Molecular dynamics simulation for all

SA Hollingsworth, RO Dror - Neuron, 2018 - cell.com
The impact of molecular dynamics (MD) simulations in molecular biology and drug discovery
has expanded dramatically in recent years. These simulations capture the behavior of …

Water in nanopores and biological channels: a molecular simulation perspective

CI Lynch, S Rao, MSP Sansom - Chemical reviews, 2020 - ACS Publications
This Review explores the dynamic behavior of water within nanopores and biological
channels in lipid bilayer membranes. We focus on molecular simulation studies, alongside …

Water is an active matrix of life for cell and molecular biology

P Ball - Proceedings of the National Academy of Sciences, 2017 - National Acad Sciences
Szent-Győrgi called water the “matrix of life” and claimed that there was no life without it.
This statement is true, as far as we know, on our planet, but it is not clear whether it must …

Bioinspired super‐wettability from fundamental research to practical applications

L Wen, Y Tian, L Jiang - Angewandte Chemie International …, 2015 - Wiley Online Library
Engineered wettability is a traditional, yet key issue in surface science and attracts
tremendous interest in solving large‐scale practical problems. Recently, different super …

Water conduction through the hydrophobic channel of a carbon nanotube

G Hummer, JC Rasaiah, JP Noworyta - nature, 2001 - nature.com
Confinement of matter on the nanometre scale can induce phase transitions not seen in bulk
systems. In the case of water, so-called drying transitions occur on this scale,,, as a result of …

Water as an active constituent in cell biology

P Ball - Chemical reviews, 2008 - ACS Publications
When Szent-Györgyi called water the “matrix of life”, 1 he was echoing an old sentiment.
Paracelsus in the 16th century said that “water was the matrix of the world and of all its …

[HTML][HTML] Hydrophobic gating in ion channels

P Aryal, MSP Sansom, SJ Tucker - Journal of molecular biology, 2015 - Elsevier
Biological ion channels are nanoscale transmembrane pores. When water and ions are
enclosed within the narrow confines of a sub-nanometer hydrophobic pore, they exhibit …

Osmotic water transport through carbon nanotube membranes

A Kalra, S Garde, G Hummer - Proceedings of the National …, 2003 - National Acad Sciences
We use molecular dynamics simulations to study osmotically driven transport of water
molecules through hexagonally packed carbon nanotube membranes. Our simulation setup …

Structure and gating mechanism of the acetylcholine receptor pore

A Miyazawa, Y Fujiyoshi, N Unwin - Nature, 2003 - nature.com
The nicotinic acetylcholine receptor controls electrical signalling between nerve and muscle
cells by opening and closing a gated, membrane-spanning pore. Here we present an atomic …

Imaging α-hemolysin with molecular dynamics: ionic conductance, osmotic permeability, and the electrostatic potential map

A Aksimentiev, K Schulten - Biophysical journal, 2005 - cell.com
Abstract α-Hemolysin of Staphylococcus aureus is a self-assembling toxin that forms a water-
filled transmembrane channel upon oligomerization in a lipid membrane. Apart from being …