The static and dynamic structural heterogeneities of B-DNA: extending Calladine-Dickerson rules

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Universal machine learning for the response of atomistic systems to external fields

Machine learned interatomic interaction potentials have enabled efficient and accurate molecular simulations of closed systems. However, external fields, which can greatly change the chemical structure and/or reactivity, have been seldom included in curren ...

Nature Portfolio2023

Landscapes of DNA Mechanics and Genomes

Thomas Antonin Zwahlen

The local physical properties - such as shape and flexibility - of the DNA double-helix is today widely believed to be influenced by nucleic acid sequence in a non-trivial way. Furthermore, there is strong evidence that these properties play a role in many ...

EPFL2023

Euclid preparation: XXVIII. Forecasts for ten different higher-order weak lensing statistics

Frédéric Courbin, Gianluca Castignani, Austin Chandler Peel, Jean-Luc Starck, Maurizio Martinelli, Yi Wang, Richard Massey, Fabio Finelli, Marcello Farina

Recent cosmic shear studies have shown that higher-order statistics (HOS) developed by independent teams now outperform standard two-point estimators in terms of statistical precision thanks to their sensitivity to the non-Gaussian features of large-scale ...

EDP SCIENCES S A2023

cgNA plus web : A Visual Interface to the cgNA plus Sequence-dependent Statistical Mechanics Model of Double-stranded Nucleic Acids

John Maddocks, Rahul Sharma, Alessandro Samuele Patelli, Lennart de Bruin

The sequence-dependent statistical mechanics of double-stranded nucleic acid, or dsNA, is believed to be essential in its biological functions. In turn, the equilibrium statistical mechanics behaviour of dsNA depends strongly both on sequence-dependent per ...

Elsevier2023

Low-Temperature Dynamics of Water Confined in Unidirectional Hydrophilic Zeolite Nanopores

Livia Eleonora Bove Kado, Umbertoluca Ranieri, Maria Rescigno

The dynamical properties of water molecules confinedin the unidirectionalhydrophilic nanopores of AlPO4-54 are investigated withquasi-elastic neutron scattering as a function of temperature downto 118 K. AlPO4-54 has among the largest pores known foralumin ...

AMER CHEMICAL SOC2023

Hybrid Quadratic Programming - Pullback Bundle Dynamical Systems Control

Aude Billard, Bernardo Fichera

Dynamical System (DS)-based closed-loop control is a simple and effective way to generate reactive motion policies that well generalize to the robotic workspace, while retaining stability guarantees. Lately the formalism has been expanded in order to handl ...

SPRINGER INTERNATIONAL PUBLISHING AG2023

Higher-order organization of multivariate time series

Enrico Amico, Andrea Santoro

Time series analysis has proven to be a powerful method to characterize several phenomena in biology, neuroscience and economics, and to understand some of their underlying dynamical features. Several methods have been proposed for the analysis of multivar ...

NATURE PORTFOLIO2023

Advancing first principle-based molecular dynamics of biological systems with machine learning

François Louis Mouvet

Molecular dynamics (MD) simulations have emerged as a transformative approach to analyse molecular systems at the atomic level, offering valuable insights into complex biological processes. Many biological phenomena can only accurately be described by inco ...

EPFL2023

A Geometric Transformer for Structural Biology: Development and Applications of the Protein Structure Transformer

Lucien Fabrice Krapp

Proteins, the central building blocks of life, play pivotal roles in nearly every biological function. To do so, these macromolecular structures interact with their surrounding environment in complex ways, leading to diverse functional behaviors. The predi ...

EPFL2023

Fast viral dynamics revealed by microsecond time-resolved cryo-EM

Marcel Drabbels, Ulrich Lorenz, Sarah Victoria Barrass, Oliver Florian Harder

Observing proteins as they perform their tasks has largely remained elusive, which has left our understanding of protein function fundamentally incom- plete. To enable such observations, we have recently proposed a technique that improves the time resoluti ...

Nature Research2023

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cgNA plus web : A Visual Interface to the cgNA plus Sequence-dependent Statistical Mechanics Model of Double-stranded Nucleic Acids

John Maddocks, Rahul Sharma, Alessandro Samuele Patelli, Lennart de Bruin

Elsevier2023