Showing papers by "Enrico Clementi published in 1987"

Structure and Dynamics of Nucleic Acids, Proteins, and Membranes

Abstract: I. Structure of Macromolecules.- Conformational Analysis of Polypeptides and Proteins for the Study of Protein Folding, Molecular Recognition, and Molecular Design.- Conformation of Non-Crystalline Proteins Viewed by NMR.- Structures and Superstructures in Periodical Polynucleotides.- Conformational Peculiarities and Biological Role of Some Nucleotide Sequences.- Multifrequency ESR of an Isotopically Enriched Copper System in the Immobilized Phase: A Monte Carlo Approach.- Neutron Scattering from Agarose Gels.- Non-Empirical Pair Potentials for the Interaction Between Amino Acids.- II. Dynamics of Macromolecules.- Molecular Dynamics of Proteins.- Proton NMR Studies of Protein Dynamics and Folding: Applications of Magnetization Transfer NMR.- Distributions and Fluctuations of Protein Structures Investigated by X-Ray Analysis and Mossbauer Spectroscopy.- Rotational Motions of Tryptophan and Tyrosine Residues in Proteins.- Protein Fluctuations and Hemeprotein Affinity for Ligand.- Cytochrome Oxidase in Energy Transduction.- Proteins and Glasses.- III. Solvation of Macromolecules.- Global Ab Initio Simulations: Study of a Liquid as an Example.- Proton Conductivity of Hydrated Lysozyme Powders, Considered Within the Framework of Percolation Theory.- Molecular Dynamics Simulations of Biomolecules in Water.- Low Frequency Coherent Vibrations of DNA: The Role of the Hydration Shell and Phosphate-Phosphate Interactions.- IV. Components of Larger Systems.- Elasticity, Structure and Dynamics of Cell Plasma Membrane and Biological Functions.- Neuronal Signaling. A Simple Thermodynamic Process Involving Complex Membrane Proteins.- Panel Discussions: Session 1. Understanding Brain Mechanisms and the Challenge of Artificial Intelligence Machines: An Interdisciplinary Approach Session 2. Sixth Generation Computers: A Sketch.- Physicists Explore Human and Artificial Intelligence.- Recognition Automata Based on Selective Neural Networks.- A Neural Theory of Preattentive Visual Information Processing: Emergent Segmentation, Cooperative-Competitive Computation, and Parallel Memory Storage.- Large-Scale Computations on a Scalar, Vector and Parallel "Supercomputer".

Numerical integration of the fluctuating hydrodynamic equations

Abstract: An approach to numerically integrate the Landau-Lifshitz fluctuating hydrodynamic equations is outlined. The method is applied to one-dimensional systems obeying the nonlinear Fourier equation and the full hydrodynamic equations for a dilute gas. Static spatial correlation functions are obtained from computer-generated sample trajectories (time series). They are found to show the emergence of long-range behavior whenever a temperature gradient is applied. The results are in very good agreement with those obtained from solving the correlation equations directly.

Hydration structure and dynamics of B- and Z-DNA in the presence of counterions via molecular dynamics simulations.

Abstract: Following our previous attempts at understanding the structural and dynamical properties of water and counterions hydrating nucleic acids, we have performed molecular dynamics simulations for B- and Z-DNA. In these simulations, the nucleic acids were held rigid. In the case of B-DNA, one turn of B-DNA double helix was considered in the presence of 1500 water molecules and 20 counterions (K+). The simulations were performed for 4.0 ps after equilibrating the system. For Z-DNA, we considered one turn of the double helix in the presence of 1851 water molecules and 24 counterions (K+). The simulations were carried out for 3.5 ps after equilibration. The average temperature of these simulations was ∼ 360 K for Z-DNA and ∼ 345 K for B-DNA. In these simulations the hydrogen atoms were explicitly taken into account. For both simulations, a fifth-order predictor-corrector was used for solving the translational equations of motion. The rotational motion of the water molecules was represented in terms of quaternion algebra and the rotational equations of motion were solved with a second-order quaternion method using a sixth-order predictor-corrector method. A time step of 0.5 · 10−15 s was used in these simulations. The structural and the dynamical properties of water solvating the counterions, and the phosphate groups of the DNA, were computed to understand the hydration structure. Diffusion coefficients and velocity correlation functions were calculated for both ions and the water molecules. The velocity correlation functions for the ions exhibit a caged behavior. The dipole correlation functions for the water molecules indicate that the water molecules close to the helix retain the memory of their initial orientations for longer periods of time than those away from the helix. During the time period of our simulation (3–4 ps) the ion probability distributions show a well-defined pattern and suggest limited mobility for the ions, being close to the helix.

Molecular dynamics of liquid water in a circularly polarized external field

Abstract: The dipole moment of the water molecule has been subjected to an external circularly polarized field of force and the effect on the molecular dynamics evaluated through novel laboratory and moving frame cross correlation functions (ccf ’s) using molecular dynamics computer simulation. The field symmetry is such as to make possible the existence in both frames off diagonal elements of the ccf ’s which disappear at field off equilibrium. The laboratory frame ccf ’s involve simultaneously the rotational and translational motion of the molecule and are not describable with contemporary theories of ‘‘rotational’’ or ‘‘translational’’ diffusion. The simulation shows laboratory frame birefringence in the orientational and rotational velocity autocorrelation functions (acf ’s) in the y (or z) and x axes for a field applied in the x axis. This birefringence is linked to the appearance of ccf elements induced by the circularly polarized field, and its experimental measurement would provide indirect information on t...

Molecular dynamics simulation of flow past a plaste

Abstract: Molecular dynamics simulations with a soft-sphere potential have been carried out to model two dimensional fluid flow obstructed by a plate. At fluid velocities large enough to obtain adequate signal to noise resolution, two counter-circulating vortices are observed behind the obstruction. The stationary state length scale of these vortices is found to be roughly proportional to the average velocity in the system, as predicted by the hydrodynamic theory.

The effect of molecular vibrations on calculated second virial coefficients

Abstract: The limitation of the rigid molecule approximation in the calculation of the second virial coefficient is examined using two different potential models for steam. Both the MCY and the ST2 potentials have been augmented by allowing bond flex and stretch according to an ab initio internal potential. Second virial coefficients are calculated within the classical approximation by the Monte Carlo method. The calculated coefficients with flexible molecules are lower than in the rigid case by up to 10% for the MCY potential and 8% for the ST2 potential.

Large-Scale Computations on a Scalar, Vector and Parallel “Supercomputer”

Abstract: We discuss two experimental parallel computer systems 1CAP-1 and 1CAP-2 which can be applied to the entire spectrum of scientific and engineering applications. These systems achieve “supercomputer” levels of performance by spreading large scale computations across multiple cooperating processors — several with vector capabilities. We outline system hardware and software, and discuss our programming strategy for migrating codes from a conventional sequential system to parallel. The performance of a variety of applications programs is analyzed to demonstrate the merits of this approach. Finally, we discuss 1CAP-3 an extension to this computing system, which has been recently assembled.

The Hylleraas‐CI method in molecular calculations: Two‐electron integrals

Abstract: In the Hylleraas-CI method, first proposed by Sims and Hagstrom, correlation factors of the type r are included into the configurations of a CI expansion. The computation of the matrix elements requires the evaluation of different two-, three-, and four-electron integrals. In this article we present formulas for the two-electron integrals over Cartesian Gaussian functions, the most used basis functions in molecular calculations. Most of the integrals have been calculated analytically in closed form (some of them in terms of the incomplete Gamma function), but in one case a numerical integration is required, although the interval for the integration is finite and the integrand well-behaved. We have also reported on partial and preliminary computations for the H2 molecule using our four-center general formulas; a basis set of s- and p-type functions yielded at R = 1.4001 A an energy of - 1.174380 a.u. to be compared with Kolos and Wolniewicz value of - 1.174475.

Nonequilibrium states by molecular dynamics: Transport coefficients in constrained fluids

Abstract: We present here a study of the behavior of fluid systems under external constraints by molecular dynamics with stochastic boundary conditions We investigate the validity of the local-equilibrium hypothesis The agreement between measured local physical properties and those predicted by a first-order Chapman-Enskog theory is remarkable We also discuss the difficulty of the measurement of local time-correlation functions © 1987 The American Physical Society

The Hylleraas–CI integrals in molecular, calculations. II. Three-and four-electron integrals and tests for two-electron many-center integrals

Abstract: In a previous paper, formulas for two-electron integrals over Cartesian Gaussian functions occurring in the Hylleraas-CI method have been given. This paper reports on the extension of those formula to three- and four-electron integrals and presents test results obtained by using the two-electron integrals for H2 With only 2 p-type polarization functions on each atom, the ground state energy calculated for H2 is only about 20 cm−1 higher than the exact value.

Hydration structures and energetics of phospholipid

Abstract: Using previously reported ab initio potentials of the intermolecular interaction energies of phospholipid (PL), Lysophosphatidyl Ethanolamine, with one Na+ ion and one water molecule, we performed Monte Carlo simulations for PL‐water and PL‐Na+‐water systems. Water‐water and PL‐water interaction energetics of PL hydration sites are analyzed to understand, in a qualitative way, why the PL head part shows hydrophilicity and the tail part shows hydrophobicity. The interaction of Na+ with PL, as well as the interaction of water with PL, is visualized from the analysis of the hydration structures near PL, and the radial distribution functions are analyzed for selected hydration sites. The PL molecule shows much stronger interaction with Na+ than with water. The Na+ ion is likely to be strongly bound to PO 4− , even to the extent of being trapped, whereas, for water, there exist two strong binding regions near NH 3+ and PO 4− . Three water molecules near NH 3+ are much more strongly bound than four water molecules near the double‐bonded oxygens of PO 4− . The hydrogens of CH2 adjacent to NH 3+ show somewhat strong hydrophilicity, while the hydrogens of CH2 adjacent to PO 4− does not show such characteristics. The CH2 groups at the PL tail part give repulsive interactions with water molecules, showing hydrophobicity. Water molecules near the PL tail are stabilized only by water‐water interactions.