General H-Theorem and Entropies That Violate the Second Law
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A Closure Scheme for Chemical Master Equations
A closure scheme for chemical master equations Patrick Smadbeck and Yiannis N. Kaznessis1 Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455 Edited by Wing Hung Wong, Stanford University, Stanford, CA, and approved July 16, 2013 (received for review April 8, 2013) Probability reigns in biology, with random molecular events dictating equation governs the evolution of the probability, PðX; tÞ,thatthe the fate of individual organisms, and propelling populations of system is at state X at time t: species through evolution. In principle, the master probability À Á equation provides the most complete model of probabilistic behavior ∂P X; t X À Á À Á À Á À Á = T X X′ P X′; t − T X′ X P X; t : [1] in biomolecular networks. In practice, master equations describing ∂t complex reaction networks have remained unsolved for over 70 X′ years. This practical challenge is a reason why master equations, for À Á all their potential, have not inspired biological discovery. Herein, we This is a probability conservation equation, where T X X′ is present a closure scheme that solves the master probability equation the transition propensity from any possible state X′ to state X of networks of chemical or biochemical reactions. We cast the master per unit time. In a network of chemical or biochemical reactions, equation in terms of ordinary differential equations that describe the the transition probabilities are defined by the reaction-rate laws time evolution of probability distribution moments. We postulate as a set of Poisson-distributed reaction propensities; these simply that a finite number of moments capture all of the necessary dictate how many reaction events take place per unit time. -
Fluctuations of Spacetime and Holographic Noise in Atomic Interferometry
General Relativity and Gravitation (2011) DOI 10.1007/s10714-010-1137-7 RESEARCHARTICLE Ertan Gokl¨ u¨ · Claus Lammerzahl¨ Fluctuations of spacetime and holographic noise in atomic interferometry Received: 10 December 2009 / Accepted: 12 December 2010 c Springer Science+Business Media, LLC 2010 Abstract On small scales spacetime can be understood as some kind of space- time foam of fluctuating bubbles or loops which are expected to be an outcome of a theory of quantum gravity. One recently discussed model for this kind of space- time fluctuations is the holographic principle which allows to deduce the structure of these fluctuations. We review and discuss two scenarios which rely on the holo- graphic principle leading to holographic noise. One scenario leads to fluctuations of the spacetime metric affecting the dynamics of quantum systems: (i) an appar- ent violation of the equivalence principle, (ii) a modification of the spreading of wave packets, and (iii) a loss of quantum coherence. All these effects can be tested with cold atoms. Keywords Quantum gravity phenomenology, Holographic principle, Spacetime fluctuations, UFF, Decoherence, Wavepacket dynamics 1 Introduction The unification of quantum mechanics and General Relativity is one of the most outstanding problems of contemporary physics. Though yet there is no theory of quantum gravity. There are a lot of reasons why gravity must be quantized [33]. For example, (i) because of the fact that all matter fields are quantized the interactions, generated by theses fields, must also be quantized. (ii) In quantum mechanics and General Relativity the notion of time is completely different. (iii) Generally, in General Relativity singularities necessarily appear where physical laws are not valid anymore. -
A Simple Method to Estimate Entropy and Free Energy of Atmospheric Gases from Their Action
Article A Simple Method to Estimate Entropy and Free Energy of Atmospheric Gases from Their Action Ivan Kennedy 1,2,*, Harold Geering 2, Michael Rose 3 and Angus Crossan 2 1 Sydney Institute of Agriculture, University of Sydney, NSW 2006, Australia 2 QuickTest Technologies, PO Box 6285 North Ryde, NSW 2113, Australia; [email protected] (H.G.); [email protected] (A.C.) 3 NSW Department of Primary Industries, Wollongbar NSW 2447, Australia; [email protected] * Correspondence: [email protected]; Tel.: + 61-4-0794-9622 Received: 23 March 2019; Accepted: 26 April 2019; Published: 1 May 2019 Abstract: A convenient practical model for accurately estimating the total entropy (ΣSi) of atmospheric gases based on physical action is proposed. This realistic approach is fully consistent with statistical mechanics, but reinterprets its partition functions as measures of translational, rotational, and vibrational action or quantum states, to estimate the entropy. With all kinds of molecular action expressed as logarithmic functions, the total heat required for warming a chemical system from 0 K (ΣSiT) to a given temperature and pressure can be computed, yielding results identical with published experimental third law values of entropy. All thermodynamic properties of gases including entropy, enthalpy, Gibbs energy, and Helmholtz energy are directly estimated using simple algorithms based on simple molecular and physical properties, without resource to tables of standard values; both free energies are measures of quantum field states and of minimal statistical degeneracy, decreasing with temperature and declining density. We propose that this more realistic approach has heuristic value for thermodynamic computation of atmospheric profiles, based on steady state heat flows equilibrating with gravity. -
LECTURES on MATHEMATICAL STATISTICAL MECHANICS S. Adams
ISSN 0070-7414 Sgr´ıbhinn´ıInstiti´uid Ard-L´einnBhaile´ Atha´ Cliath Sraith. A. Uimh 30 Communications of the Dublin Institute for Advanced Studies Series A (Theoretical Physics), No. 30 LECTURES ON MATHEMATICAL STATISTICAL MECHANICS By S. Adams DUBLIN Institi´uid Ard-L´einnBhaile´ Atha´ Cliath Dublin Institute for Advanced Studies 2006 Contents 1 Introduction 1 2 Ergodic theory 2 2.1 Microscopic dynamics and time averages . .2 2.2 Boltzmann's heuristics and ergodic hypothesis . .8 2.3 Formal Response: Birkhoff and von Neumann ergodic theories9 2.4 Microcanonical measure . 13 3 Entropy 16 3.1 Probabilistic view on Boltzmann's entropy . 16 3.2 Shannon's entropy . 17 4 The Gibbs ensembles 20 4.1 The canonical Gibbs ensemble . 20 4.2 The Gibbs paradox . 26 4.3 The grandcanonical ensemble . 27 4.4 The "orthodicity problem" . 31 5 The Thermodynamic limit 33 5.1 Definition . 33 5.2 Thermodynamic function: Free energy . 37 5.3 Equivalence of ensembles . 42 6 Gibbs measures 44 6.1 Definition . 44 6.2 The one-dimensional Ising model . 47 6.3 Symmetry and symmetry breaking . 51 6.4 The Ising ferromagnet in two dimensions . 52 6.5 Extreme Gibbs measures . 57 6.6 Uniqueness . 58 6.7 Ergodicity . 60 7 A variational characterisation of Gibbs measures 62 8 Large deviations theory 68 8.1 Motivation . 68 8.2 Definition . 70 8.3 Some results for Gibbs measures . 72 i 9 Models 73 9.1 Lattice Gases . 74 9.2 Magnetic Models . 75 9.3 Curie-Weiss model . 77 9.4 Continuous Ising model . -
Entropy and H Theorem the Mathematical Legacy of Ludwig Boltzmann
ENTROPY AND H THEOREM THE MATHEMATICAL LEGACY OF LUDWIG BOLTZMANN Cambridge/Newton Institute, 15 November 2010 C´edric Villani University of Lyon & Institut Henri Poincar´e(Paris) Cutting-edge physics at the end of nineteenth century Long-time behavior of a (dilute) classical gas Take many (say 1020) small hard balls, bouncing against each other, in a box Let the gas evolve according to Newton’s equations Prediction by Maxwell and Boltzmann The distribution function is asymptotically Gaussian v 2 f(t, x, v) a exp | | as t ≃ − 2T → ∞ Based on four major conceptual advances 1865-1875 Major modelling advance: Boltzmann equation • Major mathematical advance: the statistical entropy • Major physical advance: macroscopic irreversibility • Major PDE advance: qualitative functional study • Let us review these advances = journey around centennial scientific problems ⇒ The Boltzmann equation Models rarefied gases (Maxwell 1865, Boltzmann 1872) f(t, x, v) : density of particles in (x, v) space at time t f(t, x, v) dxdv = fraction of mass in dxdv The Boltzmann equation (without boundaries) Unknown = time-dependent distribution f(t, x, v): ∂f 3 ∂f + v = Q(f,f) = ∂t i ∂x Xi=1 i ′ ′ B(v v∗,σ) f(t, x, v )f(t, x, v∗) f(t, x, v)f(t, x, v∗) dv∗ dσ R3 2 − − Z v∗ ZS h i The Boltzmann equation (without boundaries) Unknown = time-dependent distribution f(t, x, v): ∂f 3 ∂f + v = Q(f,f) = ∂t i ∂x Xi=1 i ′ ′ B(v v∗,σ) f(t, x, v )f(t, x, v∗) f(t, x, v)f(t, x, v∗) dv∗ dσ R3 2 − − Z v∗ ZS h i The Boltzmann equation (without boundaries) Unknown = time-dependent distribution -
A Molecular Modeler's Guide to Statistical Mechanics
A Molecular Modeler’s Guide to Statistical Mechanics Course notes for BIOE575 Daniel A. Beard Department of Bioengineering University of Washington Box 3552255 [email protected] (206) 685 9891 April 11, 2001 Contents 1 Basic Principles and the Microcanonical Ensemble 2 1.1 Classical Laws of Motion . 2 1.2 Ensembles and Thermodynamics . 3 1.2.1 An Ensembles of Particles . 3 1.2.2 Microscopic Thermodynamics . 4 1.2.3 Formalism for Classical Systems . 7 1.3 Example Problem: Classical Ideal Gas . 8 1.4 Example Problem: Quantum Ideal Gas . 10 2 Canonical Ensemble and Equipartition 15 2.1 The Canonical Distribution . 15 2.1.1 A Derivation . 15 2.1.2 Another Derivation . 16 2.1.3 One More Derivation . 17 2.2 More Thermodynamics . 19 2.3 Formalism for Classical Systems . 20 2.4 Equipartition . 20 2.5 Example Problem: Harmonic Oscillators and Blackbody Radiation . 21 2.5.1 Classical Oscillator . 22 2.5.2 Quantum Oscillator . 22 2.5.3 Blackbody Radiation . 23 2.6 Example Application: Poisson-Boltzmann Theory . 24 2.7 Brief Introduction to the Grand Canonical Ensemble . 25 3 Brownian Motion, Fokker-Planck Equations, and the Fluctuation-Dissipation Theo- rem 27 3.1 One-Dimensional Langevin Equation and Fluctuation- Dissipation Theorem . 27 3.2 Fokker-Planck Equation . 29 3.3 Brownian Motion of Several Particles . 30 3.4 Fluctuation-Dissipation and Brownian Dynamics . 32 1 Chapter 1 Basic Principles and the Microcanonical Ensemble The first part of this course will consist of an introduction to the basic principles of statistical mechanics (or statistical physics) which is the set of theoretical techniques used to understand microscopic systems and how microscopic behavior is reflected on the macroscopic scale. -
Quantum Entanglement Inferred by the Principle of Maximum Tsallis Entropy
Quantum entanglement inferred by the principle of maximum Tsallis entropy Sumiyoshi Abe1 and A. K. Rajagopal2 1College of Science and Technology, Nihon University, Funabashi, Chiba 274-8501, Japan 2Naval Research Laboratory, Washington D.C., 20375-5320, U.S.A. The problem of quantum state inference and the concept of quantum entanglement are studied using a non-additive measure in the form of Tsallis’ entropy indexed by the positive parameter q. The maximum entropy principle associated with this entropy along with its thermodynamic interpretation are discussed in detail for the Einstein- Podolsky-Rosen pair of two spin-1/2 particles. Given the data on the Bell-Clauser- Horne-Shimony-Holt observable, the analytic expression is given for the inferred quantum entangled state. It is shown that for q greater than unity, indicating the sub- additive feature of the Tsallis entropy, the entangled region is small and enlarges as one goes into the super-additive regime where q is less than unity. It is also shown that quantum entanglement can be quantified by the generalized Kullback-Leibler entropy. quant-ph/9904088 26 Apr 1999 PACS numbers: 03.67.-a, 03.65.Bz I. INTRODUCTION Entanglement is a fundamental concept highlighting non-locality of quantum mechanics. It is well known [1] that the Bell inequalities, which any local hidden variable theories should satisfy, can be violated by entangled states of a composite system described by quantum mechanics. Experimental results [2] suggest that naive local realism à la Einstein, Podolsky, and Rosen [3] may not actually hold. Related issues arising out of the concept of quantum entanglement are quantum cryptography, quantum teleportation, and quantum computation. -
Entropy: from the Boltzmann Equation to the Maxwell Boltzmann Distribution
Entropy: From the Boltzmann equation to the Maxwell Boltzmann distribution A formula to relate entropy to probability Often it is a lot more useful to think about entropy in terms of the probability with which different states are occupied. Lets see if we can describe entropy as a function of the probability distribution between different states. N! WN particles = n1!n2!....nt! stirling (N e)N N N W = = N particles n1 n2 nt n1 n2 nt (n1 e) (n2 e) ....(nt e) n1 n2 ...nt with N pi = ni 1 W = N particles n1 n2 nt p1 p2 ...pt takeln t lnWN particles = "#ni ln pi i=1 divide N particles t lnW1particle = "# pi ln pi i=1 times k t k lnW1particle = "k# pi ln pi = S1particle i=1 and t t S = "N k p ln p = "R p ln p NA A # i # i i i=1 i=1 ! Think about how this equation behaves for a moment. If any one of the states has a probability of occurring equal to 1, then the ln pi of that state is 0 and the probability of all the other states has to be 0 (the sum over all probabilities has to be 1). So the entropy of such a system is 0. This is exactly what we would have expected. In our coin flipping case there was only one way to be all heads and the W of that configuration was 1. Also, and this is not so obvious, the maximal entropy will result if all states are equally populated (if you want to see a mathematical proof of this check out Ken Dill’s book on page 85). -
Semi-Classical Lindblad Master Equation for Spin Dynamics
Journal of Physics A: Mathematical and Theoretical J. Phys. A: Math. Theor. 54 (2021) 235201 (13pp) https://doi.org/10.1088/1751-8121/abf79b Semi-classical Lindblad master equation for spin dynamics Jonathan Dubois∗ ,UlfSaalmann and Jan M Rost Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Straße 38, 01187 Dresden, Germany E-mail: [email protected], [email protected] and [email protected] Received 25 January 2021, revised 18 March 2021 Accepted for publication 13 April 2021 Published 7 May 2021 Abstract We derive the semi-classical Lindblad master equation in phase space for both canonical and non-canonicalPoisson brackets using the Wigner–Moyal formal- ism and the Moyal star-product. The semi-classical limit for canonical dynam- ical variables, i.e. canonical Poisson brackets, is the Fokker–Planck equation, as derived before. We generalize this limit and show that it holds also for non- canonical Poisson brackets. Examples are gyro-Poisson brackets, which occur in spin ensembles, systems of recent interest in atomic physics and quantum optics. We show that the equations of motion for the collective spin variables are given by the Bloch equations of nuclear magnetization with relaxation. The Bloch and relaxation vectors are expressed in terms of the microscopic operators: the Hamiltonian and the Lindblad functions in the Wigner–Moyal formalism. Keywords: Lindblad master equations,non-canonicalvariables,Hamiltonian systems, spin systems, classical and semi-classical limit, thermodynamical limit (Some fgures may appear in colour only in the online journal) 1. Lindblad quantum master equation Since perfect isolation of a system is an idealization [1, 2], open microscopic systems, which interact with an environment, are prevalent in nature as well as in experiments. -
On the Exact Variance of Tsallis Entanglement Entropy in a Random Pure State
entropy Article On the Exact Variance of Tsallis Entanglement Entropy in a Random Pure State Lu Wei Department of Electrical and Computer Engineering, University of Michigan, Dearborn, MI 48128, USA; [email protected] Received: 26 April 2019; Accepted: 25 May 2019; Published: 27 May 2019 Abstract: The Tsallis entropy is a useful one-parameter generalization to the standard von Neumann entropy in quantum information theory. In this work, we study the variance of the Tsallis entropy of bipartite quantum systems in a random pure state. The main result is an exact variance formula of the Tsallis entropy that involves finite sums of some terminating hypergeometric functions. In the special cases of quadratic entropy and small subsystem dimensions, the main result is further simplified to explicit variance expressions. As a byproduct, we find an independent proof of the recently proven variance formula of the von Neumann entropy based on the derived moment relation to the Tsallis entropy. Keywords: entanglement entropy; quantum information theory; random matrix theory; variance 1. Introduction Classical information theory is the theory behind the modern development of computing, communication, data compression, and other fields. As its classical counterpart, quantum information theory aims at understanding the theoretical underpinnings of quantum science that will enable future quantum technologies. One of the most fundamental features of quantum science is the phenomenon of quantum entanglement. Quantum states that are highly entangled contain more information about different parts of the composite system. As a step to understand quantum entanglement, we choose to study the entanglement property of quantum bipartite systems. The quantum bipartite model, proposed in the seminal work of Page [1], is a standard model for describing the interaction of a physical object with its environment for various quantum systems. -
Arxiv:1707.03526V1 [Cond-Mat.Stat-Mech] 12 Jul 2017 Eq
Generalized Ensemble Theory with Non-extensive Statistics Ke-Ming Shen,∗ Ben-Wei Zhang,y and En-Ke Wang Key Laboratory of Quark & Lepton Physics (MOE) and Institute of Particle Physics, Central China Normal University, Wuhan 430079, China (Dated: October 17, 2018) The non-extensive canonical ensemble theory is reconsidered with the method of Lagrange multipliers by maximizing Tsallis entropy, with the constraint that the normalized term of P q Tsallis' q−average of physical quantities, the sum pj , is independent of the probability pi for Tsallis parameter q. The self-referential problem in the deduced probability and thermal quantities in non-extensive statistics is thus avoided, and thermodynamical relationships are obtained in a consistent and natural way. We also extend the study to the non-extensive grand canonical ensemble theory and obtain the q-deformed Bose-Einstein distribution as well as the q-deformed Fermi-Dirac distribution. The theory is further applied to the general- ized Planck law to demonstrate the distinct behaviors of the various generalized q-distribution functions discussed in literature. I. INTRODUCTION In the last thirty years the non-extensive statistical mechanics, based on Tsallis entropy [1,2] and the corresponding deformed exponential function, has been developed and attracted a lot of attentions with a large amount of applications in rather diversified fields [3]. Tsallis non- extensive statistical mechanics is a generalization of the common Boltzmann-Gibbs (BG) statistical PW mechanics by postulating a generalized entropy of the classical one, S = −k i=1 pi ln pi: W X q Sq = −k pi lnq pi ; (1) i=1 where k is a positive constant and denotes Boltzmann constant in BG statistical mechanics. -
The Master Equation
The Master Equation Johanne Hizanidis November 2002 Contents 1 Stochastic Processes 1 1.1 Why and how do stochastic processes enter into physics? . 1 1.2 Brownian Motion: a stochastic process . 2 2 Markov processes 2 2.1 The conditional probability . 2 2.2 Markov property . 2 3 The Chapman-Kolmogorov (C-K) equation 3 3.1 The C-K equation for stationary and homogeneous processes . 3 4 The Master equation 4 4.1 Derivation of the Master equation from the C-K equation . 4 4.2 Detailed balance . 5 5 The mean-field equation 5 6 One-step processes: examples 7 6.1 The Poisson process . 8 6.2 The decay process . 8 6.3 A Chemical reaction . 9 A Appendix 11 1 STOCHASTIC PROCESSES 1 Stochastic Processes A stochastic process is the time evolution of a stochastic variable. So if Y is the stochastic variable, the stochastic process is Y (t). A stochastic variable is defined by specifying the set of possible values called 'range' or 'set of states' and the probability distribution over this set. The set can be discrete (e.g. number of molecules of a component in a reacting mixture),continuous (e.g. the velocity of a Brownian particle) or multidimensional. In the latter case, the stochastic variable is a vector (e.g. the three velocity components of a Brownian particle). The figure below helps to get a more intuitive idea of a (discrete) stochastic process. At successive times, the most probable values of Y have been drawn as heavy dots. We may select a most probable trajectory from such a picture.