Bulletin of the American Physical Society
2006 APS March Meeting
Monday–Friday, March 13–17, 2006; Baltimore, MD
Session U29: Focus Session: Nonequilibrium Fluctuation in Biomolecules and Artificial Nanodevices |
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Sponsoring Units: DBP DPOLY Chair: Ioan Kosztin, University of Missouri, Columbia Room: Baltimore Convention Center 326 |
Thursday, March 16, 2006 8:00AM - 8:12AM |
U29.00001: DNA's Liaison with RNA Polymerase – Physical Consequences of a Twisted Relationship Igor Kulic, Phil Nelson RNA polymerase is the molecular motor that performs the fundamental process of transcription. Besides being the key- protagonist of gene regulation it is one of the most powerful nano-mechanical force generators known inside the cell. The fact that polymerase strictly tracks only one of DNA's strands together with DNA's helical geometry induces a force-to-torque transmission, with several important biological consequences like the ``twin supercoil domain'' effect and remote torsional interaction of genes. In the first part of the talk we theoretically explore the mechanisms of non-equilibrium transport of twist generated by a moving polymerase. We show that these equations are intrinsically non-linear in the crowded cellular environment and lead to peculiar effects like self-confinement of torsional strain by generation of alternative DNA structures like cruciforms. We demonstrate how the asymmetric conformational properties of DNA lead to a ``torsional diode'' effect, i.e. a rectification of polymerase-generated twist currents of different signs. In the second part we explore the possibility of exploiting the polymerase as a powerful workhorse for nanomechanical devices. We propose simple and easy to assemble arrangements of DNA templates interconnected by strand-hybridization that when transcribed by the polymerase linearly contract by tenfold. We show that the typical forces generated by such ``DNA stress fibers'' are in the piconewton range. We discuss their kinetics of contraction and relaxation and draw parallels to natural muscle fiber design. [Preview Abstract] |
Thursday, March 16, 2006 8:12AM - 8:24AM |
U29.00002: Enhanced Fano factor in a molecular transistor coupled to phonons and Luttinger-liquid leads So Takei, Yong Baek Kim, Aditi Mitra We study how the electron-phonon coupling {\it and} intra-lead electron interaction affect the transport properties of a molecular quantum dot coupled to leads. We consider the effects on the steady state current and DC noise for both equilibrated and unequilibrated on-dot phonons. The density matrix formalism is applied in the high temperature approximation and the resulting semi-classical rate equation is numerically solved for various strengths of electron-electron interactions in the leads and electron-phonon coupling. We have found that the Fano factor, which measures the noise to current ratio, is enhanced as the intralead electron interaction is increased, while both the current and its noise are smeared out and suppressed due to the interaction. Interestingly, the Fano factor exhibits super-poissonian behaviour as the electron-phonon coupling becomes greater than order one. [Preview Abstract] |
Thursday, March 16, 2006 8:24AM - 9:00AM |
U29.00003: Least dissipation principle for single molecule dynamics Invited Speaker: |
Thursday, March 16, 2006 9:00AM - 9:12AM |
U29.00004: Multi-scale dynamics and relaxation of a tethered membrane in a solvent by Monte Carlo simulations Ras Pandey, Kelly Anderson, Barry Farmer A tethered membrane modeled by a flexible sheet dissipates entropy as it wrinkles and crumples. Nodes of a coarse grained membrane are connected via multiple pathways for dynamical modes to propagate. We consider a sheet with nodes connected by fluctuating bonds on a cubic lattice. The empty lattice sites constitute an effective solvent medium via node-solvent interaction. Each node execute its stochastic motion with the Metropolis algorithm subject to bond fluctuations, excluded volume constraints, and interaction energy. Dynamics and conformation of the sheet are examined at a low and a high temperature with attractive and repulsive node-node interactions for the contrast in an attractive solvent medium. Variations of the mean square displacement of the center node of the sheet and that of its center of mass with the time steps are examined in detail which show different power-law motion from short to long time regimes. Relaxation of the gyration radius and scaling of its asymptotic value with the molecular weight are examined. [Preview Abstract] |
Thursday, March 16, 2006 9:12AM - 9:24AM |
U29.00005: Ion distribution inside a nanopore in the presence of a polyelectrolyte Lei Guo, Erik Luijten Experimental studies of the translocation of DNA through nanopores rely on measurements of the ionic current. In order to understand the behavior of this current, we employ molecular dynamics simulations to study the ion distribution within a nanopore in the presence of a polyelectrolyte. We characterize the ion distribution in terms of radial density profiles around the polyelectrolyte. Several factors affecting the ion distribution are studied, including the role of chain flexibility, salt concentration, nanopore size and its polarizability. Our study also provides information on the dynamics of the ions inside the pore. The combination of static and dynamic information is used to explain experimental observations. [Preview Abstract] |
Thursday, March 16, 2006 9:24AM - 9:36AM |
U29.00006: Measuring the direction of coupling between biological oscillators Jorge Brea, Alexander Neiman, David Russell The electroreceptor system of the paddle fish comprises two self-sustained noisy oscillators: one oscillator resides in the sensory epithelium and is coupled through excitatory synapse with another oscillator residing in the afferent neuron terminal. We test recently developed algorithms for estimating the directionality of their coupling from experimental recordings of spontaneous and stimulated activity. These experimental bivariate time series are structurally different: while the signal from the epithelial oscillations is represented by a continuous stochastic process, the neuron oscillations are represented by a stochastic point process. We show that the tested algorithms detect reliably directionality of coupling both in experimental and simulated data and can be used for physiologically relevant short segments of data. [Preview Abstract] |
Thursday, March 16, 2006 9:36AM - 10:12AM |
U29.00007: Applications of the ratchet effect at nano- and mesoscopic scales Invited Speaker: I will discuss the application the ratchet effect in superconducting vortex dynamics and interacting colloidal systems. We have shown theoretically how in superconductors patterned on sub-micron or nanometer scale with various pinning potentials a DC vortex transport and vortex manipulation can be achieved with an external AC drive. I will discuss several applications of the vortex ratchet effect as well as a series of experiments aimed at the detection and investigation of the vortex ratchet transport. For colloidal systems, we have recently shown that a rich variety of dynamic phases can be realized for mono- and bidisperse mixtures of interacting colloids under the influence of a symmetric flashing periodic substrate. With the addition of dc or ac drives, phase locking, jamming, and new types of ratchet effects occur. In some regimes we find that the addition of a non-ratcheting species increases the velocity of the ratcheting particles. We show that these effects occur due to the collective interactions of the colloids. [Preview Abstract] |
Thursday, March 16, 2006 10:12AM - 10:24AM |
U29.00008: On-Chip Integration of Cell-Free Gene Expression Amnon Buxboim, Margherita Morpurgo, Maya Bar-Dagan, Veronica Frydman, David Zbaida, Roy Bar-Ziv We present a synthetic approach for the study of gene networks \textit{in vitro} which is complementary to traditional \textit{in vivo} methodologies. We have developed a technology for submicron integration of functional genes and on-chip protein synthesis using a cell-free transcription/translation system. The interaction between genes is facilitated by diffusion of on-chip gene expression products from `source' genes towards `acceptor' genes. Our technology is simple and inexpensive and can serve as an improved platform for a wide variety of protein and DNA biochip applications. [Preview Abstract] |
Thursday, March 16, 2006 10:24AM - 10:36AM |
U29.00009: ``Burnt Bridge'' Mechanism of Molecular Motor Motion Tibor Antal, Paul Krapivsky Motivated by a biased diffusion of molecular motors with the bias dependent on the state of the substrate, we investigate a random walk on a one-dimensional lattice that contains weak links (called ``bridges'') which are affected by the walker. Namely, a bridge is destroyed with probability $p$ when the walker crosses it; the walker is not allowed to cross it again and this leads to a directed motion. The velocity of the walker is determined analytically for equidistant bridges. The special case of $p=1$ is more tractable --- both the velocity and the diffusion constant are calculated for uncorrelated locations of bridges, including periodic and random distributions. [Preview Abstract] |
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