[HTML][HTML] Molecular simulation of nonfacilitated membrane permeation

E Awoonor-Williams, CN Rowley - Biochimica et Biophysica Acta (BBA) …, 2016‏ - Elsevier
This is a review. Non-electrolytic compounds typically cross cell membranes by passive
diffusion. The rate of permeation is dependent on the chemical properties of the solute and …

Molecular dynamics simulation of humic substances

M Orsi - Chemical and Biological Technologies in Agriculture, 2014‏ - Springer
Humic substances (HS) are complex mixtures of natural organic material which are found
almost everywhere in the environment, and particularly in soils, sediments, and natural …

Toward atomistic resolution structure of phosphatidylcholine headgroup and glycerol backbone at different ambient conditions

A Botan, F Favela-Rosales, PFJ Fuchs… - The Journal of …, 2015‏ - ACS Publications
Phospholipids are essential building blocks of biological membranes. Despite a vast amount
of very accurate experimental data, the atomistic resolution structures sampled by the …

Permeability of small molecules through a lipid bilayer: a multiscale simulation study

M Orsi, WE Sanderson, JW Essex - The Journal of Physical …, 2009‏ - ACS Publications
The transmembrane permeation of eight small (molecular weight< 100) organic molecules
across a phospholipid bilayer is investigated by multiscale molecular dynamics simulation …

Effects of lipid composition on bilayer membranes quantified by all-atom molecular dynamics

W Ding, M Palaiokostas, W Wang… - The journal of physical …, 2015‏ - ACS Publications
Biological bilayer membranes typically contain varying amounts of lamellar and nonlamellar
lipids. Lamellar lipids, such as dioleoylphosphatidylcholine (DOPC), are defined by their …

Aggregation of model membrane proteins, modulated by hydrophobic mismatch, membrane curvature, and protein class

DL Parton, JW Klingelhoefer, MSP Sansom - Biophysical journal, 2011‏ - cell.com
Aggregation of transmembrane proteins is important for many biological processes, such as
protein sorting and cell signaling, and also for in vitro processes such as two-dimensional …

Passive membrane permeability: beyond the standard solubility-diffusion model

G Parisio, M Stocchero, A Ferrarini - Journal of Chemical Theory …, 2013‏ - ACS Publications
The spontaneous diffusion of solutes through lipid bilayers is still a challenge for theoretical
predictions. Since permeation processes remain beyond the capabilities of unbiased …

[HTML][HTML] Molecular transport through membranes: Accurate permeability coefficients from multidimensional potentials of mean force and local diffusion constants

R Sun, Y Han, JMJ Swanson, JS Tan… - The Journal of …, 2018‏ - pubs.aip.org
Estimating the permeability coefficient of small molecules through lipid bilayer membranes
plays an important role in the development of effective drug candidates. In silico simulations …

Molecular simulation of the transport of drugs across model membranes

SM Loverde - The journal of physical chemistry letters, 2014‏ - ACS Publications
This Perspective describes recent progress in the area of the molecular simulation of the
interactions of hydrophobic and hydrophilic solutes with membranes. The ability to predict …

Simulations of lipid bilayers using the CHARMM36 force field with the TIP3P-FB and TIP4P-FB water models

F Sajadi, CN Rowley - PeerJ, 2018‏ - peerj.com
The CHARMM36 force field for lipids is widely used in simulations of lipid bilayers. The
CHARMM family of force fields were developed for use with the mTIP3P water model. This …