Prerequi sites to successfully carry out the research supported by MRSEC grant include access to substantial computational facilities, access to advanced optical and electron microscopes, and microfluidic stations to operate chips made in the Brandeis Microfluidic Fab.
These four techniques – computation, optical and electron microscopy and microfluidics – form the experimental pillars on which much of the proposed research is built.
Graduate students in a microfluidics lab
IRG: Emergent Properties Due to Constraints
Thrust Area I: Polymers in a crowded and confined environment
 The goal of this project is to examine the material properties of single macromolecules (DNA and actin) in crowded and confined environments, and then apply this knowledge to chromosomes in living cells so as to relate material properties of chromosomes to their biological functions. We will use two complementary approaches. In a bottom up approach (in vitro) we will create artificial structures in which semiflexible polymers, such as DNA and actin, are confined to spaces of varying geometry and dimensionality. We will measure static and dynamic properties of these confined polymers (monomer-monomer separation, monomer diffusion) and compare them to theoretical models. Simultaneously, using a top down approach (in vivo) we will measure the same material properties of DNA in yeast cells, and use these to develop effective polymer models of chromosomes. A careful comparison between these two approaches will reveal the degree to which material properties of chromosomes influence their biological function.
Thrust II: Chiral self-assembly
 Understanding and controlling the assembly of molecules, nanoparticles and colloids into well defined three dimensional structures poses a significant challenge that spans the disciplines of biology, chemistry, physics and material science. The chirality of individual molecules imposes local constraints that compete with the global requirements of self-assembly and thereby dramatically alters the phase behavior, assembly kinetics and the macroscopic material properties of assembling systems. Cellulose, the most abundant biomolecule on earth, and collagen, the most abundant molecule in the animal kingdom, are relevant examples of structural polymers whose self-assembly into fibers is mediated by their chirality. Using a unique model system of chiral viruses we will explore how the chirality of constituent molecules controls self-assembly pathways and thus dictates the final assembled structures.
Thrust III: Active Matter 
Active matter is an assembly of microscopic objects, each of which consumes energy to generate continuous dynamics, either propagating in space or oscillating in time. The collective behavior of such an assembly emerges from the interaction between objects. During the last decade, progress has been made in establishing a theoretical framework for this class of non-equilibrium systems. Experiments have, however, lagged behind theory primarily due to the lack of precisely controllable model systems. We propose an interdisciplinary approach involving biology, chemistry and physics to develop two model systems of active matter. The creation of these two systems with precisely controlled microscopic dynamics will bring transformative change to the rapidly developing field of active matter. Our first, biologically inspired system is a dense collection of self-propelled actin filaments. The second, chemically inspired system is based on an emulsion of droplets. An oscillatory chemical reaction takes place within each droplet and droplets interact through the diffusion of reagents. Following the theme of our IRG, we will investigate the effects of confinement and frustration on the collective properties of these model systems.
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