Bulletin of the American Physical Society
2005 APS March Meeting
Monday–Friday, March 21–25, 2005; Los Angeles, CA
Session P34: Dynamics in Condensed Phase III |
Hide Abstracts |
Sponsoring Units: DCP Chair: Philip Geissler, University of California-Berkeley Room: LACC 511A |
Wednesday, March 23, 2005 11:15AM - 11:51AM |
P34.00001: Langmuir Prize Talk: Pathways to forming glass: bubbles in space-time Invited Speaker: This lecture describes a perspective of glass-forming materials that I have helped Juan P. Garrahan develop. It based upon the structure of trajectory space. Illustrations of this perspective are most often drawn from so-called ``facilitated'' or ``kinetically constrained'' lattice models. With these models, glassy dynamics emerges from the metric or geometrical constraints for molecular motion. More detailed atomistic models, and presumably natural glass formers as well, behave similarly. In the d+1 dimensions of trajectory space, one finds order-disorder phenomena that can be organized according to scaling and universality classes. Various predictions from this viewpoint, some yet to be verified experimentally, will be discussed. [Preview Abstract] |
Wednesday, March 23, 2005 11:51AM - 12:03PM |
P34.00002: Oxidative Damage to DNA Robert N. Barnett, Charles L. Cleveland, Uzi Landman, Gary B. Schuster The initial stage of the reaction of a guanine radical cation with water is investigated using ab-initio methods coupled with molecular mechanics. We explore the influence of the sugar- phosphate backbode, the complementary cytosine base, the adjacent base pairs in the B-DNA double strand, the state of hydration, and finally the distribution of counter-ions on the barrier and reaction path leading to 8-oxo-G. [Preview Abstract] |
Wednesday, March 23, 2005 12:03PM - 12:15PM |
P34.00003: Glassy Dynamics in the Immune System Prevents Auto-Immune Disorders Jun Sun, David Earl, Michael Deem A model of protein evolution is introduced. Hierarchical structures of the protein sequences or modularities play an important role in the dynamics. Computer simulations of the dynamics show that different evolving mechanisms(DNA swapping + point mutation v.s. point mutation ) lead to different stable(metastable) states. From the immunological point of view, point mutation corresponding to the metastable state has the advantage of preventing auto-immune disorders. The energy of the equilibrium states is determined only by the dynamics and independent of the initial states. Differences in initial states leads to different times of reaching equilibrium, and the binding energy is linear to the difference. Analytical arguments will be given as well to explain these features. [Preview Abstract] |
Wednesday, March 23, 2005 12:15PM - 12:51PM |
P34.00004: Invited Speaker: |
Wednesday, March 23, 2005 12:51PM - 1:03PM |
P34.00005: Novel Method for Selective Probing of Ground-State Rotational Dynamics of Solutes in Solvents Thai V. Truong, Y.R. Shen We present an optical pump/probe method that allows selective measurement of ground-state rotational dynamics of solutes in liquids. It is known that because of different solute-solvent interactions, a solute in different electronic states could have markedly different rotational dynamics in the same solvent. However, this state-specific rotational dynamics has not yet been fully explored. It is particularly difficult to measure that of the ground state since the probe often cannot distinguish responses from various molecular species (ground-state solute, excited-state solute, and solvent) present in the solution. We employ two successive pump pulses that are adjusted to create an optical linear dichroism arising from the orientational distribution of only the ground-state solute molecules, hence allowing direct measurement of the ground-state rotational dynamics of the solute. Application of the technique to a dye-solvent system shows a large difference between rotational diffusion rates of the ground state and the excited state of the dye molecules. This work was supported by National Science Foundation. [Preview Abstract] |
Wednesday, March 23, 2005 1:03PM - 1:15PM |
P34.00006: Equilibrium structure and phase separation in lipid mixture from dissipative particle dynamics simulations Jinsuo Zhang, Yi Jiang Amphiphilic lipid molecules self assemble in aqueous solutions to form various structures interesting to both biological and engineering applications. We use dissipative particle dynamics simulations to investigate the equilibruium structures of lipid assemblies and map out their phase diagram. In addition, we study the effect of phase separation in two-lipid mixtures and report the resulting shape deformation and transition between micelles, miceller disks, miceller cylinders, bilayers and vesicle. [Preview Abstract] |
Wednesday, March 23, 2005 1:15PM - 1:51PM |
P34.00007: Experimental Test of Hatano and Sasa's Nonequilibrium Steady-state Equality Invited Speaker: This abstract has not been submitted yet. [Preview Abstract] |
Wednesday, March 23, 2005 1:51PM - 2:03PM |
P34.00008: An ab initio study of crystalline and molecular biotin Milo Lin, David Prendergast, Giulia Galli The protein cofactor, biotin, has been studied due to its importance in human metabolism and its ability to selectively bind to proteins such as avidin. Understanding the selectivity of biotin from an analysis of its structural stability will help in developing new bio-sensor engineering applications. Experimental analysis of the structure of biotin is typically carried out using x-ray diffraction from crystalline samples. We analyze the differences in energetic, structural, and dynamical properties of biotin in its experimentally determined crystalline form and in its proposed molecular form. Using first principles density functional theory calculations we determine the cohesive energy of the crystalline phase. These calculations explore the limitations of density functional theory, under the generalized gradient approximation, in describing hydrogen-bonding and long-range order in molecular crystals. We analyze the structural stability of both crystalline and molecular phases by calculating the phonon spectrum. Particularly soft modes in the molecule are related to its change in conformation in transforming from the molecular to the crystalline phase. [Preview Abstract] |
Wednesday, March 23, 2005 2:03PM - 2:15PM |
P34.00009: The Transition State in a Noisy Environment Thomas Bartsch, Turgay Uzer Classical transition state theory is the cornerstone of reaction rate theory. It postulates a partition of phase space into reactant and product regions, which are separated by a dividing surface that reactive trajectories must cross. In order not to overestimate the reaction rate, the dividing surface must be chosen so that no reactive trajectory crosses back into the product region. Whereas most chemical reactions take place in a randomly fluctuating environment, as, e.g., a liquid, conventional transition state theory is not well equipped to handle this case because the no-recrossing condition is difficult to enforce in the presence of noise. To generalize the formalism of transition state theory to reactive systems driven by noise, we introduce a time-dependent dividing surface that is randomly moving in phase space so that it is crossed once and only once by each reactive trajectory. [Preview Abstract] |
Follow Us |
Engage
Become an APS Member |
My APS
Renew Membership |
Information for |
About APSThe American Physical Society (APS) is a non-profit membership organization working to advance the knowledge of physics. |
© 2024 American Physical Society
| All rights reserved | Terms of Use
| Contact Us
Headquarters
1 Physics Ellipse, College Park, MD 20740-3844
(301) 209-3200
Editorial Office
100 Motor Pkwy, Suite 110, Hauppauge, NY 11788
(631) 591-4000
Office of Public Affairs
529 14th St NW, Suite 1050, Washington, D.C. 20045-2001
(202) 662-8700