Bulletin of the American Physical Society
2005 APS March Meeting
Monday–Friday, March 21–25, 2005; Los Angeles, CA
Session A35: Energy Landscapes in Clusters, Materials, and Biology I |
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Sponsoring Units: DCP Chair: M. Gruebele, University of Illinois Room: LACC 511B |
Monday, March 21, 2005 8:00AM - 8:36AM |
A35.00001: Energy Landscapes and Beyond Invited Speaker: To understand many problems in modern science one must cope with a diversity of long-lived states or attractors. The necessary notion is that of an energy landscape. Cluster physics, protein dynamics and protein folding are key examples of problems where a landscape description is essential. In bulk condensed matter e.g. supercooled liquids and glasses, a landscape can only be meaningfully assigned to a small region of the system. Such local landscapes, however, can be constructed and used to describe the unusual slowing as the glass transition is approached and aging phenomena in quenched glasses. The resulting theory is quantitatively successful. Fully quantum glasses may also exist. $\backslash $Far-from equilibrium systems, such as cytoskeleton and gene networks require going beyond the landscape notion in new ways, which we will briefly describe. [Preview Abstract] |
Monday, March 21, 2005 8:36AM - 9:12AM |
A35.00002: Kinetics of an ultrafast folding protein analyzed with a free energy surface model Invited Speaker: Both theoretical and simulation studies have been successful in describing the kinetics of protein folding as diffusion over a one-dimensional free energy barrier, using an order parameter such as the number of ordered residues or the number of native inter-residue contacts as the reaction coordinate. In contrast, experimental results have been analyzed almost exclusively in terms of chemical kinetic schemes, with rate coefficients for transitions between well-defined thermodynamic states. We find that the two-phase relaxation kinetics of the ultra-fast folding villin subdomain following a laser temperature jump cannot be explained by a three-state kinetic model, but is readily explained by diffusion on a one-dimensional, temperature-dependent free energy profile that has a low free energy barrier separating folded and unfolded states. This analysis demonstrates the advantage of physical kinetics compared to chemical kinetics in understanding complex dynamics of protein folding, and should enable a closer connection between experiment and both theory and simulations. [Preview Abstract] |
Monday, March 21, 2005 9:12AM - 9:24AM |
A35.00003: What happens to a protein in a glassy environment? Vassiliy Lubchenko, Peter Wolynes, Hans Frauenfelder, Robert Silbey Several types of kinetic measurements reveal an intrinsic connection between processes within a protein imbedded in a glassy material and relaxations in the host itself. We use the Random First Order Transition (RFOT) theory of the glass transition to explain the microscopic origin of slaving of large scale protein conformational dynamics to the relaxations in the supercooled solvent. The slowing down of the protein motions relative to those of the solvent reflects the size of the conformational subspace explored by the protein relaxation. At {\em cryogenic} temperatures, the details of hole broadening depend on whether the chromophore is placed directly in a glass matrix, or imbedded in a protein first. We explain why spectral diffusion in proteins deviates from the usual logarithmic time dependence found in glasses. [Preview Abstract] |
Monday, March 21, 2005 9:24AM - 9:36AM |
A35.00004: Connection between the energy landscape and glass transition in a two-dimensional Lennard-Jones mixture Frank Somer Results of recent molecular dynamics simulations of a two-dimensional glass forming system are presented. The system's inherent structures are investigated over a wide range of temperature and cooling rate and compared to previous results for three-dimensional liquids and glasses. A method for analyzing the regions of the energy landscape sampled under various conditions is introduced and used to characterize the glass transition. Connections with inherent-structures theory, mode-coupling theory, and spatially inhomogeneous dynamics are discussed. [Preview Abstract] |
Monday, March 21, 2005 9:36AM - 9:48AM |
A35.00005: o-Terphenyl Self-Diffusion Near the Glass Transition Temperature Marie K. Mapes, Stephen F. Swallen, M.D. Ediger Self-diffusion coefficients (D$_{T}$) have been obtained for the fragile glassformer o-terphenyl from the glass transition temperature (T$_{g}$= 243 K) to T$_{g}$+ 32 K. Compared to the predictions of the Stokes-Einstein equation, we observe substantially enhanced translational diffusion ( $>$ 2 decades), which is a strong indicator of spatially heterogeneous dynamics. The values of D$_{T}$ are measured by isothermally annealing deuterio and protio o-terphenyl thin films. Samples are prepared as vapor-deposited glassy bilayers (100 - 1000 nm) with an initially sharp interface. When a sample is annealed, diffusion blurs the interface while supercooled o-terphenyl vaporizes at the film's surface. A mass spectrometer records deuterio and protio o-terphenyl concentrations over time, providing a profile of the diffusion that has occurred in the film. Isotope and thermal history effects on D$_{T}$ have also been investigated. Our results qualitatively agree with dynamic facilitation models and random first order transition theory. [Preview Abstract] |
Monday, March 21, 2005 9:48AM - 10:24AM |
A35.00006: Two aspects of water dynamics will be discussed; (1) intermittent collective motions and fluctuation, their experimental observation, (2) the role of these fluctuations in the water freezing process. Invited Speaker: Water exhibits intermittent collective motions associated with the hydrogen bond network rearrangement (HBNR), accompanied with large fluctuations of intermittent local collective molecular motions. We have made a theoretical analysis on multi-dimensional spectroscopy which may detect these intermittent collective motions, since this method deals with the phase space dynamics of a system. The 2-R Raman spectra obtained for CS2 and Water will be discussed A liquid to solid phase-transition goes through a nucleation process, starting with the formation of an initial nucleus, which then grows into a crystalline structure. Dynamical aspects of the nucleation processes have been explored by various studies. In simulations, simple liquids, consisting of spherical particles, are found to easily freeze to crystals. Water molecules possess strong directionality of hydrogen bonds (HB), forming a disordered three-dimensional HB network (HBN) in liquid state, and water is thus much harder to freeze than the simple liquids. A simulation, recently succeeded to reproduce the pure water freezing, revealed a role of the dynamical fluctuations intrinsic in water HBN rearrangement in a formation of the initial nucleus of the water freezing process, but large parts of its molecular mechanism have been remained unknown yet. In the present work, we use a network analysis and employ order-parameters to establish a clear molecular picture of the fragments, the transformation, the role of collective motions in this process. [Preview Abstract] |
Monday, March 21, 2005 10:24AM - 10:36AM |
A35.00007: Potential-Energy Surface of Infinite Helical Polypeptides Joel Ireta, Matthias Scheffler The potential-energy surfaces of infinite polyalanine and polyglycine chains in helical conformation are studied using density-functional theory in the Perdew, Burke and Ernzerhof approximation to the exchange-correlation functional (DFT-PBE). Minima associated to a $\pi$-helix, $\alpha$-helix and $3_{10}$-helix conformations are identified for both polypeptides. For polyalanine the $\alpha$-helix minimum is the lowest in energy. However for polyglycine $\pi$-helix and $\alpha$-helix minima are degenerated within the DFT accuracy. The $\alpha$-helix is found to undergo structural transitions to a $\pi$- or $3_{10}$-helix when the length of the helix is strainend by more than 10\%. The barriers for the structural transitions mainly associated to the breaking of the hydrogen bonds are considerably affected by the side group in polyalanine. We find this effect can not be solely attributed to repulsive interactions between the side group and the helix backbone but to sizeable changes in covalent bonds in the peptide unit of polyalanine with respect to polyglycine. [Preview Abstract] |
Monday, March 21, 2005 10:36AM - 10:48AM |
A35.00008: The role of vibrations in the kinetics of conformational isomerization of biomolecules and clusters David Leitner, Johnson Agbo, David Evans, David Wales The kinetics of conformational isomerization of sizable molecules and clusters depends both on the topography of the potential energy surface (PES), in particular barriers that separate minima corresponding to specific conformers, and the vibrational dynamics of each conformer. Incorporation of the vibrational contribution can be finessed by assuming rapid vibrational energy flow within a basin of the PES and adopting Rice-Ramsperger-Kassel-Marcus (RRKM) theory to calculate isomerization rates between pairs of conformers. However, RRKM theory often overestimates rates of conformational change due to insufficiently rapid vibrational energy flow. In this case, isomerization rates can be computed by applying a theory for quantum energy flow in many-oscillator systems to calculate corrections to RRKM theory. As an example we discuss the influence of vibrational energy flow on the kinetics of conformational isomerization of the dipeptide NATMA. [Preview Abstract] |
Monday, March 21, 2005 10:48AM - 11:00AM |
A35.00009: Amino acid and water molecules adsorbed on water clusters in a beam Ramiro Moro, Roman Rabinovitch, Vitaly Kresin Water clusters (H$_{2}$O)$_{n}$ and (D$_{2}$O)$_{n}$ ($n\le $16) are produced by supersonic expansion and pick up an additional heavy or light water molecule, respectively, or an amino acid molecule, while flying through a pick-up cell. The products are analyzed by electron bombardment ionization mass spectrometry. Ionization proceeds via well-known loss of an OH or OD group, but these have a strong predilection to come from the guest, rather than the host, molecule. e.g., even for large (D$_{2}$O)$_{n}$H$_{2}$O [or (H$_{2}$O)$_{n}$D$_{2}$O], about 50{\%} of the time the lost group is from the picked-up molecule. Similar ratios are found for amino acid guests. This suggests that proton exchange is suppressed, the host clusters are frozen into compact annealed shapes, and the adducts reside on the surface and present a dangling OH [or OD] bond where the ionization-induced hole prefers to localize dissociatively. [Preview Abstract] |
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