8.1 Reaction-Diffusion Models of Pattern Formation in Developmental Biology
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Self-Organization Principles of Intracellular Pattern Formation
Self-organization principles of intracellular pattern formation J. Halatek. F. Brauns, and E. Frey∗ Arnold{Sommerfeld{Center for Theoretical Physics and Center for NanoScience, Department of Physics, Ludwig-Maximilians-Universit¨atM¨unchen, Theresienstraße 37, D-80333 M¨unchen,Germany (Dated: February 21, 2018) Abstract Dynamic patterning of specific proteins is essential for the spatiotemporal regulation of many important intracellular processes in procaryotes, eucaryotes, and multicellular organisms. The emergence of patterns generated by interactions of diffusing proteins is a paradigmatic example for self-organization. In this article we review quantitative models for intracellular Min protein patterns in E. coli, Cdc42 polarization in S. cerevisiae, and the bipolar PAR protein patterns found in C. elegans. By analyzing the molecular processes driving these systems we derive a theoretical perspective on general principles underlying self-organized pattern formation. We argue that intracellular pattern formation is not captured by concepts such as \activators", \inhibitors", or \substrate-depletion". Instead, intracellular pattern formation is based on the redistribution of proteins by cytosolic diffusion, and the cycling of proteins between distinct conformational states. Therefore, mass-conserving reaction-diffusion equations provide the most appropriate framework to study intracellular pattern formation. We conclude that directed transport, e.g. cytosolic diffusion along an actively maintained cytosolic gradient, is the key process underlying pattern formation. Thus the basic principle of self-organization is the establishment and maintenance of directed transport by intracellular protein dynamics. Keywords: self-organization; pattern formation; intracellular patterns; reaction-diffusion; cell polarity; arXiv:1802.07169v1 [physics.bio-ph] 20 Feb 2018 NTPases 1 INTRODUCTION In biological systems self-organization refers to the emergence of spatial and temporal structure. -
Guiding Self-Organized Pattern Formation in Cell Polarity Establishment
ARTICLES https://doi.org/10.1038/s41567-018-0358-7 Guiding self-organized pattern formation in cell polarity establishment Peter Gross1,2,3,8, K. Vijay Kumar" "3,4,8, Nathan W. Goehring" "5,6, Justin S. Bois" "7, Carsten Hoege2, Frank Jülicher3 and Stephan W. Grill" "1,2,3* Spontaneous pattern formation in Turing systems relies on feedback. But patterns in cells and tissues seldom form spontane- ously—instead they are controlled by regulatory biochemical interactions that provide molecular guiding cues. The relationship between these guiding cues and feedback in controlled biological pattern formation remains unclear. Here, we explore this relationship during cell-polarity establishment in the one-cell-stage Caenorhabditis elegans embryo. We quantify the strength of two feedback systems that operate during polarity establishment: feedback between polarity proteins and the actomyosin cortex, and mutual antagonism among polarity proteins. We characterize how these feedback systems are modulated by guid- ing cues from the centrosome, an organelle regulating cell cycle progression. By coupling a mass-conserved Turing-like reac- tion–diffusion system for polarity proteins to an active-gel description of the actomyosin cortex, we reveal a transition point beyond which feedback ensures self-organized polarization, even when cues are removed. Notably, the system switches from a guide-dominated to a feedback-dominated regime well beyond this transition point, which ensures robustness. Together, these results reveal a general criterion for controlling biological pattern-forming systems: feedback remains subcritical to avoid unstable behaviour, and molecular guiding cues drive the system beyond a transition point for pattern formation. ell polarity establishment in Caenorhabditis elegans zygotes phase where myosin appears to reach a steady state (Supplementary is a prototypical example for cellular pattern formation that Fig. -
Nanostructures De Titanate De Baryum: Modélisation,Simulations
Nanostructures de titanate de Baryum : modélisation,simulations numériques et étude expérimentale. Gentien Thorner To cite this version: Gentien Thorner. Nanostructures de titanate de Baryum : modélisation,simulations numériques et étude expérimentale.. Autre. Université Paris Saclay (COmUE), 2016. Français. NNT : 2016SACLC093. tel-01427275 HAL Id: tel-01427275 https://tel.archives-ouvertes.fr/tel-01427275 Submitted on 5 Jan 2017 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. NNT : 2016SACLC093 THÈSE DE DOCTORAT DE L’UNIVERSITÉ PARIS-SACLAY PRÉPARÉE À “CENTRALESUPÉLEC” ECOLE DOCTORALE N° (573) Interfaces : approches interdisciplinaires, fondements, applications et innovation Physique Par Monsieur Gentien Thorner BARIUM TITANATE NANOSTRUCTURES: modeling, numerical simulations and experiments Thèse présentée et soutenue à Châtenay-Malabry, le 28 novembre 2016: Composition du Jury : Philippe Papet Professeur, Université de Montpellier Président Laurent Bellaiche Professeur, Université d'Arkansas Rapporteur Gregory Geneste Ingénieur de Recherche, CEA Rapporteur Christine Bogicevic Ingénieur de Recherche, CentraleSupélec Examinatrice Jean-Michel Kiat Directeur de Recherche, CentraleSupélec Directeur de thèse 3 Remerciements À un moment relativement crucial d’une thèse, quelques pensées iraient tout d’abord vers son directeur Jean-Michel Kiat pour un soutien indéfectible pendant une période s’étalant d’un premier contact lors d’un stage de recherche en deux mille dix jusqu’à la soutenance en deux mille seize. -
Pattern Formation, Social Forces, and Diffusion Instability in Games
EPJ manuscript No. (will be inserted by the editor) Pattern Formation, Social Forces, and Diffusion Instability in Games with Success-Driven Motion Dirk Helbing ETH Zurich, UNO D11, Universit¨atstr.41, 8092 Zurich, Switzerland Received: date / Revised version: date Abstract. A local agglomeration of cooperators can support the survival or spreading of cooperation, even when cooperation is predicted to die out according to the replicator equation, which is often used in evolutionary game theory to study the spreading and disappearance of strategies. In this paper, it is shown that success-driven motion can trigger such local agglomeration and may, therefore, be used to supplement other mechanisms supporting cooperation, like reputation or punishment. Success-driven motion is formulated here as a function of the game-theoretical payoffs. It can change the outcome and dynamics of spatial games dramatically, in particular as it causes attractive or repulsive interaction forces. These forces act when the spatial distributions of strategies are inhomogeneous. However, even when starting with homogeneous initial conditions, small perturbations can trigger large inhomogeneities by a pattern-formation instability, when certain conditions are fulfilled. Here, these instability conditions are studied for the prisoner's dilemma and the snowdrift game. Furthermore, it is demonstrated that asymmetrical diffusion can drive social, economic, and biological systems into the unstable regime, if these would be stable without diffusion. PACS. 02.50.Le Decision theory and game theory { 87.23.Ge Dynamics of social systems { 82.40.Ck Pattern formation in reactions with diffusion, flow and heat transfer { 87.23.Cc Population dynamics and ecological pattern formation 1 Introduction tions [17,18], which agree with replicator equations for the fitness-dependent reproduction of individuals in biology Game theory is a well-established theory of individual [19,20,21]. -
Using Neural Networks for Pattern Association for the Online Purchase
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by AIS Electronic Library (AISeL) Association for Information Systems AIS Electronic Library (AISeL) All Sprouts Content Sprouts 7-26-2009 Using Neural Networks for Pattern Association for the Online Purchase of Products Arpan Kumar Kar XLRI School of Business & Human Resources, [email protected] Supriyo Kumar De XLRI School of Business & Human Resources, [email protected] Follow this and additional works at: http://aisel.aisnet.org/sprouts_all Recommended Citation Kar, Arpan Kumar and De, Supriyo Kumar, " Using Neural Networks for Pattern Association for the Online Purchase of Products" (2009). All Sprouts Content. 281. http://aisel.aisnet.org/sprouts_all/281 This material is brought to you by the Sprouts at AIS Electronic Library (AISeL). It has been accepted for inclusion in All Sprouts Content by an authorized administrator of AIS Electronic Library (AISeL). For more information, please contact [email protected]. Working Papers on Information Systems ISSN 1535-6078 Using Neural Networks for Pattern Association for the Online Purchase of Products Arpan Kumar Kar XLRI School of Business & Human Resources, India Supriyo Kumar De XLRI School of Business & Human Resources, India Abstract Abstract: Today, a huge percentage of all the business transactions that take place in the domain of e-commerce are dominated by online shopping after the "virtual market" conceptualization of the business. This paper focuses on how pattern association rules may be obtained from the dynamic databases generated during purchases in an e-Store to maximize the profit of the marketer. -
Exploratory Modelling and the Case of Turing Patterns
to appear in: Christian, A., Hommen, D., Retzlaff, N., Schurz, G. (Eds.): Philosophy of Science. Between the Natural Sciences, the Social Sciences, and the Humanities, New York: Springer 2018. Models in Search of Targets: Exploratory Modelling and the Case of Turing Patterns Axel Gelfert Department of Philosophy, Literature, History of Science & Technology Technical University of Berlin Straße des 17. Juni 135, 10623 Berlin email: [email protected] Abstract Traditional frameworks for evaluating scientific models have tended to downplay their exploratory function; instead they emphasize how models are inherently intended for specific phenomena and are to be judged by their ability to predict, reproduce, or explain empirical observations. By contrast, this paper argues that exploration should stand alongside explanation, prediction, and representation as a core function of scientific models. Thus, models often serve as starting points for future inquiry, as proofs of principle, as sources of potential explanations, and as a tool for reassessing the suitability of the target system (and sometimes of whole research agendas). This is illustrated by a case study of the varied career of reaction- diffusion models in the study of biological pattern formation, which was initiated by Alan Turing in a classic 1952 paper. Initially regarded as mathematically elegant, but biologically irrelevant, demonstrations of how, in principle, spontaneous pattern formation could occur in an organism, such Turing models have only recently rebounded, thanks to advances in experimental techniques and computational methods. The long-delayed vindication of Turing’s initial model, it is argued, is best explained by recognizing it as an exploratory tool (rather than as a purported representation of an actual target system). -
Evolutionary Game Theory: Theoretical Concepts and Applications To
Physica A 389 (2010) 4265–4298 Contents lists available at ScienceDirect Physica A journal homepage: www.elsevier.com/locate/physa Evolutionary game theory: Theoretical concepts and applications to microbial communities Erwin Frey ∗ Ludwig-Maximilians-Universität München, Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Theresienstrasse 37, D-80333 Munich, Germany article info a b s t r a c t Article history: Ecological systems are complex assemblies of large numbers of individuals, interacting Received 30 January 2010 competitively under multifaceted environmental conditions. Recent studies using Available online 4 March 2010 microbial laboratory communities have revealed some of the self-organization principles underneath the complexity of these systems. A major role of the inherent stochasticity of its Keywords: dynamics and the spatial segregation of different interacting species into distinct patterns Population dynamics has thereby been established. It ensures the viability of microbial colonies by allowing for Game theory species diversity, cooperative behavior and other kinds of ``social'' behavior. Evolution Stochastic processes A synthesis of evolutionary game theory, nonlinear dynamics, and the theory of Nonlinear dynamics stochastic processes provides the mathematical tools and a conceptual framework for a Pattern formation deeper understanding of these ecological systems. We give an introduction into the modern formulation of these theories and illustrate their effectiveness focussing on selected examples of microbial systems. Intrinsic fluctuations, stemming from the discreteness of individuals, are ubiquitous, and can have an important impact on the stability of ecosystems. In the absence of speciation, extinction of species is unavoidable. It may, however, take very long times. We provide a general concept for defining survival and extinction on ecological time-scales. -
Exploring Reaction-Diffusion and Pattern Formation
Exploring Reaction-Diffusion and Pattern Formation Ramona Behravan1, Peter J. Bentley1, Robin Carlisle2 1 Department of Computer Science, University College London, Gower Street, London, WC1E 6BT, England 2 Glassworks Ltd., 34 Great Pulteney Street, London W1F 9NP, England Abstract. This article reviews the development of the concept of reaction- diffusion leading to pattern formation in living organisms. The article com- mences with an historical background and then describes biological develop- ment, and ideas of the formation of patterns using dynamic activator inhibitor systems. In addition to this, different models to represent such systems and their computer simulations are discussed. 1 Introduction The first steps toward the sciences arose out of the recognition of patterns and struc- tures. Patterns are all around us in the living and the non-living world. Formation of galaxies, mountains, rivers, crystals, zebra stripes, flower petals and butterfly wings are all examples of ordered structures and regular patterns. While it seems likely that evolution plays the major role in creating, selecting and exploiting features in living organisms, there can be no denying the role of physics in nature. Physical structures can emerge naturally without the selection pressure of natural evolution: sand dunes, snow flakes, clouds and cracks in the ground can all self-organise into ordered and re- petitive forms with clearly defined patterns. The existence of such natural pattern has led many researchers to hypothesise that in some of the features of life, natural evolution has exploited the automatic pattern- formation machinery provided by physics instead of creating her own from scratch. In this article we focus on this class of patterns, namely pattern formation of living or- ganisms. -
Pattern Formation in Reaction-Diffusion System on Membrane with Mechanochemical Feedback
Pattern Formation in Reaction-Diffusion System on Membrane with Mechanochemical Feedback Naoki Tamemoto and Hiroshi Noguchi* Institute for Solid State Physics, University of Tokyo, Kashiwa, Chiba 277-8581, Japan Correspondence and requests for materials should be addressed to H.N. ([email protected] tokyo.ac.jp). 1 ABSTRACT Shapes of biological membranes are dynamically regulated in living cells. Although membrane shape deformation by proteins at thermal equilibrium has been extensively studied, nonequilibrium dynamics have been much less explored. Recently, chemical reaction propagation has been experimentally observed in plasma membranes. Thus, it is important to understand how the reaction-diffusion dynamics are modified on deformable curved membranes. Here, we investigated nonequilibrium pattern formation on vesicles induced by mechanochemical feedback between membrane deformation and chemical reactions, using dynamically triangulated membrane simulations combined with the Brusselator model. We found that membrane deformation changes stable patterns relative to those that occur on a non- deformable curved surface, as determined by linear stability analysis. We further found that budding and multi-spindle shapes are induced by Turing patterns, and we also observed the transition from oscillation patterns to stable spot patterns. Our results demonstrate the importance of mechanochemical feedback in pattern formation on deforming membranes. 2 INTRODUCTION Membrane deformation is a fundamental biological process involved in many cellular functions such as vesicular transport1, cell division2, and cell motility3. To understand these phenomena, the mechanism of membrane deformation by intracellular proteins has been investigated in detail4–8. Recently, it has been shown that the deformation of biological membranes is not just a passive phenomenon but also plays physiological roles8–15. -
Vegetative Turing Pattern Formation: a Historical Perspective
Vegetative Turing Pattern Formation: A Historical Perspective Bonni J. Kealy* and David J. Wollkind Washington State University Department of Mathematics Pullman, WA 99164-3113 Joint Mathematics Meetings AMS-ALS Special Session on the Life and Legacy of Alan Turing January 2012 Bonni J. Kealy* and David J. Wollkind Washington State University Vegetative Turing Pattern Formation: A Historical Perspective Alan Turing Born Alan Mathison Turing 23 June 1912 Maida Vale, London, England Died 7 June 1954 (aged 41) Wilmslow, Chesire, England Figure: Turing at the time of his election to Fellowship of the Royal Society Bonni J. Kealy* and David J. Wollkind Washington State University Vegetative Turing Pattern Formation: A Historical Perspective Alan Turing: World Class Distance Runner Alan Turing achieved world-class Marathon standards. His best time of 2 hours, 46 minutes, 3 seconds, was only 11 minutes slower than the winner in the 1948 Olympic Games. In a 1948 cross-country race he finished ahead of Tom Richards who was to win the silver medal in the Olympics. Figure: From The Times, 25 August 1947 Figure: Running in 1946 Bonni J. Kealy* and David J. Wollkind Washington State University Vegetative Turing Pattern Formation: A Historical Perspective Paper: The Chemical Basis of Morphogenesis Figure: An example of a `dappled' Figure: Philosophical Transactions of pattern as resulting from a type (a) the Royal Society of London. Series B, morphogen system. A marker of unit Biological Sciences, Vol. 237, No. 641. length is shown. (Aug. 14, 1952), pp. 37-72. Bonni J. Kealy* and David J. Wollkind Washington State University Vegetative Turing Pattern Formation: A Historical Perspective Examples Bonni J. -
A Review: Pattern Formation and Adaptation in Multi-Robot Systems
A Review: Pattern Formation and Adaptation in Multi-Robot Systems Erkin Bahc¸eci, Onur Soysal and Erol S¸ahin CMU-RI-TR-03-43 October 2003 Robotics Institute Carnegie Mellon University Pittsburgh, Pennsylvania 15213 c Carnegie Mellon University Abstract Recent advances in robotics have started making it feasible to deploy large numbers of inexpensive robots for tasks such as surveillance and search. However, coordination of multiple robots to accomplish such tasks remains a challenging problem. This report reviews some of the recent literature in multi-robot systems. It consists of two parts. In the first part, we reviewed the studies on the pattern formation problem, that is how can a group of robots be controlled to get into and maintain a formation. The second part reviews the studies that used adaptation strategies in controlling multi- robot systems. Specifically we have investigated (1) how learning (life-long adaptation) is used to make multi-robot systems respond to changes in the environment as well in the capabilities of individual robots, and (2) how evolution is used to generate group behaviors. I Contents 1 Introduction 1 2 Pattern formation in multi-robot systems 1 2.1 Centralized pattern formation . 1 2.2 Decentralized pattern formation . 2 3 Adaptation in multi-robot systems 5 3.1 Individual level adaptation . 5 3.2 Group level adaptation . 7 4 Conclusion 9 5 Acknowledgements 9 III 1 Introduction Recent advances in robotics have started making it feasible to deploy large numbers of inexpensive robots for tasks such as surveillance and search. However, coordination of multiple robots to accomplish such tasks remains a challenging problem. -
Pattern Formation Models and Developmental Constraints GEORGE F
THE JOURNAL OF EXPERIMENTAL ZOOLOGY 251:186-202 (1989) Pattern Formation Models and Developmental Constraints GEORGE F. OSTER AND JAMES D. MURRAY Departments of Biophysics, Entomology, and Zoology, University of California, Berkeley, California 94720 (G.F.0.); Centre for Mathematical Biology, Mathematical Institute, Oxford, OX1 3LB, England (J.D.M.) ABSTRACT Most schemes for embryonic pattern formation are built around the notion of lateral inhibition. Models of this type arise in many settings, and all share some common character- istics. In this paper we examine a number of pattern formation models and show how the phenome- non of lateral inhibition constrains the possible geometries that can arise. Morphogenetic models have provided embry- how the chemical prepattern is laid down. This ologists with insight into how embryonic patterns can be modeled in one of two ways. 1) Simple may be laid down. In this chapter we shall illus- chemical gradients are established across tissues, trate the basic pattern-forming principles of these assuming that certain cells act as sources or sinks models using as an example the formation of for the chemicals, which diffuse from cell to cell bones in the vertebrate limb. The physics of the via junctions, or through the intercellular space. pattern forming process imposes constraints on 2) A chemical prepattern can arise by means of the possible cartilage patterns the limb may ex- “diffusion-driven instabilities,” a notion first pro- hibit. These constraints are reflected in the gen- posed by Turing (’52), and subsequently elabo- eral similarity one observes amongst all tretrapod rated and applied by numerous authors to a va- limbs.