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Network thermodynamics in the post-genomic era

Related publications (193)

Experimental Method to Distinguish between a Solution and a Suspension

Francesco Stellacci, Paulo Henrique Jacob Silva, Quy Ong Khac, Xufeng Xu, Ting Mao

Dispersion of objects in a fluid phase can be classified as solutions (Gibbs free energy of mixing, Delta G(mix) < 0) or suspensions (Delta G(mix) > 0) depending on their thermodynamic stability. Small objects tend to form solutions, larger ones suspension ...

WILEY2022

Thermalization and hydrodynamics of two-dimensional quantum field theories

Matthew Thomas Walters

We consider 2d QFTs as relevant deformations of CFTs in the thermodynamic limit. Using causality and KPZ universality, we place a lower bound on the timescale characterizing the onset of hydrodynamics. The bound is determined parametrically in terms of the ...

2022

Uncertainty estimation for molecular dynamics and sampling

Michele Ceriotti, Federico Grasselli, Yongbin Zhuang, Venkat Kapil, Kevin Rossi, Edgar Albert Engel, Giulio Imbalzano

Machine-learning models have emerged as a very effective strategy to sidestep time-consuming electronic-structure calculations, enabling accurate simulations of greater size, time scale, and complexity. Given the interpolative nature of these models, the r ...

2021

A genome-scale metabolic model of Saccharomyces cerevisiae that integrates expression constraints and reaction thermodynamics

Vassily Hatzimanikatis, Ljubisa Miskovic, Maria Masid Barcon, Mohammadomid Oftadeh, Pierre Guy Rémy Salvy

Eukaryotic organisms play an important role in industrial biotechnology, from the production of fuels and commodity chemicals to therapeutic proteins. To optimize these industrial systems, a mathematical approach can be used to integrate the description of ...

NATURE PORTFOLIO2021

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

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

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

Equilibrium and non-equilibrium furanose selection in the ribose isomerisation network

Paolo De Los Rios, Daniel Maria Busiello, Shiling Liang, Francesco Piazza

The exclusive presence of beta -D-ribofuranose in nucleic acids is still a conundrum in prebiotic chemistry, given that pyranose species are substantially more stable at equilibrium. However, a precise characterisation of the relative furanose/pyranose fra ...

NATURE RESEARCH2021

Fluctuation-dissipation relations in the absence of detailed balance: formalism and applications to active matter

Ignacio Pagonabarraga Mora, Sara Dal Cengio

We present a comprehensive study about the relationship between the way detailed balance is broken in non-equilibrium systems and the resulting violations of the fluctuation-dissipation theorem. Starting from stochastic dynamics with both odd and even vari ...

IOP PUBLISHING LTD2021

Dissipation-driven selection of states in non-equilibrium chemical networks

Paolo De Los Rios, Daniel Maria Busiello, Shiling Liang, Francesco Piazza

Life has most likely originated as a consequence of processes taking place in non-equilibrium conditions (e.g. in the proximity of deep-sea thermal vents) selecting states of matter that would have been otherwise unfavorable at equilibrium. Here we present ...

2021

Aggregation of discoidal particles due to depletion interaction

Depletion interactions between colloids of discoidal shape can induce their self-assembly into columnar aggregates. This is an effect of entropic origin with important implications in a range of colloidal systems, particularly in the clustering of erythroc ...

2021

On the necessity of including vapor kinetics to model the specific surface area evolution in snow

Michael Lehning, Henning Löwe

Vapor fluxes in snow are often inferred from the temperature field by assuming vapor concentrations in local thermodynamic equilibrium with the temperature. Here we give evidence that, at the pore scale, this picture is in clear contradiction with the obse ...

2021

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