Coarse-grained (CG) modeling is one of the possible solutions to fill these gaps. CG modeling does not consider all atoms in a system, but the "pseudo-atoms" or "grains", approximating groups of these atoms. This allows a significant reduction in the number of considered interactions and ...
2.2 Coarse-grained modeling The Coarse-grained models are used to gain a better understanding of the linear elastic properties of certain materials. Usually, they are applied to molecular structures where groupings or clusters are present. These groupings are represented as a single entity in the ...
Here, molecular modeling and simulations are used to study the coacervation and stabilization of the relevant polyelectrolyte mixture, systematically investigating the structural and dynamic properties that lead to stability. Atanu Baksi Hasan Zerze Gül H. Zerze ResearchOpen Access30 Sept 2024 ...
Coarse-grained approaches, in which groups of atoms are represented by single interaction sites, are very important in biological and materials sciences because they enable us to cover the size- and time-scales by several orders of magnitude larger than those available all-atom simulations, while ...
Coarse-grained modeling The numerical solution of the master equations, whereby the dynamics of each internal energy state is captured via the direct solution of the corresponding mass conservation equations, is often impractically expensive. Moreover, it is usually not required since the internal ener...
Chu JW, Izvekov S, Voth GA (2006) The multiscale challenge for biomolecular systems: coarse-grained modeling. Mol Simulat 32, 211-218.J.W. Chu, S. Izveko, G.A. Voth, The multiscale challenge for biomolecular sys- tems: Coarse-grained modeling, Mol. Simul. 32 (3) (2009) 211-218...
In this study, coarse-grained (CG) molecular dynamics (MD) simulations were used to study these properties of a polymer-drug construct in potential clinical development: poly(γ-glutamyl-glutamate)-paclitaxel-poly(ethylene glycol) nonpeptide RGD (PGG-PTX-PEG-npRGD), a linear glutamyl-glutamate ...
Recent successes in coarse‐grained modeling of DNA The growing interest in the DNA-based mesoscale systems of biological and nonbiological nature has encouraged the computational molecular science community... DA Potoyan,A Savelyev,GA Papoian - 《Wiley Interdisciplinary Reviews Computational Molecular Sc...
In this method, each molecule in the polymer chain is coarse-grained and the polymer is represented as a chain of connected beads. It is modeled as a sphere of a defined mass that repels each other via the Weeks-Chandler-Anderson potential. Common coarse-graining methods include the finite-...
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...