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Non-equilibrium kinetics and trajectory thermodynamics of synthetic molecular pumps

Publications associées (69)

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Efficient conversion of chemical energy into mechanical work by Hsp70 chaperones

Paolo De Los Rios, Alessandro Barducci, Salvatore Assenza, Alberto Stefano Sassi

Hsp70 molecular chaperones are abundant ATP-dependent nanomachines that actively reshape non-native, misfolded proteins and assist a wide variety of essential cellular processes. Here, we combine complementary theoretical approaches to elucidate the struct ...

2019

Hyperaccurate currents in stochastic thermodynamics

Daniel Maria Busiello

Thermodynamic observables of mesoscopic systems can be expressed as integrated empirical currents. Their fluctuations are bound by thermodynamic uncertainty relations. We introduce the hyperaccurate current as the integrated empirical current with the leas ...

AMER PHYSICAL SOC2019

Entropy production in master equations and Fokker-Planck equations: facing the coarse-graining and recovering the information loss

Daniel Maria Busiello, Amos Maritan

Systems operating out of equilibrium exchange energy and matter with the environment, thus producing entropy in their surroundings. Since the entropy production depends on the current flowing throughout the system, its quantification is affected by the lev ...

2019

Chaperones convert the energy from ATP into the nonequilibrium stabilization of native proteins

Paolo De Los Rios, Alessandro Barducci, Pierre Goloubinoff, Bruno Claude Daniel Fauvet, Alberto Stefano Sassi

During and after protein translation, molecular chaperones require ATP hydrolysis to favor the native folding of their substrates and, under stress, to avoid aggregation and revert misfolding. Why do some chaperones need ATP, and what are the consequences ...

2018

A comparison of Redlich-Kister polynomial and cubic spline representations of the chemical potential in phase field computations

Anirudh Raju Natarajan

Free energies play a central role in many descriptions of equilibrium and non-equilibrium properties of solids. Continuum partial differential equations (PDEs) of atomic transport, phase transformations and mechanics often rely on first and second derivati ...

Elsevier2017

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The combination of spectroscopic and diffraction methods to study chemical transformations is fundamental for the understanding of reaction mechanisms. The identification of short-lived species, likely active species, is often hindered by the contribution ...

American Chemical Society2017

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A straightforward and general way for monitoring chemical reactions is via their thermal signature. Such approach requires however an experimental setup with a high thermal stability that simultaneously allows time-resolved heat detection with high sensiti ...

Royal Soc Chemistry2015

Invariant Relationships for Heterogeneous Chemical Reaction Systems in Open Reactors

Dominique Bonvin, Julien Léo Billeter, Sriniketh Srinivasan

Many chemical and biochemical industries utilize chemical reaction processes to get desired products from raw materials. Common examples include reaction systems used to manufacture pharmaceutical drugs, vaccines and other chemicals. A chemical reaction sy ...

2014

Water dissociation on transition-metal catalysts is an important step in steam reforming and the water-gas shift reaction. To probe the effect of translational and vibrational activation on this important heterogeneous reaction, we performed state-resolved ...

Amer Assoc Advancement Science2014

70-kDa Heat shock proteins are ATP-driven molecular chaperones that perform a myriad of essential cellular tasks. Although structural and biochemical studies have shed some light on their functional mechanism, the fundamental issue of the role of energy co ...

Elife Sciences Publications Ltd2014