The implemented routines analyze the protein environment of water molecules in molecular dynamics (MD) simulations and can ... PyRod: Tracing Water Molecules in Molecular Dynamics Simulations. *David Schaller. David Schaller ... The gathered information is further processed to generate dynamic molecular interaction fields (dMIFs) for visualization and ... interpret dMIFs and purely protein-based pharmacophores that are solely based on tracing water molecules in MD simulations. ...
Molecular dynamics simulations of surface tensions of aqueous electrolytic solutions. Bhatt, D., Newman, J., & Radke, CJ. (2004 ... We present molecular-dynamics (MD) simulations of surface tension of aqueous ionic solutions of different concentrations for ... Molecular dynamics simulations of surface tensions of aqueous electrolytic solutions. Journal of Physical Chemistry B, 108(26 ... is a background dielectric continuum using MD simulations. Compared with explicit water MD simulations, SPM gives qualitatively ...
Efficient relaxation of protein-protein interfaces by discrete molecular dynamics simulations. Journal 2013 ...
Molecular Dynamics simulation of the E.coli FtsZ dimer. View ORCID ProfileVidyalakshmi C Muthukumar ... In a previous simulation study of the M.janaschii dimer it was found that the monomer-monomer contacts in the GDP bound dimer ... Simulations of the dimer were performed with GTP, GDP and ATP. We observed that the C-terminal domain rotates considerably ... We also observed the different dynamics of the GTP, GDP and ATP bound dimers due to which assembly into straight protofilaments ...
Having a precise description of water’s structure is critical to constructing accurate simulations of molecular events, ... Water, water everywhere: Polarization dramatically affects H2O structure revealed through molecular dynamics simulation. ... Gaurav Chopra and Professor Michael Levitt in the Department of Structural Biology used molecular dynamics simulations ... There were many challenges to overcome in designing and implementing QMPFF3-based molecular dynamics simulations especially to ...
Here we use microsecond molecular dynamics simulations to explore the effect of stalk deletion on enzymatic acti … ... Microsecond Molecular Dynamics Simulations of Influenza Neuraminidase Suggest a Mechanism for the Increased Virulence of Stalk- ... Here we use microsecond molecular dynamics simulations to explore the effect of stalk deletion on enzymatic activity, ... We also use these simulations to predict previously unrecognized druggable "hotspots" on the neuraminidase surface that may ...
Molecular Workbench offers 2D and 3D interactive molecular dynamics simulations for teaching physics, chemistry, and biology. ... Molecular Workbench offers 2D and 3D interactive molecular dynamics simulations for teaching physics, chemistry, and biology.. ... Molecular dynamics is a computer simulation technique widely used in academic research to assist scientists to discover new ... Molecular dynamics models can be used as a complementary tool to molecular visualization tools widely used in classrooms, such ...
In this molecular dynamics simulation study we ascertain the dynamics of the glass transition for polymer melts and ionic ... A Molecular Dynamics Simulation Study of Dynamic Processes in Molecular Glass-Forming Liquids. Technische Universität. Ph.D. ... A Molecular Dynamics Simulation Study of Dynamic Processes in Molecular Glass-Forming Liquids ... A Molecular Dynamics Simulation Study of Dynamic Processes in Molecular Glass-Forming Liquids ...
Analyzing molecular dynamics (MD) simulations is a key aspect to understand protein dynamics and function. With increasing ... Analysis of Long Molecular Dynamics Simulations Using Interactive Focus+Context Visualization. dc.contributor.author. Byška, ... Analysis of Long Molecular Dynamics Simulations Using Interactive Focus+Context Visualization. en_US. ... In case studies with different MD simulation data sets and research questions, we found that the proposed visual analysis ...
Complex Revealed by Solid-State NMR and Molecular Dynamics Simulation: Implications for Selective Antibacterial Activity for ... In this work, a combination of molecular dynamics (MD) simulations and solid-state NMR was used to present an atomistic model ... Characterization of the lipid-binding site of equinatoxin II by NMR and molecular dynamics simulation. ... Complex Revealed by Solid-State NMR and Molecular Dynamics Simulation: Implications for Selective Antibacterial Activity. ...
We introduce a molecular dynamics approach to study Aβ dimer formation. 1), We use discrete molecular dynamics simulations of a ... We introduce a molecular dynamics approach to study Aβ dimer formation. 1), We use discrete molecular dynamics simulations of a ... We introduce a molecular dynamics approach to study Aβ dimer formation. 1), We use discrete molecular dynamics simulations of a ... We introduce a molecular dynamics approach to study Aβ dimer formation. 1), We use discrete molecular dynamics simulations of a ...
Dynamical heterogeneities of rotational motion in room temperature ionic liquids evidenced by molecular dynamics simulations ... Dynamical heterogeneities of rotational motion in room temperature ionic liquids evidenced by molecular dynamics simulations ... of rotational motion in room temperature ionic liquids evidenced by molecular dynamics simulations. The Journal of Chemical ... Bonn: Molecular Spectroscopy, MPI for Polymer Research, Max Planck Society, ou_1800285 2ERC Group Hunger: Liquid dynamics, MPI ...
Nonequilibrium molecular dynamics simulation of water transport through carbon nanotube membranes at low pressure Journal ... Nonequilibrium molecular dynamics simulation of pressure-driven water transport through modified CNT membranes Journal Articles ... Distance-Based Configurational Entropy of Proteins from Molecular Dynamics Simulations Journal Articles ... predictions from an analytical classical model and nonequilibrium molecular dynamics simulations Journal Articles ...
Molecular dynamics simulations. The thermal stability of Be5C2 monolayer was evaluated by means of first-principles molecular ... Kresse, G. & Hafner, J. Ab initio molecular dynamics for liquid metals. Phys. Rev. B 47, 558 (1993). ... The structure relaxations during the PSO simulation were performed using Vienna ab initio simulation package at PBE level of ... simulations using a 2 × 2 supercell. Our three simulations at temperature of 1,000, 1,500 and 2,000 K show that Be5C2 monolayer ...
Through molecular dynamics we have analysed the stability of the ISCA1-cryptochrome complex and characterized the interaction ... Molecular dynamics simulations. The stability and dynamics of the ISCA1 and ISCA1-Cry structures were investigated through MD ... Feller, S. E., Zhang, Y., Pastor, R. W. & Brooks, B. R. Constant pressure molecular dynamics simulation: The Langevin piston ... A Universal Program for Multiscale Computer Simulations of Complex Molecular Structure and Dynamics. Journal of Computational ...
... from the relationship between the specific volumes and temperatures after the molecular dynamics experimental simulation. The ... In addition, the bulk modulus of the molecular asphalt model was determined and obtained by applying the infinitesimal strain ... The viscosity data of the molecular asphalt model was calculated using the Muller-Plathe algorithm. The predicted viscosities ... Moreover, the glass transition temperature range of the molecular asphalt model was computed ...
Prediction of EPR spectra of lyotropic liquid crystals using a combination of molecular dynamics simulations and the model-free ... We report the first application of fully atomistic molecular dynamics (MD) simulations to the prediction of the motional ... Prediction of EPR spectra of lyotropic liquid crystals using a combination of molecular dynamics simulations and the model-free ... All-atom MD simulations using the General AMBER Force Field (GAFF) have been performed on sodium dodecyl sulfate (SDS) and ...
In this paper, we propose a structural causal molecular dynamics model (SCMD), the first causality-based framework to model ... simulations describe the mechanical behaviors of molecular systems through empirical approximations of interatomic potentials. ... In the SC-VAE, the encoder and decoder infer the causal structure and temporal dynamics. All components are learned in an end- ... can enjoy a robust and flexible MD simulation model to explicitly capture the long-range and time-dependent movement dynamics. ...
2. Id phrase that more generally as the simulation volume would tend to expand. 3. But can only do so if the ensemble permits ... Could you explain the negative pressures in MD simulation simply by arguing that the force exerted by the container walls is ...
Creative Proteomics provides molecular dynamics simulation services to resolve the motions and biological functions of ... biological macromolecules and protein-small molecule interactions at the molecular level. ... Molecular dynamics (MD) simulation (Lazim et al., 2020). Molecular dynamics has a wide range of applications in the life ... Molecular Dynamics (MD) is one of the most commonly used methods in molecular simulation. Based on molecular force fields, this ...
... elastic characteristics of crossbridge components from their known atomic structures by employing molecular dynamic simulations ... Molecular Dynamics Simulations: Elastic Characteristics of Sub-molecular Structural Elements. Cross-bridge stiffness. Coupling ...
... Xiang LU1,*(. ),Xun CHEN1,Ya-Shun WANG1,Yuan-Yuan TAN1 ... Molecular dynamics (MD) simulations were performed to study the transport properties of gases (oxygen, nitrogen, and methane) ... Molecular Dynamics Simulation of Gas Transport in Amorphous Polyisoprene[J]. Acta Phys. -Chim. Sin. 2016, 32(10), 2523-2530. ... The COMPASS force field was used as the molecular mechanics force field in the simulations. Experimental values of density and ...
Nonequilibrium molecular dynamics simulations provide an efficient way of calculating transport coefficients of molecular ... 588b) Prediction of the Viscosity-Pressure Relation Using Nonequilibrium Molecular Dynamics. Conference ...
Molecular dynamics simulation of graphene growth by surface decomposition of 6H-SiC(0001) and (0001̄). In: Japanese journal of ... Molecular dynamics simulation of graphene growth by surface decomposition of 6H-SiC(0001) and (0001̄). / Iguchi, Ryosuke; ... Iguchi R, Kawamura T, Suzuki Y, Inoue M, Kangawa Y, Kakimoto K. Molecular dynamics simulation of graphene growth by surface ... Iguchi, R., Kawamura, T., Suzuki, Y., Inoue, M., Kangawa, Y., & Kakimoto, K. (2014). Molecular dynamics simulation of graphene ...
Molecular dynamics simulation of C2H2 deposition on diamond (001)-(2×1) surface. W. J. Zhu1, Z. Y. Pan1,2, Y. K. Ho3,1 and Z. Y ... We studied the deposition dynamics of C2H2 molecules on diamond reconstructed (001)-(2×1) surface by molecular dynamics method ... PACS: 79.20.Rf - Atomic, molecular, and ion beam impact and interactions with surfaces / 61.20.Ja - Computer simulation of ...
The results of molecular dynamics simulations showed that the RMSF values of cyclized AGL decreased, indicating that the ... 2.2.7. Molecular Dynamics Simulation of Cyclized α-Glucosidase. Due to the lack of suitable crystal templates, the amino acid ... Molecular Dynamics Simulation Analysis of Cyclized AGL. The three-dimensional models of cyclized AGL were simulated to explore ... The results of molecular dynamics simulations showed that the RMSF values of cyclized AGL decreased, indicating that the ...
"Molecular dynamics simulation of condensed-phase chiral molecular propellers",. abstract = "Molecular dynamics simulations were ... Molecular dynamics simulation of condensed-phase chiral molecular propellers. M. Yoneya*, Y. Tabe, H. Yokoyama. *Corresponding ... Molecular dynamics simulation of condensed-phase chiral molecular propellers. / Yoneya, M.; Tabe, Y.; Yokoyama, H. In: Journal ... Yoneya M, Tabe Y, Yokoyama H. Molecular dynamics simulation of condensed-phase chiral molecular propellers. Journal of Physical ...
Molecular dynamics simulation of palmitoyel - co a hydrolase interaction with fmn ، clofibrate و 2, 4- dichlorophenoxy acetic ... Molecular computational were simulated and were studied. Simulation in the condition that was similar to the physiological ... Then doing the required parameters molecular dynamic from trajectory and extraction simulation and analyzing of results were ... On the palmitoyl - co a hydrolase by codes of 3.1.2.2 and by using of dynamics. ...
Molecular dynamics simulations. To analyze the putative effect of variants on the RAD21 structure, the behavior of the 12 ... variant proteins were compared to that of wild type models by free molecular dynamics (MD) simulation for 60-100 ns (ns) (see ... Molecular Modelling Group, Centro de Biología Molecular Severo Ochoa, CBMSO (CSIC-UAM), Madrid, Spain ... Table 1 Molecular findings of the presently reported series of individuals with RAD21 variants. Full size table. ...