Overlay databank unlocks data-driven analyses of biomolecules for all

AM Kiirikki, HS Antila, LS Bort, P Buslaev… - Nature …, 2024 - nature.com
Tools based on artificial intelligence (AI) are currently revolutionising many fields, yet their
applications are often limited by the lack of suitable training data in programmatically …

Pathways to a shiny future: Building the foundation for computational physical chemistry and biophysics in 2050

D Biriukov, R Vácha - ACS Physical Chemistry Au, 2024 - ACS Publications
In the last quarter-century, the field of molecular dynamics (MD) has undergone a
remarkable transformation, propelled by substantial enhancements in software, hardware …

Martini 3 coarse-grained force field for cholesterol

L Borges-Araújo, AC Borges-Araújo… - Journal of Chemical …, 2023 - ACS Publications
Cholesterol plays a crucial role in biomembranes by regulating various properties, such as
fluidity, rigidity, permeability, and organization of lipid bilayers. The latest version of the …

Photophysics in Biomembranes: Computational Insight into the Interaction between Lipid Bilayers and Chromophores

S Osella, S Knippenberg - Accounts of Chemical Research, 2024 - ACS Publications
Conspectus Light is ubiquitously available to probe the structure and dynamics of
biomolecules and biological tissues. Generally, this cannot be done directly with visible light …

[HTML][HTML] Depletion of membrane cholesterol modifies structure, dynamic and activation of Nav1. 7

S Albani, VSB Eswaran, A Piergentili… - International Journal of …, 2024 - Elsevier
Cholesterol is a major component of plasma membranes and plays a significant role in
actively regulating the functioning of several membrane proteins in humans. In this study, we …

Evaluating polarizable biomembrane simulations against experiments

HS Antila, S Dixit, B Kav, JJ Madsen… - Journal of Chemical …, 2024 - ACS Publications
Owing to the increase of available computational capabilities and the potential for providing
a more accurate description, polarizable molecular dynamics force fields are gaining …

Exploring the Properties of Curved Lipid Membranes: Comparative Analysis of Atomistic and Coarse-Grained Force Fields

M Domanska, P Setny - The Journal of Physical Chemistry B, 2024 - ACS Publications
Curvature emerges as a fundamental membrane characteristic crucial for diverse biological
processes, including vesicle formation, cell signaling, and membrane trafficking …

Atherosclerotic Oxidized Lipids Affect Formation and Biophysical Properties of Supported Lipid Bilayers and Simulated Membranes

DE Santa, TP Brown, W Im… - The Journal of Physical …, 2024 - ACS Publications
Oxidized lipids arising from oxidative stress are associated with many serious health
conditions, including cardiovascular diseases. For example, KDdiA-PC and KOdiA-PC are …

Interaction of MRI Contrast Agent [Gd(DOTA)] with Lipid Membranes: A Molecular Dynamics Study

AC Oliveira, HAL Filipe, CFGC Geraldes… - Inorganic …, 2024 - ACS Publications
Contrast agents are important imaging probes in clinical MRI, allowing the identification of
anatomic changes that otherwise would not be possible. Intensive research on the …

Atomic Insights into pH-Dependent and Water Permeation of mRNA-Lipid Nanoparticles

SJ Feng, GW Chu, H Li, JF Chen - Molecular Pharmaceutics, 2025 - ACS Publications
The exposure of mRNA to water is likely to contribute to the instability of RNA vaccines upon
storage under nonfrozen conditions. Using atomistic molecular dynamics (MD) simulations …