The statistical associating fluid theory (SAFT‐γ$gamma$ Mie) model is used to correlate the thermophysical properties of oligomers and generate robust and transferrable coarse‐grained (CG) molecular parameters which can be used both in particle based molecular simulations and in equations of state ...
Coarse-grained molecular simulations of the processes of nanoparticles penetrating an asymmetric lipid bilayernanoparticlelipid bilayerpenetrationcoarse-grained molecular dynamicsWith the rapid development of nanotechnologies,nanoparticles (NPs) find widespread application in various areas,ranging from the...
Molecular mechanisms for the fusion of two droplets The fusion of phase-separated liquid-like droplets is an important mechanism for maintaining stable cellular environments when the concentration of components changes53. The residue-level CG MD simulations13,14,37 allow the investigation of inter-mole...
Through molecular dynamics simulations over a range of ELP-ELP interaction strengths, it was determined that ELP-CLP conjugates with multiple ELP strands conjugated to the CLP rigid body undergo the onset of aggregation at a lower ELP-ELP interaction strength than a corresponding system of ELP ...
IBIsCO is a parallel molecular dynamics simulation package developed specially for coarse-grained simulations with numerical potentials derived by the iterative Boltzmann inversion (IBI) method (Reith et al., J Comput Chem 2003, 24, 1624). In addition to common features of molecular dynamics programs...
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 ...
simulationsmolecularrecognitionCoarse-grained molecular dynamics (CGMD) simulation technique (MARTINI force field) is applied to monitor the aggregation of helical peptides representing the transmembrane sequence and its extension of bone marrow stromal cell antigen 2 (BST-2). One of the peptides is ...
Convergence was checked against additional shorter simulations with twofold- and fourfold-smaller time and space steps. Table 1. Particle distribution and properties for virtual cytoplasm Molecular mass range (kDa)Weight fraction (%)Average molecular mass (kDa)Radius (nm)D (μm2/s) 0–20 0.7 ...
Molecular PhysicsYamashita, K. and Daiguji, H.: Coarse-grained molecular dynamics simulations of capillary evaporation of water confined indoi: 10.1021/jp5088493, 2015. Yamashita, K. and Daiguji, H.: Coarse-grained molecular dynamics simulations of capillary evaporation of water confined in ...
We describe here raaSAFT, a Python code that enables the setup and running of coarse-grained molecular dynamics simulations in a systematic and efficient manner. The code is built on top of the popular HOOMD-blue code, and as such harnesses the computational power of GPUs. The methodology make...