The Complemented System Approach: A Novel Method for Calculating the X-ray Scattering from Computer Simulations

In this paper, we review the main problem concerning the calculation of X-ray scattering of simulated model systems, namely their finite size. A novel method based on the Rayleigh-Debye-Gans approximation was derived, which allows sidestepping this issue by complementing the missing surroundings of each particle with an average image of the system. The method was designed to operate directly on particle configurations without an intermediate step (e.g., calculation of pair distribution functions): in this way, all information contained in the configurations was preserved. A comparison of the results against those of other known methods showed that the new method combined several favourable properties: an arbitrary q-scale, scattering curves free of truncation artifacts and good behaviour down to the theoretical lower limit of the q-scale. A test of computational efficiency was also performed to establish a relative scale between the speeds of all known methods: the reciprocal lattice approach, the brute force method, the Fourier transform approach and the newly presented complemented system approach.Comment: 6 pages, 5 figures. Copyright 2010 American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Institute of Physics. The following article appeared in The Journal of Chemical Physics and may be found at http://link.aip.org/link/?jcp/133/17412

Soft-Core Attractive Model Fluid: Structure, Thermodynamics and Inter-colloidal Solvation Force †

Abstract Canonical and grand canonical Monte Carlo simulations are used to study a system of spherical particles interacting via a discontinuous potential combining a repulsive square soft core and an attractive square well. This, so-called coresoftened (CS) potential fluid is known to have both a gas-liquid critical point and a liquid-liquid critical point separating high density liquid (HDL) and low density liquid (LDL) phases. First, the spatial correlations and thermodynamic properties of homogeneous and inhomogeneous CS fluid are investigated. Using open ensemble simulation we study an equilibrium distribution of the CS fluid between the homogeneous phase and the planar pores mimicking the real porous material. The bulk radial distribution function displays discontinuities at the distances coinciding with the ranges of the successive repulsive and attractive parts in the CS potential function. The density profiles of confined CS fluid show the shapes arising from the interplay among the steric effects and the competition between the repulsive and attractive parts of the CS potential. Then, the effective force between a pair of big colloidal spheres immersed in a sea of small spheres interacting via CS potential is explored. The big-small interactions are modeled as hard core pair potentials with attractive or repulsive Yukawa tail leading to the accumulation repulsion and depletion attraction between the two colloids, respectively. For this purpose we apply a special simulation technique based on a separate sampling of the contributions arising from the Yukawa tail and hard-core (collision) parts of the big-small interaction potential to the total force between the colloidal particles

Carcinogenesis of Urethane: Simulation versus Experiment

The carcinogenesis of urethane (ethyl carbamate), a byproduct of fermentation that is consistently found in various food products, was investigated with a combination of kinetic experiments and quantum chemical calculations. The main objective of the study was to find Δ<i>G</i>^⧧, the activation free energy for the rate-limiting step of the S_N2 reaction among the ultimate carcinogen of urethane, vinyl carbamate epoxide (VCE), and different nucleobases of the DNA. In the experimental part, the second-order reaction rate constants for the formation of the main 7-(2-oxoethyl)­guanine adduct in aqueous solutions of deoxyguanosine and in DNA were determined. A series of <i>ab initio</i>, density functional theory (DFT), and semiempirical molecular orbital (MO) calculations was then performed to determine the activation barriers for the reaction between VCE and nucleobases methylguanine, methyladenine, and methylcytosine. Effects of hydration were incorporated with the use of the solvent reaction field method of Tomasi and co-workers and the Langevine dipoles model of Florian and Warshel. The computational results for the main adduct were found to be in good agreement with the experiment, thus presenting strong evidence for the validity of the proposed S_N2 mechanism. This allowed us to predict the activation barriers of reactions leading to side products for which kinetic experiments have not yet been performed. Our calculations have shown that the main 7-(2-oxoethyl)­deoxyguanosine adduct indeed forms preferentially because the emergence of other adducts either proceeds across a significantly higher activation barrier or the geometry of the reaction requires the Watson–Crick pairs of the DNA to be broken. The computational study also considered the questions of stereoselectivity, the ease of the elimination of the leaving group, and the relative contributions of the two possible reaction paths for the formation of the 1,<i>N</i>²-ethenodeoxyguanosine adduct

GNU Radio

GNU Radio is a free &amp; open-source software development toolkit that provides signal processing blocks to implement software radios. It can be used with readily-available, low-cost external RF hardware to create software-defined radios, or without hardware in a simulation-like environment. It is widely used in hobbyist, academic, and commercial environments to support both wireless communications research and real-world radio systems