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J. Miguel Rubi published an article in May 2018.
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(1970 - 2018)
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PREPRINT-CONTENT 0 Reads 0 Citations Enzymatic evolution driven by entropy production Published: 14 May 2018
bioRxiv, doi: 10.1101/319814
We show that the structural evolution of enzymes is largely influenced by the entropy produced in the enzymatic process. We have computed this quantity for the case in which the process has unstable and metastable intermediate states. By assuming that the kinetics takes place along a potential barrier, we have found that the behavior of the total entropy produced is a non-monotonic function of the intermediate state energy. By diminishing the number of metastable intermediate states, the total entropy produced decreases and consequently the enzyme kinetics and the thermodynamic efficiency are enhanced. Minimizing locally the total entropy produced for an enzymatic process with metastable intermediate states, the kinetics and the thermodynamic efficiency are raised. In contrast, in the absence of metastable intermediate states, a maximum of the entropy produced results in an improvement of the kinetic performance although the thermodynamic efficiency diminishes. Our results show that the enzymatic evolution proceeds not only to enhance the kinetics but also to optimize the total entropy produced.
Article 0 Reads 2 Citations Non-equilibrium molecular dynamics simulations of the thermal transport properties of Lennard-Jones fluids using configu... Published: 20 May 2016
Molecular Simulation, doi: 10.1080/08927022.2016.1168926
Article 0 Reads 1 Citation Theory of Casimir Forces without the Proximity-Force Approximation Published: 18 March 2016
Physical Review Letters, doi: 10.1103/physrevlett.116.110601
We analyze both the attractive and repulsive Casimir-Lifshitz forces recently reported in experimental investigations. By using a kinetic approach, we obtain the Casimir forces from the power absorbed by the materials. We consider collective material excitations through a set of relaxation times distributed in frequency according to a log-normal function. A generalized expression for these forces for arbitrary values of temperature is obtained. We compare our results with experimental measurements and conclude that the model goes beyond the proximity-force approximation. DOI:http://dx.doi.org/10.1103/PhysRevLett.116.110601 © 2016 American Physical Society
Article 0 Reads 0 Citations Thermal motion in proteins: Large effects on the time-averaged interaction energies Published: 01 March 2016
AIP Advances, doi: 10.1063/1.4945012
As a consequence of thermal motion, inter-atomic distances in proteins fluctuate strongly around their average values, and hence, also interaction energies (i.e. the pair-potentials evaluated at the fluctuating distances) are not constant in time but exhibit pronounced fluctuations. These fluctuations cause that time-averaged interaction energies do generally not coincide with the energy values obtained by evaluating the pair-potentials at the average distances. More precisely, time-averaged interaction energies behave typically smoother in terms of the average distance than the corresponding pair-potentials. This averaging effect is referred to as the thermal smoothing effect. Here, we estimate the strength of the thermal smoothing effect on the Lennard-Jones pair-potential for globular proteins at ambient conditions using x-ray diffraction and simulation data of a representative set of proteins. For specific atom species, we find a significant smoothing effect where the time-averaged interaction energy of a single atom pair can differ by various tens of cal/mol from the Lennard-Jones potential at the average distance. Importantly, we observe a dependency of the effect on the local environment of the involved atoms. The effect is typically weaker for bulky backbone atoms in beta sheets than for side-chain atoms belonging to other secondary structure on the surface of the protein. The results of this work have important practical implications for proteinsoftware relying on free energy expressions. We show that the accuracy of free energy expressions can largely be increased by introducing environment specific Lennard-Jones parameters accounting for the fact that the typical thermal motion of protein atoms depends strongly on their local environment.
Article 0 Reads 7 Citations Entropically induced asymmetric passage times of charged tracers across corrugated channels Published: 21 January 2016
The Journal of Chemical Physics, doi: 10.1063/1.4939799
We analyze the diffusion of charged and neutral tracers suspended in an electrolyte embedded in a channel of varying cross section. Making use of systematic approximations, the diffusionequation governing the motion of tracers is mapped into an effective 1Dequation describing the dynamics along the longitudinal axis of the channel where its varying-section is encoded as an effective entropic potential. This simplified approach allows us to characterize tracer diffusion under generic confinement by measuring their mean first passage time (MFPT). In particular, we show that the interplay between geometrical confinement and electrostatic interactions strongly affect the MFTP of tracers across corrugated channels hence leading to alternative means to control tracers translocation across charged pores. Finally, our results show that the MFPTs of a charged tracer in opposite directions along an asymmetric channel may differ We expect our results to be relevant for biological as well synthetic devices whose dynamics is controlled by the detection of diluted tracers.
Article 0 Reads 0 Citations Thermodynamics and energy conversion of near-field thermal radiation: Maximum work and efficiency bounds Published: 01 January 2014
EPJ Web of Conferences, doi: 10.1051/epjconf/20147901001
We analyse the process of conversion of near-field thermal radiation into usable work by considering the radiation emitted between two planar sources supporting surface phonon-polaritons. The maximum work flux that can be extracted from the radiation is obtained taking into account that the spectral flux of modes is mainly dominated by these surface modes. The thermodynamic efficiencies are discussed and an upper bound for the first law efficiency is obtained for this process.