Ewald summation and physically equivalent methods such as particle-mesh Ewald, kubic-harmonic expansions, or Lekner sums are commonly used to calculate long-range electrostatic interactions in computer simulations of polar and charged substances. The calculation of pressures in such systems is investigated. We find that the virial and thermodynamic pressures differ because of the explicit volum...

The usual thermodynamic evaluation, based solely on the Standard Gibbs Energy of reaction, does not take into account the permissible ranges of concentrations of metabolites, and it faces further difficulties when, instead of isolated reactions, we are examining whole pathways. For pathways, we seek not only to decide whether they are feasible but also to pinpoint the pathway segment that cause...

a thermodynamic analysis of the counter flow wet cooling tower (cwct) in the steelmaking unit of the khuzestan steel company (ksc) is performed in this paper. we evaluated both energy and exergy formulations for analyzing the heat and mass transfer, exergy and second-law efficiency in this cooling tower. the lewis factor le f is an indication of the relative rates of heat and mass transfer in a...

The complexes between C20 and C2 X4 , C2 X2 (X = H, F, Cl, Br) have been studied theoretically at the B3LYP/6-311G (d,p) level. The calculations include the optimized geometries, the interaction energies, aromaticity and thermodynamic. The interaction energies ranging from -60 to -101 kcal/mol and being ordered as: X = F> Cl > Br. Natural bond orbital (NBO) analysis has been performed on all ge...

Thermodynamic RNA secondary structure prediction is an important recipe for the latest generation of functional non-coding RNA finding tools. However, the predicted energy is not strong enough by itself to distinguish a single functional non-coding RNA from other RNA. Here, we analyze how well an RNA molecule folds into a particular structural class with a restricted folding algorithm called Th...

(Received December, 1988) The adaptive umbrella sampling technique, introduced recently to improve the probability ratio method and found to perform more reliably then the customary harmonic umbrella sampling, is tested and compared with other free energy methods. One of the tests applies the method to a transition involving a chemical change: calculation of the hydration free energy difference...

according to the bronsted definition, any compound which has a hydrogen atom is an acid, since itmay be lost as a proton. a thermodynamical cycle is proposed to calculate absolute pka values forbronsted acids in aqueous solution. the equilibrium of dissociation of a bronsted acid depends onthe interaction of the acid and its conjugate base with solvent molecules. there fore the pka valuedepends...

This study presents thermodynamic analysis and optimization of single effect LiCl-H2O absorption cooling system. Thermodynamic models are employed in engineering equation solver to compute the optimum performance parameters. In this study, cut off temperature to operate system has been obtained at various operating temperatures. Analysis depicts that on 3.59 % rise in evaporator temperature, th...

4-Hydroxyphenylpyruvate dioxygenase is a relevant target in both pharmaceutical and agricultural research. We report on molecular dynamics simulations and free energy calculations on this enzyme, in complex with 12 inhibitors for which experimental affinities were determined. We applied the thermodynamic integration approach and the more efficient one-step perturbation. Even though simulations ...

We describe and apply a method that reduces the time taken to calculate a single binding free energy using thermodynamic integration. This method uses a stack of grid software which we call STIMD that allows the scientist to easily distribute the necessary simulations around a computational grid (or on a high performance computer) thereby accelerating the process. We use this method to study ho...