Inhaltsbereich
Seminar: Stochastic Processes and Networks in Biology – Topics
 Overview
 Topics
If you want to give a presentation at the seminars, you should send your application to Professor Frey by email (frey@lmu.de) no later than November 6, 2020. The application must contain your CV, transcript of records, and your top 3 topics of interest.
Note: All resources below are either free to access or can be accessed via the university library. See their website for more information.

Stochastic Models for Bacterial Growth
All organisms control the size of their cells. Recent theoretical and experimental work has shown that there are quantitative laws governing cell size and its dependence on growth rate. In this seminar talk you will investigate analytically solvable theoretical models. Original publication:
Cell Size Regulation in Bacteria
Ariel Amir  Review article:
Modeling Cell Size Regulation: From SingleCellLevel Statistics to Molecular Mechanisms and PopulationLevel Effects
PoYi Ho Jie Lin Ariel Amir
 Original publication:

How Stem Cells Regulate their Population
To keep us alive, renewal of cells is crucial. On top of that, stem cells are well known for its ability to turn into other cell types; meanwhile keeping its capacity of selfreplication. In this seminar, we will understand how stem cells maintain their population using knowledge in population dynamics.
Strategies for Homeostatic Stem Cell SelfRenewal in Adult Tissues
Benjamin D. Simons Hans Clevers 
Dynamic heterogeneity as a strategy of stem cell selfrenewal
Philip Greulich Benjamin D. Simons 
Competition for Stem Cell Fate Determinants as a Mechanism for Tissue Homeostasis
David J. Jörg Yu Kitadate Shosei Yoshida Benjamin D. Simons


Physical Limits of Concentration Sensing
Cells react to biochemical cues in their environment, but what are the requirements to measure these cues? When zooming in on a biochemical receptor that detects the local density of biochemical molecules, the discrete nature of these molecules becomes apparent, in the form of molecule number fluctuations. These number fluctuations translate to a noisy receptor activity. In this seminar talk, you will investigate the physical limits where the measurement noise of bioreceptors begins to dominate over their measurement signal.
Physics of Chemoreception
Howard C. Berg Edward M. Purcell 
Physical limits to biochemical signaling
William Bialek Sima Setayeshgar 
Physical Limit to Concentration Sensing in a Changing Environment
Thierry Mora Ilya Nemenman


Brownian Ratchet and Molecular Motors
Nonequilibrium fluctuations in an isothermal medium and the anisotropic system can induce mechanical force and motion. Brownian ratchet is one of the paradigmatic examples of such phenomena. Within this seminar, we will consider how the concept of Brownian ratchet can be used to describe the movement of molecular motors along the biofilaments. Book:
Stochastic Processes in Cell Biology
Paul C. Bressloff  Review article:
Brownian ratchet models of molecular motors
Rachid AitHaddou Walter Herzog
 Book:

How to Price Derivatives – The BlackScholes Equation
The BlackScholes equation can be used to price any financial instrument deriving its value from an underlying asset. It has proven to be one of the most important tools for pricing derivatives including stock market volatility. Within this seminar we will derive the BSequation using only a few assumptions and Ito calculus. No prior knowledge about financial instruments is required. Book:
Options, Futures and Other Derivatives
John C. Hull  Original paper:
The Pricing of Options and Corporate Liabilities
Fischer Black Myron Scholes
 Book:

How Randomness can Create Order – FluctuationInduced Phase Transitions
Noise is usually thought of as a phenomenon which creates disorder. However, certain systems show the emergence of ordered states due to an interplay of noise and nonlinear effects. In this talk you will study a toy model which exhibits such a noise induced phase transition. To do so, you have to rely on Langevin equations and their correspondence to FokkerPlanck equations. Original paper:
NoiseInduced Nonequilibrium Phase Transition
C. Van den Broeck J. M. R. Parrondo R. Tora  Review article:
Nonequilibrium phase transitions induced by multiplicative noise
C. Van den Broeck J. M. R. Parrondo R. Toral R. Kawai
 Original paper:

Active Matter and Boltzmann Ansatz
Active matter is composed of large numbers of active agents, each of which can convert chemical energy to mechanical work. In the seminar, we consider how the equations of collective motion in an active matter system can be derived using the socalled Boltzmann ansatz. Original paper:
Boltzmann and hydrodynamic description for selfpropelled particles
Eric Bertin Michel Droz Guillaume Grégoire  Review article:
Hydrodynamics of soft active matter
M. C. Marchetti J. F. Joanny S. Ramaswamy T. B. Liverpool J. Prost M. Rao R. A. Simha
 Original paper:

Nonequilibrium SelfAssembly Processes
Selfassembly and selforganisation are two fundamental concepts used to explain the astonishing ability of natural systems to autonomously generate complex structures and patterns. Moreover, the artificial fabrication of complex nanostructures via selfassembly is assumed to be of great relevance for future technologies in medicine as well as in engineering. In this talk you will analyze a recently proposed generic model using concepts including Master equations and FokkerPlanckequations. 
Diffusiophoresis: How Density Gradients Can Induce Motion in Unrelated Molecules
Cells organize themselves in space and time by forming biochemical patterns and particle density gradients. In this seminar, you will investigate how density gradients can induce motion of other biomolecules without relying on specific interactions (in contrast to motor proteins that pull cargo). You will compare this phenomenon to osmosis.
Osmosis, from molecular insights to largescale applications
Sophie Marbach Lydéric Bocquet  Review article:
Diffusiophoresis in Cells: A General Nonequilibrium, Nonmotor Mechanism for the MetabolismDependent Transport of Particles in Cells
Richard P. Sear


Infection Dynamics on Networks (WKB Method)
Infection dynamics on networks are a timely topic. The nonlinear stochastic equations that are commonly used to model infection spread and exctinction are typically hard to solve analytically. You will get to know the basic mathematical framework of infection modeling and become acquainted with the use of powerful, generic methods for solving nonlinear stochastic problems. Introduction to WKB: Chapter 10 in
Stochastic Processes in Cell Biology
Paul C. Bressloff  Introduction to Infection modeling: Chapter 17 in
Networks: An Introduction
Mark Newman  Review article:
WKB theory of large deviations in stochastic populations
Michael Assaf Baruch Meerson  Optional, great paper on the general topic:
Rare event statistics in reactiondiffusion systems
Vlad Elgart Alex Kamenev  Simple application of WKB theory in infection systems:
Epidemic extinction in a generalized susceptibleinfectedsusceptible model
Hanshuang Chen Feng Huang Haifeng Zhang Guofeng Li
 Introduction to WKB: Chapter 10 in

Quantifying Irreversibility (Focus: KLDivergence)
The concept of thermodynamic irreversibility is fundamental for life. Irreversibility of a process is given by the distinguishability between the process and its time reversal, which in turn can be quantified using the KullbackLeibler divergence or relative entropy. In this seminar talk, you will read about very recent methods that allow one to detect dissipative nonequilibrium processes even in partially hidden complex systems as they occur ubiquitously in biology.
Inferring broken detailed balance in the absence of observable currents
Ignacio A. Martínez Gili Bisker Jordan M. Horowitz Juan M. R. Parrondo 
Dissipation: The PhaseSpace Perspective
R. Kawai J. M. R. Parrondo C. Van den Broeck
