Biological physics

Evolution of drug resistance

gradsDrug resistance is a very important problem in the treatment of bacterial or viral (such as HIV) infections, and in cancer. I am interested (both theoretically and experimentally) in how spatial heterogeneities in drug distribution affect the rate of evolution of drug resistance.

I am also interested in simple models (experimental and theoretical) of bacterial infections. For example, we have used the PEE Machine as an experimental model of a urinary tract infection.

Simple models for bacterial evolution with migration

source_sinkI investigate the role of migration in the evolution of genetic diversity in microbes. I am particularly interested in how evolution is affected when microbes can migrate between environments with different conditions (different nutrients, temperature etc.).

Metabolic pathways

Metabolic pathways are networks of chemical reactions used by cells to convert food into energy and other chemicals used as “building blocks”. I and Rosalind Allen are interested in how these networks evolved and how their evolution was constrained by physics and chemistry.

The physics of bacterial colonies

We use computer simulcolonyations and experiments to study the growth of bacterial colonies, fixation probabilities of beneficial mutations, and gene transfer (conjugation) between adjacent bacteria. My collaborators include D. Marenduzzo, O. Hallatschek  R. Allen, P. Cicuta, and W. C. K Poon.

Spatial models of cancer

We model gr3d_mid_plane_61_161.pngowth and treatment of metastatic lesions and primary tumours. We are in particularly interested how genetic heterogeneity of tumours is affected by replication, death, and migration of cancer cells. We collaborate on this with cancer biologists and medical researchers.

Bacteria on percolating clusters

We investigate how bacteria swim in a complicated network of connected microcompartments.

Other areas of interest

– structure of fitness landscapes in biological evolution of microbes (with M. Zagorski, see this paper about accessibility of fitness landscapes)

– relation between biological evolution, random matrix theory, and localization of eigenvectors of certain random matrices (a paper about it is here)

– simple models of oscillatory circuits in biological systems (see here for a paper with A. Garai, H. Nagel and H. Meyer-Ortmanns)

– gene expression

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