Mesoscale simulations: an indispensable approach to understand biomembranes
AL Duncan, W Pezeshkian - Biophysical Journal, 2023 - cell.com
Computer simulation techniques form a versatile tool, a computational microscope, for
exploring biological processes. This tool has been particularly effective in exploring different …
exploring biological processes. This tool has been particularly effective in exploring different …
[HTML][HTML] Deciphering photoreceptors through atomistic modeling from light absorption to conformational response
In this review, we discuss the successes and challenges of the atomistic modeling of
photoreceptors. Throughout our presentation, we integrate explanations of the primary …
photoreceptors. Throughout our presentation, we integrate explanations of the primary …
A new paradigm for molecular dynamics databases: the COVID-19 database, the legacy of a titanic community effort
D Beltrán, A Hospital, JL Gelpí… - Nucleic Acids …, 2024 - academic.oup.com
Molecular dynamics (MD) simulations are keeping computers busy around the world,
generating a huge amount of data that is typically not open to the scientific community …
generating a huge amount of data that is typically not open to the scientific community …
There and back again: bridging meso-and nano-scales to understand lipid vesicle patterning
J Cornet, N Coulonges, W Pezeshkian… - Soft Matter, 2024 - pubs.rsc.org
We describe a complete methodology to bridge the scales between nanoscale molecular
dynamics and (micrometer) mesoscale Monte Carlo simulations in lipid membranes and …
dynamics and (micrometer) mesoscale Monte Carlo simulations in lipid membranes and …
Embracing exascale computing in nucleic acid simulations
This mini-review reports the recent advances in biomolecular simulations, particularly for
nucleic acids, and provides the potential effects of the emerging exascale computing on …
nucleic acids, and provides the potential effects of the emerging exascale computing on …
Using interactive Jupyter Notebooks and BioConda for FAIR and reproducible biomolecular simulation workflows
Interactive Jupyter Notebooks in combination with Conda environments can be used to
generate FAIR (Findable, Accessible, Interoperable and Reusable/Reproducible) …
generate FAIR (Findable, Accessible, Interoperable and Reusable/Reproducible) …
Performance Modeling of Inline Compression with Software Caching for Reducing the Memory Footprint in pySDC
S Ranjan - 2023 - search.proquest.com
Modern HPC applications compute and analyze massive amounts of data. The data volume
is growing faster than memory capabilities and storage improvements leading to …
is growing faster than memory capabilities and storage improvements leading to …
Water-Glycan Interactions Drive the SARS-CoV-2 Spike Dynamics: Insights into Glycan-Gate Control and Camouflage Mechanisms
To develop therapeutic strategies against COVID-19, we introduce a high-resolution all-
atom polarizable model capturing many-body effects of protein, glycans, solvent, and …
atom polarizable model capturing many-body effects of protein, glycans, solvent, and …
Recent Advances in Modeling Membrane β-Barrel Proteins Using Molecular Dynamics Simulations: From Their Lipid Environments to Their Assemblies
Spurred by advances in AI-driven modeling and experimental methods, molecular dynamics
simulations are now acting as a platform to integrate these different approaches. This …
simulations are now acting as a platform to integrate these different approaches. This …
Check Chapter 19 updates
AL Duncan, Y Gao, E Haanappel, W Im… - … [beta]-barrel Proteins …, 2024 - books.google.com
Spurred by advances in AI-driven modeling and experimental methods, molecular dynamics
simulations are now acting as a platform to integrate these different approaches. This …
simulations are now acting as a platform to integrate these different approaches. This …