Efficient and feasible biocatalysts: Strategies for enzyme improvement. A review
Owing to the environmental friendliness and vast advantages that enzymes offer in the
biotechnology and industry fields, biocatalysts are a prolific investigation field. However, the …
biotechnology and industry fields, biocatalysts are a prolific investigation field. However, the …
Making the cut: Multiscale simulation of membrane remodeling
J Beiter, GA Voth - Current Opinion in Structural Biology, 2024 - Elsevier
Biological membranes are dynamic heterogeneous materials, and their shape and
organization are tightly coupled to the properties of the proteins in and around them …
organization are tightly coupled to the properties of the proteins in and around them …
[HTML][HTML] Introducing a force-matched united atom force field to explore larger spatiotemporal domains in molecular dynamics simulations of bitumen
This paper presents a United Atom (UA) force field for simulating hydrocarbon molecules in
bituminous materials, integrating explicit hydrogens into beads with their parent atom. This …
bituminous materials, integrating explicit hydrogens into beads with their parent atom. This …
Megamolecule Self-Assembly Networks: A Combined Computational and Experimental Design Strategy
This work describes the use of computational strategies to design megamolecule building
blocks for the self-assembly of lattice networks. The megamolecules are prepared by …
blocks for the self-assembly of lattice networks. The megamolecules are prepared by …
Computational Prediction of Coiled–Coil Protein Gelation Dynamics and Structure
Protein hydrogels represent an important and growing biomaterial for a multitude of
applications, including diagnostics and drug delivery. We have previously explored the …
applications, including diagnostics and drug delivery. We have previously explored the …
K-Means Clustering Coarse-Graining (KMC-CG): A Next Generation Methodology for Determining Optimal Coarse-Grained Map**s of Large Biomolecules
Coarse-grained (CG) molecular dynamics (MD) has become a method of choice for
simulating various large scale biomolecular processes; therefore, the systematic definition of …
simulating various large scale biomolecular processes; therefore, the systematic definition of …
Thermodynamic transferability in coarse-grained force fields using graph neural networks
Coarse-graining is a molecular modeling technique in which an atomistic system is
represented in a simplified fashion that retains the most significant system features that …
represented in a simplified fashion that retains the most significant system features that …
QM/CG-MM: Systematic Embedding of Quantum Mechanical Systems in a Coarse-Grained Environment with Accurate Electrostatics
Quantum Mechanics/Molecular Mechanics (QM/MM) can describe chemical reactions in
molecular dynamics (MD) simulations at a much lower cost than ab initio MD. Still, it is …
molecular dynamics (MD) simulations at a much lower cost than ab initio MD. Still, it is …
There and back again: bridging meso-and nano-scales to understand lipid vesicle patterning
J Cornet, N Coulonges, W Pezeshkian… - Soft Matter, 2024 - pubs.rsc.org
We describe a complete methodology to bridge the scales between nanoscale molecular
dynamics and (micrometer) mesoscale Monte Carlo simulations in lipid membranes and …
dynamics and (micrometer) mesoscale Monte Carlo simulations in lipid membranes and …
Gaussian representation of coarse-grained interactions of liquids: Theory, parametrization, and transferability
Coarse-grained (CG) interactions determined via bottom-up methodologies can faithfully
reproduce the structural correlations observed in fine-grained (atomistic resolution) systems …
reproduce the structural correlations observed in fine-grained (atomistic resolution) systems …