17 articles for “Molecular Dynamics Simulation”

Research ArticleOpen accessPhrase in the titleMolecular Dynamics Simulation and Analysis of Crystallization System in PVC Tunnel Drain-Pipe at Different TemperaturesZhongwei Hou, Xuefu Zhang, Yuanjiang ZhouAiming at the problem that carbonate and calcium ions are easy to crystallize and precipitate in the drain-pipes of limestone tunnels and then adsorb on PVC pipes in Western China, a "solid-liquid interface model" for the interaction between PVC materials and ions in aqueous solution is established by using the molecular dynamics simulation software materials studio and the microscopic mechanism … …American Journal of Biochemistry and Biotechnology, Vol. 17, Issue 1 · 9 Mar 2021 · 6,279 accessesView PDF Cite

Research ArticleOpen accessPhrase in the titleUnderstanding Material Deformation in Nanoimprint of Gold using Molecular Dynamics SimulationsAbhaysinh Gaikwad, Salil DesaiMaterial deformation in nanoimprinting is explored through Molecular Dynamics (MD) simulations. Understanding the behavior of substrate material during the nanoimprinting process is imperative for high resolution nanoscale pattern transfer. Nanoimprinting of the gold has the potential to make significant impact in diverse areas such as microelectronics and biomedical research. The deformation of gold during nanoimprinting is studied for varying depths … …American Journal of Engineering and Applied Sciences, Vol. 11, Issue 2 · 24 May 2018 · 8,710 accessesView PDF Cite

Research ArticleOpen accessPhrase in the titleDocking and Molecular Dynamics Simulations in Potential Drugs Discovery: An Application to Influenza Virus M2 ProteinMarine E. Bozdaganyan, Philipp S. Orekhov, Nicola L. Bragazzi et al.Molecular docking is a common method for searching new potential drugs. Improvement of the results of docking can be achieved by different ways-one of them is molecular dynamics simulations of protein-ligand complexes. As a model for our research we chose M2 membrane protein from influenza virus. M2 protein is a high selective tetrameric pH-gated proton channel. It was previously shown … …American Journal of Biochemistry and Biotechnology, Vol. 10, Issue 3 · 11 Nov 2014 · 8,669 accessesView PDF Cite

Research ArticleOpen accessPhrase in the titleIdentification of Pharmacological Targets Combining Docking and Molecular Dynamics SimulationsIlizaliturri-Flores Ian, Rosas-Trigueros Jorge Luis, Carrillo-Vazquez Jonathan Pablo et al.Studies that include both experimental data and computational simulations (in silico) have increased in number because the techniques are complementary. In silico methodologies are currently an essential component of drug design; moreover, identification and optimization of the best ligand based on the structures of biomolecules are common scientific challenges. Geometric structural properties of biomolecules explain their behavior and interactions and … …American Journal of Agricultural and Biological Sciences, Vol. 8, Issue 1 · 21 Mar 2013 · 8,128 accessesView PDF Cite

Research ArticleOpen accessPhrase in the titleMolecular Dynamics Simulation of DENV RNA-Dependent RNA-Polymerase with Potential Inhibitor of Disulfide Cyclic PeptideUsman Sumo Friend Tambunan, Raima Syahidah Noors, Arli Aditya Parikesit et al.Problem statement: Our researches have proposed two ligands of disulfide cyclic polypeptide, which are CDEEC and CDGSC as potential inhibitor of DENV RNA-dependent RNApolymerase by molecular docking. Approach: Methodological approach was conducted to determine the best ligand to act as inhibitor. Molecular docking simulation was conducted without a solvent in which enzyme was made rigid and ligand was left free … …OnLine Journal of Biological Sciences, Vol. 11, Issue 2 · 30 Sep 2011 · 8,441 accessesView PDF Cite

Research ArticleOpen accessEvery word in the titleSIMULATION OF NANO-SCALE CUTTING WITH MOLECULAR DYNAMICSAngelos P. Markopoulos, Kalliopi-Artemi L. Kalteremidou, Dimitrios E. ManolakosThe simulation of nanometric cutting of copper with diamond cutting tools, with the Molecular Dynamics method is considered. A 2D model of orthogonal nano-scale cutting is presented and the influence of the depth of cut and tool rake angle on chip morphology and cutting forces is investigated. For the analysis, three different depths of cut, namely 10Å, 15Å and 20Å … …Current Research in Nanotechnology, Vol. 5, Issue 2 · 20 Apr 2015 · 7,369 accessesView PDF Cite

Research ArticleOpen accessIn the keywordsIn-silico Rational Protein Engineering and Design Approach to Improve Thermostability of a Haloalkane Dehalogenase EnzymeRaghunath Satpathy, V. Badireenath Konkimalla, Jagnyeswar RathaThermostability of enzymes is a major prerequisite for use in industrial enzymology. There are as such no simple general principles for achieving thermostability in case of enzymes as many factors are required to fulfil for different enzymes. The present study describes computational methods to design thermostable haloalkane dehalogenase enzyme using the crystal structure available Protein Data Bank (PDB ID: 1EDE). … …Current Research in Bioinformatics, Vol. 4, Issue 2 · 13 Oct 2015 · 8,279 accessesView PDF Cite

Research ArticleOpen accessIn the keywordsIn silico and in vitro Structural Analysis on the Interaction of Calmodulin and Calmodulin-Binding Motif of FKBP35 from Plasmodium knowlesiSazlinawatie Aladin, Cahyo Budiman et al.FK506-binding protein 35 (FKBP35) is a peptidyl-prolyl cis-trans isomerase found in Plasmodium knowlesi, a zoonotic malaria parasite responsible for concerning cases of malaria infection in East Malaysia. This protein contains a segment known as the calmodulin-binding motif (Pk-CBM), which is predicted to facilitate interaction with calmodulin from P. knowlesi (Pk-CaM). Although this interaction is considered promising for future antimalarial drug … …OnLine Journal of Biological Sciences, Vol. 25, Issue 2 · 10 Mar 2025 · 4,846 accessesView PDF Cite

Research ArticleOpen accessIn the abstractUPLC-Q-Exactive Orbitrap-MS Analysis of Anchusa italica Retz. Flowers: Molecular Docking, Dynamics Modeling, and Pharmacokinetics for Cardiovascular DiseaseLinyang Wang, Yan Chen, Ainiwaer Aikemu, Shuge TianThis study builds on prior UPLC-Q-Exactive Orbit rap-MS analyses of Anchusa italica Retz. Flowers (Airfs) to explore their anti-cardiovascular mechanis·ms and key bioactive markers. UPLC-Q-Exactive Orbitrap-MS identified 30 major compounds, including polyphenols and flavonoids with strong antioxidant activity. The potential active ingredients were then screened using Lipinski's rule of five, and a network pharmacology method was employed to construct an … …American Journal of Biochemistry and Biotechnology, Vol. 21, Issue 2 · 25 Oct 2025 · 2,599 accessesView PDF Cite

Research ArticleOpen accessIn the abstractMechanism Analysis of Artemisinin and Artesunate as Lung Cancer Therapy Agents Through in Silico MethodDidik Harmoko, Vivitri Dewi Prasasty, Adi YulandiSeveral in vitro studies have focused on the ability of artemisinin and its derivatives to suppress lung cancer cells, but there are still many biological processes and mechanisms, such as the interactions between the active compounds (ligands) and receptors that are not well understood and require further research. Drug targeting for lung cancer will be more precise and the inhibition … …OnLine Journal of Biological Sciences, Vol. 24, Issue 3 · 15 Feb 2024 · 6,144 accessesView PDF Cite