Molecular Dynamics Simulation Concept

subject area of

• A conformational landscape for alginate secretion across the outer membrane ofPseudomonas aeruginosa  Journal Articles
• A reactive molecular dynamics study of thermal pyrolysis behavior and mechanisms of lignin during the hydrothermal process: The function of the water molecules  Journal Articles
• A revisit of the two-form kinetic model of prothrombinase: A rebuttal  Journal Articles
• Allosteric pluripotency as revealed by protein kinase A  Journal Articles
• An atomic charge model for graphene oxide for exploring its bioadhesive properties in explicit water  Journal Articles
• Anesthetics significantly increase the amount of intramembrane water in lipid membranes  Journal Articles
• Anomalous and anisotropic nanoscale diffusion of hydration water molecules in fluid lipid membranes  Journal Articles
• Binding of solvated peptide (EPLQLKM) with a graphene sheet via simulated coarse-grained approach  Journal Articles
• Blood bank storage of red blood cells increases RBC cytoplasmic membrane order and bending rigidity  Journal Articles
• Computational Structural Pharmacology and Toxicology of Voltage-Gated Sodium Channels  Chapters
• Computational Study of the Binding Modes of Caffeine to the Adenosine A_2AReceptor  Journal Articles
• Curcumin Protects Membranes through a Carpet or Insertion Model Depending on Hydration  Journal Articles
• Design of Hydrated Porphyrin-Phospholipid Bilayers with Enhanced Magnetic Resonance Contrast  Journal Articles
• Detergent-mediated protein aggregation  Journal Articles
• Distance-Based Configurational Entropy of Proteins from Molecular Dynamics Simulations  Journal Articles
• Divergent allostery reveals critical differences between structurally homologous regulatory domains of Plasmodium falciparum and human protein kinase G  Journal Articles
• Domains on a Sphere: Neutron Scattering, Models, and Mathematical Formalism  Journal Articles
• Drug release by pH-responsive molecular tweezers: Atomistic details from molecular modeling  Journal Articles
• Effect of cholesterol on the lateral nanoscale dynamics of fluid membranes  Journal Articles
• Effects of Cu Ions and Explicit Water Molecules on the Copper Binding Domain of Amyloid Precursor Protein APP(131–189): A Molecular Dynamics Study  Journal Articles
• Elastic properties and line tension of self-assembled bilayer membranes  Journal Articles
• Empirical prediction of protein pK_avalues with residue mutation  Journal Articles
• Erythro-VLPs: Anchoring SARS-CoV-2 spike proteins in erythrocyte liposomes  Journal Articles
• Ethanol enhances collective dynamics of lipid membranes  Journal Articles
• Favorable adsorption of capped amino acids on graphene substrate driven by desolvation effect  Journal Articles
• Hopping of Water in a Glassy Polymer Studied via Transition Path Sampling and Likelihood Maximization  Journal Articles
• Identification of a conserved 8 aa insert in the PIP5K protein in the Saccharomycetaceae family of fungi and the molecular dynamics simulations and structural analysis to investigate its potential functional role  Journal Articles
• Impact of confinement on proteins concentrated in lithocholic acid based organic nanotubes  Journal Articles
• Ionizable amino lipid interactions with POPC: implications for lipid nanoparticle function  Journal Articles
• Lipid Rafts: Buffers of Cell Membrane Physical Properties  Journal Articles
• Mechanism of allosteric inhibition in the Plasmodium falciparum cGMP-dependent protein kinase  Conferences
• Membrane Cholesterol Reduces Polymyxin B Nephrotoxicity in Renal Membrane Analogs  Journal Articles
• Membrane Remodeling by the Lytic Fragment of SticholysinII: Implications for the Toroidal Pore Model  Journal Articles
• Membrane charge and lipid packing determine polymyxin-induced membrane damage  Journal Articles
• Membrane-Modulating Drugs can Affect the Size of Amyloid-β25–35 Aggregates in Anionic Membranes  Journal Articles
• Molecular Dynamics of Fibrinogen Adsorption onto Graphene, but Not onto Poly(ethylene glycol) Surface, Increases Exposure of Recognition Sites That Trigger Immune Response  Journal Articles
• Molecular Mechanism for the (−)-Epigallocatechin Gallate-Induced Toxic to Nontoxic Remodeling of Aβ Oligomers  Journal Articles
• Nonequilibrium molecular dynamics simulation of pressure-driven water transport through modified CNT membranes  Journal Articles
• Nonequilibrium molecular dynamics simulation of water transport through carbon nanotube membranes at low pressure  Journal Articles
• Order and disorder—An integrative structure of the full-length human growth hormone receptor  Journal Articles
• Partitioning of caffeine in lipid bilayers reduces membrane fluidity and increases membrane thickness  Journal Articles
• Prediction of homoprotein and heteroprotein complexes by protein docking and template‐based modeling: A CASP‐CAPRI experiment  Journal Articles
• Protein-Protein Interactions in Membranes  Journal Articles
• Quantum Mechanics/Molecular Mechanics Strategies for Docking Pose Refinement: Distinguishing between Binders and Decoys in CytochromecPeroxidase  Journal Articles
• Reducing deformation anisotropy to achieve ultrahigh strength and ductility in Mg at the nanoscale  Journal Articles
• Role of Dimers in the cAMP-Dependent Activation of Hyperpolarization-Activated Cyclic-Nucleotide-Modulated (HCN) Ion Channels  Journal Articles
• Role of Dynamics in the Autoinhibition and Activation of the Exchange Protein Directly Activated by Cyclic AMP (EPAC)  Journal Articles
• Role of Dynamics in the Autoinhibition and Activation of the Hyperpolarization-activated Cyclic Nucleotide-modulated (HCN) Ion Channels  Journal Articles
• Simulations reveal the role of composition into the atomic-level flexibility of bioactive glass cements  Conferences
• State-dependent inter-repeat contacts of exceptionally conserved asparagines in the inner helices of sodium and calcium channels  Journal Articles
• Steroid–steroid interactions in biological membranes: Cholesterol and cortisone  Journal Articles
• The Effect of Benzannulation on the Structures, Reactivity and Molecular Dynamics of Indenes, Pentalenes, Azulenes and Related Molecules  Journal Articles
• The Effects of Resveratrol, Caffeine, β‐Carotene, and Epigallocatechin Gallate (EGCG) on Amyloid‐β25--35 Aggregation in Synthetic Brain Membranes  Journal Articles
• The Influence of Ser-154, Cys-113, and the Phosphorylated Threonine Residue on the Catalytic Reaction Mechanism of Pin1  Journal Articles
• The Lipid Bilayer Provides a Site for Cortisone Crystallization at High Cortisone Concentrations  Journal Articles
• The Nanostructured Origin of Deformation Twinning  Journal Articles
• The Projection Analysis of NMR Chemical Shifts Reveals Extended EPAC Autoinhibition Determinants  Journal Articles
• The bending rigidity of the red blood cell cytoplasmic membrane  Journal Articles
• The complete N-terminal extension of heparin cofactor II is required for maximal effectiveness as a thrombin exosite 1 ligand  Journal Articles
• The organization of melatonin in lipid membranes  Journal Articles
• Thermal conductivity reduction through isotope substitution in nanomaterials: predictions from an analytical classical model and nonequilibrium molecular dynamics simulations  Journal Articles
• Transient Structural Properties of the Rho GDP-Dissociation Inhibitor.  Journal Articles