The aim of this workshop is to bring in contact a small number of high-profile research groups working at the interface between mathematical physics and biochemistry, united by the common interest for the role of large chemical networks in the regulation of cellular behavior.

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Slides

Slides for most of the talks of the conference are available at this link. For those who would still like to contribute their slides, please send them to the conference organizers.

 

Program

Book of abstracts:

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Workshop schedule:

 

Tue 13

Wed 14

Thu 15

Fri 16

8.30 – 10.30

Salutation

Rein ten Wolde

Malaguti

Ouldridge

Schuster

Ewald

Fleming

Peliti

Estevez-Torres

Qian

De Buyl

Bo

10.30 – 11.00

☕

☕

☕

☕

11.00 – 13.00

Baez

Pollard

Smith

Krishnamurthy

Stelling

Yordanov

Skupin

Rao

Wachtel

Carlon

Bravi

Soons

Greetings

13.00 – 14.00

☕

☕

☕

☕

14.00 – 16.00

Craciun

Ebenhöh

Raguin

Poolman

 

Gaspard

Nghè

Mueller

De Martino

Roldan

16.00 – 16.30

☕

☕

☕

16.30 – 18.00

Flamm

Merkle

Mast

Keil

Bar-Even

Noor

 18.00 – 18.30

Poster intro

 

Plesa

19.00 – 22.00

Poster session

Gala dinner

Legend:

20’ Communication
40′ Invited Talk

40′ Invited Talk

or

Group Slot

Speakers

Invited

Prof. John Baez (U. C. Riverside, California; Centre for Quantum Technologies, Singapore) works on information and network theory. He is expert on the mathematical techniques for the study of the topology and dynamics of Chemical Networks. He also coordinates the Azimuth Project, a way for scientists, engineers and mathematicians to do something about the global ecological crisis.

Dr. Arren Bar-Even (Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam, Systems and Synthetic Metabolism group) and his group study the biochemical logic and design principles of metabolic pathways and their applications in metabolic engineering of microbes, focusing on engineering synthetic alternatives to central metabolic pathways, aiming to uncover optimality in metabolic designs and to offer novel solutions for humanity’s needs in chemical and energy production.

Prof. Gheorghe Craciun (University of Wisconsin-Madison) works on mathematical and computational methods in the modelling in biology and medicine, in particular the deterministic and stochastic description of mass-action kinetics. He has recently proven the Global Attractor Conjecture.

Prof. Oliver Ebenhöh (Institute for Quantitative and Theoretical Biology, University Düsseldorf) develops mathematical models of plant energy metabolism and photosynthesis, with focus on acclimation processes of the electron transport chain, methods to simulate and describe the production and degradation of biopolymers, and the timing of metabolism: how are key processes regulated by the diurnal rhythm and the circadian clock?

Dr. Andre Estevez-Torres (Laboratoire Jean Perrin, Paris) and his group assemble chemical systems based on DNA and RNA which reproduce the behavior of the dynamics of population networks. They are taking a biomimetic approach with two goals: on the one hand, by studying simple molecular systems that emulate their biological analogues, they hope to better understand the emergence of complex biological behaviors such as genetic regulation or morphogenesis. On the other hand, these dynamical molecular systems can be seen as new materials that mimic living organisms, and which are able to adapt and response autonomously to their environment.

Prof. Christoph Flamm (Institute for Theoretical Chemistry, Wien) works on (hyper)graph-theoretic concepts related to the analysis of Chemical Networks: motifs, pathways, transformation rules, with a special attention to their computational implementation.

Prof. Pierre Gaspard (Université Libre de Bruxelles), a major expert on the theory of chaotic dynamical systems and of Markov processes for thermodynamic modelling, has recently turned his attention to the role of fluctuations in Chemical Networks and to the stochastic dynamics of copolimerization.

Dr. Supriya Krishnamurthy (Physics Department, Stockholm University) is interested in both fundamental and interdisciplinary applications of non-equilibrium statistical mechanics. Recent work includes understanding combinatorial satisfiability problems on random graphs, evolutionary game theoretical problems, using large deviation theory for estimating work distributions of stochastic processes, and most recently also solving moment hierarchies for chemical reaction networks.

Dr. Christof Mast (Systems Biophysics Group, Ludwig Maximilians Universität München, Germany) works in the group of Prof. Dieter Braun and is interested in the effects of thermal and chemical non- equilibria on the orgin of life, e.g. the emergence of structure and information and the physical driving of the first biochemical reactions.

Prof. Daniel Merkle (University of Southern Denmark) works on Cheminformatics, with special interest in new algorithmic approaches, combining graph theory and chemistry, and computational complexity questions.

Dr. Philippe Nghe (ESPCI, Paris) and his team are at the interface between statistical physics and systems biology, and focuses on interaction networks (catalytic or regulatory). A major challenge in this field is to go beyond a mere description of connectivity, and understand the relations between structure and function.

Dr. Thomas Ouldridge (Imperial College, London) and his group probe the fundamental principles underlying complex biochemical systems through theoretical modelling, simulation and experiment, focusing in particular on the interplay between the detailed biochemistry and the overall output of a process such as sensing, replication or self-assembly. They are inspired by natural systems, and aim to explore the possibilities of engineering artificial analogs.

Dr. Luca Peliti has been professor of physics at the University of Naples “Federico II” and member of several prestigious international institutions, working among many other topics on statistical models of evolving populations, the origin of biological order, kinetic proofreading. He is editor of the book Biologically inspired physics.

Dr. Mark Poolman (Oxford Brookes University) works on genome-scale metabolic modelling and metabolic control of biological systems.

Prof. Hong Qian (University of Washington) works on the mathematical approach to and physical understanding of biological systems, especially in terms of stochastic mathematics and nonequilibrium statistical physics. In recent years, he has been particularly interested in a nonlinear, stochastic, open system approach to cellular dynamics.

Prof. Stefan Schuster (Friedrich Schiller Universität Jena) is an expert on the regulation and reconstruction of metabolic networks. He is coauthor of the important monograph The regulation of cellular systems and has taught numerous courses on biophysiscs, chemical network dynamics, bioinformatics, etc.

Prof. Eric Smith is currently a professor at Tokyo Institute of Technology and a Principle Investigator of the Earth-Life Science Institute, a World Premier International Focus Center of the Japanese government that operates as part of Tokyo Tech.  He is also external professor at the Santa Fe Institute, and an affiliated research scientist at the Georgia Institute of Technology, working on the NASA Astrobiology Institute node “Reliving the Past: Experimental Evolution of Major Transitions”.  His interests include theoretical problems in modern non-equilibrium statistical mechanics and associated statistical inference, and applications of these ideas to the emergence of robust order in organic geochemistry on early planets, and its relation to origins and subsequent evolution of life.  He is also interested in population processes and questions of multi-level architecture and information flows in evolving systems, and how these cause our understanding of the living state to be related to understanding of other topics like the nature of individuality.

Prof. Jorg Stelling (ETH, Zurich) is head of the Computational System Biology group, which comprises biologists, computer scientists, engineers, and mathematicians who perform interdisciplinary research in systems and synthetic biology. The CSB focuses on developing and applying computational methods and mechanistic mathematical models to study complex cellular networks, to elucidate their operating principles, and to enable their rational re-design. Biological applications rely on the group’s experimental biology part that uses budding yeast as a model organism, and on various external collaborations.

Prof. Pieter Rein ten Wolde (AMOLF, Amsterdam) and his group’s aim is to unravel the design principles of Chemical Networks and the computations performed by molecules using a combination of database analyses, theory and computer simulation.

Contributed talks

Dr. Stefano Bo (NORDITA, Stockholm). His research concerned the thermodynamics of small systems out of equilibrium where fluctuations play a prominent role. He focused on how changing the amount of details available for studying a system affects the description of its thermodynamics. Lately, he has become interested in the relation between information and entropy in small systems and in exploring its applications to the problem of sensing in living organisms.

Dr. Sophie de Buyl (Vrije Universiteit Brussel) has an education in Theoretical and Mathematical Physics. She is working on the design of genetic regulatory networks to develop synthetic biology with Archaea. Her research interests include deriving thermodynamical constraints on information transmission and computational capacity of gene regulatory networks, as well as modelling the dynamics of microbial communities.

Dr. Daniele De Martino (IST Austria, Klosterneuburg) has as his main research focus statistical mechanics and its applications beyond condensed matter systems.
He gave contributions on the study of phase transitions in disordered systems and
in the last years he has been working on the  theoretical physico-chemical  basis of cell metabolism and on the development of related computational methods for data analysis in particular to model cell growth and overflows with maximum entropy approaches.

Dr. Barbara Bravi (Ecole Polytechnique Fédérale de Lausanne) works on Statistical Physics inspired approximation methods for complex biochemical networks, including dynamical mean-field approaches and coarse-graining techniques. She is broadly interested in modelling out-of-equilibrium phenomena and stochastic processes with a particular emphasis on the applications to Systems Biology.

Prof. Enrico Carlon (Theoretical Physics, KU Leuven, Belgium) has a
background in statistical mechanics and works on various systems at the interface between physics and biology. The main focus of recent research has been the mechanical and dynamical properties of DNA and the dynamics of small oscillating genetic circuits.

Dr. Edgar Roldan (MPI for the Physics of Complex Systems, Dresden)

Dr. Stefan Müller (Faculty of Mathematics, University of Vienna) works in chemical reaction network theory and metabolic pathway analysis. In the latter field, he studies optimal resource allocation based on stoichiometric and kinetic information. In particular, he aims to clarify the relation between linear and nonlinear aspects of metabolic optimality, thereby using polyhedral geometry and oriented matroids.

Local speakers

Prof. Massimiliano Esposito and Dr. Matteo Polettini (University of Luxembourg, Complex Systems and Statistical Mechanics Group) work on the thermodynamics of nonequilibrium processes, and have recently started analyzing the thermodynamics of Chemical Networks and its relation to topology, both at the mean-field and for systems described by the Chemical Master Equation.

Dr. Ronan Fleming (University of Luxemboug, LCSB) leads the Systems Biochemistry Group, an interdiscipinary research group of mathematical, computational and experimental biologists. The fundamental interest is to develop scalable mathematical and numerical analysis techniques that increase the predictive fidelity of biomolecular network models, by incorporating physico-chemical constraints, motivated by optimality principles. Their applied interest is in the aetiopathogenesis and amelioration of Parkinson’s disease.

Dr. Alexander Skupin (University of Luxembourg, Integrative Cell Signalling group) and his group combine state-of-the-art imaging and single cell techniques with mechanistic modelling and bioinformatics analyses to investigate how the emergent behaviour of cells, organs and organisms originates from molecular entities.

Information

Contact

Please write to matteo.polettini or to massimiliano.esposito followed by at uni.lu, or fill in the form below.