arXiv subjects

J. Rubio

Publications and source records attributed to J. Rubio.

6 recordsLinked to original sources

arXiv2023

Fluctuation relations to calculate protein redox potentials from molecular dynamics simulations

The tunable design of protein redox potentials promises to open a range of applications in biotechnology and catalysis. Here we introduce a method to calculate redox potential changes by combining fluctuation relations with molecular dynamics simulations. It involves the simulation of reduced and oxidized states, followed by the instantaneous conversion between them. Energy differences introduced by the perturbations are obtained using the Kubo-Onsager approach. Using a detailed fluctuation relation coupled with Bayesian inference, these are post-processed into estimates for the redox potentials in an efficient manner. This new method, denoted MD+CB, is tested on a de novo four-helix bundle heme protein (the m4D2 `maquette') and five designed mutants, including some mutants characterized experimentally in this work. The MD+CB approach is found to perform reliably, giving redox potential shifts with reasonably good correlation (0.85) to the experimental values for the mutants. The MD+CB approach also compares well with redox potential shift predictions using a continuum electrostatic method. The estimation method employed within the MD+CB approach is straightforwardly transferable to standard equilibrium MD simulations, and holds promise for redox protein engineering and design applications.

physics.bio-ph↗

arXiv2019

Electromagnetic probes of primordial black holes as dark matter

The LIGO discoveries have rekindled suggestions that primordial black holes (BHs) may constitute part to all of the dark matter (DM) in the Universe. Such suggestions came from 1) the observed merger rate of the BHs, 2) their unusual masses, 3) their low/zero spins, and 4) also from the independently uncovered cosmic infrared background (CIB) fluctuations signal of high amplitude and coherence with unresolved cosmic X-ray background (CXB). Here we summarize the prospects to resolve this important issue with electromagnetic observations using the instruments and tools expected in the 2020's. These prospects appear promising to make significant, and potentially critical, advances. We demonstrate that in the next decade, new space- and ground-borne electromagnetic instruments, combined with concurrent theoretical efforts, should shed critical light on the long-considered link between primordial BHs and DM. Specifically the new data and methodologies under this program will involve: I) Probing with high precision the spatial spectrum of source-subtracted CIB with Euclid and WFIRST, and its coherence with unresolved cosmic X-ray background using eROSITA and Athena, II) Advanced searches for microlensing of Galactic stars by the intervening Galactic Halo BHs with OGLE, Gaia, LSST and WFIRST, III) Supernovae (SNe) lensing in the upcoming surveys with WFIRST, LSST and also potentially with Euclid and JWST, IV) Advanced theoretical work to understand the details of PBH accretion and evolution and their influence on cosmic microwave background (CMB) anisotropies in light of the next generation CMB experiments, V) Better new samples and theoretical understanding involving stability and properties of ultra faint dwarf galaxies, pulsar timing, and cosmological quasar lensing.

astro-ph.CO↗

arXiv2006

Computing spectral sequences

In this paper, a set of programs enhancing the Kenzo system is presented. Kenzo is a Common Lisp program designed for computing in Algebraic Topology, in particular it allows the user to calculate homology and homotopy groups of complicated spaces. The new programs presented here entirely compute Serre and Eilenberg-Moore spectral sequences, in particular the groups and differential maps for arbitrary r. They also determine when the spectral sequence has converged and describe the filtration of the target homology groups induced by the spectral sequence.

cs.SC↗

arXiv2004

The one-particle Green's function of one.dimensional insulating materials

The single particle spectral-weight function (SWF) of the ionic Hubbard model at half filling is calculated in the cluster perturbation theory approximation. An abrupt change of regime in the low-energy region, near the chemical potential, is found at a critical value, $U_{c}$, of the coupling constant (Hubbard $U$). The SWF at the Fermi points $k_{F}$=$\pm{\pi}/2$ jumps, as $U$ increases, from a two-peak structure, the gap edges, to a four-peak structure accompanied by a (non-vanishing) minimum of the charge-gap. The two inner peaks of this structure show very small dispersion (flat bands) away from the Fermi points, whereas the outer peaks mark the edges of the Hubbard bands. No other signatures of abrupt change are detected in the SWF. The two regimes are physically realized in the angle-resolved photoelectron spectra of $(TaSe_{4})_{2}I$, and the blue-bronze $K_{0.3}MoO_{3}$, respectively.

cond-mat.str-el↗

arXiv2002

Spectral-weight function of the ionic Hubbard model

The one-electron spectral-weight function of the half-filled ionic Hubbard model is calculated by means of Quantum Monte Carlo. A metallic regimen occurs between two values of the coupling constant (Hubbard U) U1 < U2 . The system is a band insulator below U1, and an increasingly antiferromagnetic (AF) insulator above U2 evolving into a Mott insulator as U tends to infinity . The intermediate regimen which is both AF and dimerized, is caused by a two-peak structure at k = 0,5 pi (the Fermi surface). As U increases both peaks approach each other, overlap, and separate again, the system becoming metallic in the overlap region.

cond-mat.str-el↗

arXiv2001

The one-electron Green's function of the half-filled Hubbard model on a triangular lattice

The one-electron density of states for the half-filled Hubbard model on a triangular lattice is studied as a function of both temperature and Hubbard U using Quantum Monte Carlo. We find three regimes: (1) a strong-coupling Mott-Hubbard regime, characterized by a gap which persists even at high temperatures; (2) a weak-coupling paramagnetic regime, characterized by the absence of a pseudogap at any finite temperature; and (3) an intermediate-coupling (spiral) spin-density-wave regime, characterized by a pseudogap which appears when U is increased beyond a critical (temperature dependent) value. The behavior of the sqrt(3) times sqrt{3} adlayer structures on fourth-group semiconductor surfaces is briefly commented upon in the light of the above discussion.

cond-mat.str-el↗