Optimal use of data in parallel tempering simulations for the construction of discrete-state Markov models of biomolecular dynamics

Parallel tempering (PT) molecular dynamics simulations have been extensively investigated as a means of efficient sampling of the configurations of biomolecular systems. Recent work has demonstrated how the short physical trajectories generated in PT simulations of biomolecules can be used to construct the Markov models describing biomolecular dynamics at each simulated temperature. While this approach describes the temperature-dependent kinetics, it does not make optimal use of all available PT data, instead estimating the rates at a given temperature using only data from that temperature. This can be problematic, as some relevant transitions or states may not be sufficiently sampled at the temperature of interest, but might be readily sampled at nearby temperatures. Further, the comparison of temperature-dependent properties can suffer from the false assumption that data collected from different temperatures are uncorrelated. We propose here a strategy in which, by a simple modification of the PT protocol, the harvested trajectories can be reweighted, permitting data from all temperatures to contribute to the estimated kinetic model. The method reduces the statistical uncertainty in the kinetic model relative to the single temperature approach and provides estimates of transition probabilities even for transitions not observed at the temperature of interest. Further, the method allows the kinetics to be estimated at temperatures other than those at which simulations were run. We illustrate this method by applying it to the generation of a Markov model of the conformational dynamics of the solvated terminally blocked alanine peptide.     

Mass spectrometry of halo-pyrazolium salts

Eleven halogen substituted 1-methyl-2-phenylpyrazolium bromides or chlorides were investigated by field desorption, field ionization, and electron impact mass spectrometry. Dealkylation was found to be the predominant thermal decomposition. An exchange between covalent and ionic halogen prior to dealkylation was observed and is discussed in detail.     

Thermal conduction through loose and granular two-phase materials at normal pressure

The integrated theory derived for the lattice-type dispersions is modified and extended to estimate the effective thermal conductivity of loose and granular two-phase materials at normal pressure assuming an effective continuous media approximation. A comparison of calculated values ofλ _e with the reported experimental results over a wide range of loose and granular two-phase materials shows a good agreement.     

Effective thermal conductivity of granulated two-phase systems at interstitial air pressures

Considering the htermal conduction through molecular collisions an expression for the effective thermal conductivityλ _e of loose and granular two-phase materials at different interstitial air pressure has been derived. The dependence ofλ _e on pore and particle sizes, characteristic pressure and radiative heat transfer is also discussed. Calculated values ofλ _e of glass beads and loose building materials are compared with reported results.     

Microdetermination of indoles with N-bromoacetamide in acetic acid medium

Summary A titrimetric method for the microdetermination of indole and its derivatives withN-bromoacetamide is described. It has been observed thatN-bromoacetamide brominates the compound containing indole nucleus in the presence of acetic acid. The usual reaction time is 15 minutes and the reaction is carried out at room temperature. The relative errors are less than ±1.5% at the mg level.

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Zusammenfassung Die maßanalytische Bestimmung von Indol und seinen Derivaten mitN-Bromacetamid wurde beschrieben. Dieses Reagens bromiert in Gegenwart von Essigsäure indolhältige Verbindungen innerhalb 15 min bei Zimmertemperatur. Der rel. Fehler ist geringer als ±1,5%.

     

Bounds on the effective thermal conductivity of two-phase systems

The weighted geometric mean of resistors considered for determining the effective thermal conductivityK _E of two-phase systems has been optimised. Solutions of the equations lead to a useful set of bounds. When compared with other bounds the present bounds give the better results in estimating the upper and lower values of the effective thermal conductivity of a two-phase system.     

On the effects of uniform high suction on the steady hydromagnetic flow due to a rotating disc

Summary The effect of uniform high suction on the steady flow of conducting viscous liquid due to a rotating disc, in the presence of a transverse magnetic field is considered. Series solutions for velocity components are obtained in descending powers of the suction parameter (a). The solutions, thus obtained, are valid for small values of m (= B ₀ ² /). Tables for displacement thickness, momentum thickness, and velocity components are given for different values of a and m.     

The Ricci identity

Summary The Ricci identities have been established by C.I. Ispas [1] and H. Rund [2] in a Finsler space. Here we shall discuss some identities based on the principle of mathematical induction [3], [4].     

Low temperature heat capacity of LaRu2 by a.c. technique

The low temperature heat capacity data of a small bulk sample of LaRu₂ show that the structural transformation occurring at T_m ～ 29.5K is rather spread out. The electronic heat capacity coefficient, γ, and Debye temperature, θ_D, are found to be respectively $\text{8.5}\text{mJ}\text{g}$. atom K² and 164 K. The multiple anomalies below T_m and T_c (4.45 K) are discussed.