An explicit time-domain finite element method for room acoustics simulations: Comparison of the performance with implicit methods

This paper presents the applicability of an explicit time-domain finite element method (TD-FEM) using a dispersion reduction technique called modified integration rules (MIR) on room acoustics simulations with a frequency-independent finite impedance boundary. First, a dispersion error analysis and a stability analysis are performed to derive the dispersion relation and the stability condition of the present explicit TD-FEM for three-dimensional room acoustics simulations with an infinite impedance boundary. Secondly, the accuracy and efficiency of the explicit TD-FEM are presented by comparing with implicit TD-FEM using MIR through room acoustics simulations in a rectangular room with infinite impedance boundaries. Thirdly, the stability condition of the explicit TD-FEM is investigated numerically in the case with finite impedance boundaries. Finally, the performance of the explicit TD-FEM in room acoustics simulations with finite impedance boundaries is demonstrated in a comparison with the implicit TD-FEM. Although the stability of the present explicit TD-FEM is dependent on the impedance values given at boundaries, the explicit TD-FEM is computationally more efficient than the implicit method from the perspective of computational time for acoustics simulations of a room with larger impedance values at boundaries.     

二维等离子体并行PIC模拟的性能分析及应用

通过区域分解法实现了二维等离子体粒子模拟程序并行化,并将此程序运行在由16个Pentium Ⅲ 1.6G CPU组成的微机机群上,对其性能进行了测试.结果表明,在计算规模一定的情况下,并行程序的并行效率随计算结点的增加而降低;而在计算节点不变的情况下,并行效率随计算规模的增加而增加,并行计算更适合于计算规模大的物理问题.利用此并行程序计算了等离子体中的束流不稳定性,结果表明,在波动激发的线性增长阶段,等离子体束流激发的Alfv啨n波基本上沿背景磁场方向传播,其波数满足共振条件ω-kV_b=-Ω_i,其中ω和k分别为Alfvén波的频率和波数,V_b为束流的速度,Ω_i为离子的回旋频率.     

Soyasapogenol-B as a Potential Multitarget Therapeutic Agent for Neurodegenerative Disorders: Molecular Docking and Dynamics Study

Neurodegenerative disorders involve various pathophysiological pathways, and finding a solution for these issues is still an uphill task for the scientific community. In the present study, a combination of molecular docking and dynamics approaches was applied to target different pathways leading to neurodegenerative disorders such as Alzheimer’s disease. Initially, abrineurin natural inducers were screened using physicochemical properties and toxicity assessment. Out of five screened compounds, a pentacyclic triterpenoid, i.e., Soyasapogenol B appeared to be the most promising after molecular docking and simulation analysis. Soyasapogenol B showed low TPSA (60.69), high absorption (82.6%), no Lipinski rule violation, and no toxicity. Docking interaction analysis revealed that Soyasapogenol B bound effectively to all of the targeted proteins (AChE, BuChE MAO-A, MAO-B, GSK3β, and NMDA), in contrast to other screened abrineurin natural inducers and inhibitors. Importantly, Soyasapogenol B bound to active site residues of the targeted proteins in a similar pattern to the native ligand inhibitor. Further, 100 ns molecular dynamics simulations analysis showed that Soyasapogenol B formed stable complexes against all of the targeted proteins. RMSD analysis showed that the Soyasapogenol B–protein complex exhibited average RMSD values of 1.94 Å, 2.11 Å, 5.07 Å, 2.56 Å, 3.83 Å and 4.07 Å. Furthermore, the RMSF analysis and secondary structure analysis also indicated the stability of the Soyasapogenol B–protein complexes.     

Diclofenac Ion Hydration: Experimental and Theoretical Search for Anion Pairs

Self-assembly of organic ions in aqueous solutions is a hot topic at the present time, and substances that are well-soluble in water are usually studied. In this work, aqueous solutions of sodium diclofenac are investigated, which, like most medicinal compounds, is poorly soluble in water. Classical MD modeling of an aqueous solution of diclofenac sodium showed equilibrium between the hydrated anion and the hydrated dimer of the diclofenac anion. The assignment and interpretation of the bands in the UV, NIR, and IR spectra are based on DFT calculations in the discrete-continuum approximation. It has been shown that the combined use of spectroscopic methods in various frequency ranges with classical MD simulations and DFT calculations provides valuable information on the association processes of medical compounds in aqueous solutions. Additionally, such a combined application of experimental and calculation methods allowed us to put forward a hypothesis about the mechanism of the effect of diclofenac sodium in high dilutions on a solution of diclofenac sodium.     

Bioactive Phytoconstituents as Potent Inhibitors of Tyrosine-Protein Kinase Yes (YES1): Implications in Anticancer Therapeutics

Tyrosine-protein kinase Yes (YES1) belongs to the Tyrosine-protein kinase family and is involved in several biological activities, including cell survival, cell–cell adhesion, cell differentiation, and cytoskeleton remodeling. It is highly expressed in esophageal, lung, and bladder cancers, and thus considered as an attractive drug target for cancer therapy. In this study, we performed a virtual screening of phytoconstituents from the IMPPAT database to identify potential inhibitors of YES1. Initially, the molecules were retrieved on their physicochemical properties following the Lipinski rule of five. Then binding affinities calculation, PAINS filter, ADMET, and PASS analyses followed by an interaction analysis to select safe and clinically better hits. Finally, two compounds, Glabrene and Lupinisoflavone C (LIC), with appreciable affinities and a specific interaction towards the AlphaFold predicted structure of YES1, were identified. Their time-evolution analyses were carried out using an all-atom molecular dynamics (MD) simulation, principal component analysis, and free energy landscapes. Altogether, we propose that Glabrene and LIC can be further explored in clinical settings to develop anticancer therapeutics targeting YES1 kinase.     

半导体量子点结构的特性及力学研究进展

量子点结构具有独特而优异的光学和电学等性能, 是当前国际研究的热点问题之一.量子点异质结构中的弹性场会对量子点结构的制备、加工及其光学和电学等物理性能产生重要影响. 本文以此为背景, 从低维量子限制系统所遵循的量子力学规律及其特点、半导体量子点的物理性能及表征、半导体量子点制备技术等方面较为全面地介绍半导体量子点结构的研究进展, 并着重介绍在半导体量子点结构的力学研究方面以及力学性能与物理性能耦合研究等方面的一些研究结果.      

Identification and Evaluation of Traditional Chinese Medicine Natural Compounds as Potential Myostatin Inhibitors: An In Silico Approach

Myostatin (MSTN), a negative regulator of muscle mass, is reported to be increased in conditions linked with muscle atrophy, sarcopenia, and other muscle-related diseases. Most pharmacologic approaches that treat muscle disorders are ineffective, emphasizing the emergence of MSTN inhibition. In this study, we used computational screening to uncover natural small bioactive inhibitors from the Traditional Chinese Medicine database (~38,000 compounds) for the MSTN protein. Potential ligands were screened, based on binding affinity (150), physicochemical (53) and ADMET properties (17). We found two hits (ZINC85592908 and ZINC85511481) with high binding affinity and specificity, and their binding patterns with MSTN protein. In addition, molecular dynamic simulations were run on each complex to better understand the interaction mechanism of MSTN with the control (curcumin) and the hit compounds (ZINC85592908 and ZINC85511481). We determined that the hits bind to the active pocket site (Helix region) and trigger conformational changes in the MSTN protein. Since the stability of the ZINC85592908 compound was greater than the MSTN control, we believe that ZINC85592908 has therapeutic potential against the MSTN protein and may hinder downstream singling by inhibiting the MSTN protein and increasing myogenesis in the skeletal muscle tissues.     

Stereocomplex Crystallization in Asymmetric Diblock Copolymers Studied by Dynamic Monte Carlo Simulations

Stereocomplex crystallization in asymmetric diblock copolymers was studied using dynamic Monte Carlo simulations, and the key factor dominating the formation of stereocomplex crystallites(SCs) was uncovered. The asymmetric diblock copolymers with higher degree of asymmetry exhibit larger difference between volume fractions of beads of different blocks, and local miscibility between different kinds of beads is lower, leading to lower SC content. To minimize the interference from volume fraction of beads, the SC formation in blends of asymmetric diblock copolymers was also studied. For the cases where the volume fractions of beads of different blocks are the same, similar local miscibility between beads of different blocks and similar SC content was observed. These findings indicate that the volume fraction of beads of different blocks is a key factor controlling the SC formation in the asymmetric diblock copolymers. The SC content can be regulated by adjusting the difference between the contents of beads of different blocks in asymmetric diblock copolymers.     

Structural Investigations and Binding Mechanisms of Oseltamivir Drug Resistance Conferred by the E119V Mutation in Influenza H7N9 Virus

The use of vaccinations and antiviral medications have gained popularity in the therapeutic management of avian influenza H7N9 virus lately. Antiviral medicines are more popular due to being readily available. The presence of the neuraminidase protein in the avian influenza H7N9 virus and its critical role in the cleavage of sialic acid have made it a target drug in the development of influenza virus drugs. Generally, the neuraminidase proteins have common conserved amino acid residues and any mutation that occurs around or within these conserved residues affects the susceptibility and replicability of the influenza H7N9 virus. Herein, we investigated the interatomic and intermolecular dynamic impacts of the experimentally reported E119V mutation on the oseltamivir resistance of the influenza H7N9 virus. We extensively employed molecular dynamic (MD) simulations and subsequent post-MD analyses to investigate the binding mechanisms of oseltamivir-neuraminidase wildtype and E119V mutant complexes. The results revealed that the oseltamivir-wildtype complex was more thermodynamically stable than the oseltamivir-E119V mutant complex. Oseltamivir exhibited a greater binding affinity for wildtype (−15.46 ± 0.23 kcal/mol) relative to the E119V mutant (−11.72 ± 0.21 kcal/mol). The decrease in binding affinity (−3.74 kcal/mol) was consistent with RMSD, RMSF, SASA, PCA, and hydrogen bonding profiles, confirming that the E119V mutation conferred lower conformational stability and weaker protein–ligand interactions. The findings of this oseltamivir-E119V mutation may further assist in the design of compounds to overcome E119V mutation in the treatment of influenza H7N9 virus patients.     

Potential Efficacy of β-Amyrin Targeting Mycobacterial Universal Stress Protein by In Vitro and In Silico Approach

The emergence of drug resistance and the limited number of approved antitubercular drugs prompted identification and development of new antitubercular compounds to cure Tuberculosis (TB). In this work, an attempt was made to identify potential natural compounds that target mycobacterial proteins. Three plant extracts (A. aspera, C. gigantea and C. procera) were investigated. The ethyl acetate fraction of the aerial part of A. aspera and the flower ash of C. gigantea were found to be effective against M. tuberculosis H₃₇Rv. Furthermore, the GC-MS analysis of the plant fractions confirmed the presence of active compounds in the extracts. The Mycobacterium target proteins, i.e., available PDB dataset proteins and proteins classified in virulence, detoxification, and adaptation, were investigated. A total of ten target proteins were shortlisted for further study, identified as follows: BpoC, RipA, MazF4, RipD, TB15.3, VapC15, VapC20, VapC21, TB31.7, and MazF9. Molecular docking studies showed that β-amyrin interacted with most of these proteins and its highest binding affinity was observed with Mycobacterium Rv1636 (TB15.3) protein. The stability of the protein-ligand complex was assessed by molecular dynamic simulation, which confirmed that β-amyrin most firmly interacted with Rv1636 protein. Rv1636 is a universal stress protein, which regulates Mycobacterium growth in different stress conditions and, thus, targeting Rv1636 makes M. tuberculosis vulnerable to host-derived stress conditions.