DOCSLIB.ORG

Nonequilibrium Critical Phenomena: Exact Langevin Equations, Erosion of Tilted Landscapes

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Nonequilibrium Critical Phenomena: Exact Langevin Equations, Erosion of Tilted Landscapes Nonequilibrium critical phenomena : exact Langevin equations, erosion of tilted landscapes. Charlie Duclut To cite this version: Charlie Duclut. Nonequilibrium critical phenomena : exact Langevin equations, erosion of tilted landscapes.. Physics [physics]. Université Pierre et Marie Curie - Paris VI, 2017. English. NNT : 2017PA066241. tel-01690438 HAL Id: tel-01690438 https://tel.archives-ouvertes.fr/tel-01690438 Submitted on 23 Jan 2018 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. UNIVERSITÉ PIERRE ET MARIE CURIE ÉCOLE DOCTORALE PHYSIQUE EN ÎLE-DE-FRANCE THÈSE pour obtenir le titre de Docteur de l’Université Pierre et Marie Curie Mention : PHYSIQUE THÉORIQUE Présentée et soutenue par Charlie DUCLUT Nonequilibrium critical phenomena: exact Langevin equations, erosion of tilted landscapes. Thèse dirigée par Bertrand DELAMOTTE préparée au Laboratoire de Physique Théorique de la Matière Condensée soutenue le 11 septembre 2017 devant le jury composé de : M. Andrea GAMBASSI Rapporteur M. Michael SCHERER Rapporteur M. Giulio BIROLI Examinateur Mme Leticia CUGLIANDOLO Présidente du jury M. Andrei FEDORENKO Examinateur M. Bertrand DELAMOTTE Directeur de thèse Remerciements First of all, I would like to thank the referees Andrea Gambassi and Michael Scherer for taking the time to carefully read the manuscript. I also thank the other jury members, Giulio Biroli, Leticia Cugliandolo, and Andrei Fedorenko, for accepting to get into my work and evaluate it. Mes remerciements vont ensuite à Bertrand Delamotte, mon directeur de thèse, pour l’im- mense pédagogie dont il a su faire preuve pendant mes trois années de thèse. Je le remercie pour toutes les explications et les nombreux éclaircissements qu’il m’a donnés, pour le recul qu’il m’a permis de prendre sur mon travail. Sans lui, ce manuscrit n’aurait bien évidemment pas pu voir le jour. Je remercie également chaleureusement Julien Vidal, parrain de thèse et d’escalade, pour ses nombreux conseils, son soutien, et les nombreuses escapades à Fontainebleau et en montagne, qui je l’espère continueront après mon départ du laboratoire. Je le remercie également, ainsi qu’Ivan Dornic, pour leur relecture de mon manuscrit. Merci aussi à Hugues Chaté et Ivan, avec lesquels j’ai beaucoup apprécié collaborer, pour leurs conseils et recommandations pour ma recherche de postdoc. Mon séjour de trois ans au LPTMC n’aurait pas été le même sans toutes les personnes qui le composent : en particulier, je remercie vivement Pascal Viot, son directeur, pour sa présence et sa disponibilité. Merci également aux secrétaires et comptables du laboratoire, Diane Domand, Sylvie Dalla Foglia et Liliane Cruzel pour leur gentillesse, leur patience et leur aide. Merci également à Michel Quaggetto pour les nombreux problèmes informatiques qu’il m’a aidé à résoudre. Merci à Boris Mantisi et Annie Lemarchand pour leurs crumbles et autres gâteaux improvisés qui ont pu adoucir et réchauffer certaines après-midis d’hiver. Merci aux anciens thésards et post- docs qui m’ont précédé au laboratoire, Thibault Debelhoir, Frédéric Léonard, Simon Moulieras, Elena Tarquini, et Andréas Tresmontant pour toutes les pauses café et les soirées autour d’un verre. Merci en particulier à Fred et Thibault pour les discussions politiques, les ateliers pancar- tes et les discosoupes. Merci aussi à Fred de m’avoir initié à la gymnastique, et à Thibault pour toutes les discussions, pour sa gentillesse et son altruisme. Un grand merci également aux doctorants de mon année avec lesquels j’ai beaucoup appré- cié passer du temps dans et hors du labo : Chloé, Charlotte, Elsa, Félix, Nico et Stanley. En trois années ils sont devenus bien plus que des collègues et ils me manqueront beaucoup en Allemagne ! Merci en particulier à Chloé et Elsa pour avoir rendu bien plus faciles nos longues soirées de rédaction. Merci à mes compagnons de grimpe, qui sans cesse me rappellent la valeur d’un sandwiche et d’un verre d’eau. Un immense merci à sketchy Tonio, le premier compagnon des sorties régulières à Bleau, à Alexis le téméraire, à Jean et à ses messages ambivalents voire ambidextres, et à John qui les déteste, à Édith le panda, à Quentin qui pourrait s’acheter un sac de sport, à Marion l’alpiniste qui revient de loin, et merci bien sûr à Léo, celui qui a choisi l’autre voie et qui m’a beaucoup fait douté. Merci aussi à Guillaume et Raphaël qui prennent la relève des grimpeurs parisiens ! Merci évidemment à l’AS de Jussieu (et ses nombreuses ramifications) et surtout à ses membres tous passionnés et passionnants : Adeline, Charlotte, Christophe, Constant, Flavien, Goki, Horace, Jeanne, Julia, Kévin, Lucie, Manu, Maria Belen, Marie, Maud, i ii Romain, Thomas, Thomas... Merci également à mes colocataires pour les repas et tous les moments partagés, merci à Édouard – le seul vrai – pour les risottos, les mille-feuilles, et tous ses petits plats, et merci à ceux qui se sont succédés mais qui hantent encore les lieux : en particulier Baptiste, Marguerite, Joris, Arman et Thibaut. Un gigantesque merci à celles et ceux qui ne font pas (encore) d’escalade mais qui comptent beaucoup quand même : Delphine, Muriel, Marc l’insaisissable, Aïcha, Charlotte, Corentin, Erwan, Maxime mais également Lucie, Thibaut, Éléonore, David et bien d’autres. Merci bien sûr aussi à Maya, à Paul et à Édouard, qui sont là depuis si longtemps, qui ont toujours cru en moi, ont toujours su me donner beaucoup de confiance et que je n’oublie pas une seconde. Je remercie également mes parents, mon frère et ma sœur pour être simplement là, pour avoir su balayer mes hésitations lorsque j’en ai eues, pour m’avoir sans cesse soutenu dans mes choix et mes études. To Bibu Contents Introduction 1 I Scale invariance, universality and renormalization group7 I.1 Scale invariance and phase transitions........................8 I.1.1 Phase transitions................................8 I.1.2 Universality in the second-order phase transitions.............. 10 I.2 Renormalization group................................. 12 I.2.1 Integrating the microscopic degrees of freedom step by step........ 12 I.2.2 Universality seen by the renormalization group............... 15 I.2.3 An example: the central-limit theorem seen by the RG........... 19 I.3 The nonperturbative renormalization group..................... 20 I.3.1 Exact renormalization group equation for the action............ 20 I.3.2 The effective average action method..................... 21 I.3.3 An example: the φ4 theory........................... 28 I.3.4 Results...................................... 32 I.4 NPRG: some answers to its criticisms......................... 36 I.4.1 NPRG results.................................. 36 I.4.2 Retrieving the one-loop perturbative results................. 39 I.4.3 Controlling the approximations........................ 43 I.5 Conclusion....................................... 46 II Out-of-equilibrium phase transitions 49 II.1 Summary of the different Langevin equations.................... 51 II.2 Mesoscopic description: the Langevin equation................... 51 II.2.1 A phenomenological approach........................ 52 II.2.2 Numerical resolution of a Langevin equation................. 55 II.2.3 Field theory for a Langevin equation..................... 57 II.3 Microscopic description: the master equation.................... 60 II.3.1 Reaction-diffusion processes.......................... 60 II.3.2 Master equation for reaction-diffusion processes............... 67 II.3.3 Field theory for reaction-diffusion processes: the Doi-Peliti formalism... 69 II.4 Langevin equations for reaction-diffusion processes................. 73 II.4.1 Approximate derivation of a Langevin equation............... 74 II.4.2 Microscopic Langevin equation and imaginary noise............ 76 II.5 Microscopic Langevin equation and duality formalism................ 81 II.5.1 Langevin equation in the duality formalism................. 81 II.5.2 Duality in the field-theoretical context.................... 83 II.5.3 Duality in the probability-generating function formalism.......... 90 II.6 Conclusion....................................... 91 v vi CONTENTS III Frequency regulator 93 III.1 NPRG approach to nonequilibrium.......................... 96 III.1.1 Effective average action and exact flow equation.............. 96 III.1.2 Some general properties of the out-of-equilibrium regulator........ 97 III.2 The model A as a benchmark............................. 98 III.2.1 Model A, field theory and fluctuation-dissipation theorem......... 98 III.2.2 NPRG formulation............................... 100 III.2.3 NPRG results without a frequency regulator................. 104 III.2.4 NPRG results with a frequency regulator................... 106 III.3 Conclusion....................................... 110 IV Landscape erosion 111 IV.1 Experimental facts and models............................ 112 IV.1.1 Experimental data............................... 112 IV.1.2 Minimal ingredients for an erosion model.................. 115 IV.1.3 Large length scale: the Kardar-Parisi-Zhang
Load more

Recommended publications
  • The Effect of Compression and Expansion on Stochastic Reaction Networks
    IMT School for Advanced Studies, Lucca Lucca, Italy The Effect of Compression and Expansion on Stochastic Reaction Networks PhD Program in Institutions, Markets and Technologies Curriculum in Computer Science and Systems Engineering (CSSE) XXXI Cycle By Tabea Waizmann 2021 The dissertation of Tabea Waizmann is approved. Program Coordinator: Prof. Rocco De Nicola, IMT Lucca Supervisor: Prof. Mirco Tribastone, IMT Lucca The dissertation of Tabea Waizmann has been reviewed by: Dr. Catia Trubiani, Gran Sasso Science Institute Prof. Michele Loreti, University of Camerino IMT School for Advanced Studies, Lucca 2021 To everyone who believed in me. Contents List of Figures ix List of Tables xi Acknowledgements xiii Vita and Publications xv Abstract xviii 1 Introduction 1 2 Background 6 2.1 Multisets . .6 2.2 Reaction Networks . .7 2.3 Ordinary Lumpability . 11 2.4 Layered Queuing Networks . 12 2.5 PEPA . 16 3 Coarse graining mass-action stochastic reaction networks by species equivalence 19 3.1 Species Equivalence . 20 3.1.1 Species equivalence as a generalization of Markov chain ordinary lumpability . 27 3.1.2 Characterization of SE for mass-action networks . 27 3.1.3 Computation of the maximal SE and reduced net- work . 28 vii 3.2 Applications . 31 3.2.1 Computational systems biology . 31 3.2.2 Epidemic processes in networks . 33 3.3 Discussion . 36 4 DiffLQN: Differential Equation Analysis of Layered Queuing Networks 37 4.1 DiffLQN .............................. 38 4.1.1 Architecture . 38 4.1.2 Capabilities . 38 4.1.3 Syntax . 39 4.2 Case Study: Client-Server dynamics . 41 4.3 Discussion .
    [Show full text]
  • Intrinsic Noise Analyzer: a Software Package for the Exploration of Stochastic Biochemical Kinetics Using the System Size Expansion
    Intrinsic Noise Analyzer: A Software Package for the Exploration of Stochastic Biochemical Kinetics Using the System Size Expansion Philipp Thomas1,2,3., Hannes Matuschek4., Ramon Grima1,2* 1 School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom, 2 SynthSys Edinburgh, University of Edinburgh, Edinburgh, United Kingdom, 3 Department of Physics, Humboldt University of Berlin, Berlin, Germany, 4 Institute of Physics and Astronomy, University of Potsdam, Potsdam, Germany Abstract The accepted stochastic descriptions of biochemical dynamics under well-mixed conditions are given by the Chemical Master Equation and the Stochastic Simulation Algorithm, which are equivalent. The latter is a Monte-Carlo method, which, despite enjoying broad availability in a large number of existing software packages, is computationally expensive due to the huge amounts of ensemble averaging required for obtaining accurate statistical information. The former is a set of coupled differential-difference equations for the probability of the system being in any one of the possible mesoscopic states; these equations are typically computationally intractable because of the inherently large state space. Here we introduce the software package intrinsic Noise Analyzer (iNA), which allows for systematic analysis of stochastic biochemical kinetics by means of van Kampen’s system size expansion of the Chemical Master Equation. iNA is platform independent and supports the popular SBML format natively. The present implementation is the first to adopt a complementary approach that combines state-of-the-art analysis tools using the computer algebra system Ginac with traditional methods of stochastic simulation. iNA integrates two approximation methods based on the system size expansion, the Linear Noise Approximation and effective mesoscopic rate equations, which to-date have not been available to non-expert users, into an easy-to-use graphical user interface.
    [Show full text]
  • System Size Expansion Using Feynman Rules and Diagrams
    System size expansion using Feynman rules and diagrams Philipp Thomas∗y, Christian Fleck,z Ramon Grimay, Nikola Popovi´c∗ October 2, 2018 Abstract Few analytical methods exist for quantitative studies of large fluctuations in stochastic systems. In this article, we develop a simple diagrammatic approach to the Chemical Master Equation that allows us to calculate multi-time correlation functions which are accurate to a any desired order in van Kampen's system size expansion. Specifically, we present a set of Feynman rules from which this diagrammatic perturbation expansion can be constructed algo- rithmically. We then apply the methodology to derive in closed form the leading order corrections to the linear noise approximation of the intrinsic noise power spectrum for general biochemical reaction networks. Finally, we illustrate our results by describing noise-induced oscillations in the Brusselator reaction scheme which are not captured by the common linear noise approximation. 1 Introduction The quantification of intrinsic fluctuations in biochemical networks is becoming increasingly important for the study of living systems, as some of the key molecular players are expressed in low numbers of molecules per cell [1]. The most commonly employed method for investigating this type of cell-to-cell variability is the stochastic simulation algorithm (SSA) [2]. While the SSA allows for the exact sampling of trajectories of discrete intracellular biochemistry, it is computationally expensive, which often prevents one from obtaining statistics for large ranges of the biological parameter space. A widely used approach to overcome these limitations has been the linear noise approximation (LNA) [3, 4, 5]. The LNA is obtained to leading order in van Kampen's system size expansion [6].
    [Show full text]
  • Approximate Probability Distributions of the Master Equation
    Approximate probability distributions of the master equation Philipp Thomas∗ School of Mathematics and School of Biological Sciences, University of Edinburgh Ramon Grimay School of Biological Sciences, University of Edinburgh Master equations are common descriptions of mesoscopic systems. Analytical solutions to these equations can rarely be obtained. We here derive an analytical approximation of the time-dependent probability distribution of the master equation using orthogonal polynomials. The solution is given in two alternative formulations: a series with continuous and a series with discrete support both of which can be systematically truncated. While both approximations satisfy the system size expansion of the master equation, the continuous distribution approximations become increasingly negative and tend to oscillations with increasing truncation order. In contrast, the discrete approximations rapidly converge to the underlying non-Gaussian distributions. The theory is shown to lead to particularly simple analytical expressions for the probability distributions of molecule numbers in metabolic reactions and gene expression systems. I. INTRODUCTION first few moments [12{14]; alternative methods are based on moment closure [15]. It is however the case that the Master equations are commonly used to describe fluc- knowledge of a limited number of moments does not al- tuations of particulate systems. In most instances, how- low to uniquely determine the underlying distribution ever, the number of reachable states is so large that their functions. Reconstruction of the probability distribution combinatorial complexity prevents one from obtaining therefore requires additional approximations such as the analytical solutions to these equations. Explicit solutions maximum entropy principle [16] or the truncated moment are known only for certain classes of linear birth-death generating function [17] which generally yield different processes [1], under detailed balance conditions [2], or results.
    [Show full text]
  • How Reliable Is the Linear Noise Approximation Of
    Thomas et al. BMC Genomics 2013, 14(Suppl 4):S5 http://www.biomedcentral.com/1471-2164/14/S4/S5 RESEARCH Open Access How reliable is the linear noise approximation of gene regulatory networks? Philipp Thomas1,2, Hannes Matuschek3, Ramon Grima1* From IEEE International Conference on Bioinformatics and Biomedicine 2012 Philadelphia, PA, USA. 4-7 October 2012 Abstract Background: The linear noise approximation (LNA) is commonly used to predict how noise is regulated and exploited at the cellular level. These predictions are exact for reaction networks composed exclusively of first order reactions or for networks involving bimolecular reactions and large numbers of molecules. It is however well known that gene regulation involves bimolecular interactions with molecule numbers as small as a single copy of a particular gene. It is therefore questionable how reliable are the LNA predictions for these systems. Results: We implement in the software package intrinsic Noise Analyzer (iNA), a system size expansion based method which calculates the mean concentrations and the variances of the fluctuations to an order of accuracy higher than the LNA. We then use iNA to explore the parametric dependence of the Fano factors and of the coefficients of variation of the mRNA and protein fluctuations in models of genetic networks involving nonlinear protein degradation, post-transcriptional, post-translational and negative feedback regulation. We find that the LNA can significantly underestimate the amplitude and period of noise-induced oscillations in genetic oscillators. We also identify cases where the LNA predicts that noise levels can be optimized by tuning a bimolecular rate constant whereas our method shows that no such regulation is possible.
    [Show full text]
  • Computation of Biochemical Pathway Fluctuations Beyond the Linear Noise Approximation Using
    Computation of biochemical pathway fluctuations beyond the linear noise approximation using iNA Philipp Thomas∗†‡ ¶, Hannes Matuschek§¶ and Ramon Grima∗† ∗School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom †SynthSys Edinburgh, University of Edinburgh, Edinburgh, United Kingdom ‡Department of Physics, Humboldt University of Berlin, Berlin, Germany §Institute of Physics and Astronomy, University of Potsdam, Potsdam, Germany ¶These authors contributed equally. Abstract—The linear noise approximation is commonly used the first software package enabling a fluctuation analysis of to obtain intrinsic noise statistics for biochemical networks. biochemical networks via the Linear Noise Approximation These estimates are accurate for networks with large numbers (LNA) and Effective Mesoscopic Rate Equation (EMRE) of molecules. However it is well known that many biochemical networks are characterized by at least one species with a approximations of the CME. The former gives the variance small number of molecules. We here describe version 0.3 of and covariance of concentration fluctuations in the limit of the software intrinsic Noise Analyzer (iNA) which allows for large molecule numbers while the latter gives the mean accurate computation of noise statistics over wide ranges of concentrations for intermediate to large molecule numbers molecule numbers. This is achieved by calculating the next and is more accurate than the conventional Rate Equations order corrections to the linear noise approximation’s estimates of variance and covariance of concentration fluctuations. The (REs). efficiency of the methods is significantly improved by auto- In this proceeding we develop and efficiently implement mated just-in-time compilation using the LLVM framework in iNA, the Inverse Omega Square (IOS) method comple- leading to a fluctuation analysis which typically outperforms menting the EMRE method by providing estimates for the that obtained by means of exact stochastic simulations.
    [Show full text]
  • Stochastic Analysis of Biochemical Systems
    ON MOMENTS AND TIMING { STOCHASTIC ANALYSIS OF BIOCHEMICAL SYSTEMS by Khem Raj Ghusinga A dissertation submitted to the Faculty of the University of Delaware in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Electrical and Computer Engineering Summer 2018 c 2018 Khem Raj Ghusinga All Rights Reserved ON MOMENTS AND TIMING { STOCHASTIC ANALYSIS OF BIOCHEMICAL SYSTEMS by Khem Raj Ghusinga Approved: Kenneth E. Barner, Ph.D. Chair of the Department of Electrical and Computer Engineering Approved: Babatunde Ogunnaike, Ph.D. Dean of the College of Engineering Approved: Ann L. Ardis, Ph.D. Senior Vice Provost for Graduate and Professional Education I certify that I have read this dissertation and that in my opinion it meets the academic and professional standard required by the University as a dissertation for the degree of Doctor of Philosophy. Signed: Abhyudai Singh, Ph.D. Professor in charge of dissertation I certify that I have read this dissertation and that in my opinion it meets the academic and professional standard required by the University as a dissertation for the degree of Doctor of Philosophy. Signed: Ryan Zurakowski, Ph.D. Member of dissertation committee I certify that I have read this dissertation and that in my opinion it meets the academic and professional standard required by the University as a dissertation for the degree of Doctor of Philosophy. Signed: Gonzalo R. Arce, Ph.D. Member of dissertation committee I certify that I have read this dissertation and that in my opinion it meets the academic and professional standard required by the University as a dissertation for the degree of Doctor of Philosophy.
    [Show full text]
  • An Alternative Route to the System-Size Expansion
    Home Search Collections Journals About Contact us My IOPscience An alternative route to the system-size expansion This content has been downloaded from IOPscience. Please scroll down to see the full text. 2017 J. Phys. A: Math. Theor. 50 395003 (http://iopscience.iop.org/1751-8121/50/39/395003) View the table of contents for this issue, or go to the journal homepage for more Download details: IP Address: 129.215.109.91 This content was downloaded on 05/09/2017 at 12:10 Please note that terms and conditions apply. You may also be interested in: Symmetry and Collective Fluctuations in Evolutionary Games: Symmetry and collective fluctuations: large deviations and scaling in population processes E Smith and S Krishnamurthy Approximation and inference methods for stochastic biochemical kinetics—a tutorial review David Schnoerr, Guido Sanguinetti and Ramon Grima System size expansion using Feynman rules and diagrams Philipp Thomas, Christian Fleck, Ramon Grima et al. Master equations and the theory of stochastic path integrals Markus F Weber and Erwin Frey Stochastic switching in biology: from genotype to phenotype Paul C Bressloff Multi-compartment linear noise approximation Joseph D Challenger, Alan J McKane and Jürgen Pahle Modeling stochasticity in biochemical reaction networks P H Constantino, M Vlysidis, P Smadbeck et al. Fundamentals of higher order stochastic equations P D Drummond How limit cycles and quasi-cycles are related in systems with intrinsic noise Richard P Boland, Tobias Galla and Alan J McKane IOP Journal of Physics A: Mathematical and Theoretical J. Phys. A: Math. Theor. Journal of Physics A: Mathematical and Theoretical J.
    [Show full text]
  • How Reliable Is the Linear Noise Approximation of Gene Regulatory Networks?
    Mathematisch-Naturwissenschaftliche Fakultät Philipp Thomas | Hannes Matuschek | Ramon Grima How reliable is the linear noise approximation of gene regulatory networks? Suggested citation referring to the original publication: BMC Genomics 14 (2013) S5 DOI https://doi.org/10.1186/1471-2164-14-S4-S5 ISSN (online) 1471-2164 Postprint archived at the Institutional Repository of the Potsdam University in: Postprints der Universität Potsdam Mathematisch-Naturwissenschaftliche Reihe ; 876 ISSN 1866-8372 https://nbn-resolving.org/urn:nbn:de:kobv:517-opus4-435028 DOI https://doi.org/10.25932/publishup-43502 Thomas et al. BMC Genomics 2013, 14(Suppl 4):S5 http://www.biomedcentral.com/1471-2164/14/S4/S5 RESEARCH Open Access How reliable is the linear noise approximation of gene regulatory networks? Philipp Thomas1,2, Hannes Matuschek3, Ramon Grima1* From IEEE International Conference on Bioinformatics and Biomedicine 2012 Philadelphia, PA, USA. 4-7 October 2012 Abstract Background: The linear noise approximation (LNA) is commonly used to predict how noise is regulated and exploited at the cellular level. These predictions are exact for reaction networks composed exclusively of first order reactions or for networks involving bimolecular reactions and large numbers of molecules. It is however well known that gene regulation involves bimolecular interactions with molecule numbers as small as a single copy of a particular gene. It is therefore questionable how reliable are the LNA predictions for these systems. Results: We implement in the software package intrinsic Noise Analyzer (iNA), a system size expansion based method which calculates the mean concentrations and the variances of the fluctuations to an order of accuracy higher than the LNA.
    [Show full text]
  • Optimal Experimental Design Applied to Models of Microbial Gene Regulation
    Optimal Experimental Design Applied to Models of Microbial Gene Regulation by Nathan Braniff A thesis presented to the University of Waterloo in fulfillment of the thesis requirement for the degree of Doctor of Philosophy in Applied Mathematics Waterloo, Ontario, Canada, 2020 c Nathan Braniff 2020 Examining Committee Membership The following served on the Examining Committee for this thesis. The decision of the Examining Committee is by majority vote. External Examiner: Julio Banga Professor, IIM-CISC Supervisor: Brian Ingalls Professor, Applied Mathematics, University of Waterloo Internal Members: Matt Scott Assoc. Professor, Applied Mathematics, University of Waterloo Kirsten Morris Professor, Applied Mathematics, University of Waterloo Internal-External Member: Trevor Charles Professor, Biology, University of Waterloo ii Authour's Declaration This thesis consists of material all of which I authored or co-authored: see Statement of Contributions included in the thesis. This is a true copy of the thesis, including any required final revisions, as accepted by my examiners. I understand that my thesis may be made electronically available to the public. iii Statement of Contributions Chapters1,2,7,&8 : I am the sole author of this material, under the supervision of Brian Ingalls. This material has not been previously published. Chapter3 : This material has been previously published as: \New opportunities for optimal design of dynamic experiments in systems and synthetic biology" by Nathan Braniff, and Brian Ingalls in Current Opinion in Systems Biology 9 (2018): 42-48 I co-authored this manuscript with Brian Ingalls. My contribution was gathering the candidate references and in selecting the initial areas of focus for the article.
    [Show full text]
  • Arxiv:1810.05368V2 [Q-Bio.PE] 20 Feb 2019 a Rusaeemergent, Are Groups Mal .Introduction 1
    Deriving mesoscopic models of collective behaviour for finite populations Jitesh Jhawar1 , Richard G. Morris2, Vishwesha Guttal1 1. Centre for Ecological Sciences, Indian Institute of Science, Bengaluru, 560012 2. National Centre for Biological Sciences, TIFR, Bengaluru, 560012 Abstract Animal groups exhibit many emergent properties that are a consequence of local interactions. Link- ing individual-level behaviour, which is often stochastic and local, to coarse-grained descriptions of animal groups has been a question of fundamental interest from both biological and mathe- matical perspectives. In this book chapter, we present two complementary approaches to derive coarse-grained descriptions of collective behaviour at so-called mesoscopic scales, which account for the stochasticity arising from the finite sizes of animal groups. We construct stochastic dif- ferential equations (SDEs) for a coarse-grained variable that describes the order/consensus within a group. The first method of construction is based on van Kampen’s system-size expansion of transition rates. The second method employs Gillespie’s chemical Langevin equations. We apply these two methods to two microscopic models from the literature, in which organisms stochasti- cally interact and choose between two directions/choices of foraging. These ‘binary-choice’ models differ only in the types of interactions between individuals, with one assuming simple pairwise interactions, and the other incorporating ternary effects. In both cases, the derived mesoscopic SDEs have multiplicative/state-dependent noise, i.e., the strength of the noise depends on the current state of the system. However, the different models demonstrate the contrasting effects of noise: increasing the order/consensus in the pairwise interaction model, whilst reducing the order/consensus in the higher-order interaction model.
    [Show full text]
  • Chemical Kinetics Roots and Methods to Obtain the Probability Distribution Function Evolution of Reactants and Products in Chemi
    Review Chemical Kinetics Roots and Methods to Obtain the Probability Distribution Function Evolution of Reactants and Products in Chemical Networks Governed by a Master Equation José-Luis Muñoz-Cobo 1,2,* and Cesar Berna 2 1 Department of Chemical and Nuclear Engineering, Universitat Politècnica de València, 46022 Valencia, Spain 2 Instituto Universitario de Ingeniería Energética, Universitat Politècnica de València, 46022 Valencia, Spain; [email protected] * Correspondence: [email protected]; Tel.: +34-96-387-7631 Received: 24 January 2019; Accepted: 11 February 2019; Published: 14 February 2019 Abstract: In this paper first, we review the physical root bases of chemical reaction networks as a Markov process in multidimensional vector space. Then we study the chemical reactions from a microscopic point of view, to obtain the expression for the propensities for the different reactions that can happen in the network. These chemical propensities, at a given time, depend on the system state at that time, and do not depend on the state at an earlier time indicating that we are dealing with Markov processes. Then the Chemical Master Equation (CME) is deduced for an arbitrary chemical network from a probability balance and it is expressed in terms of the reaction propensities. This CME governs the dynamics of the chemical system. Due to the difficulty to solve this equation two methods are studied, the first one is the probability generating function method or z-transform, which permits to obtain the evolution of the factorial moment of the system with time in an easiest way or after some manipulation the evolution of the polynomial moments.
    [Show full text]