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Molecular Dynamics Inc explicit solvent models
Explicit Solvent Models, supplied by Molecular Dynamics Inc, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/explicit/dynamics+explicit+gfn2+models+molecular+solvation+xtb+%C2%B7+%C2%B7/pm41872054-564-13-1
Average 86 stars, based on 1 article reviews
explicit solvent models - by Bioz Stars, 2026-10
86/100 stars

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Article Title: Bioinformatics-Guided structural characterization and immunogenicity assessment of multi-epitope vaccine candidates against Zika virus
Article Snippet: Molecular dynamics (MD) simulations were conducted to evaluate the structural stability and dynamic behavior of the multi-epitope vaccine (MEV) in complex with the human Toll-like receptor 3 (TLR3)., , The simulation system was prepared by solvating the complex in an explicit water box using the TIP3P water model, selected for its widespread use and validated accuracy in representing aqueous environments for protein dynamics. .

Article Title: A novel mRNA-based multi-epitope vaccine for rabies virus computationally designed via reverse vaccinology and immunoinformatics.
Article Snippet: Vaccine-TLR4 complex molecular dynamic (MD) simulation To evaluate the dynamic behavior and stability of the docked TLR4–vaccine complex, an explicit all-atom Molecular Dynamics Simulation (MDS) was performed using GROMACS 2023.168, compiled with CUDA support to leverage GPU acceleration.

Article Title: A novel mRNA-based multi-epitope vaccine for rabies virus computationally designed via reverse vaccinology and immunoinformatics
Article Snippet: To evaluate the dynamic behavior and stability of the docked TLR4–vaccine complex, an explicit all-atom Molecular Dynamics Simulation (MDS) was performed using GROMACS 2023.1 , compiled with CUDA support to leverage GPU acceleration.

Article Title: Solvent Effects on the Selectivity of Ambimodal Dipolar/Diels-Alder Cycloadditions: A Study Using Explicit Solvation Models.
Article Snippet: Keywords: explicit solvation models · GFN2-xTB · molecular dynamics · nonequilibrium solvation effects · post-transition state bifurcation [1] D. G. Truhlar, B. C. Garrett, S. J. Klippenstein, J. Phys.

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Article Title: K16F/E22F Mutation Promotes Oligomerization and Alters β-Sheet Topology of Aβ16-22 Peptides: Insights from Molecular Dynamics Simulations.
Article Snippet: .. Accelerated Molecular Dynamics for Peptide Folding: Benchmarking Different Combinations of Force Fields and Explicit Solvent Models. ..

Article Title: Differential Glycosylation does not modulate the Conformational Heterogeneity of Humanised IgGk NIST Monoclonal Antibody
Article Snippet: .. Molecular dynamics simulations Explicit solvent molecular dynamics simulations. .. The proposed NISTmAb structure2 was subjected to explicit solvent molecular dynamics simulations to generate a conformational ensemble as input for the computation of ion moblity spectra using the structure relaxation approximation (SRA, below).

Article Title: Food byproduct-derived as sustainable nano-stabilizers for Pickering emulsions influenced by macronutrient composition.
Article Snippet: We explored how nanoparticle source and concentration affect stability and rheology of fish oil Pickering emulsions (FO-PE).. Nano fish bone (NFB), insoluble okara dietary fiber (IDF), and myofibrillar protein (MFP) nanoparticles (0.5–2.5 %) were fabricated via wet nanosizing and characterized.. NFB-stabilized FO-PE showed the highest stability among three stabilizers, with droplet sizes (D3,2) ranging from 2.08 μm (at 2.5 % NFB) to 2.76 μm (at 0.5 % NFB) and zeta-potential from − 36.66 to − 33.56 mV, attributed to its calcium phosphate crystalline structure forming strong interfacial networks, H-bonds, and electrostatic repulsion, supported by molecular docking.

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Article Title: Food byproduct-derived as sustainable nano-stabilizers for Pickering emulsions influenced by macronutrient composition.
Article Snippet: We explored how nanoparticle source and concentration affect stability and rheology of fish oil Pickering emulsions (FO-PE).. Nano fish bone (NFB), insoluble okara dietary fiber (IDF), and myofibrillar protein (MFP) nanoparticles (0.5–2.5 %) were fabricated via wet nanosizing and characterized.. NFB-stabilized FO-PE showed the highest stability among three stabilizers, with droplet sizes (D3,2) ranging from 2.08 μm (at 2.5 % NFB) to 2.76 μm (at 0.5 % NFB) and zeta-potential from − 36.66 to − 33.56 mV, attributed to its calcium phosphate crystalline structure forming strong interfacial networks, H-bonds, and electrostatic repulsion, supported by molecular docking.

Article Title: Thermodynamic Insights into the WT and Y220C TP53 DBDs Reveals that the Oncogenic Y220C Variant is a Loss of Function Mutation for Zn 2+ -binding at Physiological Temperature
Article Snippet: .. Molecular dynamics (MD) simulations were performed using Cresset Flare v10 software, utilizing the Open Force Field (OpenFF) 2.2.0 with explicit TIP4Pew water molecules. ..



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Flowchart for Abaqus/EXPLICIT secondary development.

Journal: Sensors (Basel, Switzerland)

Article Title: Delamination Localization in CFRP Laminates Using One-Way Mixing of Ultrasonic Guided Waves

doi: 10.3390/s26061912

Figure Lengend Snippet: Flowchart for Abaqus/EXPLICIT secondary development.

Article Snippet: Subsequently, the Abaqus/EXPLICIT kernel is triggered to execute the script command, and the model definitions are then generated into an .inp file.

Techniques:

Flowchart for Abaqus/EXPLICIT secondary development.

Journal: Sensors (Basel, Switzerland)

Article Title: Delamination Localization in CFRP Laminates Using One-Way Mixing of Ultrasonic Guided Waves

doi: 10.3390/s26061912

Figure Lengend Snippet: Flowchart for Abaqus/EXPLICIT secondary development.

Article Snippet: This study employs Python script files to bypass the graphical interface of Abaqus/EXPLICIT, enabling direct interaction with the Abaqus/EXPLICIT software kernel.

Techniques: