Effective atom volumes for implicit solvent models: comparison between Voronoi volumes and minimum fluctuation volumes

An essential element of implicit solvent models, such as the generalized Born method, is a knowledge of the volume associated with the individual atoms of the solute. Two approaches for determining atomic volumes for the generalized Born model are described; one is based on Voronoi polyhedra and the other, on minimizing the fluctuations in the overall volume of the solute. Volumes to be used with various parameter sets for protein and nucleic acids in the CHARMM force field are determined from a large set of known structures. The volumes resulting from the two different approaches are compared with respect to various parameters, including the size and solvent accessibility of the structures from which they are determined. The question of whether to include hydrogens in the atomic representation of the solute volume is examined. Copyright 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1857-1879, 2001     

Small angle X-ray scattering investigations of thermodynamic properties of fluid mixtures

Absolute small angle X-ray studies of concentration fluctuations were performed in order to determine thermodynamic properties of a model blend, consisting ofn-hexane and perfluoro-n-hexane. The quantities which we determined were the second derivate of the Gibbs free energy of mixing with respect to the concentration of the components, the location of the spinodal, interaction and solubility parameters, the energy gradient density coefficient as well as the correlation length of the fluctuations at various compositions and temperatures, particularly in the neighbourhood of the spinodal and the critical point. The data obtained were compared with those obtainable from the well known location of the binodal, to test the reliability of the scattering method.     

Origin of the Landau-Lifshitz hydrodynamic fluctuations in nonequilibrium systems and a new method for reducing the Boltzmann equation

The Landau-Lifshitz fluctuating fluxes in fluctuating hydrodynamics are derived from the deterministic Boltzmann equation with the aid of a reduction method developed by Fujisaka and Mori. Thus it is shown that the hydrodynamic fluctuations innonequilibrium systems are generated by the reduction of variables from the-space distribution function to its five momentum moments, i.e., the hydrodynamic variables. This differs from the Bixon-Zwanzig and Fox-Uhlenbeck theories, in which the Landau-Lifshitz fluctuating fluxes are derived from the molecular fluctuating force in thestochastic Boltzmann-Langevin equation, which is, however, negligible in nonequilibrium systems. Thus the present method improves the Chapman-Enskog reduction method so as to include the hydrodynamic fluctuations generated by the reduction of variables.Supported in part by the Scientific Research Fund of the Ministry of Education.     

On fluctuations in μ-space

A master equation is derived microscopically to describe the fluctuating motion of the particle density in . space. This equation accounts for the drift motion of particles and is valid for any inhomogeneous gas. The Boltzmann equation is obtained from the first moment of this equation by neglecting the second cumulant (the pair correlation function). The successive moments form coarse-grained BBGKY-like hierarchy equations, in which small spatial regions with r_ij < the force range are smeared out. These hierarchy equations are convenient for investigating the nonequilibrium long-range pair correlation function, which arises mainly from sequences of isolated binary collisions and gives rise to the much-discussed long-time tail and the logarithmic term in the density expansion of transport coefficients. It is shown to have a spatial long tail, like the Coulombic potential, in a steady laminar flow. The stochastic nature of the nonlinear Boltzmann-Langevin equation is also investigated; the random source term is found to be expressed as a linear superposition of Poisson random variables and to become Gaussian in special cases.     

Time-dependent fluctuations in infrared vsCH2 frequencies in acyl chain membranes of Acholeplasma laidlawii cells

We measured FT-IR spectra of intact Acholeplasma laidlawii cells grown at 37 °C on palmitic acid (C16:0) or on binary palmitic acid-d31/oleic acid (C16:0-d31/C18:1(9)) at an initial mole ratio of 2:3, which have been previously reported to produce significant fluctuations in CH₂ symmetric stretching (ν_sCH₂) and CD₂ asymmetric stretching (ν_aCD₂) frequencies (Biochim. Biophys. Acta 1279 (1996) 49). Time courses for acyl chain ν_sCH₂ and ν_aCD₂ frequencies determined from fourth derivative spectra are presented. Fluctuations were detected with the C16:0 enriched cells at temperatures above 40 °C as well as with the cells enriched in 2:3 C16:0-d₃₁/C18:1(9). These observations at temperatures above 40 °C for the C16:0 enriched cells were not in agreement with the conclusion in the previous work by Moore et al. Our results have suggested that the 2850 cm⁻¹ ν_sCH₂ band comprises two components arising from trans and gauche conformations, and that the fluctuations in ν_sCH₂ frequency are caused by random temporal changes in the relative intensities of these two components.     

The stochastic Boltzmann equation and hydrodynamic fluctuations

Based on the assumption of a kinetic equation in space, a stochastic differential equation of the one-particle distribution is derived without the use of the linear approximation. It is just the Boltzmann equation with a Langevin-fluctuating force term. The result is the general form of the linearized Boltzmann equation with fluctuations found by Bixon and Zwanzig and by Fox and Uhlenbeck. It reduces to the general Landau-Lifshitz equations of fluid dynamics in the presence of fluctuations in a similar hydrodynamic approximation to that used by Chapman and Enskog with respect to the Boltzmann equation.This work received financial support from the Alexander von Humboldt Foundation.     

Statistics of transfer matrices for disordered quantum thin metallic slabs

In the quantum transport problem of a tight-binding Anderson model, the statistics of eigenvalues for the transfer matrices of thin disordered slabs is studied. Numerical simulations indicate that the probability distribution of nearest neighbor eigenvalue spacing and the ₃ statistics have already become close to that of the Gaussian orthogonal ensemble for sample lengths of the order of the mean free path, provided that transverse localization effects are not important. An intuitive argument is given why this should occur independently of the size of the matrix. Therefore, good mixing of the channels is not essential for obtaining Gaussian orthogonal ensemble type statistics and universal conductance fluctuations.     

Phenomenology of nonlocal cellular automata

Dynamical systems with nonlocal connections have potential applications to economic and biological systems. This paper studies the dynamics of nonlocal cellular automata. In particular, all two-state, three-input nonlocal cellular automata are classified according to the dynamical behavior starting from random initial configurations and random wirings, although it is observed that sometimes a rule can have different dynamical behaviors with different wirings. The nonlocal cellular automata rule space is studied using a mean-field parametrization which is ideal for the situation of random wiring. Nonlocal cellular automata can be considered as computers carrying out computation at the level of each component. Their computational abilities are studied from the point of view of whether they contain many basic logical gates. In particular, I ask the question of whether a three-input cellular automaton rule contains the three fundamental logical gates: two-input rules AND and OR, and one-input rule NOT. A particularly interesting edge-of-chaos nonlocal cellular automaton, the rule 184, is studied in detail. It is a system of coupled selectors or multiplexers. It is also part of the Fredkin's gate—a proposed fundamental gate for conservative computations. This rule exhibits irregular fluctuations of density, large coherent structures, and long transient times.     

Novel aromatic carboxamides from dehydroabietylamine as potential fungicides: Design,synthesis and antifungal evaluation

The present study was carried out to design and synthesize a number of novel aromatic carboxamide derivatives of dehydroabietylamine. The preliminary antifungal assay indicated that most of title compounds displayed moderate to good antifungal activity toward the six fungal strains in vitro. Compounds 3i, 3q, 4b and 4d showed significant antifungal activity against Sclerotinia sclerotiorum, with EC₅₀ values ranging from 0.067 ～ 0.393 mg/L. Compounds 3i, 4b and 4d also showed pronounced mycelial growth inhibition activities against B. cinerea and A. solani. Furthermore, in the in vivo assay, compound 4b exhibited brilliant protective activity against S. sclerotiorum-infected rape leaves. Meanwhile, the in vivo bioassay on tomato plants infected by B. cinerea showed that compound 3i and 4d displayed excellent protective activity at 200 mg/L, which were near to boscalid. Primary mechanistic study revealed that 4b could inhibit sclerotia formation as well as reduce the exopolysaccharide level. SEM and TEM analysis indicated that 4b possessed a strong ability to destroy the surface morphology of mycelia, cell structure and seriously interfere with the growth of the fungal pathogen. In addition, 4b exhibited good inhibitory activity (IC₅₀ = 23.3 ± 1.6 μM) toward succinate dehydrogenase (SDH). Molecular modeling study confirmed the binding modes between compound 4b and SDH. The above antifungal results and fungicidal mechanism study revealed that this class of dehydroabietylamine derivatives could be potential SDH inhibitors and lead compounds for novel fungicides development.     

Escape of Brownian particles and stochastic resonance with low-temperature quantum fluctuations

In this paper, we investigate the escape of Brownian particles and stochastic resonance (SR) with low-temperatures quantum fluctuations by using the quantum Smoluchowski equations at low-temperature. Two specific examples have been considered: one is the example of bistable system, and the other is the example of metastable system. The explicit expressions of the mean-first passage time (MFPT) and signal-to-noise ratio (SNR) for both specific examples are obtained, respectively. Based on the numerical compu...