Maximally robust unravelings of quantum master equations

The stationary state of an open quantum system has infinitely many representations as an ensemble of pure states. We argue that the most natural ensemble is the most robust physically realizable ensemble. Robustness is quantified by the survival probability. Physical realization requires monitoring the environment to “unravel” the dissipative evolution.     

Configuration-specific kinetic theory applied to the elastic collisions of hard spherical molecules

Classical trajectory simulations can be used to glean a wealth of information on the geometric details of gas-phase molecular collision events for which the standard theoretical treatment lacks the ability to predict. For instance, the standard treatment gives no information on configuration-specific collision parameters. A configuration-specific parameter is defined here as the average value for a collision parameter that is exclusive to either an ensemble of front-end or an ensemble of rear-end molecular collisions. This paper presents statistical results of simulation "measurements" on several configuration-specific parameters, including the configuration-specific collision frequencies. The simulations use single-component systems of hard spherical molecules confined within a spherical boundary. To complement the simulation effort, a systematic mathematical analysis for the configuration-specific parameters is presented. This analysis uses the Maxwell-Boltzmann distribution of molecular speeds as usual, but exploits the distinction between front-end and rear-end collision space, and uses the line-of-centers speed rather than the relative speed. The configuration-specific expressions derived from this analysis are in very good agreement with the simulation measurements for every molecular collision parameter studied in this work.     

Grand canonical Monte Carlo simulation of ligand-protein binding

A new application of the grand canonical thermodynamics ensemble to compute ligand-protein binding is described. The described method is sufficiently rapid that it is practical to compute ligand-protein binding free energies for a large number of poses over the entire protein surface, thus identifying multiple putative ligand binding sites. In addition, the method computes binding free energies for a large number of poses. The method is demonstrated by the simulation of two protein-ligand systems, thermolysin and T4 lysozyme, for which there is extensive thermodynamic and crystallographic data for the binding of small, rigid ligands. These low-molecular-weight ligands correspond to the molecular fragments used in computational fragment-based drug design. The simulations correctly identified the experimental binding poses and rank ordered the affinities of ligands in each of these systems.     

Fluorocyclohexanes-II Cis- and trans- 1H:3H- and 1H:4H-decafluorocyclohexanes

An extension of the methods employed in the isolation of (trans) 1H/2H-decafluorocyclohexane,¹ (I) from the polyfluorocyclohexane mixture obtained by the vapour phase fluorination of benzene with cobaltic fluoride at about 150°, has afforded the four remaining members of the series of decafluorocyclohexanes [the cis- and trans-1H:3H- and 1H:4H-isomers (1H:3H/-(IV), 1H/3H-(III), 1H:4H/-(VII), and 1H/4H-(VIII), respectively)] and also the cis-1H:2H-decafluorocyclohexane (II), obtained previously^1,2 by the lithium aluminium hydride reduction of 1:2-dichlorodecafluorocyclohexane. The structures of the 1H:3H- and 1H:4H-decafluorides have been established by dehydrofluorination studies. The six decafluorocyclohexanes have been related to two new nonafluorocyclohexanes³ (IX and X) by further fluorination of the latter. 2H-Heptafluoroadipic acid has been obtained from 3H-nonafluorocyclohex-1-ene (V), one of the dehydrofluorination products of the 1H:3H-decafluorides.