Publication

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

Publications associées (43)

Structure and dynamics of liquid water from ab initio simulations: adding Minnesota density functionals to Jacob's ladder

Ursula Röthlisberger, Justin Villard, Martin Peter Bircher

The accurate representation of the structural and dynamical properties of water is essential for simulating the unique behavior of this ubiquitous solvent. Here we assess the current status of describing liquid water using ab initio molecular dynamics, wit ...

Cambridge2024

cgNA+: A sequence-dependent coarse-grain model of double-stranded nucleic acids

Rahul Sharma

DNA mechanics plays a crucial role in many biological processes, including nucleosome positioning and protein-DNA interactions. It is believed that nature employs epigenetic modifications in DNA to further regulate gene expression. Moreover, double-strande ...

EPFL2023

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

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 ...

2023

Relative, local and global dimension in complex networks

Alexis Arnaudon

Dimension is a fundamental property of objects and the space in which they are embedded. Yet ideal notions of dimension, as in Euclidean spaces, do not always translate to physical spaces, which can be constrained by boundaries and distorted by inhomogenei ...

NATURE PORTFOLIO2022

Sequence-dependent structural properties of B-DNA: what have we learned in 40 years?

John Maddocks, Daiva Petkeviciute, Rahul Sharma, Marco Pasi, Paolo Carloni

The structure of B-DNA, the physiological form of the DNA molecule, has been a central topic in biology, chemistry and physics. Far from uniform and rigid, the double helix was revealed as a flexible and structurally polymorphic molecule. Conformational ch ...

London2021

Coupled dynamical systems are omnipresent in everyday life. In general, interactions between individual elements composing the system are captured by complex networks. The latter greatly impact the way coupled systems are functioning and evolving in time. ...

EPFL2020

A complex networks approach to traffic flow theory: measures and models

Leonardo Bellocchi

In this thesis, we developed a research direction that combines the theoretical concepts of complex networks with practical needs and applications in the field of transportation engineering. As a first objective we analyzed the phenomenon of congestion pr ...

EPFL2020

Quantifying uncertain system outputs via the multilevel Monte Carlo method — Part I: Central moment estimation

Fabio Nobile, Sebastian Krumscheid, Michele Pisaroni

In this work we introduce and analyze a novel multilevel Monte Carlo (MLMC) estimator for the accurate approximation of central moments of system outputs affected by uncertainties. Central moments play a central role in many disciplines to characterize a r ...

2020

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While most models of randomly connected neural networks assume single-neuron models with simple dynamics, neurons in the brain exhibit complex intrinsic dynamics over multiple timescales. We analyze how the dynamical properties of single neurons and recurr ...

2019

Knots are interesting objects to experiment since their topological properties are combined with mechanical properties, fluid mechanics or dynamical properties like unknotting under the excitation of the thermal energy. Knots play also a role in biology be ...

SPRINGER HEIDELBERG2019

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