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.

Announcement

Subscription is open for contributed 20′ talks and posters on topics related to: methods for CN analysis (stochastic or deterministic); signalling and information processing in CNs; metabolic analysis. There will be the opportunity to append posters at the conference premises and discuss them during coffee breaks. We are also planning to organize a poster session. Participation is free of charge, lunch and coffee breaks will be offered.
We can only accept a very limited number of applications. Registration is mandatory. Please write to the organizers, or in the box below, specifying 1) Generalities 2) Short motivation for participation 3) Title and abstract of contributed talk / poster 4) Date of arrival 5) Date of departure 6) Special dietary requirements.

 

Invited speakers

Confirmed

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. 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.

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. 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. 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. 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. Stefan Müller (Radon Institute for Computational and Applied Mathematics, Austrian Academy of Sciences) 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.