Preconditioned Bi-Conjugate Gradient Method for Radiative Transfer in Spherical Media

A robust numerical method called the Preconditioned Bi-Conjugate Gradient (Pre-BiCG)method is proposed for the solution of radiative transfer equation in spherical geometry.A variant of this method called Stabilized Preconditioned Bi-Conjugate Gradient (Pre-BiCG-STAB) is also presented. These are iterative methods based on the construction of a set of bi-orthogonal vectors. The application of Pre-BiCG method in some benchmark tests show that the method is quite versatile, and can handle hard problems that may arise in astrophysical radiative transfer theory.Comment: 19 pages, 12 figure

Absolute FKBP binding affinities obtained via non-equilibrium unbinding simulations

We compute absolute binding affinities for two ligands bound to the FKBP protein using non-equilibrium unbinding simulations. The methodology is straight-forward, requiring little or no modification to many modern molecular simulation packages. The approach makes use of a physical pathway, eliminating the need for complicated alchemical decoupling schemes. Results of this study are promising. For the ligands studied here the binding affinities are typically estimated within less than 4.0 kJ/mol of the target values; and the target values are within less than 1.0 kJ/mol of experiment. These results suggest that non-equilibrium simulation could provide a simple and robust means to estimate protein-ligand binding affinities.Comment: 9 pages, 3 figures (no necessary color). Changes made to methodology and results between revision

Luminosity indicators in dusty photoionized environments

The luminosity of the central source in ionizing radiation is an essential parameter in a photoionized environment, and one of the most fundamental physical quantities one can measure. We outline a method of determining luminosity for any emission-line region using only infrared data. In dusty environments, grains compete with hydrogen in absorbing continuum radiation. Grains produce infrared emission, and hydrogen produces recombination lines. We have computed a very large variety of photoionization models, using ranges of abundances, grain mixtures, ionizing continua, densities, and ionization parameters. The conditions were appropriate for such diverse objects as H II regions, planetary nebulae, starburst galaxies, and the narrow and broad line regions of active nuclei. The ratio of the total thermal grain emission relative to H$\beta$ (IR/H$\beta$) is the primary indicator of whether the cloud behaves as a classical Str\"{o}mgren sphere (a hydrogen-bounded nebula) or whether grains absorb most of the incident continuum (a dust-bounded nebula). We find two global limits: when $IR/H\beta<100$ infrared recombination lines determine the source luminosity in ionizing photons; when $IR/H\beta\gg100$ the grains act as a bolometer to measure the luminosity.Comment: 12 pages 3 figures. Accepted ASP Sept.9

The Work-Hamiltonian Connection and the Usefulness of the Jarzynski Equality for Free Energy Calculations

The connection between work and changes in the Hamiltonian for a system with a time-dependent Hamiltonian has recently been called into question, casting doubt on the usefulness of the Jarzynski equality for calculating free energy changes. In this paper, we discuss the relationship between two possible definitions of free energy and show how some recent disagreements regarding the applicability of the Jarzynski equality are the result of different authors using different definitions of free energy. Finally, in light of the recently raised doubts, we explicitly demonstrate that it is indeed possible to obtain physically relevant free energy profiles from molecular pulling experiments by using the Jarzynski equality and the results of Hummer and Szabo.Comment: 3 page

Mocassin: A fully three-dimensional Monte Carlo photoionization code

The study of photoionized environments is fundamental to many astrophysical problems. Up to the present most photoionization codes have numerically solved the equations of radiative transfer by making the extreme simplifying assumption of spherical symmetry. Unfortunately very few real astronomical nebulae satisfy this requirement. To remedy these shortcomings, a self-consistent, three-dimensional radiative transfer code has been developed using Monte Carlo techniques. The code, Mocassin, is designed to build realistic models of photoionized nebulae having arbitraries geometry and density distributions with both the stellar and diffuse radiation fields treated self-consistently. In addition, the code is capable of tretating on or more exciting stars located at non-central locations. The gaseous region is approximated by a cuboidal Cartesian grid composed of numerous cells. The physical conditions within each grid cell are determined by solving the thermal equilibrium and ionization balance equations This requires a knowledge of the local primary and secondary radiation fields, which are calculated self-consistently by locally simulating the individual processes of ionization and recombination. The main structure and computational methods used in the Mocassin code are described in this paper. Mocassin has been benchmarked against established one-dimensional spherically symmetric codes for a number of standard cases, as defined by the Lexington/Meudon photoionization workshops (Pequignot et al., 1986; Ferland et al., 1995; Pequignot et al., 2001)\citep{pequignot86,ferland95, pequignot01}. The results obtained for the benchmark cases are satisfactory and are presented in this paper. A performance analysis has also been carried out and is discussed here.Comment: 17 pages, 4 figures, 1 appendix Changes: appendix adde