Abstract: In this work, we present a simple decomposition scheme of the Kohn-Sham optimized orbitals which is able to provide a reduced basis set, made of localized polycentric orbitals, specifically designed for Quantum Monte Carlo. The decomposition follows a standard Density functional theory (DFT) calculation and is based on atomic connectivity and shell structure. The new orbitals are used to construct a compact correlated wave function of the Slater–Jastrow form which is optimized at the Variational Monte Carlo level and then used as the trial wave function for a final Diffusion Monte Carlo accurate energy calculation. We are able, in this way, to capture the basic information on the real system brought by the Kohn-Sham orbitals and use it for the calculation of the ground state energy within a strictly variational method. Here, we show test calculations performed on some small selected systems to assess the validity of the proposed approach in a molecular fragmentation, in the calculation of a barrier height of a chemical reaction and in the determination of intermolecular potentials. The final Diffusion Monte Carlo energies are in very good agreement with the best literature data within chemical accuracy.
Abstract: In tissue engineering, porous biodegradable scaffolds are used as templates for regenerating required tissues. With the advances in computational tools, many modeling approaches have been considered. For example, fluid flow through porous medium can be modeled using the Brinkman equation where permeability of the porous medium has to be defined. In this review, we summarize various models recently reported for defining permeability and non-invasive pressure drop monitoring as a tool to validate dynamic changes in permeability. We also summarize some models used for scaffold degradation and integrating mass transport in the simulation.
Abstract: The chief objective of this study is the proposal design and CFD simulation of a new compacted copper wire woven fin heat exchanger and silica gel adsorbent bed used as part of an adsorption refrigeration system. This type of heat exchanger design has a large surface area because of the wire woven fin design. It is estimated that this will help improve the coefficient of performance (COP) of the adsorption phase and increase the heat transfer in this system arrangement. To study the heat transfer between the fins and porous adsorbent reactor bed, two experiments were carried out and matched to computational fluid dynamics (CFD) results.
Abstract: In population genetics, information about evolutionary forces, e.g., mutation, selection and genetic drift, is often inferred from DNA sequence information. Generally, DNA consists of two long strands of nucleotides or sites that pair via the complementary bases cytosine and guanine (C and G), on the one hand, and adenine and thymine (A and T), on the other. With whole genome sequencing, most genomic information stored in the DNA has become available for multiple individuals of one or more populations, at least in humans and model species, such as fruit flies of the genus Drosophila. In a genome-wide sample of L sites for M (haploid) individuals, the state of each site may be made binary, by binning the complementary bases, e.g., C with G to C/G, and contrasting C/G to A/T, to obtain a “site frequency spectrum” (SFS). Two such samples of either a single population from different time-points or two related populations from a single time-point are called joint site frequency spectra (joint SFS). While mathematical models describing the interplay of mutation, drift and selection have been available for more than 80 years, calculation of exact likelihoods from joint SFS is difficult. Sufficient statistics for inference of, e.g., mutation or selection parameters that would make use of all the information in the genomic data are rarely available. Hence, often suites of crude summary statistics are combined in simulation-based computational approaches. In this article, we use a bi-allelic boundary-mutation and drift population genetic model to compute the transition probabilities of joint SFS using orthogonal polynomials. This allows inference of population genetic parameters, such as the mutation rate (scaled by the population size) and the time separating the two samples. We apply this inference method to a population dataset of neutrally-evolving short intronic sites from six DNA sequences of the fruit fly Drosophila melanogaster and the reference sequence of the related species Drosophila sechellia.
Abstract: The accurate and exhaustive description of the conformational ensemble sampled by small molecules in solution, possibly at different physiological conditions, is of primary interest in many fields of medicinal chemistry and computational biology. Recently, we have built an on-line database of compounds with antimicrobial properties, where we provide all-atom force-field parameters and a set of molecular properties, including representative structures extracted from cluster analysis over μs-long molecular dynamics (MD) trajectories. In the present work, we used a medium-sized antibiotic from our sample, namely ampicillin, to assess the quality of the conformational ensemble. To this aim, we compared the conformational landscape extracted from previous unbiased MD simulations to those obtained by means of Replica Exchange MD (REMD) and those originating from three freely-available conformer generation tools widely adopted in computer-aided drug-design. In addition, for different charge/protonation states of ampicillin, we made available force-field parameters and static/dynamic properties derived from both Density Functional Theory and MD calculations. For the specific system investigated here, we found that: (i) the conformational statistics extracted from plain MD simulations is consistent with that obtained from REMD simulations; (ii) overall, our MD-based approach performs slightly better than any of the conformer generator tools if one takes into account both the diversity of the generated conformational set and the ability to reproduce experimentally-determined structures.