Featured Researches

Chemical Physics

"The numerical accuracy of truncated Ewald sums for periodic systems with long-range Coulomb interactions"

Ewald summation is widely used to calculate electrostatic interactions in computer simulations of condensed-matter systems. We present an analysis of the errors arising from truncating the infinite real- and Fourier-space lattice sums in the Ewald formulation. We derive an optimal choice for the Fourier-space cutoff given a screening parameter η . We find that the number of vectors in Fourier space required to achieve a given accuracy scales with η 3 . The proposed method can be used to determine computationally efficient parameters for Ewald sums, to assess the quality of Ewald-sum implementations, and to compare different implementations.

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Chemical Physics

A Blocking Technique for Emulating Very Large Polyelectrolytes

A new Monte Carlo method for computing thermodynamical properties of very large polyelectrolytes is presented. It is based on a renormalization group relating the original polymer to a smaller system, where in addition to the naively rescaled forces, a corrective nearest-neighbor interaction originating from the short distance Coulomb cutoff is introduced. The method is derived for low T but is in the unscreened case valid for all T. Large polymers with N monomers are emulated by Monte Carlo calculations on smaller systems, K=N/Q. The computational gain of the method is Q^3. It is explored with emphasis on room temperature. Results for N=10000 are presented.

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Chemical Physics

A Computational Study of Thirteen-atom Ar-Kr Cluster Heat Capacities

Heat capacity curves as functions of temperature were calculated using Monte Carlo methods for the series of Ar_{13-n}Kr_n clusters (0 <= n <= 13). The clusters were modeled classically using pairwise additive Lennard-Jones potentials. J-walking (or jump-walking) was used to overcome convergence difficulties due to quasiergodicity present in the solid-liquid transition regions, as well as in the very low temperature regions where heat capacity anomalies arising from permutational isomers were observed. Substantial discrepancies between the J-walking results and the results obtained using standard Metropolis Monte Carlo methods were found. Results obtained using the atom-exchange method, another Monte Carlo variant designed for multi-component systems, were mostly similar to the J-walker results. Quench studies were also done to investigate the clusters' potential energy surfaces; in each case, the lowest energy isomer had an icosahedral-like symmetry typical of homogeneous thirteen-atom rare gas clusters, with an Ar atom being the central atom.

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Chemical Physics

A Criterion That Determines Fast Folding of Proteins: A Model Study

We consider the statistical mechanics of a full set of two-dimensional protein-like heteropolymers, whose thermodynamics is characterized by the coil-to-globular ( T θ ) and the folding ( T f ) transition temperatures. For our model, the typical time scale for reaching the unique native conformation is shown to scale as τ f ∼F(M)exp(σ/ σ 0 ) , where σ=1− T f / T θ , M is the number of residues, and F(M) scales algebraically with M . We argue that T f scales linearly with the inverse of entropy of low energy non-native states, whereas T θ is almost independent of it. As σ→0 , non-productive intermediates decrease, and the initial rapid collapse of the protein leads to structures resembling the native state. Based solely on {\it accessible} information, σ can be used to predict sequences that fold rapidly.

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Chemical Physics

A Dynamical Theory of Electron Transfer: Crossover from Weak to Strong Electronic Coupling

We present a real-time path integral theory for the rate of electron transfer reactions. Using graph theoretic techniques, the dynamics is expressed in a formally exact way as a set of integral equations. With a simple approximation for the self-energy, the rate can then be computed analytically to all orders in the electronic coupling matrix element. We present results for the crossover region between weak (nonadiabatic) and strong (adiabatic) electronic coupling and show that this theory provides a rigorous justification for the salient features of the rate expected within conventional electron transfer theory. Nonetheless, we find distinct characteristics of quantum behavior even in the strongly adiabatic limit where classical rate theory is conventionally thought to be applicable. To our knowledge, this theory is the first systematic dynamical treatment of the full crossover region.

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Chemical Physics

A Heuristic Molecular Model of Hydrophobic Interactions

Hydrophobic interactions provide driving forces for protein folding, membrane formation, and oil-water separation. Motivated by information theory, the poorly understood nonpolar solute interactions in water are investigated. A simple heuristic model of hydrophobic effects in terms of density fluctuations is developed. This model accounts quantitatively for the central hydrophobic phenomena of cavity formation and association of inert gas solutes; it therefore clarifies the underlying physics of hydrophobic effects and permits important applications to conformational equilibria of nonpolar solutes and hydrophobic residues in biopolymers.

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Chemical Physics

A Hybrid Decomposition Parallel Implementation of the Car-Parrinello Method

We have developed a flexible hybrid decomposition parallel implementation of the first-principles molecular dynamics algorithm of Car and Parrinello. The code allows the problem to be decomposed either spatially, over the electronic orbitals, or any combination of the two. Performance statistics for 32, 64, 128 and 512 Si atom runs on the Touchstone Delta and Intel Paragon parallel supercomputers and comparison with the performance of an optimized code running the smaller systems on the Cray Y-MP and C90 are presented.

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Chemical Physics

A Monte Carlo study of temperature-programmed desorption spectra with attractive lateral interactions

We present results of a Monte Carlo study of temperature-programmed desorption in a model system with attractive lateral interactions. It is shown that even for weak interactions there are large shifts of the peak maximum temperatures with initial coverage. The system has a transition temperature below which the desorption has a negative order. An analytical expression for this temperature is derived. The relation between the model and real systems is discussed.

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Chemical Physics

A Symmetry Adapted Approach to Molecular Spectroscopy: The Anharmonic Oscillator Symmetry Model

We apply the Anharmonic Oscillator Symmetry Model to the description of vibrational excitations in D 3h and T d molecules. A systematic procedure can be used to establish the relation between the algebraic and configuration space formulations, by means of which new interactions are found in the algebraic model, leading to reliable spectroscopic predictions. We illustrate the method for the case of D 3h -triatomic molecules and the T d Be-cluster.

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Chemical Physics

A Variational Approach for Minimizing Lennard-Jones Energies

A variational method for computing conformational properties of molecules with Lennard-Jones potentials for the monomer-monomer interactions is presented. The approach is tailored to deal with angular degrees of freedom, {\it rotors}, and consists in the iterative solution of a set of deterministic equations with annealing in temperature. The singular short-distance behaviour of the Lennard-Jones potential is adiabatically switched on in order to obtain stable convergence. As testbeds for the approach two distinct ensembles of molecules are used, characterized by a roughly dense-packed ore a more elongated ground state. For the latter, problems are generated from natural frequencies of occurrence of amino acids and phenomenologically determined potential parameters; they seem to represent less disorder than was previously assumed in synthetic protein studies. For the dense-packed problems in particular, the variational algorithm clearly outperforms a gradient descent method in terms of minimal energies. Although it cannot compete with a careful simulating annealing algorithm, the variational approach requires only a tiny fraction of the computer time. Issues and results when applying the method to polyelectrolytes at a finite temperature are also briefly discussed.

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