Light-driven and phonon-assisted dynamics in organic and semiconductor nanostructures

S Kilina, D Kilin, S Tretiak - Chemical reviews, 2015 - ACS Publications
Rapid advances in chemical synthesis and fabrication techniques have led to a boost in
manufacturing and design of novel nanostructured materials that exhibit unique and often …

[HTML][HTML] The good, the bad and the user in soft matter simulations

J Wong-Ekkabut, M Karttunen - Biochimica et Biophysica Acta (BBA) …, 2016 - Elsevier
Molecular dynamics (MD) simulations have become popular in materials science,
biochemistry, biophysics and several other fields. Improvements in computational resources …

Structural basis for directional chitin biosynthesis

W Chen, P Cao, Y Liu, A Yu, D Wang, L Chen… - Nature, 2022 - nature.com
Chitin, the most abundant aminopolysaccharide in nature, is an extracellular polymer
consisting of N-acetylglucosamine (GlcNAc) units. The key reactions of chitin biosynthesis …

Hydrophobicity of arginine leads to reentrant liquid-liquid phase separation behaviors of arginine-rich proteins

Y Hong, S Najafi, T Casey, JE Shea, SI Han… - Nature …, 2022 - nature.com
Intrinsically disordered proteins rich in cationic amino acid groups can undergo Liquid-
Liquid Phase Separation (LLPS) in the presence of charge-balancing anionic counterparts …

Pressure control using stochastic cell rescaling

M Bernetti, G Bussi - The Journal of Chemical Physics, 2020 - pubs.aip.org
Molecular dynamics simulations require barostats to be performed at a constant pressure.
The usual recipe is to employ the Berendsen barostat first, which displays a first-order …

Tinker 8: software tools for molecular design

JA Rackers, Z Wang, C Lu, ML Laury… - Journal of chemical …, 2018 - ACS Publications
The Tinker software, currently released as version 8, is a modular molecular mechanics and
dynamics package written primarily in a standard, easily portable dialect of Fortran 95 with …

i-PI 2.0: A universal force engine for advanced molecular simulations

V Kapil, M Rossi, O Marsalek, R Petraglia… - Computer Physics …, 2019 - Elsevier
Progress in the atomic-scale modeling of matter over the past decade has been tremendous.
This progress has been brought about by improvements in methods for evaluating …

Non-encapsulation approach for high-performance Li–S batteries through controlled nucleation and growth

H Pan, J Chen, R Cao, V Murugesan, NN Rajput… - Nature Energy, 2017 - nature.com
High-surface-area, nanostructured carbon is widely used for encapsulating sulfur and
improving the cyclic stability of Li–S batteries, but the high carbon content and low packing …

Structural basis of outer membrane protein insertion by the BAM complex

Y Gu, H Li, H Dong, Y Zeng, Z Zhang, NG Paterson… - Nature, 2016 - nature.com
All Gram-negative bacteria, mitochondria and chloroplasts have outer membrane proteins
(OMPs) that perform many fundamental biological processes. The OMPs in Gram-negative …

The coupling between stability and ion pair formation in magnesium electrolytes from first-principles quantum mechanics and classical molecular dynamics

NN Rajput, X Qu, N Sa, AK Burrell… - Journal of the American …, 2015 - ACS Publications
In this work we uncover a novel effect between concentration dependent ion pair formation
and anion stability at reducing potentials, eg, at the metal anode. Through comprehensive …