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Statistical Mechanics (statistical + mechanic)
Selected AbstractsStudies of molecular docking between fibroblast growth factor and heparin using generalized simulated annealingINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 13 2008Samuel Silva da Rocha Pita Abstract Since the middle 70s, the main molecular docking problem consists in limitations to treat adequately the degrees of freedom of protein (or a receptor) due to the energy landscape roughness and the high computational cost. Until recently, only few algorithms considering flexible simultaneously both ligand and receptor at low computational cost were developed. As a recent proposed Statistical Mechanics, generalized simulated annealing (GSA) has been employed at diverse works concerning global optimization problems. In this work, we used this method exploring the molecular docking problem taking into account the FGF-2 and heparin complex. Since the requirements of an efficient docking algorithm are accuracy and velocity, we tested the influence of GSA parameters qA (new configuration acceptance index), qV (energy surface visiting index), and qT (temperature decreasing control) on the performance of GSADOCK program. Our simulations showed that as temperature parameter qT increases, qA parameter follows this behavior in the interval ranging from 1.1 to 2.3. We found that the GSA parameters have the best performance for the qA values ranging from 1.1 to 1.3, qV values from 1.3 to 1.5, and qT values from 1.1 to 1.7. Most of good qV values were equal or next the good qT values. Finally, the implemented algorithm is trustworthy and can be employed as a tool of molecular modeling methods. The final version of the program will be free of charge and will be accessible at our home-page or could be requested to the authors for e-mail. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008 [source] The Small World of Canadian Capital Markets: Statistical Mechanics of Investment Bank Syndicate Networks, 1952,1989CANADIAN JOURNAL OF ADMINISTRATIVE SCIENCES, Issue 4 2004Joel A.C. Baum We investigate the structure of investment bank syndicate networks in Canada. We consider two banks to be connected if they have participated in an underwriting syndicate together, and construct networks of such connections using data drawn from the Record of New Issues (Financial Data Group). We show that these interfirm networks form "small worlds", in which banks are both locally clustered and globally connected by short paths of intermediate banks, and are "scale free", in which the connectivity of the network is highly skewed and with most banks tied to a small set of prominent banks. We examine changes over time in the network's small-world and scale-free properties, and demonstrate their theoretical and practical implications for the structure and operation of Canadian capital markets by linking these properties to the network's cliquey-ness, resilience, and speed of information transmission. Résumé Cette étude porte sur la structure des réseaux que for-ment les syndicats d'émission des banques d'investissement au Canada. Nous posons que deux banques sont liées si elles ont participé ensemble à un syndicat d'émission, et nous retraçons les réseaux de liens en utilisant des données extraites du Record of New Issues (Financial Data Group). Nous montrons que ces réseaux interorganisationnels (RIO)forment des petits mondes dans lesquels les banques sont à la fois localement regroupées et mondialement reliées par des courts chemins de banques intermédiaires. Les RIO sont également sans échelle (scale free): la connectivité dans le réseau est fortement inégale et la plupart des banques sont liées à un petit nombre de banques dominantes. Nous examinons l'évolution des propriétés de petit monde et d'absence d'échelle du réseau et mettons en Evidence leurs implications théoriques et pratiques pour la structure et le fonctionnement du marché canadien des capitaux en reliant ces propriétés aux caractères de clique, de résilience et de vitesse de transmission de l'information du réseau. [source] Rigid-body dynamics in the isothermal-isobaric ensemble: A test on the accuracy and computational efficiencyJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 8 2003Wataru Shinoda Abstract We have developed a time-reversible rigid-body (rRB) molecular dynamics algorithm in the isothermal-isobaric (NPT) ensemble. The algorithm is an extension of rigid-body dynamics [Matubayasi and Nakahara, J Chem Phys 1999, 110, 3291] to the NPT ensemble on the basis of non-Hamiltonian statistical mechanics [Martyna, G. J. et al., J Chem Phys 1994, 101, 4177]. A series of MD simulations of water as well as fully hydrated lipid bilayer systems have been undertaken to investigate the accuracy and efficiency of the algorithm. The rRB algorithm was shown to be superior to the state-of-the-art constraint-dynamics algorithm SHAKE/RATTLE/ROLL, with respect to computational efficiency. However, it was revealed that both algorithms produced accurate trajectories of molecules in the NPT as well as NVT ensembles, as long as a reasonably short time step was used. A couple of multiple time-step (MTS) integration schemes were also examined. The advantage of the rRB algorithm for computational efficiency increased when the MD simulation was carried out using MTS on parallel processing computer systems; total computer time for MTS-MD of a lipid bilayer using 64 processors was reduced by about 40% using rRB instead of SHAKE/RATTLE/ROLL. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 920,930, 2003 [source] Simulation of binary mixture adsorption of methane and CO2 at supercritical conditions in carbonsAICHE JOURNAL, Issue 3 2006Yohanes Kurniawan Abstract Knowledge of the adsorption behavior of coal-bed gases, mainly under supercritical high-pressure conditions, is important for optimum design of production processes to recover coal-bed methane and to sequester CO2 in coal-beds. Here, we compare the two most rigorous adsorption methods based on the statistical mechanics approach, which are Density Functional Theory (DFT) and Grand Canonical Monte Carlo (GCMC) simulation, for single and binary mixtures of methane and carbon dioxide in slit-shaped pores ranging from around 0.75 to 7.5 nm in width, for pressure up to 300 bar, and temperature range of 308-348 K, as a preliminary study for the CO2 sequestration problem. For single component adsorption, the isotherms generated by DFT, especially for CO2, do not match well with GCMC calculation, and simulation is subsequently pursued here to investigate the binary mixture adsorption. For binary adsorption, upon increase of pressure, the selectivity of carbon dioxide relative to methane in a binary mixture initially increases to a maximum value, and subsequently drops before attaining a constant value at pressures higher than 300 bar. While the selectivity increases with temperature in the initial pressure-sensitive region, the constant high-pressure value is also temperature independent. Optimum selectivity at any temperature is attained at a pressure of 90-100 bar at low bulk mole fraction of CO2, decreasing to approximately 35 bar at high bulk mole fractions. © 2005 American Institute of Chemical Engineers AIChE J, 2006 [source] Density functional theory for chemical engineering: From capillarity to soft materialsAICHE JOURNAL, Issue 3 2006Jianzhong Wu Abstract Understanding the microscopic structure and macroscopic properties of condensed matter from a molecular perspective is important for both traditional and modern chemical engineering. A cornerstone of such understanding is provided by statistical mechanics, which bridges the gap between molecular events and the structural and physiochemical properties of macro- and mesoscopic systems. With ever-increasing computer power, molecular simulations and ab initio quantum mechanics are promising to provide a nearly exact route to accomplishing the full potential of statistical mechanics. However, in light of their versatility for solving problems involving multiple length and timescales that are yet unreachable by direct simulations, phenomenological and semiempirical methods remain relevant for chemical engineering applications in the foreseeable future. Classical density functional theory offers a compromise: on the one hand, it is able to retain the theoretical rigor of statistical mechanics and, on the other hand, similar to a phenomenological method, it demands only modest computational cost for modeling the properties of uniform and inhomogeneous systems. Recent advances are summarized of classical density functional theory with emphasis on applications to quantitative modeling of the phase and interfacial behavior of condensed fluids and soft materials, including colloids, polymer solutions, nanocomposites, liquid crystals, and biological systems. Attention is also given to some potential applications of density functional theory to material fabrications and biomolecular engineering. © 2005 American Institute of Chemical Engineers AIChE J, 2006 [source] Matrix formalism for site-specific binding of unstructured proteins to multicomponent lipid membranes,JOURNAL OF PEPTIDE SCIENCE, Issue 4 2008Vladimir B. Teif Abstract We describe a new approach to calculate the binding of flexible peptides and unfolded proteins to multicomponent lipid membranes. The method is based on the transfer matrix formalism of statistical mechanics recently described as a systematic tool to study DNA,protein,drug binding in gene regulation. Using the energies of interaction of the individual polymer segments with different membrane lipid species and the scaling corrections due to polymer looping, we calculate polymer adsorption characteristics and the degree of sequestration of specific membrane lipids. The method is applied to the effector domain of the MARCKS (myristoylated alanine rich C kinase substrate) protein known to be involved in signal transduction through membrane binding. The calculated binding constants of the MARCKS(151,175) peptide and a series of related peptides to mixed PC/PS/PIP2 membranes are in satisfactory agreement with in vitro experiments. Copyright © 2008 European Peptide Society and John Wiley & Sons, Ltd. [source] A Nonequilibrium Statistical Mechanical Model of Structural Relaxation in GlassJOURNAL OF THE AMERICAN CERAMIC SOCIETY, Issue 3 2006John C. Mauro We derive a new model of structural relaxation in glass based on nonequilibrium statistical mechanics and the Stillinger model of inherent structures. Our model follows the evolution of a system from its equilibrium liquid state through an arbitrary cooling path and allows for the computation of macroscopic properties as a function of time. Using this new model, we have numerically demonstrated for the first time the connection between the topography of a potential energy landscape in 1-D and its corresponding fragility. [source] Applying centrality measures to impact analysis: A coauthorship network analysisJOURNAL OF THE AMERICAN SOCIETY FOR INFORMATION SCIENCE AND TECHNOLOGY, Issue 10 2009Erjia Yan Many studies on coauthorship networks focus on network topology and network statistical mechanics. This article takes a different approach by studying micro-level network properties with the aim of applying centrality measures to impact analysis. Using coauthorship data from 16 journals in the field of library and information science (LIS) with a time span of 20 years (1988,2007), we construct an evolving coauthorship network and calculate four centrality measures (closeness centrality, betweenness centrality, degree centrality, and PageRank) for authors in this network. We find that the four centrality measures are significantly correlated with citation counts. We also discuss the usability of centrality measures in author ranking and suggest that centrality measures can be useful indicators for impact analysis. [source] Notes on ferromagnetic p -spin and REMMATHEMATICAL METHODS IN THE APPLIED SCIENCES, Issue 7 2009Adriano Barra Abstract In this paper we apply some of the recent mathematical techniques (mainly based on interpolation) developed in the spin glass theory to the ferromagnetic p -spin model. We introduce two Hamiltonians and derive their thermodynamics. This is a second step toward an alternative and rigorous formulation of the statistical mechanics of simple systems on lattice. A first step has been performed in J. Stat. Phys. (2007; arXiv:0712.1344) where the techniques have been tested on the two-body Ising model. For completeness the adaptation of the well-known random energy model to the context of the ferromagnetism is presented. At the end a discussion on the extension of these techniques to Gaussian-disordered p -spin models is also briefly outlined. Copyright © 2008 John Wiley & Sons, Ltd. [source] On the clustering phase transition in self-gravitating N -body systemsMONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY, Issue 1 2001Monica Cerruti-Sola The thermodynamic behaviour of self-gravitating N -body systems has been worked out by borrowing a standard method from molecular dynamics. The link between dynamics and thermodynamics is made in the microcanonical ensemble of statistical mechanics. Through the computation of basic thermodynamic observables and of the equation of state in the plane, the clustering phase transition appears to be of the second-order type. The dynamical,microcanonical averages are compared with their corresponding canonical ensemble averages, obtained through standard Monte Carlo computations. The latter seem to have completely lost any information about the phase transition. Finally, our results , obtained in a ,microscopic' framework , are compared with some existing theoretical predictions , obtained in a ,macroscopic' (thermodynamic) framework: qualitative and quantitative agreement is found, with an interesting exception. [source] A competitive coexistence principle?OIKOS, Issue 10 2009Cathy Neill Competitive exclusion , n species cannot coexist on fewer than n limiting resources in a constant and isolated environment , has been a central ecological principle for the past century. Since empirical studies cannot universally demonstrate exclusion, this principle has mainly relied on mathematical proofs. Here we investigate the predictions of a new approach to derive functional responses in consumer/resource systems. Models usually describe the temporal dynamics of consumer/resource systems at a macroscopic level , i.e. at the population level. Each model may be pictured as one time-dependent macroscopic trajectory. Each macroscopic trajectory is, however, the product of many individual fates and from combinatorial considerations can be realized in many different ways at the microscopic , or individual , level. Recently it has been shown that, in systems with large enough numbers of consumer individuals and resource items, one macroscopic trajectory can be realized in many more ways than any other at the individual , or microscopic , level. Therefore, if the temporal dynamics of an ecosystem are assumed to be the outcome of only statistical mechanics , that is, chance , a single trajectory is near-certain and can be described by deterministic equations. We argue that these equations can serve as a null to model consumer-resource dynamics, and show that any number of species can coexist on a single resource in a constant, isolated environment. Competition may result in relative rarity, which may entail exclusion in finite samples of discrete individuals, but exclusion is not systematic. Beyond the coexistence/exclusion outcome, our model also predicts that the relative abundance of any two species depends simply on the ratio of their competitive abilities as computed from , and only from , their intrinsic kinetic and stoichiometric parameters. [source] From molecules to meteorology via turbulent scale invarianceTHE QUARTERLY JOURNAL OF THE ROYAL METEOROLOGICAL SOCIETY, Issue 650 2010A. F. Tuck Abstract This review attempts to interpret the generalized scale invariance observed in common atmospheric variables,wind, temperature, humidity, ozone and some trace species,in terms of the computed emergence of ring currents (vortices) in simulations of populations of Maxwellian molecules subject to an anisotropy in the form of a flux. The data are taken from ,horizontal' tracks of research aircraft and from ,vertical' trajectories of research dropsondes. It is argued that any attempt to represent the energy distribution in the atmosphere quantitatively must have a proper basis in molecular physics, a prerequisite to accommodate the observed long-tailed velocity probability distributions and the implied effects on radiative transfer, atmospheric chemistry, turbulent structure and the definition of temperature itself. The relationship between fluctuations and dissipation is discussed in a framework of non-equilibrium statistical mechanics, and a link between maximization of entropy production and scale invariance is hypothesized. Copyright © 2010 Royal Meteorological Society [source] Manifestly covariant classical correlation dynamics I. General theoryANNALEN DER PHYSIK, Issue 10-11 2009C. Tian Abstract In this series of papers we substantially extend investigations of Israel and Kandrup on nonequilibrium statistical mechanics in the framework of special relativity. This is the first one devoted to the general mathematical structure. Based on the action-at-a-distance formalism we obtain a single-time Liouville equation. This equation describes the manifestly covariant evolution of the distribution function of full classical many-body systems. For such global evolution the Bogoliubov functional assumption is justified. In particular, using the Balescu-Wallenborn projection operator approach we find that the distribution function of full many-body systems is completely determined by the reduced one-body distribution function. A manifestly covariant closed nonlinear equation satisfied by the reduced one-body distribution function is rigorously derived. We also discuss extensively the generalization to general relativity especially an application to self-gravitating systems. [source] Manifestly covariant classical correlation dynamics I. General theoryANNALEN DER PHYSIK, Issue 10-11 2009C. Tian Abstract In this series of papers we substantially extend investigations of Israel and Kandrup on nonequilibrium statistical mechanics in the framework of special relativity. This is the first one devoted to the general mathematical structure. Based on the action-at-a-distance formalism we obtain a single-time Liouville equation. This equation describes the manifestly covariant evolution of the distribution function of full classical many-body systems. For such global evolution the Bogoliubov functional assumption is justified. In particular, using the Balescu-Wallenborn projection operator approach we find that the distribution function of full many-body systems is completely determined by the reduced one-body distribution function. A manifestly covariant closed nonlinear equation satisfied by the reduced one-body distribution function is rigorously derived. We also discuss extensively the generalization to general relativity especially an application to self-gravitating systems. [source] Ultra-fast dynamics in solids: non-equilibrium behaviour of magnetism and atomic structureANNALEN DER PHYSIK, Issue 7-8 2009K.H. Bennemann Abstract Non-equilibrium physics is of fundamental interest, for example, for extensions of statistical mechanics and thermodynamics. In particular, it is important to understand how conservation laws like energy conservation and angular-momentum conservation in magnetic solids control the time scale of the dynamics. Laser irradiation may cause intense electronic excitations and thus a strong non-equilibrium state. Results are presented for the ultra-fast response of magnetism in ferromagnetic transition metals like Ni, Co, Fe, and Gd and furthermore of the atomic structure in semiconductors like Si, Ge, and InSb. Non-thermal melting is a most spectacular example of ultra-fast bond breaking. Time-resolved magnetooptical experiments yielding sub-picosecond spin dynamics are discussed. The spin dynamics is accompanied by THz light emission. The structural changes in semiconductors, bond changes sp3 , s2p2, and phase transitions occur within about 100 fs. The results also shed light on electron-transfer processes, on ionization, and on molecular dissociation dynamics, which may occur during fs and as times. We discuss the application of time-resolved analysis to tunnelling problems and the phase diagram of high-Tc superconductivity. [source] Ultra-fast dynamics in solids: non-equilibrium behaviour of magnetism and atomic structureANNALEN DER PHYSIK, Issue 7-8 2009K.H. Bennemann Abstract Non-equilibrium physics is of fundamental interest, for example, for extensions of statistical mechanics and thermodynamics. In particular, it is important to understand how conservation laws like energy conservation and angular-momentum conservation in magnetic solids control the time scale of the dynamics. Laser irradiation may cause intense electronic excitations and thus a strong non-equilibrium state. Results are presented for the ultra-fast response of magnetism in ferromagnetic transition metals like Ni, Co, Fe, and Gd and furthermore of the atomic structure in semiconductors like Si, Ge, and InSb. Non-thermal melting is a most spectacular example of ultra-fast bond breaking. Time-resolved magnetooptical experiments yielding sub-picosecond spin dynamics are discussed. The spin dynamics is accompanied by THz light emission. The structural changes in semiconductors, bond changes sp3 , s2p2, and phase transitions occur within about 100 fs. The results also shed light on electron-transfer processes, on ionization, and on molecular dissociation dynamics, which may occur during fs and as times. We discuss the application of time-resolved analysis to tunnelling problems and the phase diagram of high-Tc superconductivity. [source] Nonequilibrium quantum anharmonic oscillator and scalar field: high temperature approximationsANNALEN DER PHYSIK, Issue 6 2009R.F. Alvarez-Estrada Abstract We treat a relativistic quantum boson gas, described by a scalar quantum field, with quartic self-interaction (,4) in three spatial dimensions: we review the known equilibrium case and present new proposals off-equilibrium. For high temperature and large spatial scales, the behaviour of the gas at equilibrium simplifies nonperturbatively (equilibrium dimensional reduction or EDR): its thermodynamics is described by classical statistical mechanics with some quantum field effects. By assumption, the initial state of the gas off-equilibrium includes interactions and inhomogeneities and is not far from thermal equilibrium. We employ real-time generating functionals and obtain the free nonequilibrium correlators at non-zero temperature. The nonequilibrium quantum gas appears to simplify nonperturbatively in the regime of high temperature and large temporal and spatial scales (nonequilibrium dimensional reduction or NEDR), its dynamics being described by classical statistical mechanics with some quantum field effects. We outline the renormalization of the ,4 theory, the nonequilibrium statistical mechanics of a quantum anharmonic oscillator and the high temperature simplifications, all of which provide very useful hints for NEDR in the field case. Our main proposals are NEDR and the associated new (renormalized) real-time nonequilibrium generating functionals for the ,4 theory. [source] Nonequilibrium statistical mechanics of swarms of driven particlesCOMPLEXITY, Issue 4 2003Werner Ebeling Abstract As a rough model for the collective motions of cells and organisms we develop here the statistical mechanics of swarms of self-propelled particles. Our approach is closely related to the recently developed theory of active Brownian motion and the theory of canonical-dissipative systems. Free motion and motion of a swarms confined in an external field is studied. Briefly, the case of particles confined on a ring and interacting by repulsive forces is studied. In more detail we investigate self-confinement by Morse-type attracting forces. We begin with pairs N = 2; the attractors and distribution functions are discussed, then the case N > 2 is discussed. Simulations for several dynamical modes of swarms of active Brownian particles interacting by Morse forces are presented. In particular we study rotations, drift, fluctuations of shape, and cluster formation. © 2003 Wiley Periodicals, Inc. [source] | |||||||||||||||||||