Associate Professor (Canada Research Chair Tier II)
Department of Physics
Simon Fraser University
Burnaby, BC V5A 1S6
Left to Right: Sara Sadeghi, Saeed Saberi, EE
Left to Right: EE, Pau Farre, Saeed Saberi
Current Graduate Students:
Regulation and Chromatin Structure:
Every cell in an organism contains the same genome - the set of all genes that are written in the DNA. Despite this fact that cells all share the same list of genes, there is a huge variety of cell types. This arises in part because different cells use differing sets of genes. What allows a cell to turn on only a certain set of its genes? Many genes are controlled by specific programs encoded in the DNA that turn them on or off in response to particular spacial and/or temporal cues. The structure of the DNA also influences how genes are regulated. In higher organisms the genome is meticulously packaged into a structure called chromatin. In collaboration with several experimental groups we are analyzing factors that regulate chromatin structure, and developing models for how the structure of DNA influences gene expression.
There are a variety of filamentous proteins that are key structural elements in many tissues. These tissues have a variety of mechanical properties that depends on the structure of the filamentous protein that make them. A fundamental question is how does a filament's response to external forces depend on the underlying protein sequence? Single-molecule experiments using optical tweezers or atomic force microscopes provide the opportunity to measure the mechanical response of individual proteins. My group is developing simple atomistic models to predict the observed mechanical behaviours of a variety of different filamentous protein structures.
Biochemical Networks and Cellular Decision Making:
My lab is also interested in the dynamical properties of biological networks. Given a set of interacting genes and their various regulatory interactions, can one model the temporal behaviour of the entire network and make predictions about its function. In particular, how do physical constraints influence the types of biochemical calculations that bacteria need to perform in order to carry out the tasks that they need to perform in order to survive. Recently we have developed a model for the network which regulates the circadian rhythms in photosynthetic bacteria. We are now working on a model for the cell cycle in the asymmetrically dividing bacteria Caulobacter Crescentus.
List of publications
PHYS-847: Quantitative Biology
PHYS-347: Introduction to Biophysics