Aleksandra Walczak

 

 

 

walczak(at)physics.ucsd.edu

phone: (858) 822 5528

 

Urey Hall 6230

La Jolla, CA 92093-0371

 

 

 

 

 

 

 

 

I am graduate student, working with Professor Peter G. Wolynes,  at the Department of Physics and Center for Theoretical Biological Physics at the University of California, San Diego.

                                  HOST: Mac OS X 10.3.9

 

Curriculum Vitae

 

 

Currently, I am working on two types of complex systems: glasses and gene networks/switches.

      

My current research is related to studying the effects of the stochastic nature of genetic networks. The relatively small numbers of protein molecules of a given type present in the cell and the nonlinear nature of chemical reactions result in emergent behaviours, which are not easily predicted. I am interested in how noise on all levels of the regulatory system affects the complex collective characteristics of systems observed experimentally.

I am also trying to understand the particular phases that arise in the stripe glass Hamiltonian model, which describes the interplay of competing interactions on short and long length scales. I am especially interested in the existence and dynamics of the glass phase. This system is an interesting example of self-generated randomness- no quenched disorder is needed to result in glassy behaviour.  

 

In the future I would like to continue working on theoretically understanding the collective behaviour that arises in both biological and non-animate many body systems.        

 

More specifically, I have been trying to understand the role of DNA binding state fluctuations in the regulation of genes. I have worked on constructing simple models and approximations [2, 3, 4], which allow for, at least some, analytical progress in these problems. These have allowed us to understand, on the example of toy models, how the DNA binding state fluctuations influence the steady state properties and lifetimes of attractors of simple gene systems. I have shown, that for fast binding and unbinding from the DNA, the DNA binding state may be taken to be in equilibrium for highly cooperative binding, when predicting steady state properties. However, if proteins are produced in bursts, the DNA binding state fluctuations must be taken into account explicitly, even in the steady state [4]. Furthermore, even if the steady state probability distributions are not influenced by the DNA binding state fluctuations, the escape rate in biologically relevant regimes strongly depends on transcription factor-DNA binding rates [2].

   

Publications

  1. F. Alet, A. M. Walczak and M. P. A. Fisher, "Exotic quantum phase transitions in correlated matter", Physica A, to be published in Proceedings of the XI School on Fundamental Problems in Statistical Physics, cond-mat/0511516
  2.  A. M. Walczak, J. N. Onuchic and P. G. Wolynes, "Absolute rate theories of epigenetic stability", Proc. Natl. Acad. Sci. USA (102), 18926, (2005)
  3. J. E. M. Hornos, D. Schultz, G. C. P. Innocentini, J. Wang, A. M. Walczak, J. N. Onuchic and P. G. Wolynes, "Self-regulating gene: an exact solution", Phys. Rev. E (72), 051907-1-5, (2005)
  4. A. M. Walczak, M. Sasai, P.G. Wolynes, "Self-Consistent Proteomic Field Theory of Stochastic Gene Switches", Biophys. J. (88), 828-850 (2005)
  5. A. M. Walczak, J.M. Antosiewicz, "Langevin Dynamics of Proteins at Constant pH", Phys. Rev, E (66), 051911 (2002).

 

 

 

Canadian-American-Mexican Graduate Student Conference (an APS meeting I co-organized)