LMU-UT Joint Workshop on Statistical and Biological Physics
October 29(Mon.), 30(Tue.), 2018
Abstracts

Erwin Frey - Emergence and Self-Organisation in Biological Systems
Abstract:
Isolated systems tend to evolve towards thermal equilibrium, a special state that has been a research
focus in physics for more than a century. By contrast, most processes studied in biological systems
are far from equilibrium. A fundamental overarching hallmark of all these processes is the
emergence of structure, order, and information, and we are facing the major challenge to identify
the underlying physical principles. Two particular exciting problems are the self-organised
formation of spatio-temporal patterns and the robust self-assembly of complex structures. In bothfields there are recent advances in understanding the underlying physics that will be reviewed inthis talk.

Shuji Ishihara - From cells to tissue: a continuum model for passive and active tissue
deformation
Abstract: Morphogenesis is a process in which both chemical and mechanical interactions amongcells play an essential role for determining shape of tissue and bodies. We have developed methods
to quantify mechanical force and deformation in a growing epithelial tissue in terms of stress anddeformation tensors. To relate these quantities, we also developed a continuum model for twodimensional epithelial tissue, where a field variable representing coarse-grained cellular shape isincluded. Employing formalism developed in active gel theory, active terms were included into themodel, by which new mechanism for cotraction-elongation, a typical morohogenetic process, wasidentified.

Fridtjof Brauns - Phase space geometry of reaction–diffusion systems
Abstract:
The dynamics of any physical system are encoded in the (flow) structure of the system's phasespace. Phase space flow for low dimensional ODE dynamics can be studied in terms of geometricstructures like nullclines and fixed points in phase space. This approach is at the core of Nonlinear
Dynamics. Recent advances suggest that a general phase space geometric framework can be
developed for mass-conserving reaction--diffusion systems.
Here we develop a comprehensive theory for pattern formation in two-component mass-conserving
reaction--diffusion systems. These systems serve as paradigmatic class of systems able to form
(stationary) patterns --- a prominent application is intracellular polarization. Based on the core
concepts of mass redistribution and local chemical equilibria, we introduce geometric structures inphase space that explicitly reveal the interplay between reaction- and diffusion-processes. The
nonlinear chemical interactions are captured by a line of chemical equilibria. We show that all
aspects of pattern formation --- ranging from linear instability and excitability to the characteristics
and bifurcations of stationary patterns --- can be extracted from the geometric features of the line ofchemical equilibria. In particular, we find that a mass-redistribution instability is at the core ofpattern formation. Furthermore, our analysis points towards a deep connection to equilibrium phaseseparation as described by Model~B dynamics. Challenges for future research will be tosystematically work out this connection, to generalize the framework to mass-conserving systems

with more components and more conserved quantities, and to tackle issues like non-linear
wavelength selection in such systems.

Taihei Fujimori - Tissue self-organization based on collective cell migration in Dictyostelium
development
Abstract:
Although directional cell migration often has a crucial role in tissue patterning, the molecular anddevelopmental complexity of higher animals hinders the exact identification of navigational rules ofindividual cell movement. We focused on a simple form of multicellular organization present in thedevelopment of Dictyostelium discoideum, one of the social amoeba. Upon starvation,
Dictyostelium cells aggregate, differentiate into prestalk or prespore cells, and form segregatedpattern where prestalk cell cluster sits on prespore cell mass. Despite the system being wellstudied, the exact navigational rules underlying their morphogenesis remain elusive. By
spatiotemporal manipulation of the chemoattractant and the cell-cell contact signal using
microfluidics and purified adhesion protein, here we show that there is contact-dependentnavigation in addition to their well known chemotaxis toward cAMP. Our analysis revealed thatcell-cell adhesion promotes constitutive F-actin formation which gives rise to contact following
motion, and the polarity induced by cell-cell contact competes with those induced by chemotaxis.
Surprisingly, the mechanism is an inversion of the so-called contact inhibition of locomotion – acanonical scheme of collective cell migration in metazoans. Furthermore, we demonstrate that bothsignals are required for pattern formation. Isolated prestalk and prespore cells can protrude towards
the contact signal as well as chemotax towards cAMP, however when given both signals, prestalkcells orient towards the chemoattractant whereas prespore cells choose the contact signal. We
propose that the difference in prioritization to navigational cues works as an efficient and rapidmeans of cell segregation and that a similar mechanism may underlie tissue patterning in othersystems.

Nen Saito - Self-organization via membrane deformation and reaction diffusion: 3D modelingfor macropinocytosis of ameboid cell
Abstract:
Ameboid cell shows drastic deformation of cell shapes. Sometimes topology of cell shape canchange (e.g. endocytosis). Macropinocytosis is clathrin-independent endocytosis and allows
internalization of large volume of extracellular fluid. D. discoideum and tumor cells show
constitutive macropinocytosis for uptake of nutrients from extracellular fluid. The mechanism of it
remains still unclear.
We introduce a mathematical model based on 3D phase-field method, which enables to simulate
reaction-diffusion process on the cell membrane and large membrane deformation simultaneously.
Simulation results indicate that simple chemical reactions lead to drastic membrane deformation,
which results in an engulfment of extracellular fluid. This study provides a new insight for
macropinocytosis as a self-organization phenomenon via feedback between drastic deformation of
membrane and reaction-diffusion on it.

Felix Kempf - Active Matter Invasion into Capillaries
Abstract:
Biological active materials such as bacterial biofilms and eukaryotic cells thrive in confined microspaces. Here, we numerically show that combining growth dynamics with their intrinsic activity
cells can use confinement as a mechanical guidance to achieve distinct modes of collective
invasion. We assess the dynamics of the growing interface and classify these collective modes ofinvasion based on the activity of the cells. While at small and moderate activities the active material

grows as a coherent unit, we find blobs of active materials collectively detaching from the cohort
above an activity threshold in a process reminiscent of the intravasation in cancer cells. We further
characterise the mechanical mechanisms of transition between different modes of invasion.

Tetsuya Hiraiwa - Theory on dynamics and stress generation in an actomyosin cytoskeleton
Abstract:
This talk focuses on active mechanics of a cortical cytoskeleton, which is a network structure
consisting of actin and myosin filaments and crosslinker proteins located underneath the cell
membrane. Mechanical properties of a cortical cytoskeleton govern not only cell‘s resistances todeformation but also contractility induced by the motor protein, myosin. Motor-induced contractile
stress in a cortical cytoskeleton plays crucial roles in dynamic cellular behaviors, such as
cytokinesis and cell migration.
In this talk, I would like to explain our theoretical work on dynamics and stress generation in a
cortical cytoskeleton. I will propose a mechanical model of motor-induced stress in an isotropic
actomyosin network with crosslinkers and share the results of the model about motor-induced¬¬
contractility. In particular, since a cortical cytoskeleton in a living cell should be flowable, we study
the case of fluidic networks, in which there are only few amount of crosslinkers and/or network
elements can undergo stochastic turnover processes. We found that a finite amount of crosslinkers
is significant for motor-induced contractility. We also investigated how turnover of crosslinkers andactin filaments influences motor-induced stress. Furthermore, we looked at the dynamic local
density inhomogeneity of the network with such contractility.

Manon Wigbers - A Cascade of Protein Patterns Senses Cell Shape in Starfish Oocyte during
MeiosisAbstract:
Cells are constantly subject to mechanical stresses, for example during migration, cell division anddevelopment. These mechanical stresses generate shape deformations and cytoplasmic flows,
modulating the reaction diffusion dynamics of biochemical processes inside these cells. The generalmechanisms of such mechanochemical feedback, underlying the formation of self-organizedspatiotemporal patterns that are important during development, have remained largely unexplored.
Here, we study how the Rho GTPase signaling pathway drives mechanical contraction waves post
anaphase in starfish oocytes. We can modulate the speed of the contraction waves by manipulating
the cell shape of the oocytes in micro-fabricated PDMS chambers of defined geometry. We
combine our experimental results with a reaction-diffusion model and show how a cascade ofprotein patterns allows the RhoGTPase pathway to sense cell shape, giving rise to a close interplay
between cell geometry and biochemical regulation in biological pattern formation.

Tomohiro Shima - Kinesin-binding–triggered conformation switching of microtubules
contributes to polarized transport
Abstract:
Kinesin-1, the founding member of the kinesin superfamily of proteins, is known to use only asubset of microtubules for transport in living cells. This biased use of microtubules is proposed as
the guidance cue for polarized transport in neurons, but the underlying mechanisms are still poorly
understood. Here, we report that kinesin-1 binding on microtubules promotes additional kinesin-1
binding by inducing conformational switching of the microtubules. Our data demonstrate that thispositive feedback spontaneously provide a subset of high affinity microtubules from other low
affinity microtubules, shedding light on the mechanism behind polarized transport in cells.

Philipp Geiger - Topologically Robust Zero-Sum Games
Abstract:
To explore how the topology of interaction networks determines the robustness of dynamicalsystems, we study the antisymmetric Lotka-Volterra equation (ALVE). The ALVE is the replicator
equation of zero-sum games in evolutionary game theory, in which the strengths of pairwiseinteractions between strategies are defined by an antisymmetric matrix such that typically somestrategies go extinct over time. Here we show that there also exist topologically robust zero-sum
games, such as the rock-paper-scissors game, for which all strategies coexist for all choices ofinteraction strengths. We refer to such zero-sum games as coexistence networks and constructcoexistence networks with an arbitrary number of strategies. By mapping the long-time dynamics of
the ALVE to the algebra of antisymmetric matrices, we identify simple graph-theoretical rules bywhich coexistence networks are constructed. In particular, we characterize the kernel of anantisymmetric matrix in terms of Pfaffians and their relation to near-perfect matchings. Our results
show that the topology of interaction networks alone can determine the long-time behavior ofnonlinear dynamical systems, and may help to identify robust network motifs arising, for example,
in ecology.

Yuma Fujimoto - Evolution of Intention through mutual recognition in Game Theory
Abstract:
Intention recognition is an important characteristic of intelligent agents. In their interactions withothers, they try to read others' intentions and make an image of others to choose their actions
accordingly. While the way in which players choose their actions depending on such intentions has
been investigated in game theory, how dynamic changes in intentions by mutually reading others'
intentions are incorporated into game theory has not been explored. We present a novel formulationof game theory in which players read others' intentions and change their own through an iterated
game. Here, intention is given as a function of the other's action and the own action to be taken
accordingly as the dependent variable, while the mutual recognition of intention is represented as
the functional dynamics. It is shown that a player suffers no disadvantage when he/she recognizes
the other's intention, whereas the functional dynamics reach equilibria in which both players'
intentions are optimized. These cover a classical Nash and Stackelberg equilibria but we extend
them in this study: Novel equilibria exist depending on the degree of mutual recognition. Moreover,the degree to which each player recognizes the other can also differ. This formulation is applied toresource competition, duopoly, and prisoner's dilemma games. For example, in the resourcecompetition game with player-dependent capacity on gaining the resource, the superior player's
recognition leads to the exploitation of the other, while the inferior player's recognition leads tocooperation through which both players' payoffs increase.

David Muramatsu - Range Expansions in a Stochastic Metapopulation Model
Abstract:
In range expansions, the colonization of a territory by an invading species, the front between
invaded and new territory roughens due to stochastic fluctuations.
To investigate the growth laws describing the front width of a given system, large sized systems
have to be considered, since finite size effects may otherwise obscure the dynamics that govern theinterface.
Naive implementations of exact simulation algorithms like the Gillespie algorithm scale
unfavorably in the system size such that the simulation of ensembles of large systems with complex
interactions quickly becomes unfeasible.

We address this problem by implementing a parallelized version of the Gillespie algorithm, whichscales linearly in the system size, suited for lattice based systems that display local fast dynamics
while having a low rate of particle exchange between lattice sites.
We employ this algorithm to determine the growth law governing the front width of a system which
has been inaccessible to previously used simulation methods.

Tetsuhiro Hatakeyama - Reciprocity between Robustness and Plasticity as a Universal Law in
Biology
Abstract:
Robustness and plasticity are important characteristics in biological systems and have therefore
attracted much attention from not only biologists but also physicists. Whereas robustness concerns
insensitivity to perturbations, plasticity concerns the variability of external inputs. How the two
phenomena are compatible with each other is an important question to be addressed.
We investigate the compatibility of the two distinguishable properties in some biological systems,e.g., circadian clocks and reaction-diffusion systems, and we found the reciprocity between
robustness and plasticity as a quantitative relationship. For example, the robustness of period andplasticity of phase against environmental changes such as temperature and nutrient conditions arecompatible in circadian clocks. We found a quantitative relationship between them: higher
robustness in the period implies higher plasticity in the phase, where changes in period and phasefollow a linear relationship with a negative coefficient.

Yongtae Hwang - Collective behaviors of cardiac myosin molecules for effective cardiac
function
Abstract:
For effective heart contractions, it is extremely important to maintain high and stable ventricularpressure during systole and release the pressure immediately during the following relaxation.
However, myosin and actin filaments are distributed in a complex 3D arrangement in heart andthus, one can imagine that contractile forces are somehow coordinated among myosins and there
must be a key molecular property of cardiac myosin for such functional demands in heart. In thisstudy, in order to reveal molecular properties of cardiac myosins for functional demands in heart,
forces generated by synthetic cardiac myosin filaments were measured by optical tweezers at highspatiotemporal resolution. Back and forth stepwise force curves were frequently observed at highATP and ADP concentrations. Combined with simulation results, one key feature for back andforth force generations is the ADP state of myosin, which remains bound to actin and causes thereverse strokes and subsequent detachments more frequently at higher loads. These molecularproperties appeared to be suitable to maintain high systolic pressure and achieve pressure release
quickly during the following relaxation.

Sakurako Tanida - Self-organizations of microtubule filaments gliding on kinesin motors
Abstract:
Microtubules are the common substrates to eukaryotic cells and some bacteria.In those cells, thefilamentous proteins micortubules interact with motor proteins, and show coordinated motion. Such
motions play an important role in cell dynamics, for example, division, intraceller transportation,and migration.While other proteins are known to often help the self-organization process, thekinetics of microtubules itself also responsible for the self-organization process. In this study, weinvestigated the relation between dynamical self-organization and the microtubules' motion
generated by motor proteins. By using a simple experimental system in which the microtubules
glide on the carpet of the kinesin motor, we found that a subtle interaction difference whether
microtubules overlap each other makes a big difference in the large-scale self-organization.

Patrick Wilke - Two-Species Active Transport along Cylindrical Biofilaments is Limited byEmergent Topological Hindrance
Abstract:
Active motion of molecules along filamentous structures is a crucial feature of cell biology and isoften modeled with the paradigmatic asymmetric simple exclusion process. Motivated by recent
experimental studies that have addressed the stepping behavior of kinesins on microtubules, weinvestigate a lattice gas model for simultaneous transport of two species of active particles on acylinder. The species are distinguished by their different gaits: While the first species moves
straight ahead, the second follows a helical path. We show that the collective properties of such
systems critically differ from those of one-species transport in a way that cannot be accounted forby standard models. This is most evident in a jamming transition far below full occupation, as wellas in non-equilibrium pattern formation. The altered behavior arises because -- unlike the case insingle-species transport -- any given position may be targeted by two particles from different
directions at the same time. However, a particle can leave a given position only in one direction.
This simple change in connectivity significantly amplifies the impact of steric interactions and thus
becomes a key determinant of mixed species transport. We computationally characterize this type ofhindrance and develop a comprehensive theory for collective two-species transport along a cylinder.
Our observations show high robustness against model extensions that account for additional
biomolecular features and demonstrate that even small fractions of a second species cansignificantly alter transport. This suggests that our analysis is also relevant in a biological context.

Renan A. L. Almeida - Coarsening & percolation in twisted nematic liquid crystals
Coarsening & percolation in twisted nematic liquid crystals
Abstract:
When the two-dimensional Ising-Glauber (2DIG) model is quenched from the paramagnetic to theferromagnetic phase, locally equilibrated regions of spins up and down spontaneously form amid
the system and coarsen over time. Some aspects of this coarsening dynamics can be described byphenomenological scaling theories that suggest universal behaviours out-of-equilibrium. However,these universal behaviours remain to be experimentally substantiated in many directions: functional
forms of space-time scaling functions are just a few, but some of the notable examples. Beyond
that, recent simulations of the 2DIG model surprisingly indicated that, along with the coarsening,
the statistics of certain length scales might be in the universality class of the critical percolation
model (a purely static model). In this seminar, I will address both of these universal aspects coarsening and percolation - by analysing the two-dimensional ordering dynamics of twisted
nematic liquid crystals quenched from a hydrodynamic turbulent state. The ordering is featured inthis case by the disentangling and shrinking of topological defects that lie in between twisted
domains. I will give experimental evidence that the celebrated Ohta-Jasnow-Kawasaki scaling
theory well describes functional forms for space and for time scaling functions. Finally, but notleast important, it will be argued that universal exponents related to the critical percolation model
are indeed measured along the out-of-equilibrium ordering dynamics.

Kazumasa Takeuchi - Turbulent liquid crystal and competing bacteria: possible universal
relaxation at criticality
Abstract:
On the basis of experiments on turbulent liquid crystal under a twist alignment and simulations onbacteria strains competing in a microfluidic channel, I argue that critical relaxation dynamics inthose apparently different problems may be governed by a single universality class, namely thevoter universality class. The voter class is theoretically believed to describe phase transitions into

absorbing states in the presence of the Ising-like up-down symmetry, but so far remains
experimentally elusive. Here I describe two possible situations, showing some experimental andnumerical observations akin to the voter class dynamics, and discuss underlying mechanisms. The
work on competing bacteria is due to collaboration with Takuro Shimaya (arXiv:1804.09895).