Stochastic biochemistry
From Ilya Nemenman
This is one of the Projects of Ilya Nemenman's lab. Email Ilya for details.
Contents |
What is this about?
Here we are interested in understanding how signals propagate through stochastic biochemical networks of various complexity.
Specific questions include:
- Deriving (asymptotocally) exact results for coarse-graining biochemical kinetics in the context of dynamical signals (e.g., concentrations of various chemicals that change over time due to external influences and/or due to noise). The methods used involve WKB (mesoscopic molecular copy numbers) techniques, full counting statistics methods, and Doi-Peliti formalism. We are specifically interested in simple model reactions, like Michaelis-Menten (or particle transport), Hill cooperative reactions, protein-DNA binding, and others.
- Deriving correct coarse-grained descriptions (that is, integrating our the internal dynamics) for common signal transduction mechanisms, like futile cycle and two-component signaling. In particular, what are frequency response characteristics of these systems? Their channel capacity? Does the systems have built-in mechanisms for adaptation to maximize, say, information transmission?
- Understanding infromation-theretic characteristis of signal transduction in large biochemical networks, specifically effects of topological properties of the networks on the former.
- Building tools for fast, yet exact simulation of large stochastic biochemical systems.
Internal project pages (you have to be a collaborator to view these).
Results
Bibliography
These are the papers relevant for this topic.
Simple stochastic kinetics
- Pump current and all that
- The Berry phase in stochastic kinetics
- Tools and approximations for stochastic analysis
- Signal processing in the Futile Cycle
Szabo et al., Ao and Thouless, 1993, Thouless et al., 1996, Hannay, 1985, J. H. Hannay, J. Phys. A. 18, 221 (1985), Schilling et al, 2007, R. Schilling, M. Vogelsberger, D. A. Garanin, Garrison and Wright, 1988, J. C. Garrison, E.M. Wright, Phys. Lett. A, 128, 177 (1988),
