Statistical Mechanics and Computer Simulations with Applications in Micro- and Nano-Fluidics and Biological Physics

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Over the last 10-15 years, we have witnessed a remarkable convergence of the experimental and computational sciences. Indeed, while experimentalists can now study single molecules such as DNA or proteins, or even build nanoscopic systems (e.g., nanochannels) made of a very small number of molecules, theoreticians now possess the theoretical and computational tools to study the very same systems, molecule by molecule. Massive computers make it possible to make molecular movies and detailed predictions. This convergence opens incredible possibilities in a number of disciplines, including biophysics and the separation sciences. In this grant application, we propose to investigate several problems at the interfaces between soft matter physics, analytical chemistry, biotechnology, computational science, and biophysics: (1) We will use molecular-level computer simulations to study micro- and nanofluidic systems used to separate and analyze DNA and proteins (what is often called lab-on-a-chip systems in the media). (2) We will continue the development of our revolutionary lattice model of diffusion and drift. We will extend our work to study the separation of biomolecules with high and pulsed electric fields, ratchet systems, networks of cavities, drug-delivery systems (e.g., gel-based pills), complex geometries, ... (3) We will continue the study and development of new microfluidic technologies. In particular, we will examine the separation of long DNA molecules, the use of artificial media as a substitute to fragile gels, and the design of devices based on thermodynamic ratchet systems. (4) We will model the passage of DNA through narrow pores, the process that will most likely be behind the next generation of DNA sequencers. We will examine the role of noise, the utilization of pulsed electric fields, and finally some biological aspects of this process as it occurs in live cells. (5) Finally, we will model the collective motion of swimming bacteria in asymmetric devices to see if these devices can be used to separate the cells according to their biophysical properties.