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37 articles for “molecular dynamics”
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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 PDFCite
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 PDFCite
Research ArticleOpen accessPhrase 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 PDFCite
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 PDFCite
Research ArticleOpen accessPhrase in the titleHOMOLOGY MODELING AND MOLECULAR DYNAMICS STUDIES OF EC1 DOMAIN OF VE-CADHERIN TO ELUCIDATE DOCKING INTERACTION WITH CADHERIN-DERIVED PEPTIDEVivitri Dewi Prasasty, Usman Sumo Friend Tambunan, Teruna Jaya SiahaanVE-cadherin is a protein in the cadherin family that is found at the adherens junctions of the microvessel endothelial cells of the Blood-Brain Barrier (BBB). It is recognized as the homotypic cell adhesion molecules and there is limited structural information on how VE-cadherins mediate cell-cell adhesion. It has been shown that the EC1 domain of cadherins is important for the … …OnLine Journal of Biological Sciences, Vol. 14, Issue 2 · 25 Jun 2014 · 7,530 accessesView PDFCite
Research ArticleOpen accessPhrase in the titleStructural Consequences of the Polymorphism Q223R in the Human Leptin Receptor: A Molecular Dynamics StudyJonathan P. Carrillo-Vázquez, Brenda Chimal-Vega, Beatriz Zamora-López et al.Leptin Receptor (LEPR) is a component of a signaling pathway related to appetite and energy expenditure. Single Nucleotide Polymorphisms (SNP) of Leptin receptor gene (lepr) have been proposed as possible modulator of adipose tissue and body weight. The main phenomenological consequence reported of these SNPs is the modulation of the LEP-LEPR interaction promoting the weight gain. Particularly, Q223R polymorphism has … …American Journal of Agricultural and Biological Sciences, Vol. 8, Issue 3 · 23 Sep 2013 · 7,835 accessesView PDFCite
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 PDFCite
Research ArticleOpen accessPhrase in the titleMolecular Dynamics Investigation of Cutting Force in Nanometric Cutting of Monocrystalline SiliconY.H. Chen, F.Z. Fang, X.D. Zhang, X.T. HuProblem statement: Ultra-precision machining of monocrystalline silicon has become tremendously important in microelectronic, micromechanical and optical element manufacturing and the mechanism of nanometric cutting monocrystalline silicon has been a focused research topic. Molecular Dynamics (MD) simulation is developed as an effective way for studying the material removal process at nanometric scale. Approach: Molecular Dynamics (MD) simulation of nanometric cutting is … …Current Research in Nanotechnology, Vol. 1, Issue 2 · 21 Jun 2011 · 8,403 accessesView PDFCite
Research ArticleOpen accessPhrase in the titleMolecular Dynamics Studies of Human β-GlucuronidaseIbrahim Ali Noorbatcha, Ayesha Masrur Khan, Hamzah Mohd SallehProblem statement: The enzyme β-glucuronidase is being used as a reporter molecule in the area of genetic engineering, as a component of prodrug therapy in cancer treatment and in the scouring process of cotton fabrics. However, a detailed understanding of the factors responsible for the stability and the activity of this enzyme is still not available. Molecular Dynamics (MD) simulations … …American Journal of Applied Sciences, Vol. 7, Issue 6 · 30 Jun 2010 · 7,613 accessesView PDFCite
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 PDFCite