Coarse grained MD simulation of bulk and interfacial behavior of mixture of CTAB/SDS surfactantsMolecular dynamicsSurfactant-surface interactionsCorrosion inhibitorsCoarse-grained simulationsMARTINI force field modelMOLECULAR-DYNAMICS SIMULATIONANIONIC SURFACTANTS...
Residue-level coarse-grained (CG) molecular dynamics (MD) simulation is widely used to investigate slow biological processes that involve multiple proteins, nucleic acids, and their complexes. Biomolecules in a large simulation system are distributed non-uniformly, limiting computational efficiency with co...
Coarse-grained models can be simulated within a MD framework as long as there is sufficient knowledge of the interaction characteristics of the individual beads. Methods have been developed to augment the MD simulation of coarse-grained models, such as the Brownian dynamics method40 and the dissipat...
Similar observations can be made in the field of biomolecular simulation. It would certainly be interesting to use the equations discussed in Section 3.2 in these research contexts in order to have a more controlled approach to coarse-grained non-equilibrium dynamics. In the final section of this...
(ref.22), but the long-time stability of such MD models has not been demonstrated and their great computational expense prevents such models being used to examine capsid self-assembly. Coarse-grained (CG) models using simpler molecular representations34,35provide an appealing alternative; for ...
A coarse-grained (CG) model of polyethylene glycol (PEG) was developed and implemented in CG molecular dynamics (MD) simulations of PEG chains with degree of polymerization (DP) 20 and 40. In the model, two repeat units of PEG are grouped as one CG bead. Atomistic MD simulation of PEG ...
coarse-grained simulation of dna using lammps an implementation of the oxdna model and its applications During the last decade coarse-grained nucleotide models have emerged that allow us to study DNA and RNA on unprecedented time and length scales. Among them is oxDNA, a coarse-grained, sequence...
To help elucidate its mechanism of membrane-lytic activity, we performed a total of 8μs of coarse-grained molecular dynamics (CG-MD) simulations of M1.1 in the presence of zwitterionic phospholipid membranes. Several systems were simulated in which the peptide/lipid ratio was varied. At a low...
Fundamental understanding of mechanisms associated with PEI-based gene delivery can enable systematic and fast design of the carriers including their molecular functionalization. All-atom (AA)42,43,44and coarse-grained (CG)45,46,47,48molecular dynamics (MD) simulations serve as valuable tools in exp...
A potential solution to these issues is to adopt coarse-grained (CG) modeling, which is a well-established framework in protein molecular dynamics (MD) simulation, designed to effectively strike a balance between maintaining essential molecular details and enhancing computational efficiency. CG-scale re...