currently in progress

NON-EQUILIBRIUM CHEMISTRY OF DYNAMICALLY EVOLVING PRESTELLAR CORES. II. IONIZATION AND MAGNETIC FIELD

International Nuclear Information System (INIS)

Tassis, Konstantinos; Willacy, Karen; Yorke, Harold W.; Turner, Neal J.

2012-01-01

We study the effect that non-equilibrium chemistry in dynamical models of collapsing molecular cloud cores has on measurements of the magnetic field in these cores, the degree of ionization, and the mean molecular weight of ions. We find that OH and CN, usually used in Zeeman observations of the line-of-sight magnetic field, have an abundance that decreases toward the center of the core much faster than the density increases. As a result, Zeeman observations tend to sample the outer layers of the core and consistently underestimate the core magnetic field. The degree of ionization follows a complicated dependence on the number density at central densities up to 10 5 cm –3 for magnetic models and 10 6 cm –3 in non-magnetic models. At higher central densities, the scaling approaches a power law with a slope of –0.6 and a normalization which depends on the cosmic-ray ionization rate ζ and the temperature T as (ζT) 1/2 . The mean molecular weight of ions is systematically lower than the usually assumed value of 20-30, and, at high densities, approaches a value of 3 due to the asymptotic dominance of the H + 3 ion. This significantly lower value implies that ambipolar diffusion operates faster.

Introduction to crystal growth and characterization

CERN Document Server

Benz, Klaus-Werner

2014-01-01

This new textbook provides for the first time a comprehensive treatment of the basics of contemporary crystallography and crystal growth in a single volume. The reader will be familiarized with the concepts for the description of morphological and structural symmetry of crystals. The architecture of crystal structures of selected inorganic and molecular crystals is illustrated. The main crystallographic databases as data sources of crystal structures are described. Nucleation processes, their kinetics and main growth mechanism will be introduced in fundamentals of crystal growth. Some phase d

Non-equilibrium condensation process in holographic superconductor with nonlinear electrodynamics

Energy Technology Data Exchange (ETDEWEB)

Liu, Yunqi; Gong, Yungui [School of Physics, Huazhong University of Science and Technology,Wuhan, Hubei 430074 (China); Wang, Bin [IFSA Collaborative Innovation Center, Department of Physics and Astronomy, Shanghai Jiao Tong University,Shanghai 200240 (China)

2016-02-17

We study the non-equilibrium condensation process in a holographic superconductor with nonlinear corrections to the U(1) gauge field. We start with an asymptotic Anti-de-Sitter(AdS) black hole against a complex scalar perturbation at the initial time, and solve the dynamics of the gravitational systems in the bulk. When the black hole temperature T is smaller than a critical value T{sub c}, the scalar perturbation grows exponentially till saturation, the final state of spacetime approaches to a hairy black hole. In the bulk theory, we find the clue of the influence of nonlinear corrections in the gauge filed on the process of the scalar field condensation. We show that the bulk dynamics in the non-equilibrium process is completely consistent with the observations on the boundary order parameter. Furthermore we examine the time evolution of horizons in the bulk non-equilibrium transformation process from the bald AdS black hole to the AdS hairy hole. Both the evolution of apparent and event horizons show that the original AdS black hole configuration requires more time to finish the transformation to become a hairy black hole if there is nonlinear correction to the electromagnetic field. We generalize our non-equilibrium discussions to the holographic entanglement entropy and find that the holographic entanglement entropy can give us further understanding of the influence of the nonlinearity in the gauge field on the scalar condensation.

Nonequilibrium and generalized-ensemble molecular dynamics simulations for amyloid fibril

Energy Technology Data Exchange (ETDEWEB)

Okumura, Hisashi [Research Center for Computational Science, Institute for Molecular Science, Okazaki, Aichi 444-8585 (Japan); Department of Structural Molecular Science, The Graduate University for Advanced Studies, Okazaki, Aichi 444-8585 (Japan)

2015-12-31

Amyloids are insoluble and misfolded fibrous protein aggregates and associated with more than 20 serious human diseases. We perform all-atom molecular dynamics simulations of amyloid fibril assembly and disassembly.

Shear flow simulations of biaxial nematic liquid crystals

Science.gov (United States)

Sarman, Sten

1997-08-01

We have calculated the viscosities of a biaxial nematic liquid crystal phase of a variant of the Gay-Berne fluid [J. G. Gay and B. J. Berne, J. Chem. Phys. 74, 3316 (1981)] by performing molecular dynamics simulations. The equations of motion have been augmented by a director constraint torque that fixes the orientation of the directors. This makes it possible to fix them at different angles relative to the stream lines in shear flow simulations. In equilibrium simulations the constraints generate a new ensemble. One finds that the Green-Kubo relations for the viscosities become linear combinations of time correlation function integrals in this ensemble whereas they are complicated rational functions in the conventional canonical ensemble. We have evaluated these Green-Kubo relations for all the shear viscosities and all the twist viscosities. We have also calculated the alignment angles, which are functions of the viscosity coefficients. We find that there are three real alignment angles but a linear stability analysis shows that only one of them corresponds to a stable director orientation. The Green-Kubo results have been cross checked by nonequilibrium shear flow simulations. The results from the different methods agree very well. Finally, we have evaluated the Miesowicz viscosities [D. Baalss, Z. Naturforsch. Teil A 45, 7 (1990)]. They vary by more than 2 orders of magnitude. The viscosity is consequently highly orientation dependent.

Experimental approaches for studying non-equilibrium atmospheric plasma jets

Energy Technology Data Exchange (ETDEWEB)

Shashurin, A., E-mail: ashashur@purdue.edu [School of Aeronautics & Astronautics, Purdue University, West Lafayette, Indiana 47907 (United States); Keidar, M. [Department of Mechanical and Aerospace Engineering, The George Washington University, Washington, District of Columbia 20052 (United States)

2015-12-15

This work reviews recent research efforts undertaken in the area non-equilibrium atmospheric plasma jets with special focus on experimental approaches. Physics of small non-equilibrium atmospheric plasma jets operating in kHz frequency range at powers around few Watts will be analyzed, including mechanism of breakdown, process of ionization front propagation, electrical coupling of the ionization front with the discharge electrodes, distributions of excited and ionized species, discharge current spreading, transient dynamics of various plasma parameters, etc. Experimental diagnostic approaches utilized in the field will be considered, including Rayleigh microwave scattering, Thomson laser scattering, electrostatic streamer scatterers, optical emission spectroscopy, fast photographing, etc.

Identifying self-interstitials of bcc and fcc crystals in molecular dynamics

Science.gov (United States)

Bukkuru, S.; Bhardwaj, U.; Warrier, M.; Rao, A. D. P.; Valsakumar, M. C.

2017-02-01

Identification of self-interstitials in molecular dynamics (MD) simulations is of critical importance. There exist several criteria for identifying the self-interstitial. Most of the existing methods use an assumed cut-off value for the displacement of an atom from its lattice position to identify the self-interstitial. The results obtained are affected by the chosen cut-off value. Moreover, these chosen cut-off values are independent of temperature. We have developed a novel unsupervised learning algorithm called Max-Space Clustering (MSC) to identify an appropriate cut-off value and its dependence on temperature. This method is compared with some widely used methods such as effective sphere (ES) method and nearest neighbor sphere (NNS) method. The cut-off radius obtained using our method shows a linear variation with temperature. The value of cut-off radius and its temperature dependence is derived for five bcc (Cr, Fe, Mo, Nb, W) and six fcc (Ag, Au, Cu, Ni, Pd, Pt) crystals. It is seen that the ratio of the cut-off values "r" to the lattice constant "a" lies between 0.23 and 0.3 at 300 K and this ratio is on an average smaller for the fcc crystals. Collision cascade simulations are carried out for Primary knock-on Atom (PKA) energies of 5 keV in Fe (at 300 K and 1000 K) and W (at 300 K and 2500 K) and the results are compared using the various methods.

Dynamical ion transfer between coupled Coulomb crystals in a double-well potential.

Science.gov (United States)

Klumpp, Andrea; Zampetaki, Alexandra; Schmelcher, Peter

2017-09-01

We investigate the nonequilibrium dynamics of coupled Coulomb crystals of different sizes trapped in a double well potential. The dynamics is induced by an instantaneous quench of the potential barrier separating the two crystals. Due to the intra- and intercrystal Coulomb interactions and the asymmetric population of the potential wells, we observe a complex reordering of ions within the two crystals as well as ion transfer processes from one well to the other. The study and analysis of the latter processes constitutes the main focus of this work. In particular, we examine the dependence of the observed ion transfers on the quench amplitude performing an analysis for different crystalline configurations ranging from one-dimensional ion chains via two-dimensional zigzag chains and ring structures to three-dimensional spherical structures. Such an analysis provides us with the means to extract the general principles governing the ion transfer dynamics and we gain some insight on the structural disorder caused by the quench of the barrier height.

Extension of CE/SE method to non-equilibrium dissociating flows

KAUST Repository

Wen, C.Y.

2017-12-08

In this study, the hypersonic non-equilibrium flows over rounded nose geometries are numerically investigated by a robust conservation element and solution element (CE/SE) code, which is based on hybrid meshes consisting of triangular and quadrilateral elements. The dissociating and recombination chemical reactions as well as the vibrational energy relaxation are taken into account. The stiff source terms are solved by an implicit trapezoidal method of integration. Comparison with laboratory and numerical cases are provided to demonstrate the accuracy and reliability of the present CE/SE code in simulating hypersonic non-equilibrium flows.

Importance of thermal nonequilibrium considerations for the simulation of nuclear reactor LOCA transients

International Nuclear Information System (INIS)

Fischer, S.R.; Nelson, R.A.; Sullivan, L.H.

1980-01-01

The purpose of this paper is to show the importance of considering thermal nonequilibrium effects in computer simulations of the refill and reflood portions of pressurized water reactor (PWR) loss-of-coolnat accident (LOCA) transients. Although RELAP4 assumes thermodynamic equilibrium between phases, models that account for the nonequilibrium phenomena associated with the mixing of subcooled emergency cooling water with steam and the superheating of vapor in the presence of liquid droplets have recently been incorporated into the code. Code calculated results, both with and without these new models, have been compared with experimental test data to assess the importance of including thermal nonequilibrium phenomena in computer code simulations

Potential and flux field landscape theory. II. Non-equilibrium thermodynamics of spatially inhomogeneous stochastic dynamical systems

International Nuclear Information System (INIS)

Wu, Wei; Wang, Jin

2014-01-01

We have established a general non-equilibrium thermodynamic formalism consistently applicable to both spatially homogeneous and, more importantly, spatially inhomogeneous systems, governed by the Langevin and Fokker-Planck stochastic dynamics with multiple state transition mechanisms, using the potential-flux landscape framework as a bridge connecting stochastic dynamics with non-equilibrium thermodynamics. A set of non-equilibrium thermodynamic equations, quantifying the relations of the non-equilibrium entropy, entropy flow, entropy production, and other thermodynamic quantities, together with their specific expressions, is constructed from a set of dynamical decomposition equations associated with the potential-flux landscape framework. The flux velocity plays a pivotal role on both the dynamic and thermodynamic levels. On the dynamic level, it represents a dynamic force breaking detailed balance, entailing the dynamical decomposition equations. On the thermodynamic level, it represents a thermodynamic force generating entropy production, manifested in the non-equilibrium thermodynamic equations. The Ornstein-Uhlenbeck process and more specific examples, the spatial stochastic neuronal model, in particular, are studied to test and illustrate the general theory. This theoretical framework is particularly suitable to study the non-equilibrium (thermo)dynamics of spatially inhomogeneous systems abundant in nature. This paper is the second of a series

Understanding Molecular Conduction: Old Wine in a New Bottle?

Science.gov (United States)

Ghosh, Avik

2007-03-01

Molecules provide an opportunity to test our understanding of fundamental non-equilibrium transport processes, as well as explore new device possibilities. We have developed a unified approach to nanoscale conduction, coupling bandstructure and electrostatics of the channel and contacts with a quantum kinetic theory of current flow. This allows us to describe molecular conduction at various levels of detail, -- from quantum corrected compact models, to semi-empirical models for quick physical insights, and `first-principles' calculations of current-voltage (I-V) characteristics with no adjustable parameters. Using this suite of tools, we can quantitatively explain various experimental I-Vs, including complex reconstructed silicon substrates. We find that conduction in most molecules is contact dominated, and limited by fundamental electrostatic and thermodynamic restrictions quite analogous to those faced by the silicon industry, barring a few interesting exceptions. The distinction between molecular and silicon electronics must therefore be probed at a more fundamental level. Ultra-short molecules are unique in that they possess large Coulomb energies as well as anomalous vibronic couplings with current flow -- in other words, strong non-equilibrium electron-electron and electron-phonon correlations. These effects yield prominent experimental signatures, but require a completely different modeling approach -- in fact, popular approaches to include correlation typically do not work for non-equilibrium. Molecules exhibit rich physics, including the ability to function both as weakly interacting current conduits (quantum wires) as well as strongly correlated charge storage centers (quantum dots). Theoretical treatment of the intermediate coupling regime is particularly challenging, with a large `fine structure constant' for transport that negates orthodox theories of Coulomb Blockade and phonon-assisted tunneling. It is in this regime that the scientific and

Controlling Non-Equilibrium Structure Formation on the Nanoscale.

Science.gov (United States)

Buchmann, Benedikt; Hecht, Fabian Manfred; Pernpeintner, Carla; Lohmueller, Theobald; Bausch, Andreas R

2017-12-06

Controlling the structure formation of gold nanoparticle aggregates is a promising approach towards novel applications in many fields, ranging from (bio)sensing to (bio)imaging to medical diagnostics and therapeutics. To steer structure formation, the DNA-DNA interactions of DNA strands that are coated on the surface of the particles have become a valuable tool to achieve precise control over the interparticle potentials. In equilibrium approaches, this technique is commonly used to study particle crystallization and ligand binding. However, regulating the structural growth processes from the nano- to the micro- and mesoscale remains elusive. Here, we show that the non-equilibrium structure formation of gold nanoparticles can be stirred in a binary heterocoagulation process to generate nanoparticle clusters of different sizes. The gold nanoparticles are coated with sticky single stranded DNA and mixed at different stoichiometries and sizes. This not only allows for structural control but also yields access to the optical properties of the nanoparticle suspensions. As a result, we were able to reliably control the kinetic structure formation process to produce cluster sizes between tens of nanometers up to micrometers. Consequently, the intricate optical properties of the gold nanoparticles could be utilized to control the maximum of the nanoparticle suspension extinction spectra between 525 nm and 600 nm. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Strong dielectric liquid crystal polymer (Part 3)

Energy Technology Data Exchange (ETDEWEB)

Kurata, Hideaki; Shibasaki, Akira

1988-11-01

Influence of change of molecular parameters on liquid crystal condition is studied to get the correlation between molecular structure of liquid crystal and phase structure or visco-elastic properties. Eight kinds of biphenyl type liquid crystals with polyacrilate main chain and triphenyl type liquid crystals were used as samples. Followings were found by a ploarizing microscope and X-ray diffraction: Phases are transferred from isotropic phase S/sub A/ phase S/sup *//sub C/ phase S/sub 1/ phase to solid on temperature desending sequence. Degree of polymerization changes only these transfer point but spacer length affects not only transfer points and layer distance but also liquid crystal structure itself. Visco-elasticity of isotropic phase shows Newtonian viscosity and is affected by the main chain length. Macroscopic and microscopic structures influence on viscoelasticity in S/sub A/ phase and S/sup *//sub C/ phase. Two rapid rises of viscoelasticity are found in low molecular weight liquid crystal when S/sub A/ transfer and S/sub A/ to S/sup *//sub C/ transfer occur by temperature desending from the isotropic phase. Viscoelastic behavior is contributed by the properties of domain itself and interaction between domains, and the interaction is changed by polymerization. 6 references, 13 figures, 1 table.

Nonequilibrium effects in Isoscaling

International Nuclear Information System (INIS)

Dorso, C. O.; Lopez, J. A.

2007-01-01

In this work we study within a simple model different properties of the system that allow us to understand the properties of the isoscaling observable. We first show that isoscaling is a general property of fragmenting systems. We show this by using a simple generalized percolation model. We show that the usual isoscaling property can be obtained in the case of bond percolation in bichromatic lattices with any regular topology. In this case the probabilities of each color (isospin) are independent. We then explore the effect of introducing 'non-equilibrium' effects

Instabilities and nonequilibrium structures

International Nuclear Information System (INIS)

Tirapegui, E.; Villarroel, D.

1987-01-01

Physical systems can be studied both near to and far from equilibrium where instabilities appear. The behaviour in these two regions is reviewed in this book, from both the theoretical and application points of view. The influence of noise in these situations is an essential feature which cannot be ignored. It is therefore discussed using phenomenological and theoretical approaches for the numerous problems which still remain in the field. This volume should appeal to mathematicians and physicists interested in the areas of instability, bifurcation theory, dynamical systems, pattern formation, nonequilibrium structures and statistical mechanics. (Auth.)

Emergence of a fluctuation relation for heat in nonequilibrium Landauer processes

Science.gov (United States)

Taranto, Philip; Modi, Kavan; Pollock, Felix A.

2018-05-01

In a generalized framework for the Landauer erasure protocol, we study bounds on the heat dissipated in typical nonequilibrium quantum processes. In contrast to thermodynamic processes, quantum fluctuations are not suppressed in the nonequilibrium regime and cannot be ignored, making such processes difficult to understand and treat. Here we derive an emergent fluctuation relation that virtually guarantees the average heat produced to be dissipated into the reservoir either when the system or reservoir is large (or both) or when the temperature is high. The implication of our result is that for nonequilibrium processes, heat fluctuations away from its average value are suppressed independently of the underlying dynamics exponentially quickly in the dimension of the larger subsystem and linearly in the inverse temperature. We achieve these results by generalizing a concentration of measure relation for subsystem states to the case where the global state is mixed.

Non-equilibrium scaling analysis of the Kondo model with voltage bias

International Nuclear Information System (INIS)

Fritsch, Peter; Kehrein, Stefan

2009-01-01

The quintessential description of Kondo physics in equilibrium is obtained within a scaling picture that shows the buildup of Kondo screening at low temperature. For the non-equilibrium Kondo model with a voltage bias, the key new feature are decoherence effects due to the current across the impurity. In the present paper, we show how one can develop a consistent framework for studying the non-equilibrium Kondo model within a scaling picture of infinitesimal unitary transformations (flow equations). Decoherence effects appear naturally in third order of the β-function and dominate the Hamiltonian flow for sufficiently large voltage bias. We work out the spin dynamics in non-equilibrium and compare it with finite temperature equilibrium results. In particular, we report on the behavior of the static spin susceptibility including leading logarithmic corrections and compare it with the celebrated equilibrium result as a function of temperature.

Identifying self-interstitials of bcc and fcc crystals in molecular dynamics

International Nuclear Information System (INIS)

Bukkuru, S.; Bhardwaj, U.; Warrier, M.; Rao, A.D.P.; Valsakumar, M.C.

2017-01-01

Identification of self-interstitials in molecular dynamics (MD) simulations is of critical importance. There exist several criteria for identifying the self-interstitial. Most of the existing methods use an assumed cut-off value for the displacement of an atom from its lattice position to identify the self-interstitial. The results obtained are affected by the chosen cut-off value. Moreover, these chosen cut-off values are independent of temperature. We have developed a novel unsupervised learning algorithm called Max-Space Clustering (MSC) to identify an appropriate cut-off value and its dependence on temperature. This method is compared with some widely used methods such as effective sphere (ES) method and nearest neighbor sphere (NNS) method. The cut-off radius obtained using our method shows a linear variation with temperature. The value of cut-off radius and its temperature dependence is derived for five bcc (Cr, Fe, Mo, Nb, W) and six fcc (Ag, Au, Cu, Ni, Pd, Pt) crystals. It is seen that the ratio of the cut-off values “r” to the lattice constant “a” lies between 0.23 and 0.3 at 300 K and this ratio is on an average smaller for the fcc crystals. Collision cascade simulations are carried out for Primary knock-on Atom (PKA) energies of 5 keV in Fe (at 300 K and 1000 K) and W (at 300 K and 2500 K) and the results are compared using the various methods. - Highlights: • Max-Space Clustering (MSC) method is developed to identify interstitials in crystals. • MSC provides a structured way to identify the temperature dependent cut-off radius. • It is compared with widely used sphere methods and found to be better. • MSC coupled with graph tree optimization can be used to obtain diffusion trajectory. • Cascade simulations of Fe, W are carried out and results are compared with various methods.

Identifying self-interstitials of bcc and fcc crystals in molecular dynamics

Energy Technology Data Exchange (ETDEWEB)

Bukkuru, S., E-mail: srinivasaraobukkuru@gmail.com [Dept. of Nuclear Physics, Andhra University, Visakhapatnam 530003 (India); Bhardwaj, U., E-mail: haptork@gmail.com [Computational Analysis Division, BARC, Visakhapatnam 530012, Andhra Pradesh (India); Warrier, M., E-mail: manoj.warrier@gmail.com [Computational Analysis Division, BARC, Visakhapatnam 530012, Andhra Pradesh (India); Rao, A.D.P., E-mail: adp_rao_99@yahoo.com [Dept. of Nuclear Physics, Andhra University, Visakhapatnam 530003 (India); Valsakumar, M.C., E-mail: mc.valsakumar@gmail.com [IIT Palakkad, Kozhippara P.O., Palakkad 678557, Kerala (India)

2017-02-15

Identification of self-interstitials in molecular dynamics (MD) simulations is of critical importance. There exist several criteria for identifying the self-interstitial. Most of the existing methods use an assumed cut-off value for the displacement of an atom from its lattice position to identify the self-interstitial. The results obtained are affected by the chosen cut-off value. Moreover, these chosen cut-off values are independent of temperature. We have developed a novel unsupervised learning algorithm called Max-Space Clustering (MSC) to identify an appropriate cut-off value and its dependence on temperature. This method is compared with some widely used methods such as effective sphere (ES) method and nearest neighbor sphere (NNS) method. The cut-off radius obtained using our method shows a linear variation with temperature. The value of cut-off radius and its temperature dependence is derived for five bcc (Cr, Fe, Mo, Nb, W) and six fcc (Ag, Au, Cu, Ni, Pd, Pt) crystals. It is seen that the ratio of the cut-off values “r” to the lattice constant “a” lies between 0.23 and 0.3 at 300 K and this ratio is on an average smaller for the fcc crystals. Collision cascade simulations are carried out for Primary knock-on Atom (PKA) energies of 5 keV in Fe (at 300 K and 1000 K) and W (at 300 K and 2500 K) and the results are compared using the various methods. - Highlights: • Max-Space Clustering (MSC) method is developed to identify interstitials in crystals. • MSC provides a structured way to identify the temperature dependent cut-off radius. • It is compared with widely used sphere methods and found to be better. • MSC coupled with graph tree optimization can be used to obtain diffusion trajectory. • Cascade simulations of Fe, W are carried out and results are compared with various methods.

Development of Nanostructured Water Treatment Membranes Based on Thermotropic Liquid Crystals: Molecular Design of Sub-Nanoporous Materials.