Carbon nanodots from an in silico perspective

F Mocci, L de Villiers Engelbrecht, C Olla… - Chemical …, 2022 - ACS Publications
Carbon nanodots (CNDs) are the latest and most shining rising stars among
photoluminescent (PL) nanomaterials. These carbon-based surface-passivated …

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 …

Lipid14: the amber lipid force field

CJ Dickson, BD Madej, ÅA Skjevik… - Journal of chemical …, 2014 - ACS Publications
The AMBER lipid force field has been updated to create Lipid14, allowing tensionless
simulation of a number of lipid types with the AMBER MD package. The modular nature of …

Derivation and systematic validation of a refined all-atom force field for phosphatidylcholine lipids

JPM Jämbeck, AP Lyubartsev - The journal of physical chemistry …, 2012 - ACS Publications
An all-atomistic force field (FF) has been developed for fully saturated phospholipids. The
parametrization has been largely based on high-level ab initio calculations in order to keep …

Mechanism of activation of protein kinase JAK2 by the growth hormone receptor

AJ Brooks, W Dai, ML O'Mara, D Abankwa, Y Chhabra… - Science, 2014 - science.org
Introduction Class I cytokines regulate key processes such as growth, lactation,
hematopoiesis, and immune function and contribute to oncogenesis. Although the …

Receptor-mediated endocytosis of nanoparticles of various shapes

R Vácha, FJ Martinez-Veracoechea, D Frenkel - Nano letters, 2011 - ACS Publications
Cellular uptake through endocytosis is crucial for drug delivery and nanomedicine.
However, the conditions under which passive endocytosis (ie, not ATP driven) takes place …

An extension and further validation of an all-atomistic force field for biological membranes

JPM Jambeck, AP Lyubartsev - Journal of chemical theory and …, 2012 - ACS Publications
Biological membranes are versatile in composition and host intriguing molecular processes.
In order to be able to study these systems, an accurate model Hamiltonian or force field (FF) …

Mesoscopic simulation of cell membrane damage, morphology change and rupture by nonionic surfactants

RD Groot, KL Rabone - Biophysical journal, 2001 - cell.com
A new simulation method, dissipative particle dynamics, is applied to model biological
membranes. In this method, several atoms are united into a single simulation particle. The …

The different interactions of lysine and arginine side chains with lipid membranes

L Li, I Vorobyov, TW Allen - The journal of physical chemistry B, 2013 - ACS Publications
The basic amino acids lysine (Lys) and arginine (Arg) play important roles in membrane
protein activity, the sensing of membrane voltages, and the actions of antimicrobial, toxin …

Effect of lipid peroxidation on the properties of lipid bilayers: a molecular dynamics study

J Wong-Ekkabut, Z Xu, W Triampo, IM Tang… - Biophysical journal, 2007 - cell.com
Lipid peroxidation plays an important role in cell membrane damage. We investigated the
effect of lipid peroxidation on the properties of 1-palmitoyl-2-linoleoyl-sn-glycero-3 …