Physics of the Genome
How forces and interactions between DNA, RNA and proteins give rise to observed structure and dynamics for nuclear material and to observed nonlinear behavior for the expression of genes in different types of cells. These studies are enabled by the world-leading program in genome structure and dynamics in the CTBP lab of Erez Aiden.
Biomolecular Physics And Cellular Processes
Cells are large and complex in molecular terms but small in terms of the ordinary mechanical objects we encounter. Also, many of these molecular processes operate out of equilibrium. Thus, the usual paradigm of condensed matter physics - put many microscopic objects together; derive a free energy and, using various analytical approximations and simulations, calculate a few bulk properties - needs to be fundamentally re-worked for biological matter. We are still learning about how the interactions between these types of elements create higher-level functional behavior. And we strongly believe that lessons learned at one biological level can directly inform research at other level, both in terms of concepts and methods - we have seen this repeatedly in our CTBP history.
Regulatory Control Of Biological Active Processes
Much of CTBP research has focused on coupling molecular-based control systems (for example in the form of genetic circuits) with biophysical processes such as metabolism, genome folding and cell motion. These processes implement the actual functionality of living systems and their regulation enables those systems to take appropriate actions in response to information about the current environment. These projects take advantage of the unique capabilities of the CTBP, where expertise in different aspects of the task at hand can be brought together to make rapid progress.
As we progress with our own research agenda, we are also interested in making newly developed tools available for general use by the community. Current efforts here include the AWSEM approach for molecular level biophysics, the SMOG method for structure-based analysis of biomolecules and the DCA approach for combining comparative genomes with structural biology data to enhance capabilities in protein-protein interactions in the context of cell signaling. Our newest efforts in this direction include the NDB website for our research into genomic structure and the RACIPE methodology for analyzing the robust features of biological networks.
Physics of the Genome