Physics-inspired structural representations for molecules and materials
The first step in the construction of a regression model or a data-driven analysis, aiming to
predict or elucidate the relationship between the atomic-scale structure of matter and its …
predict or elucidate the relationship between the atomic-scale structure of matter and its …
The SIRAH force field: a suite for simulations of complex biological systems at the coarse-grained and multiscale levels
The different combinations of molecular dynamics simulations with coarse-grained
representations have acquired considerable popularity among the scientific community …
representations have acquired considerable popularity among the scientific community …
LiPyphilic: A Python toolkit for the analysis of lipid membrane simulations
Molecular dynamics simulations are now widely used to study emergent phenomena in lipid
membranes with complex compositions. Here, we present LiPyphilic—a fast, fully tested …
membranes with complex compositions. Here, we present LiPyphilic—a fast, fully tested …
Layer-by-layer unsupervised clustering of statistically relevant fluctuations in noisy time-series data of complex dynamical systems
Complex systems are typically characterized by intricate internal dynamics that are often
hard to elucidate. Ideally, this requires methods that allow to detect and classify in an …
hard to elucidate. Ideally, this requires methods that allow to detect and classify in an …
Living supramolecular polymerization of fluorinated cyclohexanes
The development of powerful methods for living covalent polymerization has been a key
driver of progress in organic materials science. While there have been remarkable reports …
driver of progress in organic materials science. While there have been remarkable reports …
Mechanistic understanding from molecular dynamics in pharmaceutical research 2: lipid membrane in drug design
We review the use of molecular dynamics (MD) simulation as a drug design tool in the
context of the role that the lipid membrane can play in drug action, ie, the interaction …
context of the role that the lipid membrane can play in drug action, ie, the interaction …
Classifying soft self-assembled materials via unsupervised machine learning of defects
Unlike molecular crystals, soft self-assembled fibers, micelles, vesicles, etc., exhibit a certain
order in the arrangement of their constitutive monomers but also high structural dynamicity …
order in the arrangement of their constitutive monomers but also high structural dynamicity …
Integrating machine learning in the coarse-grained molecular simulation of polymers
E Ricci, N Vergadou - The Journal of Physical Chemistry B, 2023 - ACS Publications
Machine learning (ML) is having an increasing impact on the physical sciences,
engineering, and technology and its integration into molecular simulation frameworks holds …
engineering, and technology and its integration into molecular simulation frameworks holds …
DADApy: Distance-based analysis of data-manifolds in Python
DADApy is a Python software package for analyzing and characterizing high-dimensional
data manifolds. It provides methods for estimating the intrinsic dimension and the probability …
data manifolds. It provides methods for estimating the intrinsic dimension and the probability …
Detecting dynamic domains and local fluctuations in complex molecular systems via timelapse neighbors shuffling
M Crippa, A Cardellini, C Caruso… - Proceedings of the …, 2023 - National Acad Sciences
It is known that the behavior of many complex systems is controlled by local dynamic
rearrangements or fluctuations occurring within them. Complex molecular systems …
rearrangements or fluctuations occurring within them. Complex molecular systems …