Water at charged interfaces

G Gonella, EHG Backus, Y Nagata… - Nature Reviews …, 2021 - nature.com
The ubiquity of aqueous solutions in contact with charged surfaces and the realization that
the molecular-level details of water–surface interactions often determine interfacial functions …

Computational modeling of realistic cell membranes

SJ Marrink, V Corradi, PCT Souza, HI Ingolfsson… - Chemical …, 2019 - ACS Publications
Cell membranes contain a large variety of lipid types and are crowded with proteins,
endowing them with the plasticity needed to fulfill their key roles in cell functioning. The …

Lipid21: complex lipid membrane simulations with AMBER

CJ Dickson, RC Walker, IR Gould - Journal of chemical theory and …, 2022 - ACS Publications
We extend the modular AMBER lipid force field to include anionic lipids, polyunsaturated
fatty acid (PUFA) lipids, and sphingomyelin, allowing the simulation of realistic cell …

Life in the lumen: The multivesicular endosome

J Gruenberg - Traffic, 2020 - Wiley Online Library
The late endosomes/endo‐lysosomes of vertebrates contain an atypical phospholipid,
lysobisphosphatidic acid (LBPA)(also termed bis [monoacylglycero] phosphate [BMP]) …

A practical guide to biologically relevant molecular simulations with charge scaling for electronic polarization

E Duboue-Dijon, M Javanainen, P Delcroix… - The Journal of …, 2020 - pubs.aip.org
Molecular simulations can elucidate atomistic-level mechanisms of key biological
processes, which are often hardly accessible to experiment. However, the results of the …

Charge scaling manifesto: A way of reconciling the inherently macroscopic and microscopic natures of molecular simulations

BJ Kirby, P Jungwirth - The journal of physical chemistry letters, 2019 - ACS Publications
Electronic polarization effects play an important role in the interactions of charged species in
biologically relevant aqueous solutions, such as those involving salt ions, proteins, nucleic …

Effective inclusion of electronic polarization improves the description of electrostatic interactions: The prosECCo75 biomolecular force field

R Nencini, C Tempra, D Biriukov… - Journal of Chemical …, 2024 - ACS Publications
prosECCo75 is an optimized force field effectively incorporating electronic polarization via
charge scaling. It aims to enhance the accuracy of nominally nonpolarizable molecular …

Quantitative comparison against experiments reveals imperfections in force fields' descriptions of popc–cholesterol interactions

M Javanainen, P Heftberger, JJ Madsen… - Journal of Chemical …, 2023 - ACS Publications
Cholesterol is a central building block in biomembranes, where it induces orientational
order, slows diffusion, renders the membrane stiffer, and drives domain formation. Molecular …

Molecular dynamics simulations of the effects of lipid oxidation on the permeability of cell membranes

D Wiczew, N Szulc, M Tarek - Bioelectrochemistry, 2021 - Elsevier
The formation of transient pores in their membranes is a well-known mechanism of
permeabilization of cells exposed to high-intensity electric pulses. However, the formation of …

Superlubricity of zwitterionic bottlebrush polymers in the presence of multivalent ions

V Adibnia, M Olszewski, G De Crescenzo… - Journal of the …, 2020 - ACS Publications
In this study, we report lubrication properties of physisorbed zwitterionic bottlebrush
polymers in the presence of multivalent ions using the surface force apparatus. Unlike …