Using technology such as optical tweezers, single molecules can be held at their ends and stretched, much like rubber bands. Beyond the technical difficulty of performing these precise measurements, there remains the theoretical challenge of recovering what their mechanical properties would be without such manipulation. For example, how likely is it that the molecule will have a certain end-to-end distance versus another? It has been previously understood how to calculate this property from repeatedly pulling the molecule in a single direction. Our group has developed a novel method, based on optimally using the time reversal of paths that the molecule takes after being pulled in the opposite direction, to more reliably calculate the relative probabilities of molecular lengths. This method leads to a substantial gain in efficiency, and should find use in both computational and experimental settings. Another topic addressed by our group is concerned with """"""""crowded"""""""" molecular environments. As a first step towards understanding how the motion of proteins is affected by the presence of other molecules in the cell (""""""""crowders""""""""), we have investigated the diffusion of idealized molecules in the presence of random spherical objects -- the so-called Lorentz gas. We have derived a simple analytic formula that predicts how the diffusivity of such idealized molecules depends on the concentration of crowding molecules. This result should pave the way to a more thorough characterization of crowding effects in the cell.
| Minh, David D L; Adib, Artur B (2009) Path integral analysis of Jarzynski's equality: analytical results. Phys Rev E Stat Nonlin Soft Matter Phys 79:021122 |
| Mittal, Jeetain (2009) Using compressibility factor as a predictor of confined hard-sphere fluid dynamics. J Phys Chem B 113:13800-4 |
| Minh, David D L; Adib, Artur B (2008) Optimized free energies from bidirectional single-molecule force spectroscopy. Phys Rev Lett 100:180602 |
| Adib, Artur B (2008) Stochastic actions for diffusive dynamics: reweighting, sampling, and minimization. J Phys Chem B 112:5910-6 |
| Adib, Artur B (2008) Random-walk approach to the d-dimensional disordered Lorentz gas. Phys Rev E Stat Nonlin Soft Matter Phys 77:021118 |
