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Molecular thermodynamics of metabolism: hydration quantities and the equation-of-state approach

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Publications associées (45)

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Bridging Native and Intrinsic Structures of Microhydrated Biomolecules by Cold Ion Spectroscopy

Andrei Zviagin

Solving native structures of such large molecules, like biomolecules, is often challenging, particularly due to the potentially infinite number of non-covalent interactions with water. In this thesis, we report the use of cold ion gas-phase action spectros ...

EPFL2023

Liposomes and Lipid Droplets Display a Reversal of Charge-Induced Hydration Asymmetry

Sylvie Roke, Nathan Dupertuis, Saranya Pullanchery Sankara Narayanan

The unique properties of water are critical for life. Water molecules have been reported to hydrate cations and anions asymmetrically in bulk water, being a key element in the balance of biochemical interactions. We show here that this behavior extends to ...

Amer Chemical Soc2023

Predicting hot-electron free energies from ground-state data

Michele Ceriotti, Federico Grasselli, Chiheb Ben Mahmoud

Machine-learning potentials are usually trained on the ground-state, Born-Oppenheimer energy surface, which depends exclusively on the atomic positions and not on the simulation temperature. This disregards the effect of thermally excited electrons, that i ...

AMER PHYSICAL SOC2022

Effects of surface wettability on (001)-WO3 and (100)-WSe2: A spin-polarized DFT-MD study

Kevin Sivula

An extensive understanding of WO3 and WSe2 bulk crystalline structures and explicit solvent effects on (001)-WO3 and (100)-WSe2 facets are essential for design of efficient (photo) electrocatalysts. The atomistic level understanding of both WO(3 )and WSe2 ...

ELSEVIER2022

Individual and combined benefits of different nonequilibrium proofreading mechanisms

Paolo De Los Rios, Daniel Maria Busiello, Stefano Zamuner, Adélaïde Alice Mohr

Genome duplication, transcription, and translation are among many crucial cellular processes that need to be performed with high fidelity. However, those extremely low error rates cannot be explained with simple equilibrium thermodynamic considerations. Th ...

Amer Physical Soc2023

Revealing the Structure of Tryptophan in Microhydrated Complexes by Cold Ion Spectroscopy

Oleg Boyarkine, Natalia Nagornova, Manuel Dömer, Andrei Zviagin, Ruslan Yamaletdinov

The geometry of biomolecules isolated in the gas phaseusuallydiffers substantially from their native structures in aqueous solution,which are the only ones truly relevant to life science. To connectthe high resolution of cold ion spectroscopy that can be a ...

2023

A comprehensive framework for hard-magnetic beams: Reduced-order theory, 3D simulations, and experiments

Pedro Miguel Nunes Pereira de Almeida Reis, Dong Yan, Arefeh Abbasi

Thin beams made of magnetorheological elastomers embedded with hard-magnetic particles (hard-MREs) are capable of large deflections under an applied magnetic field. We propose a comprehensive framework, comprising a beam model and 3D finite element modelin ...

PERGAMON-ELSEVIER SCIENCE LTD2022

Spectral Coarse Spaces for the Substructured Parallel Schwarz Method

Tommaso Vanzan

The parallel Schwarz method (PSM) is an overlapping domain decomposition (DD) method to solve partial differential equations (PDEs). Similarly to classical nonoverlapping DD methods, the PSM admits a substructured formulation, that is, it can be formulated ...

2022

Low-Rank Tensor Methods for High-Dimensional Problems

Christoph Max Strössner

In this thesis, we propose and analyze novel numerical algorithms for solving three different high-dimensional problems involving tensors. The commonality of these problems is that the tensors can potentially be well approximated in low-rank formats. Ident ...

EPFL2023

Nonparametric estimation for SDE with sparsely sampled paths: An FDA perspective

Victor Panaretos, Leonardo Vincenzo Santoro, Neda Mohammadi Jouzdani

We consider the problem of nonparametric estimation of the drift and diffusion coefficients of a Stochastic Differential Equation (SDE), based on n independent replicates {Xi(t) : t is an element of [0 , 1]}13 d B(t), where alpha is an element of {0 , 1} a ...

Elsevier2024

Self-Assembly of N-Rich Triimidazoles on Ag(111): Mixing the Pleasures and Pains of Epitaxy and Strain

Ulrich Aschauer, Christian Wäckerlin

In the present report, homochiral hydrogen-bonded assemblies of heavily N-doped (C9H6N6) heterocyclic triimidazole (TT) molecules on an Ag(111) substrate were investigated using scanning tunneling microscopy (STM) and low energy electron diffraction (LEED) ...

Amer Chemical Soc2023

Conservation of Forces and Total Work at the Interface Using the Internodes Method

Simone Deparis

The Internodes method is a general purpose method to deal with non-conforming discretizations of partial differential equations on 2D and 3D regions partitioned into disjoint subdomains. In this paper we are interested in measuring how much the Internodes ...

2022

Stabilized isogeometric discretizations on trimmed and union geometries, and weak imposition of the boundary conditions for the Darcy flow

Riccardo Puppi

Modern manufacturing engineering is based on a ``design-through-analysis'' workflow. According to this paradigm, a prototype is first designed with Computer-aided-design (CAD) software and then finalized by simulating its physical behavior, which usually i ...

EPFL2022

Quadrature-free immersed isogeometric analysis

Pablo Antolin Sanchez, Thibaut Hirschler

This paper presents a novel method for solving partial differential equations on three-dimensional CAD geometries by means of immersed isogeometric discretizations that do not require quadrature schemes. It relies on a newly developed technique for the eva ...

SPRINGER2022

Cryogenic electron tomography to determine thermodynamic quantities for nanoparticle dispersions

Francesco Stellacci, Quy Ong Khac, Paulo Henrique Jacob Silva, Davide Demurtas, Xufeng Xu, Francesca Olgiati, Anna Murello, Ting Mao

Here we present a method to extract thermodynamic quantities for nanoparticle dispersions in solvents. The method is based on the study of tomograms obtained from cryogenic electron tomography (cryoET). The approach is demonstrated for gold nanoparticles ( ...

Royal Society of Chemistry2022

Pivotal Role of Intersite Hubbard Interactions in Fe-Doped alpha-MnO2

Iurii Timrov

We present a first-principles investigation of the structural, electronic, and magnetic properties of the pristine and Fe-doped alpha-MnO2 using density-functional theory with extended Hubbard functionals. The onsite U and intersite V Hubbard parameters ar ...

AMER CHEMICAL SOC2022

Acceleration of gossip algorithms through the Euler-Poisson-Darboux Equation

Raphaël Jean Berthier

Gossip algorithms and their accelerated versions have been studied exclusively in discrete time on graphs. In this work, we take a different approach and consider the scaling limit of gossip algorithms in both large graphs and large number of iterations. T ...

OXFORD UNIV PRESS2022

Analytic modelling of passive microfluidic mixers

Jean-Michel Sallese

This paper deals with a new analytical model for microfluidic passive mixers. Two common approaches already exist for such a purpose. On the one hand, the resolution of the advection-diffusion-reaction equation (ADRE) is the first one and the closest to ph ...

AMER INST MATHEMATICAL SCIENCES-AIMS2022

Mechanistic Insight into Supramolecular Polymerization in Water Tunable by Molecular Geometry

Lukas Pfeifer

Supramolecular self-assembly in water based on non-covalent bonding is attracting major attention due to the potential of hydrogels and aqueous polymers in biomedical applications. Although supramolecular polymerization in organic solvents is well establis ...

CHINESE CHEMICAL SOC2022

Repair or Degrade: the Thermodynamic Dilemma of Cellular Protein Quality-Control

Paolo De Los Rios, Bruno Claude Daniel Fauvet, Satyam Tiwari, Mathieu Rebeaud

Life is a non-equilibrium phenomenon. Owing to their high free energy content, the macromolecules of life tend to spontaneously react with ambient oxygen and water and turn into more stable inorganic molecules. A similar thermodynamic picture applies to th ...

FRONTIERS MEDIA SA2021