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Acta Mechanica Sinica 2023年第1期39卷 23-29页

作者：王林李二垒周宗彦张百成余艾冰 ARC Hub for Computational Particle Technology Department of Chemical & Biological Engineering Monash University Clayton VIC 3800 Australia Delft University of Technology Stevinweg 1 2628 CN Delft The Netherlands Jiangxi Provincial Key Laboratory for Simulation and Modelling of Particulate Systems Jiangxi University of Science and Technology Nanchang 330013 China Beijing Advanced Innovation Center Materials Genome Engineering Advanced Material & Technology Institute University of Science and Technology Beijing Beijing 100083 China

粉末床熔融增材制造技术已应用于功能梯度材料的制造.文献中报道了一种材料成分沿垂直于粉末铺粉方向变化的新设计.基于此设计,本工作采用离散单元数值模拟研究了两种密度差异较大的金属粉末在铺粉过程中颗粒的偏析情况.结果发现,在铺... 详细信息

粉末床熔融增材制造技术已应用于功能梯度材料的制造.文献中报道了一种材料成分沿垂直于粉末铺粉方向变化的新设计.基于此设计,本工作采用离散单元数值模拟研究了两种密度差异较大的金属粉末在铺粉过程中颗粒的偏析情况.结果发现,在铺粉过程中,较大密度粉末(重颗粒)一侧的铺粉量小于较小密度粉末(轻颗粒)的一侧的铺粉量.这种现象表明重颗粒从粉末密度大的一侧向粉末密度较小的一侧扩散.这种扩散受铺粉速度影响较大,铺粉速度越快,扩散越明显.但粉末层厚度对扩散影响不大.结果还表明,重颗粒与轻颗粒间的粒径差异影响扩散较大,减小重颗粒的粒径可能是控制颗粒偏析的一种方案.

关键词：材料成分颗粒偏析功能梯度材料离散单元金属粉末密度差异增材制造技术扩散影响

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Probing the unfolded configurations of a β-hairpin using sketch-map

arXiv

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arXiv 2023年

作者： Ardevol, Albert Tribello, Gareth A. Ceriotti, Michele Parrinello, Michele Computational Science Department of Chemistry and Applied Biosciences ETH Zurich USI-Campus Via Giuseppe Buffi 13 LuganoC-6900 Switzerland Atomistic Simulation Centre School of Mathematics and Physics Queen’s University Belfast BelfastBT7 1NN United Kingdom Laboratory of Computational Science and Modelling EPFL Switzerland

This work examines the conformational ensemble involved in β-hairpin folding by means of advanced molecular dynamics simulations and dimensionality reduction. A fully atomistic description of the protein and the surrounding solvent molecules is used and this complex energy landscape is sampled by means of parallel tempering metadynamics simulations. The ensemble of configurations explored is analysed using the recently proposed sketch-map algorithm. Further simulations allow us to probe how mutations affect the structures adopted by this protein. We find that many of the configurations adopted by a mutant are the same as those adopted by the wild type protein. Furthermore, certain mutations destabilize secondary structure containing configurations by preventing the formation of hydrogen bonds or by promoting the formation of new intramolecular contacts. Our analysis demonstrates that machine-learning techniques can be used to study the energy landscapes of complex molecules and that the visualizations that are generated in this way provide a natural basis for examining how the stabilities of particular configurations of the molecule are affected by factors such as temperature or structural mutations. Copyright © 2023, The Authors. All rights reserved.

关键词： Proteins

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Using data-reduction techniques to analyse biomolecular trajectories

arXiv

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arXiv 2019年

作者： Tribello, Gareth A. Gasparotto, Piero Atomistic Simulation Centre School of Mathematics and Physics Queen’s University Belfast BelfastBT7 1NN United Kingdom Laboratory of Computational Science and Modelling National Centre for Computational Design and Discovery of Novel Materials MARVEL IMX École Polytechnique Fédérale de Lausanne Lausanne1015 Switzerland

This chapter discusses the way in which dimensionality reduction algorithms such as diffusion maps and sketch-map can be used to analyze molecular dynamics trajectories. The first part discusses how these various algorithms function as well as practical issues such as landmark selection and how these algorithms can be used when the data to be analyzed comes from enhanced sampling trajectories. In the later parts a comparison between the results obtained by applying various algorithms to two sets of sample data are performed and Copyright © 2019, The Authors. All rights reserved.

关键词： Trajectories

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Invariance principles in the theory and computation of transport coefficients

arXiv

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arXiv 2021年

作者： Grasselli, Federico Baroni, Stefano COSMO Laboratory of Computational Science and Modelling IMX École Polytechnique Fédérale de Lausanne Lausanne1015 Switzerland SISSA - Scuola Internazionale Superiore di Studi Avanzati Trieste34136 Italy CNR-IOM DEMOCRITOS Simulation Center SISSA Trieste34136 Italy

In this work we elaborate on two recently discovered invariance principles, according to which transport coefficients are, to a large extent, independent of the microscopic definition of the densities and currents of the conserved quantities being transported (energy, momentum, mass, charge). The first such principle, gauge invariance, allows one to define a quantum adiabatic energy current from density-functional theory, from which the heat conductivity can be uniquely defined and computed using equilibrium ab initio molecular dynamics. When combined with a novel topological definition of atomic oxidation states, gauge invariance also sheds new light onto the mechanisms of charge transport in ionic conductors. The second principle, convective invariance, allows one to extend the analysis to multi-component systems. These invariance principles can be combined with new spectral analysis methods for the current time series to be fed into the Green-Kubo formula to obtain accurate estimates of transport coefficients from relatively short molecular dynamics simulations. Copyright © 2021, The Authors. All rights reserved.

关键词： Molecular dynamics

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Particle-Scale modelling of Injected Hydrogen and Coke Co-Combustion in the Raceway of an Ironmaking Blast Furnace

SSRN

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SSRN 2022年

作者： Dianyu, E. Zhou, Peng Ji, Langyong Cui, Jiaxin Xu, Qiang Guo, Liejin Yu, Aibing International Institute for Innovation Jiangxi University of Science and Technology Ganzhou341000 China Jiangxi Provincial Key Laboratory for Simulation and Modelling of Particulate Systems Jiangxi University of Science and Technology Ganzhou341000 China State Key Laboratory of Multiphase Flow in Power Engineering Xi’an Jiaotong University Xi’an710049 China ARC Research Hub for Computational Particle Technology Department of Chemical Engineering Monash University VIC3800 Australia Centre for Simulation and Modelling of Particulate Systems Southeast University Monash University Joint Research Institute Suzhou215123 China

Hydrogen is an environmentally friendly fuel that does not produce greenhouse gas (GHG) emissions. Its applications have attracted significant attention from many industries, especially the ironmaking industry, which consumes massive amounts of fossil energy. The injection of hydrogen into a blast furnace (BF) is one of the most promising low-carbon ironmaking routines. In this study, an experimentally validated CFD-DEM model is adopted to investigate the dynamics, microstructure and thermochemical behaviours in the raceway of a BF with hydrogen injection operations (HIOs), which include raceway evolution, force distribution and the co-combustion characteristics of hydrogen and coke. Some significant features are obtained through comparison analyses between HIOs and air injection operations (AIOs). In particular, the effects of the hydrogen injection concentration on the raceway size, gas temperature and components are studied. The simulation results show that a smaller raceway is formed under HIOs in comparison with that of AIOs. In addition, the gas temperature is higher near the tuyere but lower along the tuyere axis, and the oxygen consumption is larger and produces more CO. As the hydrogen injection concentration increases: (i) the raceway size and gas temperature decrease;(ii) the CO is generated at the early stage and the maximum CO2 concentration moves to inlet direction along the tuyere axis. The results provide insights on the fundamental understanding of low-carbon ironmaking BF technology. © 2022, The Authors. All rights reserved.

关键词： Blast furnaces

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GPU-enabled molecular dynamics simulations of ankyrin kinase complex

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AIP Conference Proceedings 2014年第1期1621卷 112-115页

作者： Vertika Gautam Wei Lim Chong Tanchanok Wisitponchai Piyarat Nimmanpipug Sharifuddin M. Zain Noorsaadah Abd. Rahman Chatchai Tayapiwatana Vannajan Sanghiran Lee Drug Design and Development Research Group Department of Chemistry Faculty of Science University of Malaya 50603 Lembah Pantai Kuala Lumpur Malaysia Division of Clinical Immunology Department of Medical Technology / Biomedical Technology Research Unit National Center for Genetic Engineering and Biotechnology National Science and Technology Development Agency Faculty of Associated Medical Scie Thailand Computational Simulation Modelling Laboratory (CSML) Department of Chemistry and Center of Excellence for Innovation in Chemistry and Materials Science Research Center Faculty of Science Chiang Mai University Chiang Mai 50200 Thailand Drug Design and Development Research Group Department of Chemistry Faculty of Science University of Malaya 50603 Lembah Pantai Kuala Lumpur Malaysia and Computational Simulation Modelling Laboratory (CSML) Department of Chemistry and Center of E Thailand

The ankyrin repeat (AR) protein can be used as a versatile scaffold for protein–protein interactions. It has been found that the heterotrimeric complex between integrin-linked kinase (ILK), PINCH, and parvin is an essential signaling platform, serving as a convergence point for integrin and growth-factor signaling and regulating cell adhesion, spreading, and migration. Using ILK-AR with high affinity for the PINCH1 as our model system, we explored a structure-based computational protocol to probe and characterize binding affinity hot spots at protein–protein interfaces. In this study, the long time scale dynamics simulations with GPU accelerated molecular dynamics (MD) simulations in AMBER12 have been performed to locate the hot spots of protein-protein interaction by the analysis of the Molecular Mechanics–Poisson-Boltzmann Surface Area/Generalized Born Solvent Area (MM-PBSA/GBSA) of the MD trajectories. Our calculations suggest good binding affinity of the complex and also the residues critical in the binding.

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Peptide docking of HIV-1 p24 with single chain fragment variable (scFv) by CDOCKER algorithm

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AIP Conference Proceedings 2014年第1期1621卷 98-102页

作者： Hana Atiqah Abdul Karim Chatchai Tayapiwatana Piyarat Nimmanpipug Sharifuddin M. Zain Noorsaadah Abdul Rahman Vannajan Sanghiran Lee Drug Design and Development Research Group Department of Chemistry Faculty of Science University of Malaya 50603 Lembah Pantai Kuala Lumpur Malaysia Division of Clinical Immunology Department of Medical Technology / Biomedical Technology Research Unit National Center for Genetic Engineering and Biotechnology National Science and Technology Development Agency Faculty of Associated Medical Scie Thailand Computational Simulation Modelling Laboratory (CSML) Department of Chemistry and Center of Excellence for Innovation in Chemistry and Materials Science Research Center Faculty of Science Chiang Mai University Chiang Mai 50200 Thailand Drug Design and Development Research Group Department of Chemistry Faculty of Science University of Malaya 50603 Lembah Pantai Kuala Lumpur Malaysia and Computational Simulation Modelling Laboratory (CSML) Department of Chemistry and Center of E Thailand

In search for the important residues that might have involve in the binding interaction between the p24 caspid protein of HIV-1 fragment (MET68 - PRO90) with the single chain fragment variable (scFv) of FAB23.5, modern computational chemistry approach has been conducted and applied. The p24 fragment was initially taken out from the 1AFV protein molecule consisting of both light (VL) and heavy (VH) chains of FAB23.5 as well as the HIV-1 caspid protein. From there, the p24 (antigen) fragment was made to dock back into the protein pocket receptor (antibody) by using the CDOCKER algorithm to conduct the molecular docking process. The score calculated from the CDOCKER gave 15 possible docked poses with various docked ligand's positions, the interaction energy as well as the binding energy. The best docked pose that imitates the original antigen's position was determined and further processed to the In Situ minimization to obtain the residues interaction energy as well as to observe the hydrogen bonds interaction in the protein-peptide complex. Based on the results demonstrated, the specific residues in the complex that have shown immense lower interaction energies in the 5Å vicinity region from the peptide are from the heavy chain (VH:TYR105) and light chain (VL: ASN31, TYR32, and GLU97). Those residues play vital roles in the binding mechanism of Antibody-Antigen (Ab-Ag) complex of p24 with FAB23.5.

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Balancing Ventilation Performance and Energy Conservation: An Integrated Multi-Objective Optimization and Preference Decision-Making Model for Optimizing Impinging Jet Ventilation

SSRN

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SSRN 2023年

作者： Dianyu, E. Tan, Cong Li, Jing Shi, Guangsi Liu, Sida Yi, Lei Zhou, Zongyan Cui, Jiaxin Jiangxi Provincial Key Laboratory for Simulation and Modelling of Particulate Systems Jiangxi University of Science and Technology Nanchang330013 China International Institute for Innovation Jiangxi University of Science and Technology Nanchang330013 China ARC Research Hub for Computational Particle Technology Department of Chemical and Biological Engineering Monash University VIC3800 Australia

Balancing the requirements for thermal comfort (TC) and indoor air quality (IAQ) while minimizing energy consumption (EC) is a challenging trade-off problem in impinging jet ventilation (IJV), which has great potential for energy savings. Multi-criteria decision-making (MCDM) technology is a rapid and effective approach to address this issue in response to changing outdoor weather conditions. However, conflicting ventilation performances, such as TC (e.g. DR, PMV), IAQ (e.g. ACE, LMAA) and EC, may present challenges in identifying optimal ventilation parameters. This study therefore proposes an integrated multi-objective optimization (MOO) and MCDM model to overcome this limitation. The former, which yields Pareto solutions, is to maintain ventilation performance indicators with good TC or IAQ standards within an acceptable range (e.g. -0.5 © 2023, The Authors. All rights reserved.

关键词： Energy conservation

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Study on Effects of Operation Parameters on Ventilation Performances for a Floor-Standing Air Conditioner

SSRN

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SSRN 2022年

作者： Dianyu, E. Tan, Cong Li, Jing Liu, Sida Zhou, Zongyan Cui, Jiaxin Yi, Lei Jiangxi Provincial Key Laboratory for Simulation and Modelling of Particulate Systems Jiangxi University of Science and Technology Nanchang330013 China International Institute for Innovation Jiangxi University of Science and Technology Nanchang330013 China ARC Research Hub for Computational Particle Technology Department of Chemical and Biological Engineering Monash University VIC3800 Australia

The floor-standing air conditioners (FSACs) have been widely used in civil and office buildings because of its advantages of high cooling/heating capacity and easy installation. The major challenge of FSACs is to meet the requirements of thermal comfort and indoor air quality (IAQ) while the operation energy consumption should be minimized. This study extensively examines the effects of some key operation parameters on the FSAC performance using validated computational fluid dynamics (CFD) method. The operation parameters include controllable supply vane angle, supply air velocity, supply air temperature, and uncontrollable outdoor weather condition. The main ventilation performance is assessed by indices such as predicted mean vote (PMV), predicted percent dissatisfied (PPD), draught rate (DR), local mean age of air (LMAA), and energy consumption (P system ). The relative importance of the operation parameters for each ventilation performance index is identified through evaluating the individual effects of the operation parameters on the ventilation performance. By comparing the individual effects and combined effects of the operation parameters on the ventilation performance, it is found that the variations of PMV, PPD, DR, LMAA and P system caused by the combined effects can be accounted by the corresponding most important operation parameters by 90.6%, 97.4%, 77.1%, 95.1% and 79.2%, respectively. Additionally, the outdoor weather conditions do not significantly affect DR, PPD and LMAA, but can shift PMV to uncomfortable levels. Finally, the constant-air-volume (CAV) system is recommended for FSACs during the steady stage and a simplified and optimized operation strategy is proposed. © 2022, The Authors. All rights reserved.

关键词： Sensitivity analysis

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O-desmethylquinine as a cyclooxygenase-2 (COX-2) inhibitors using AutoDock Vina

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AIP Conference Proceedings 2014年第1期1621卷 103-107页

作者： Sophi Damayanti Andhika Bintang Mahardhika Slamet Ibrahim Wei Lim Chong Vannajan Sanghiran Lee Daryono Hadi Tjahjono Pharmacochemistry Research Group School of Pharmacy Bandung Institute of Technology Ganesa 10 Bandung 40132 Indonesia Department of Chemistry Faculty of Science University of Malaya Kuala Lumpur 50603 Malaysia Department of Chemistry Faculty of Science University of Malaya Kuala Lumpur 50603 Malaysia and Computational Simulation Modelling Laboratory (CSML) Department of Chemistry and Center of Excellence for Innovation in Chemistry and Materials Scien Thailand

computational approach was employed to evaluate the biological activity of novel cyclooxygenase-2 COX-2 inhibitor, O-desmethylquinine, in comparison to quinine as common inhibitor which can also be used an agent of antipyretic, antimalaria, analgesic and antiinflamation. The molecular models of the compound were constructed and optimized with the density function theory with at the B3LYP/6-31G (d,p) level using Gaussian 09 program. Molecular docking studies of the compounds were done to obtain the COX-2 complex structures and their binding energies were analyzed using the AutoDock Vina. The results of docking of the two ligands were comparable and cannot be differentiated from the energy scoring function with AutoDock Vina.

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