(3ca) Theory and Modeling of Artificial Molecular Machines in Biological Systems

Living organisms offer numerous examples of molecular machines that convert different forms of energy into mechanical work in the form of directed movement or conformational change of other biological components. Within the past two decades, a considerable scientific research has been invested in understanding the biophysics of the molecular machines. In specific, artificial molecular machines that perform useful tasks on molecular scales or their cooperative assemblies capable of converting energy into mechanical work in scales much larger than individual molecules have presented a great promise in the fields of nanotechnology and alternative energy resources.

World of molecular machines is in many respects quite different than that of their macroscopic counterparts. Molecular machines operate in a domain where gravity and inertia are outplayed, by orders of magnitude, by Van der Waals, electrostatic and other types of molecular interaction and their far-from-equilibrium motion is always accompanied with considerable thermal fluctuations. To gain further understanding of the performance of the artificial molecular machines, we study the conformational change of several biological molecules under external mechanical force. We use theories of nonequilibrium thermodynamics along with novel molecular simulation techniques to investigate Helix-coil transition of peptides, deconstruction of coiled-coiled structures and unzipping of dsDNA under the action of artificial molecular machines. We are currently collaborating with Fraser Stoddart group at Northwestern University to implement our design principles in synthesis of molecular machines with mechanically interlocked molecules such as rotaxanes or cantenanes.  We hope our theoretical studies guide the experiments and provide physical insight to the biophysics of the artificial molecular machines and their applications within biological systems.