Single Molecules: From Observation to Manipulation
Final Report Abstract
In the last years there has been a major increase in activity in studies of dynamics in nanoscale confinements. A substantial progress in understanding the leading factors that determine the dynamics of confining systems has opened new possibilities to modify and control motion at these small scales. The difficulties in realizing efficient ways to control confined motion are related to the complexity of the task, namely dealing with systems with many degrees of freedom under strict size limitations, which leaves very limited access to interfere with the system in order to be able to control. One way to deal with small-scale systems, in particular those related to biomolecules, has been probing them on a single molecule level. This information one obtains on single molecules is more detailed than in ensemble measurements. In the framework of our DFG project we investigated the effect of normal and lateral vibrations of a substrate on diffusivity, mobility and friction at the nanoscale. We demonstrated that manipulations by mechanical excitations when applied at the right frequency and amplitude can dramatically increase surface diffusion and mobility that has a resonance nature, the reduction of friction does not exhibit pronounce resonance features. We have found a sharp transition from the state with a small tip-surface separation to the state with a large separation as the vibration frequency or/and amplitude increase. With another working direction, we focused on the study of diffusion process of molecules or small particles in narrow confining systems. In fact, the diffusion process in higher dimensional (2D or 3D) confined system is an insightful model to study the influence of entropic effects, which also plays a prominent role in the dynamics of biomolecules and their folding. The higher dimensional problem could approximati veiy be described by an one-dimensional kinetic equation with geometrical restrictions giving rise to entropic contributions to the effective energy function, where the barrier height scales with temperature. Biased diffusion of molecules or small particles through narrow, confined geometries exhibits peculiar properties which are radically different from what one would generally observe in purely energetic systems: the average particle current decreases upon increasing the strength of the thermal noise, contrary to the behavior that usually found in purely energetic systems. Similar to purely energetic systems, we observed an enhancement in the effective diffusion coefficient whose maximum always exceeds the bulk diffusion constant. Surprisingly, in confined systems, these transport behaviors can be controlled by a single parameter, which is a ratio of external work applied to the particle and thermal energy, whereas applied bias and temperature are independent parameters in purely energetic systems. Moreover, we were able to show the effect of Stochastic Resonance, i. e. the anomalous signal amplification due to noise, in presence of entropic barriers.
Publications
- Entropic transport in confined media, Ph.D thesis, Augsburg, Germany, 2008
P.S. Burada
- Fractons in Proteins: Can They Lead to Anomalously Decaying Time Autocorrelations?, Phys. Rev. Lett. 95, 098106 (2005)
R. Granek and J. Klafter
- Tuning Diffusion and Friction in Microscopic Contacts By Mechanical Excitations., Phys. Rev. Lett. 95, 016101 (2005)
Z. Tshiprut, A. E. Filippov, and M. Urbakh
- Entropic transport: Kinetics, scaling and control mechanisms, Phys. Rev. Lett. 96, 130603 (2006)
D. Reguera, G. Schmid, P.S. Burada, M. Rubi, and P. Hänggi
- The Basic of Nanoscale Friction and Ways to Control it. Nanotribiology, eds. E. Meyer and E. Gnecco. Spinger, 143 (2006)
J. Klafter and M. Urbakh
- The escape of a particle from a driven harmonic potential to art attractive surface, J. Chem. Phys. 125, 204705 (2006)
Z. Tshiprut, J. Klafter and M. Urbakh
- Biased diffusion in confined media, in: Noise and Fluctuations, ICNF 2007, edited by M. Tacano, Y. Yamamoto, and M. Nakao, AIP Conf. Proc, 922, pp. 513-518 (2007)
P.S. Burada, G. Schmid, D. Reguera, M. Rubi, and P. Hänggi
- Biased diffusion in confined media: Test of the Fick-Jacobs approximation and validity criteria, Phys. Rev. E 75, 051111 (2007)
P.S. Burada, G. Schmid, D. Reguera, M. Rubi, and P. Hänggi
- Directed transport induced by asymmetric surface vibrations. Making use of friction, J. of Phys: Condensed Matter 19, 096004 (2007)
D. Fleishman, Y. Asscher and M. Urbakh
- The effect of Lateral Vibrations on Transport and Friction in Nanoscale Contacts, Tribilogy International 40, 967 (2007)
Z. Tshiprut, A. E. Filippov, and M. Urbakh
- Entropic paHicle transport in periodic channels, BioSystems 93, 16 (2008)
P.S. Burada, G. Schmid, P. Talkner, P. Hänggi, D. Reguera, and J.M. Rubi
- Entropic Stochastic Resonance, Phys. Rev. Lett. 101, 130602 (2008)
P.S. Burada, G. Schmid, D. Reguera, M.H. Vainstein, J.M. Rubi, and P. Hänggi
- Double Entropic Stochastic Resonance, Europhys. Lett. 87, 50003(2009)
P.S. Burada, G. Schmid, D. Reguera, J.M. Rubi, and P. Hänggi
- Entropic transport - A test bed for the Fick-Jacobs approximation, Phil. Trans. R. Soc. A 367, 3157 (2009)
P.S. Burada, G. Schmid, and P. Hänggi
