Self-assembly, interfacial properties, interactions with macromolecules and molecular modelling and simulation of microbial bio-based amphiphiles (biosurfactants). A …

N Baccile, C Seyrig, A Poirier, S Alonso-de Castro… - Green …, 2021 - pubs.rsc.org
Chemical surfactants are omnipresent in consumer products, but they are the subject of
environmental concerns. For this reason, the complete replacement of petrochemical …

Enhanced sampling molecular dynamics simulations correctly predict the diverse activities of a series of stiff-stilbene G-quadruplex DNA ligands

MP O'Hagan, S Haldar, JC Morales, AJ Mulholland… - Chemical …, 2021 - pubs.rsc.org
Ligands with the capability to bind G-quadruplexes (G4s) specifically, and to control G4
structure and behaviour, offer great potential in the development of novel therapies …

How well does molecular simulation reproduce environment-specific conformations of the intrinsically disordered peptides PLP, TP2 and ONEG?

LM Reid, I Guzzetti, T Svensson, AC Carlsson… - Chemical …, 2022 - pubs.rsc.org
Understanding the conformational ensembles of intrinsically disordered proteins and
peptides (IDPs) in their various biological environments is essential for understanding their …

Exploration and validation of force field design protocols through QM-to-MM mapping

C Ringrose, JT Horton, LP Wang… - Physical Chemistry …, 2022 - pubs.rsc.org
The scale of the parameter optimisation problem in traditional molecular mechanics force
field construction means that design of a new force field is a long process, and sub-optimal …

Catalytic mechanism of the colistin resistance protein MCR-1

R Suardíaz, E Lythell, P Hinchliffe… - Organic & …, 2021 - pubs.rsc.org
The mcr-1 gene encodes a membrane-bound Zn2+-metalloenzyme, MCR-1, which
catalyses phosphoethanolamine transfer onto bacterial lipid A, making bacteria resistant to …

Benchmarking polarizable and non-polarizable force fields for Ca2+–peptides against a comprehensive QM dataset

KS Amin, X Hu, DR Salahub, C Baldauf… - The Journal of …, 2020 - pubs.aip.org
Explicit description of atomic polarizability is critical for the accurate treatment of inter-
molecular interactions by force fields (FFs) in molecular dynamics (MD) simulations aiming …

Ionic liquids and Graphene: The ultimate combination for High-Performance supercapacitors

A Ghahari, H Raissi - Journal of Molecular Liquids, 2024 - Elsevier
Ionic liquids (ILs), due to their tunable propensities and properties, are discussed as a new
class of solvents for scientific and industrial applications. Developing novel processes and …

Resistance to the “last resort” antibiotic colistin: a single-zinc mechanism for phosphointermediate formation in MCR enzymes

E Lythell, R Suardíaz, P Hinchliffe… - Chemical …, 2020 - pubs.rsc.org
MCR (mobile colistin resistance) enzymes catalyse phosphoethanolamine (PEA) addition to
bacterial lipid A, threatening the “last-resort” antibiotic colistin. Molecular dynamics and …

Efficient Interrogation of the kinetic barriers demarcating catalytic states of a tyrosine kinase with optimal physical descriptors and mixture models

P Dutta, N Sengupta - ChemPhysChem, 2023 - Wiley Online Library
Computer simulations are increasingly used to access thermo‐kinetic information underlying
structural transformation of protein kinases. Such information are necessary to probe their …

The automated optimisation of a coarse-grained force field using free energy data

J Caceres-Delpiano, LP Wang… - Physical Chemistry …, 2021 - pubs.rsc.org
Atomistic models provide a detailed representation of molecular systems, but are sometimes
inadequate for simulations of large systems over long timescales. Coarse-grained models …