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arXiv 2021年

作者： Pols, Mike Vicent-Luna, José Manuel Filot, Ivo van Duin, Adri C.T. Tao, Shuxia Materials Simulation & Modelling Department of Applied Physics Eindhoven University of Technology Eindhoven5600 MB Netherlands Laboratory of Inorganic Materials Chemistry Schuit Institute of Catalysis Department of Chemical Engineering and Chemistry Eindhoven University of Technology P.O. Box 513 Eindhoven5600 MB Netherlands Center for Computational Energy Research Department of Applied Physics Eindhoven University of Technology Eindhoven5600 MB Netherlands Department of Mechanical Engineering Pennsylvania State University University ParkPA16802 United States

Halide perovskites make efficient solar cells due to their exceptional optoelectronic properties, but suffer from several stability issues. The characterization of the degradation processes is challenging because of the limitations in the spatio-temporal resolution in experiments and the absence of efficient computational methods to study the reactive processes. Here, we present the first effort in developing reactive force fields for large scale molecular dynamics simulations of the phase instability and the defect-induced degradation reactions in inorganic CsPbI3. We find that the phase transitions are driven by a combination of the anharmonicity of the perovskite lattice with the thermal entropy. At relatively low temperatures, the Cs cations tend to move away from the preferential positions with good contacts with the surrounding metal halide framework, potentially causing its conversion to a non-perovskite phase. Our simulations of defective structures reveal that, although both iodine vacancies and interstitials are very mobile in the perovskite lattice, the vacancies have a detrimental effect on the stability, initiating the decomposition reactions of perovskites to PbI2. Our work puts ReaxFF forward as an effective computational framework to study reactive processes in halide perovskites. © 2021, CC BY-NC-SA.

关键词： Molecular dynamics

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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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Theoretical study of intermolecular interactions in protic ionic liquids: a single ion pair picture

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Journal of Physics: Conference Series 2021年第1期1719卷

作者： P Nanthanasit N Chattrapiban M Jitvisate P Nimmanpipug S Rimjaem Ph.D. Degree Program in Physics (International Program) Department of Physics and Materials Science Faculty of Science Chiang Mai University Chiang Mai 50200 Thailand Plasma and Beam Physics Research Facility Department of Physics and Materials Science Faculty of Science Chiang Mai University Chiang Mai 50200 Thailand Thailand Center of Excellence in Physics Ministry of Higher Education Science Research and Innovation Bangkok 10400 Thailand The Establishment of Research Center for Quantum Technology Faculty of Science Chiang Mai University Chiang Mai 50200 Thailand Computational Simulation and Modelling Laboratory Faculty of Science and Center of Excellence for Innovation in Analytical Science and Technology Chiang Mai University Chiang Mai 50200 Thailand

Protic ionic liquids are made via intermolecular transfer between cation and anion. This research employs theoretical calculation to gain understanding of the intermolecular interactions at single-ion-pair level and their consequences to the macroscopic properties of the ionic liquids. The protic ionic liquids used in this study are ethylammonium nitrate (EAN), propylammonium nitrate (PAN), and butylammonium nitrate (BAN). Molecular structures of ions and ion pair of each liquid are optimized using the density functional theory. The ion pair binding energies and infrared spectra of optimized structures are investigated. Infrared spectra of separated cation and anion are compared with cation-anion ion pair to specify the vibrational band shifts due to intermolecular interactions. The infrared-spectra show the hydrogen-bond stretching modes in the far-infrared region at the wavenumber between 108-252 cm−1 and the red shifts of four vibrational bands due to intermolecular interactions between the ions. Three vibrational band shifts are mainly due to Coulomb force, and the other shift is caused by combination of intermolecular interactions. Moreover, the energy calculations show that the binding energy decreases as the alkyl chain length increases.

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Verification benchmarks for single-phase flow in three-dimensional fractured porous media

arXiv

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arXiv 2020年

作者： Berre, Inga Boon, Wietse M. Flemisch, Bernd Fumagalli, Alessio Gläser, Dennis Keilegavlen, Eirik Scotti, Anna Stefansson, Ivar Tatomir, Alexandru Brenner, Konstantin Burbulla, Samuel Devloo, Philippe Duran, Omar Favino, Marco Hennicker, Julian Lee, I-Hsien Lipnikov, Konstantin Masson, Roland Mosthaf, Klaus Chiara Nestola, Maria Giuseppina Ni, Chuen-Fa Nikitin, Kirill Schädle, Philipp Svyatskiy, Daniil Yanbarisov, Ruslan Zulianp, Patrick Department of Mathematics University of Bergen Allégaten 41 Bergen5007 Norway Department of Mathematics KTH Royal Institute of Technology Lindstedtsvägen 25 Stockholm11428 Sweden Department of Hydromechanics and Modelling of Hydrosystems University of Stuttgart Pfaffenwaldring 61 Stuttgart70569 Germany Laboratory for Modeling and Scientific Computing MOX Politecnico di Milano p.za Leonardo da Vinci 32 Milano20133 Italy Department of Applied Geology Geosciences Center University of Göttingen Goldschmidtstrasse 3 Göttingen37077 Germany Department of Earth Sciences Uppsala University Villavägen 16 UppsalaS-75236 Sweden University of Côte d’Azur CNRS INRIA LJAD Nice France Institute of Applied Analysis and Numerical Simulation University of Stuttgart Pfaffenwaldring 57 Stuttgart70569 Germany FEC Universidade Estadual de Campinas Cidade Universitária R. Josiah Willard Gibbs 85 Campinas-SPCEP 13083-839 Brazil Institute of Earth Sciences University of Lausanne Building Geopolis UNIL-Mouline Lausanne1015 Switzerland Section de Mathématiques Université de Genève 2-4 rue du Lièvre CP 64 Genève1211 Switzerland Graduate Institute of Applied Geology National Central University Taiwan Center for Environmental Studies National Central University Taiwan Los Alamos National Laboratory New Mexico United States Department of Environmental Engineering Technical University of Denmark Bygningstorvet Building 115 Kgs. Lyngby2800 Denmark Numerical Simulation in Science Medicine and Engineering Group Institute of Computational Science Università della Svizzera italiana. Via G. Buffi 13 Lugano Ticino6900 Switzerland Marchuk Institute of Numerical Mathematics of Russian Academy of Sciences Moscow Russia ETH Zürich Geothermal Energy and Geofluids Group Institute of Geophysics Zürich8092 Switzerland

Flow in fractured porous media occurs in the earth’s subsurface, in biological tissues, and in man-made materials. Fractures have a dominating influence on flow processes, and the last decade has seen an extensive development of models and numerical methods that explicitly account for their presence. To support these developments, we present a portfolio of four benchmark cases for single-phase flow in three-dimensional fractured porous media. The cases are specifically designed to test the methods’ capabilities in handling various complexities common to the geometrical structures of fracture networks. Based on an open call for participation, results obtained with 17 numerical methods were collected. This paper presents the underlying mathematical model, an overview of the features of the participating numerical methods, and their performance in solving the benchmark cases. Copyright © 2020, The Authors. All rights reserved.

关键词： Numerical methods

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Nucleotide binding domain 1 pharmacophore modeling for visualization and analysis of P-glycoprotein-flavonoid molecular interactions

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Frontiers in Biology 2016年第5期11卷 391-395页

作者： Pathomwat Wongrattanakamon Vannajan Sanghiran Lee Piyarat Nimmanpipug Supat Jiranusomkul Laboratory for Molecular Design and Simulation (LMDS) Department of Pharmaceutical Sciences Faculty of Pharmacy Chiang Mai University Chiang Mai 50200 Thailand Department of Chemistry Faculty of Science University of Malaya Kuala Lumpur 50603 Malaysia Computational Simulation and Modelling Laboratory (CSML) Department of Chemistry Faculty of Science Chiang Mai University Chiang Mai 50200 Thailand

BACKGROUND： P-glycoprotein （P-gp） is a 170-kDa membrane protein. It provides a barrier function and help to excrete toxins from the body as a transporter. Some bioflavonoids have been shown to block P-gp activity. OBJECTIVE： To evaluate the important amino acid residues within nucleotide binding domain 1 （NBD l） of P-gp that play a key role in molecular interactions with flavonoids using structure-based pharmacophore model. METHODS： In the molecular docking with NBD 1 models, a putative binding site of flavonoids was proposed and compared with the site for ATP. The binding modes for ligands were achieved using LigandScout to generate the P-gp-flavonoid pharmacophore models. RESULTS： The binding pocket for flavonoids was investigated and found these inhibitors compete with the ATP for binding site in NBD1 including the NBD1 amino acid residues identified by the in silico techniques to be involved in the hydrogen bonding and van der Waals （hydrophobic） interactions with flavonoids. CONCLUSION： These flavonoids occupy with the same binding site of ATP in NBD1 proffering that they may act as an ATP competitive inhibitor.

关键词： P-glycoprotein Nucleotide-binding domain 1 pharmacophore model flavonoid competitive inhibition herb-drug interaction

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Nucleotide-binding domain 1 modelling: A novel molecular docking approach for screening of P-glycoprotein inhibitory activity of bioflavonoids

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Chemical Data Collections 2016年 2卷 10-16页

作者： Pathomwat Wongrattanakamon Vannajan Sanghiran Lee Piyarat Nimmanpipug Supat Jiranusornkul Laboratory for Molecular Design and Simulation (LMDS) Department of Pharmaceutical Sciences Faculty of Pharmacy Chiang Mai University Chiang Mai 50200 Thailand Department of Chemistry Faculty of Science University of Malaya Kuala Lumpur 50603 Malaysia Computational Simulation and Modelling Laboratory (CSML) Department of Chemistry Faculty of Science Chiang Mai University Chiang Mai 50200 Thailand

Modulation of P-glycoprotein (P-gp)’s function may lead to significant changes in the prescription drugs’ pharmacokinetic profiles and increase potential risks in occurring of drug-drug including herb-drug interactions. This computational structured-based study aimed to screen bioflavonoids which play a role in herb-drug interactions as a P-gp inhibitor utilising molecular docking analysis. 25 flavonoids were used as ligands for docking study. The mouse P-gp (code: 4Q9H) was acquired from the Protein Data Bank (PDB). Docking analysis was operated utilising AutoDock 4.2.6. A lowest estimated free energy of binding value in a cluster of each flavonoid against nucleotide-binding domain 1 (NBD1) of P-gp was analysed. The result points out the high correlation between the estimated free energies of binding and percentage of inhibitory efficiency values of flavonoids applied in the molecular modelling that is powerful and capable to predict potential P-gp interactions among flavonoids and its substrates.

关键词： Nucleotide-binding domain 1 P-glycoprotein Flavonoids Molecular docking Herb-drug interactions

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Estimation of inhibitory effect against tyrosinase activity through homology modeling and molecular docking

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Enzyme Research 2015年第1期2015卷 262364页

作者： Nokinsee, Daungkamon Shank, Lalida Lee, Vannajan Sanghiran Nimmanpipug, Piyarat Computational Simulation and Modelling Laboratory (CSML) Department of Chemistry Center of Excellence for Innovation in Chemistry 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 Kuala Lumpur 50603 Malaysia

Tyrosinase is a key enzyme in melanogenesis. Generally, mushroom tyrosinase from A. bisporus had been used as a model in skin-whitening agent tests employed in the cosmetic industry. The recently obtained crystal structure of bacterial tyrosinase from B. megaterium has high similarity (33.5%) to the human enzyme and thus it was used as a template for constructing of the human model. Binding of tyrosinase to a series of its inhibitors was simulated by automated docking calculations. Docking and MD simulation results suggested that N81, N260, H263, and M280 are involved in the binding of inhibitors to mushroom tyrosinase. E195 and H208 are important residues in bacterial tyrosinase, while E230, S245, N249, H252, V262, and S265 bind to inhibitors and are important in forming pi interaction in human tyrosinase. © 2015 Daungkamon Nokinsee et al.

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26th Annual computational Neuroscience Meeting (CNS*2017): Part 3 Antwerp, Belgium. 15-20 July 2017 Abstracts

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BMC NEUROSCIENCE 2017年第SUPPL 1期18卷 95-176页

作者： [Anonymous] Department of Neuroscience Yale University New Haven CT 06520 USA Department Physiology & Pharmacology SUNY Downstate Brooklyn NY 11203 USA NYU School of Engineering 6 MetroTech Center Brooklyn NY 11201 USA Departament de Matemàtica Aplicada Universitat Politècnica de Catalunya Barcelona 08028 Spain Institut de Neurobiologie de la Méditerrannée (INMED) INSERM UMR901 Aix-Marseille Univ Marseille France Center of Neural Science New York University New York NY USA Aix-Marseille Univ INSERM INS Inst Neurosci Syst Marseille France Laboratoire de Physique Théorique et Modélisation CNRS UMR 8089 Université de Cergy-Pontoise 95300 Cergy-Pontoise Cedex France Department of Mathematics and Computer Science ENSAT Abdelmalek Essaadi’s University Tangier Morocco Laboratory of Natural Computation Department of Information and Electrical Engineering and Applied Mathematics University of Salerno 84084 Fisciano SA Italy Department of Medicine University of Salerno 84083 Lancusi SA Italy Dipartimento di Fisica Università degli Studi Aldo Moro Bari and INFN Sezione Di Bari Italy Data Analysis Department Ghent University Ghent Belgium Coma Science Group University of Liège Liège Belgium Cruces Hospital and Ikerbasque Research Center Bilbao Spain BIOtech Department of Industrial Engineering University of Trento and IRCS-PAT FBK 38010 Trento Italy Department of Data Analysis Ghent University Ghent 9000 Belgium The Wellcome Trust Centre for Neuroimaging University College London London WC1N 3BG UK Department of Electronic Engineering NED University of Engineering and Technology Karachi Pakistan Blue Brain Project École Polytechnique Fédérale de Lausanne Lausanne Switzerland Departement of Mathematics Swansea University Swansea Wales UK Laboratory for Topology and Neuroscience at the Brain Mind Institute École polytechnique fédérale de Lausanne Lausanne Switzerland Institute of Mathematics University of Aberdeen Aberdeen Scotland UK Department of Integrativ

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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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