Bulletin of the American Physical Society
2005 APS March Meeting
Monday–Friday, March 21–25, 2005; Los Angeles, CA
Session H35: Energy Landscapes in Clusters, Materials, and Biology III |
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Sponsoring Units: DCP DBP Chair: J. Onuchic, University of California-San Diego Room: LACC 511B |
Tuesday, March 22, 2005 8:00AM - 8:36AM |
H35.00001: The Energy Landscape of Proteins Invited Speaker: Energy levels have been seminal concepts in physics for a long time, presumably starting with the Balmer series in hydrogen and continuing with the energy levels in more complex atoms, and in molecules, solids, nuclei, and particles. In complex systems, energy levels change to energy landscapes (EL), because they can assume a large number of different conformations. Understanding the energy landscape is important because transitions in the landscape correspond to fluctuations, relaxations, and reactions. For any complex system, the exploration of the EL is a formidable problem. Glasses and proteins are the systems where the energy landscapes are beginning to emerge from experimental, theoretical, and computational studies. Both systems are important; glasses for their many applications and proteins for their roles as building blocks of living matter. The energy landscape of even a simple protein is extremely complex. It is organized hierarchically into a number of tiers. Different tiers have characteristic properties and different functional roles. Two tiers stand out; fluctuations in these tiers are similar to the alpha and beta relaxations in glasses. In contrast to glasses, these fluctuations do not depend only on the protein, the environment (solvent) and the hydration shell of the protein, are crucially involved. Studies of these fluctuations, particularly using neutron scattering and the M\"ossbauer effect, promise to give more insight into protein functions and also into the physics of complex systems. [Preview Abstract] |
Tuesday, March 22, 2005 8:36AM - 9:12AM |
H35.00002: Exploring the protein funnel energy landscape for folding and function Invited Speaker: Globally the energy landscape of a folding protein resembles a partially rough funnel. Using minimalist model simulations together with analytical theory, we learn about good (minimally frustrated) folding sequences and non-folding (frustrated) sequences In addition to the need to minimize energetic frustration, the fold topology also plays a major role in the folding mechanism. Some folding motifs are easier to design than others, suggesting the possibility that evolution not only selected sequences with sufficiently small energetic frustration but also more easily designable native structures. We have demonstrated for several proteins (such as CI2 and SH3) that they are sufficiently well designed (i.e., reduced energetic frustration) that much of the heterogeneity observed in their transition state ensemble (TSE) is determined by topology. Topological effects go beyond the TSE. The overall structure of the on-route and off-route (traps) intermediates for the folding of more complex proteins and protein dimers is also strongly influenced by topology.this theoretical framework, simulations of minimalist models and their connections to more computationally-expensive all-atom simulations, we are now in the process of obtaining a quantitative understanding of the folding problem, which allows for a direct comparison to a new generation of folding experiments. Connections between the folding landscape and protein function will also be discussed. [Preview Abstract] |
Tuesday, March 22, 2005 9:12AM - 9:48AM |
H35.00003: Protein Folding and Amyloid Formation: Good Questions for Solid State NMR Invited Speaker: Recent results from two ongoing projects will be described. These projects illustrate the expanding capability of solid state NMR spectroscopy to provide unique information about the molecular structure of complex biochemical systems that are of current interest in the biophysical and biomedical research communities. Methodological advances that facilitate progress on these projects will be discussed briefly. In the area of protein folding, we are using solid state NMR spectroscopy to characterize the distributions of molecular structures in unfolded and partially folded states of relatively simple model proteins. The measurements are carried out on frozen glassy solutions at low temperatures. Initial results for the chemical denaturation of the 35-residue helical protein HP35 show that unfolding does not occur by a simple two-state process and that local conformational distributions in the unfolded state are remarkably non-uniform. In the area of amyloid fibrils, we are using solid state NMR to develop experimentally-based models for the molecular structure of peptide fibrils associated with Alzheimer's disease and other amyloid diseases, and to develop an understanding of the interactions that stabilize amyloid fibril structures in general. The NMR data also reveal molecular-level polymorphism in amyloid fibrils, with implications for biomedical issues such as the etiological role of fibrils in amyloid diseases and the structural basis for strains in prion diseases. [Preview Abstract] |
Tuesday, March 22, 2005 9:48AM - 10:00AM |
H35.00004: Distribution of Defects on Curved Crystals Yaroslav Chushak, Alex Travesset Topological defects, namely, dislocations and disclinations, play a crucial role in two-dimensional curved crystals. They are needed to reduce an excess strain that is produced by curved geometries. In this talk we present a detailed analysis of the actual distribution of defects in concrete examples that include a spherical cap, a Gaussian bump and a toroidal patch. [Preview Abstract] |
Tuesday, March 22, 2005 10:00AM - 10:12AM |
H35.00005: Fast Electronic Relaxation in Metal Clusters via Excitation of Coherent Shape Deformations: Slipping Through a Bottleneck Vitaly Kresin, Yuri Ovchinnikov, Vladimir Kresin We introduce and describe a fast electronic relaxation channel which is particular to free metallic nanoclusters. This channel overcomes the possibility of a phonon bottleneck by invoking the essential role of cluster shape deformations. Such a deformation entails the appearance of coherent surface phonon excitations and enables internal conversion at the level crossing point, thus allowing large energy transfer from an excited electron to the ionic subsystem. As a result, one can show that (unlike usual multiphonon processes) the shape deformation channel is capable of producing short electronic relaxation times, much less than a picosecond. The calculations are in agreement with recent pump-probe photoelectron measurements of relaxation in Al$_{n}^{-}$ clusters. [Preview Abstract] |
Tuesday, March 22, 2005 10:12AM - 10:24AM |
H35.00006: Planar graph model of energy landscapes Joseph Snider, Clare Yu Energy landscape models of glasses generally assume that unusual energy distributions are required for slow, glassy dynamics, for example ``trap'' models with infinitely deep holes. Here, we model energy landscapes with planar graphs where vertices represent configurations and edges represent possible transitions. The vertices are embedded in a two-dimensional plane and assigned energies. The edges are drawn such that only nearby vertices are accessible from any given vertex. In this case, we find two phases: a ``glassy'' one with sub-exponential relaxation and ``normal'' one with slightly super-exponential relaxation. [Preview Abstract] |
Tuesday, March 22, 2005 10:24AM - 10:36AM |
H35.00007: A Novel Approach to Kinetics on Complex Potential Energy Surface Jun Lu, R. Stephen Berry Understanding the kinetics and dynamics of the underlying potential energy surface (PES) is essential to many scientific problems, e.g. the dynamics of the molecular clusters and polymers, the folding of proteins, the complicated phenomenology of glasses, and even the optimal design of nanoparticle materials. However, the complexity and the huge number of dimensions of the PES of typical systems of interest forces us to statistically simplify it in order to understand and even manipulate the underlying kinetics. These challenges are addressed by using a novel approach of constructing PES-like networks of stationary points. If constructed with proper regularity, the kinetics of the artificial PES is easy to predict and understand; thus by tuning the stationary points in these PES networks, we have a useful channel to study the complexity of kinetics on an irregular PES. The Master Equation is used to study the kinetics on a PES and the strategies of statistical sampling for a multi-dimensional surface. It is the largest eigenvalues and their corresponding eigenvectors that provide the most important kinetic information. Furthermore, one can measure the robustness of the sampling strategies by comparing the eigenvalue and eigenvector spectra of full and sample PESs. [Preview Abstract] |
Tuesday, March 22, 2005 10:36AM - 10:48AM |
H35.00008: Metal Cluster Anions Produced by Attachment of Slow Electrons: Readjustment and Blurring of the Magic Numbers Roman Rabinovitch, Ramiro Moro, Chunlei Xia, Vitaly Kresin The high electric polarizabilities of metal clusters enable them to attach low-energy electrons with large cross sections: electrons are captured by a strong long-range polarization potential. But the last stage of the collision process is not understood: where and how fast is the captured electron's energy deposited? The question is closely related to the problem of electron relaxation in size-quantized nanosystems. To explore this, we have measured the mass spectra of sodium cluster anions born in the electron-cluster interaction region. If the energy deposited by the captured electron is quickly thermalized and is sufficient to cause rapid cluster evaporation, there should be a rearrangement of the cluster abundances and a shift of the magic numbers from Na$_{n}$ to $\mbox{Na}_{\mbox{n-1}}^{\mbox{-}}$. Such a shift is clearly observed at shell closings near $n$=20 and $n$=40. However, near $n$=58 and $n$=92 the shell closings become completely blurred. This interesting change may be due to a bottleneck in electron relaxation and/or to insufficiently fast evaporation. [Preview Abstract] |
Tuesday, March 22, 2005 10:48AM - 11:00AM |
H35.00009: Alloy surface segregation in reactive environments via density functional theory and atomistic thermodyanamics John Kitchin, Karsten Reuter, Matthias Scheffler The chemical and materials properties of an alloy surface depend sensitively on its detailed surface composition and structure, which in turn can differ substantially from the one of the bulk alloy due to segregation of one species to the surface. Concerning the alloy function e.g. in catalytic or corrosive environments, this surface segregation can furthermore depend on the partial pressures and temperatures in the surrounding if one alloy component interacts more strongly with a gas-phase species than the other. Instead of solely predicting the chemical and materials properties on the basis of the formal bulk composition, this requires a theory that explicitly considers the effect of the reactive environment. As a first step in this endeavor, we are extending the concepts of {\em ab initio atomistic thermodynamics} to address segregation in binary transition metal alloys in the presence of a reactive gas phase. We apply the approach to the (111) surface of Ag$_3$Pd in an O$_2$ atmosphere, and find that contrary to the situation in ultra-high vacuum, Pd segregates to the surface at high oxygen pressures. We discuss the difficulties and possible inaccuracies of the {\em ab initio atomistic thermodynamic approach} with respect to the limited exploration of configuration space and the steps necessary to proceed beyond it. [Preview Abstract] |
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