Results 11 to 20 of about 9,251,104 (264)

Molecular Dynamics Simulations of the Breathing Phase Transition of MOF Nanocrystallites II: Explicitly Modeling the Pressure Medium

open access: yesFrontiers in Chemistry, 2021
One of the most investigated properties of porous crystalline metal-organic frameworks (MOFs) is their potential flexibility to undergo large changes in unit cell size upon guest adsorption or other stimuli, referred to as “breathing”.
Larissa Schaper   +2 more
doaj   +1 more source

Deployment-to-dwell metrics and supply-based force sustainment [PDF]

open access: yesJournal of Defense Analytics and Logistics, 2018
Purpose – In the present fast-paced and globalized age of war, special operations forces have a comparative advantage over conventional forces because of their small, highly-skilled units.
Sarah E. Evans, Gregory Steeger
doaj   +1 more source

MutDock: A computational docking approach for fixed-backbone protein scaffold design

open access: yesFrontiers in Molecular Biosciences, 2022
Despite the successes of antibodies as therapeutic binding proteins, they still face production and design challenges. Alternative binding scaffolds of smaller size have been developed to overcome these issues.
Varun M. Chauhan, Robert J. Pantazes
doaj   +1 more source

Comprehensive Evaluation of End-Point Free Energy Techniques in Carboxylated-Pillar[6]arene Host–Guest Binding: III. Force-Field Comparison, Three-Trajectory Realization and Further Dielectric Augmentation

open access: yesMolecules, 2023
Host–guest binding, despite the relatively simple structural and chemical features of individual components, still poses a challenge in computational modelling.
Xiao Liu   +5 more
doaj   +1 more source

Automatically Constructed Neural Network Potentials for Molecular Dynamics Simulation of Zinc Proteins

open access: yesFrontiers in Chemistry, 2021
The development of accurate and efficient potential energy functions for the molecular dynamics simulation of metalloproteins has long been a great challenge for the theoretical chemistry community.
Mingyuan Xu   +6 more
doaj   +1 more source

Probing the Suitability of Different Ca2+ Parameters for Long Simulations of Diisopropyl Fluorophosphatase

open access: yesMolecules, 2021
Organophosphate hydrolases are promising as potential biotherapeutic agents to treat poisoning with pesticides or nerve gases. However, these enzymes often need to be further engineered in order to become useful in practice.
Alexander Zlobin   +3 more
doaj   +1 more source

RNA-protein complexes and force field polarizability

open access: yesFrontiers in Chemistry, 2023
Molecular dynamic (MD) simulations offer a way to study biomolecular interactions and their dynamics at the atomistic level. There are only a few studies of RNA-protein complexes in MD simulations, and here we wanted to study how force fields differ when
Hanna Baltrukevich, Piia Bartos
doaj   +1 more source

Bridging the 12-6-4 Model and the Fluctuating Charge Model

open access: yesFrontiers in Chemistry, 2021
Metal ions play important roles in various biological systems. Molecular dynamics (MD) using classical force field has become a popular research tool to study biological systems at the atomic level.
Pengfei Li
doaj   +1 more source

Force Field for Calculation of the Vapor-Liquid Phase Equilibrium of trans-Decalin

open access: yesChemEngineering, 2023
Based on the TraPPE force field, previously unknown values of the parameters of the intermolecular interaction potential of trans-decalin were determined.
Ivan P. Anashkin, Alexander V. Klinov
doaj   +1 more source

Identifying Systematic Force Field Errors Using a 3D-RISM Element Counting Correction

open access: yesMolecules, 2023
Hydration free energies of small molecules are commonly used as benchmarks for solvation models. However, errors in predicting hydration free energies are partially due to the force fields used and not just the solvation model.
Lizet Casillas   +2 more
doaj   +1 more source

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