Preface

Thirty three years ago, because of the dramatic increase in the power and utility of computer simulations, The University of Georgia formed the first institutional unit devoted to the application of simulations in research and teaching: The Center for Simulational Physics. Then, as the international simulations community expanded further, we sensed the need for a meeting place for both experienced simulators and newcomers to discuss inventive algorithms and recent results in an environment that promoted lively discussion. As a consequence, the Center for Simulational Physics established an annual workshop series on Recent Developments in Computer Simulation Studies in Condensed Matter Physics. This year’s highly interactive workshop was the 32nd in the series marking our efforts to promote high quality research in simulational physics. The continued interest shown by the scientific community amply demonstrates the useful purpose that these meetings have served. The latest workshop was held at The University of Georgia from February 18-22, 2019. These Proceedings provide a “status report” on a number of important topics. This on-line “volume” is published with the goal of timely dissemination of the material to a wider audience. These Proceedings contain both invited papers and contributed presentations on problems in both classical and quantum condensed matter physics. The Workshop was prefaced by a special tutorial presented by colleagues from Oak Ridgr National Laboratory on a powerful software suite: OWL (Oak Ridge Wang-Landau). The first manuscript in this Proceedings is devoted to this tutorial material. The Workshop topics, as usual, ranged from hard and soft condensed matter to biologically inspired problems and purely methodological advances. We hope that readers will benefit from specialized results as well as profit from exposure to new algorithms, methods of analysis, and conceptual developments. D. P. Landau M. Bachmann S. P. Lewis H.-B. Schüttler

Hands-on with OWL: the Oak–Ridge Wang–Landau Monte Carlo software suite

The Oak–Ridge Wang–Landau (OWL) package is an open-source scientific software specialized for large-scale, Monte Carlo simulations for the study of materials properties at finite temperature. In this paper, we discuss the main features and capabilities of OWL, followed by detailed descriptions of building and running the code. The readers will be guided through the usage and functionality of the code with a few hands-on examples. This paper is based on a tutorial on OWL given at the 32nd Center for Simulational Physics Workshop on Recent Developments in Computer Simulation Studies in Condensed Matter Physics.

A Novel Approach based on Lifting Wavelet Transform for MIMO-OFDM Systems

In this article, two methods are proposed to further increase the advantages of MIMO-OFDM systems such as high access quality, high data rates and spectral efficiency. The first of these is the combination of the MIMO-OFDM system with the fast Walsh Hadamard transform (FWHT) due to its high accomplishment with the ability to spread the data versus the disturbing influences of the channel. The second is the combination of Lifting wavelet transform (LWT), due to its superior advantages such as good time-frequency localization properties, ICI and ISI suppression capabilities due to its orthonormal structure, unlike fast Fourier transform (FFT), with MIMO-OFDM scheme. Computer simulation studies are carried out to verify the accomplishment of the suggested methods over the bit error rate (BER) and peak to average power ratio (PAPR) benchmark. From the acquired outcomes, it is noticed that approximately 6 dB of SNR gain and approximately 2 dB of PAPR gain are achieved with the proposed method.

The Interconnection and Damping Assignment Passivity-Based Control Synthesis via the Optimal Control Method for Electric Vehicle Subsystems

The interconnection between optimal control theory and the theory of energy-shaping control is described in our paper. For linear and nonlinear systems, the application of the theory of optimal control for the synthesis of parameters of energy-shaping control matrices is demonstrated in detail. The use of a Riccati equation allows us to form an optimality criterion and to synthesize the energy-shaping control system that provides the desired transient processes. The proposed approach was applied to the synthesis of control influences for electric vehicle subsystems, such as a two-mass system and a permanent magnets synchronous motor. The results of computer simulation studies, as well as those conducted on real experimental installations, are given in this paper.

An approximate point-based alternative for the estimation of variance under big BAF sampling

Background A new variance estimator is derived and tested for big BAF (Basal Area Factor) sampling which is a forest inventory system that utilizes Bitterlich sampling (point sampling) with two BAF sizes, a small BAF for tree counts and a larger BAF on which tree measurements are made usually including DBHs and heights needed for volume estimation. Methods The new estimator is derived using the Delta method from an existing formulation of the big BAF estimator as consisting of three sample means. The new formula is compared to existing big BAF estimators including a popular estimator based on Bruce’s formula. Results Several computer simulation studies were conducted comparing the new variance estimator to all known variance estimators for big BAF currently in the forest inventory literature. In simulations the new estimator performed well and comparably to existing variance formulas. Conclusions A possible advantage of the new estimator is that it does not require the assumption of negligible correlation between basal area counts on the small BAF factor and volume-basal area ratios based on the large BAF factor selection trees, an assumption required by all previous big BAF variance estimation formulas. Although this correlation was negligible on the simulation stands used in this study, it is conceivable that the correlation could be significant in some forest types, such as those in which the DBH-height relationship can be affected substantially by density perhaps through competition. We derived a formula that can be used to estimate the covariance between estimates of mean basal area and the ratio of estimates of mean volume and mean basal area. We also mathematically derived expressions for bias in the big BAF estimator that can be used to show the bias approaches zero in large samples on the order of $\frac {1}{n}$ 1 n where n is the number of sample points.

Investigating the network consequences of focal brain lesions through comparisons of real and simulated lesions

Given the increased interest in the functional human connectome, a number of computer simulation studies have sought to develop a better quantitative understanding of the effects of focal lesions on the brain’s functional network organization. However, there has been little work evaluating the predictions of this simulation work vis a vis real lesioned connectomes. One of the few relevant studies reported findings from real chronic focal lesions that only partially confirmed simulation predictions. We hypothesize that these discrepancies arose because although the effects of focal lesions likely consist of two components: short-term node subtraction and long-term network re-organization, previous simulation studies have primarily modeled only the short-term consequences of the subtraction of lesioned nodes and their connections. To evaluate this hypothesis, we compared network properties (modularity, participation coefficient, within-module degree) between real functional connectomes obtained from chronic stroke participants and “pseudo-lesioned” functional connectomes generated by subtracting the same sets of lesioned nodes/connections from healthy control connectomes. We found that, as we hypothesized, the network properties of real-lesioned connectomes in chronic stroke differed from those of the pseudo-lesioned connectomes which instantiated only the short-term consequences of node subtraction. Reflecting the long-term consequences of focal lesions, we found re-organization of the neurotopography of global and local hubs in the real but not the pseudo-lesioned connectomes. We conclude that the long-term network re-organization that occurs in response to focal lesions involves changes in functional connectivity within the remaining intact neural tissue that go well beyond the short-term consequences of node subtraction.

NOVEL LIGANDS OF HUMAN CYP7 ENZYMES – POSSIBLE MODULATORS OF CHOLESTEROL BLOOD LEVEL: COMPUTER SIMULATION STUDIES

Our in vitro studies showed that a couple of perspective steroidal derivatives showed previously biomedical potential via enzyme inhibition, receptor binding or antiproliferative effect against the cancer cells of reproductive tissues are able to bind to human CYP7 enzymes – key enzymes taking part in hydroxylation of cholesterol, 25-, 27-hydroxycholesterol and a number of steroidal hormones. In silico screening of binding affinity of the modified steroids toward CYP7 enzymes showed that interaction energy for the new ligands is comparable with consequent values, calculated for the ‘essential’ substrates of the enzymes – cholestenone (CYP7A1) and DHEA (CYP7B1). However, no correlation between binding energy and the affinity of the ligand was found. Novel ligands interact with conserved amino acids taking part in stabilization of natural substrates of CYP7 enzymes. A couple of structural features, governing ligand binding, were identified. Among which are planar structure of A-ring for CYP7A1 ligands, absence of many polar fragments in side-chain and presence of polar group at C3 position. Analysis of the docking results showed that CYP7B1 higher selectivity in comparison with CYP7A1 is connected by the structure of the cavity formed by α-helices I and B`. The data obtained will be used for the explanation of ligand specificity of human sterol- hydroxylases.

An Approximate Point-based Alternative for the Estimation of Variance under Big BAF Sampling

BackgroundA new variance estimator is derived and tested for big BAF (Basal Area Factor) sampling which is a forest inventory system that utilizes two BAF sizes, a small BAF for tree counts and a larger BAF on which tree measurements are made usually including \dbh s and heights needed for volume estimation.MethodsThe new estimator is derived using the \Dm\ from an existing formulation of the big BAF estimator as consisting of three sample means. The new formula is compared to existing big BAF estimators including a popular estimator based on Bruce's formula.ResultsSeveral computer simulation studies were conducted comparing the new variance estimator to all known variance estimators for big BAF currently in the forest inventory literature. In simulations the new estimator performed well and comparably to existing variance formulas.ConclusionsA possible advantage of the new estimator is that it does not require the assumption of negligible correlation between basal area counts on the small BAF factor and volume-basal area ratios based on the large BAF factor selection trees, an assumption required by all previous big BAF variance estimation formulas. Although this correlation was negligible on the simulation stands used in this study, it is conceivable that the correlation could be significant in some forest types, such as those in which the \dbh-height relationship can be affected substantially by density perhaps through competition. We also mathematically derived expressions for bias in the big BAF estimator that can be used to show the bias approaches zero in large samples on the order of 1/n where n is the number of sample points.