Publications associées à Influence of Long-range Electrostatic Treatments on the Folding of the N-terminal H4 Histone Tail Peptide

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 ...

Royal Soc Chemistry2024

Searching for the Thinnest Metallic Wire

Nicola Marzari, Davide Campi

One-dimensional materials have gained much attention in the last decades: from carbon nanotubes to ultrathin nanowires to few-atom atomic chains, these can all display unique electronic properties and great potential for next-generation applications. Exfol ...

Amer Chemical Soc2024

Stability: a search for structure

Wouter Jongeneel

In this thesis we study stability from several viewpoints. After covering the practical importance, the rich history and the ever-growing list of manifestations of stability, we study the following. (i) (Statistical identification of stable dynamical syste ...

EPFL2024

Stochastic pairwise preference convergence in Bayesian agents

Max-Olivier Hongler

Beliefs inform the behaviour of forward-thinking agents in complex environments. Recently, sequential Bayesian inference has emerged as a mechanism to study belief formation among agents adapting to dynamical conditions. However, we lack critical theory to ...

2024

From Sequence to Dynamics to Function: Computational Design of Allostery and Ligand Selectivity in G-Protein Coupled Receptors

Mahdi Hijazi

The phenomenon of allostery, a general property in proteins that has been heralded as "the second secret of life" remains elusive to our understanding and even more challenging to incorporate into protein design. One example of allosteric proteins with gre ...

EPFL2024

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

Inferring free-energy barriers and kinetic rates from molecular dynamics via underdamped Langevin models

Fabio Pietrucci, Sara Bonella, David Daniel Girardier

Rare events include many of the most interesting transformation processes in condensed matter, from phase transitions to biomolecular conformational changes to chemical reactions. Access to the corresponding mechanisms, free-energy landscapes and kinetic r ...

Aip Publishing2023

Advancing Computational Chemistry with Stochastic and Artificial Intelligence Approaches

Justin Villard

Computational chemistry aims to simulate reactions and molecular properties at the atomic scale, advancing the design of novel compounds and materials with economic, environmental, and societal implications. However, the field relies on approximate quantum ...

EPFL2023

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

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

Yaolong Zhang

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

Spectral and thermodynamic properties of interacting electrons with dynamical functionals

Tommaso Chiarotti

Empowered by ever-increasing computational power and algorithmic developments, electronic-structure simulations continue to drive research and innovation in materials science. In this context, ab-initio calculations offer an unbiased platform for the under ...

EPFL2023

Computational design of dynamic receptor—peptide signaling complexes applied to chemotaxis

Andreas Füglistaler, Aurélien Laurent Jean-Charles Oggier, Mahdi Hijazi, Patrick Daniel Barth, Robert Everett Jefferson, Ana Paola Rico Villarreal

Engineering protein biosensors that sensitively respond to specific biomolecules by triggering precise cellular responses is a major goal of diagnostics and synthetic cell biology. Previous biosensor designs have largely relied on binding structurally well ...

Nature Research2023

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

Temperature- and pressure-dependence of the hydrogen bond network in plastic ice VII

Livia Eleonora Bove Kado, Umbertoluca Ranieri, Maria Rescigno

We model, via classical molecular dynamics simulations, the plastic phase of ice VII across a wide range of the phase diagram of interest for planetary investigations. Although structural and dynamical properties of plastic ice VII are mostly independent o ...

AIP Publishing2022

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

Engineering and characterizing nonclassical states of light in quantum optical networks

Kilian Robert Seibold

The exploration of open quantum many-body systems -systems of microscopic size exhibiting quantum coherence and interacting with their surrounding- has emerged as a key research area over the last years. The recent advances in controlling and preserving qu ...

EPFL2022

Real space and reciprocal space investigations of the spin dynamics in skyrmion-hosting materials

Le Yu

Magnetic skyrmions are whirl-like spin configurations with particle-like properties protected by non-trivial topology. Due to their unique spin structures and dynamical properties, they have attracted tremendous interests over the past decade, from fundame ...

EPFL2022

Dynamical properties of a driven dissipative dimerized S=1/2 chain

Bruce Normand

We consider the dynamical properties of a gapped quantum spin system coupled to the electric field of a laser, which drives the resonant excitation of specific phonon modes that modulate the magnetic interactions. We deduce the quantum master equations gov ...

2021

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

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

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 ...

Springernature2021

Is a Single Conformer Sufficient to Describe the Reorganization Energy of Amorphous Organic Transport Materials?

Anne-Clémence Corminboeuf, Kun-Han Lin, Iwona Swiderska, Hélène Wu, Raimon Fabregat I De Aguilar-Amat, Jacob Terence Blaskovits

The reorganization energy (lambda), which quantifies the structural rearrangement of a molecule when accommodating a charge, is a key parameter in the evaluation of charge mobility in molecular solids. However, it is unclear how lambda is influenced by con ...

AMER CHEMICAL SOC2021