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Nelson A. Alves

Publications and source records attributed to Nelson A. Alves.

At least 19 recordsLinked to original sources
arXiv2020

Featuring ACE2 binding SARS-CoV and SARS-CoV-2 through a conserved evolutionary pattern of amino acid residues

Spike (S) glycoproteins mediate the coronavirus entry into the host cell. The S1 subunit of S-proteins contains the receptor-binding domain (RBD) that is able to recognize different host receptors, highlighting its remarkable capacity to adapt to their hosts along the viral evolution. While RBD in spike proteins is determinant for the virus-receptor interaction, the active residues lie at the receptor-binding motif (RBM), a region located in RBD that plays a fundamental role binding the outer surface of their receptors. Here, we address the hypothesis that SARS-CoV and SARS-CoV-2 strains able to use angiotensin-converting enzyme 2 (ACE2) proteins have adapted their RBM along the viral evolution to explore specific conformational topology driven by the residues YGF to infect host cells. We also speculate that this YGF-based mechanism can act as a protein signature located at the RBM to distinguish coronaviruses able to use ACE2 as a cell entry receptor.

q-bio.BM↗
arXiv2015

Superstatistics and the quest of generalized ensembles equivalence in a system with long-range interactions

The so-called $χ^{2}$-superstatistics of Beck and Cohen (BC) is employed to investigate the infinite-range Blume-Capel model, a well-known representative system displaying inequivalence of canonical and microcanonical phase diagrams. While not being restricted to any of those particular thermodynamic limits, our analytical result can smoothly recover both canonical and microcanonical ensemble solutions as its nonextensive parameter $q$ is properly tuned. Additionally, we compare our findings to ones previously obtained from a generalized canonical framework named Extended Gaussian ensemble (EGE). Finally, we show that both EGE and BC solutions are equivalent at the thermodynamic level.

cond-mat.stat-mech↗
arXiv2015

Microcanonical thermostatistics analysis without histograms: cumulative distribution and Bayesian approaches

Microcanonical thermostatistics analysis has become an important tool to reveal essential aspects of phase transitions in complex systems. An efficient way to estimate the microcanonical inverse temperature $β(E)$ and the microcanonical entropy $S(E)$ is achieved with the statistical temperature weighted histogram analysis method (ST-WHAM). The strength of this method lies on its flexibility, as it can be used to analyse data produced by algorithms with generalised sampling weights. However, for any sampling weight, ST-WHAM requires the calculation of derivatives of energy histograms $H(E)$, which leads to non-trivial and tedious binning tasks for models with continuous energy spectrum such as those for biomolecular and colloidal systems. Here, we discuss two alternative methods that avoid the need for such energy binning to obtain continuous estimates for $H(E)$ in order to evaluate $β(E)$ by using ST-WHAM: (i) a series expansion to estimate probability densities from the empirical cumulative distribution function (CDF), and (ii) a Bayesian approach to model this CDF. Comparison with a simple linear regression method is also carried out. The performance of these approaches is evaluated considering coarse-grained protein models for folding and peptide aggregation.

physics.comp-ph↗
arXiv2012

Microcanonical thermostatistics of coarse-grained proteins with amyloidogenic propensity

The formation of fibrillar aggregates seems to be a common characteristic of polypeptide chains, although the observation of these aggregates may depend on appropriate experimental conditions. Partially folded intermediates seem to have an important role in the generation of protein aggregates, and a mechanism for this fibril formation considers that these intermediates also correspond to metastable states with respect to the fibrillar ones. Here, using a coarse-grained (CG) off-lattice model, we carry out a comparative analysis of the thermodynamic aspects characterizing the folding transition with respect to the propensity for aggregation of four different systems: two isoforms of the amyloid $β$-protein, the Src SH3 domain, and the human prion proteins (hPrP). Microcanonical analysis of the data obtained from replica exchange method (REM) is conducted to evaluate the free-energy barrier and latent heat in these models. The simulations of the amyloid $β$ isoforms and Src SH3 domain indicated that the folding process described by this CG model is related to a negative specific heat, a phenomenon that can only be verified in the microcanonical ensemble in first-order phase transitions. The CG simulation of the hPrP heteropolymer yielded a continuous folding transition. The absence of a free-energy barrier and latent heat favors the presence of partially unfolded conformations, and in this context, this thermodynamic aspect could explain the reason why the hPrP heteropolymer is more aggregation-prone than the other heteropolymers considered in this study. We introduced the hydrophobic radius of gyration as an order parameter and found that it can be used to obtain reliable information about the hydrophobic packing and the transition temperatures in the folding process.

physics.bio-ph↗
arXiv2012

Stripe-tetragonal phase transition in the 2D Ising model with dipole interactions: Partition-function zeros approach

We have performed multicanonical simulations to study the critical behavior of the two-dimensional Ising model with dipole interactions. This study concerns the thermodynamic phase transitions in the range of the interaction δwhere the phase characterized by striped configurations of width h=1 is observed. Controversial results obtained from local update algorithms have been reported for this region, including the claimed existence of a second-order phase transition line that becomes first order above a tricritical point located somewhere between δ=0.85 and 1. Our analysis relies on the complex partition function zeros obtained with high statistics from multicanonical simulations. Finite size scaling relations for the leading partition function zeros yield critical exponents νthat are clearly consistent with a single second-order phase transition line, thus excluding such tricritical point in that region of the phase diagram. This conclusion is further supported by analysis of the specific heat and susceptibility of the orientational order parameter.

cond-mat.stat-mech↗
arXiv2011

Multicanonical entropy like-solution of statistical temperature weighted histogram analysis method (ST-WHAM)

A multicanonical update relation for calculation of the microcanonical entropy $S_{micro}(E)$ by means of the estimates of the inverse statistical temperature $β_S$, is proposed. This inverse temperature is obtained from the recently proposed statistical temperature weighted histogram analysis method (ST-WHAM). The performance of ST-WHAM concerning the computation of $S_{micro}(E)$ from canonical measures, in a model with strong free-energy barriers, is also discussed on the basis of comparison with the multicanonical simulation estimates.

cond-mat.stat-mech↗
arXiv2010

The extended gaussian ensemble and metastabilities in the Blume-Capel model

The Blume-Capel model with infinite-range interactions presents analytical solutions in both canonical and microcanonical ensembles and therefore, its phase diagram is known in both ensembles. This model exhibits nonequivalent solutions and the microcanonical thermodynamical features present peculiar behaviors like nonconcave entropy, negative specific heat, and a jump in the thermodynamical temperature. Examples of nonequivalent ensembles are in general related to systems with long-range interactions that undergo canonical first-order phase transitions. Recently, the extended gaussian ensemble (EGE) solution was obtained for this model. The gaussian ensemble and its extended version can be considered as a regularization of the microcanonical ensemble. They are known to play the role of an interpolating ensemble between the microcanonical and the canonical ones. Here, we explicitly show how the microcanonical energy equilibrium states related to the metastable and unstable canonical solutions for the Blume-Capel model are recovered from EGE, which presents a concave "extended" entropy as a function of energy.

cond-mat.stat-mech↗
arXiv2010

Extended gaussian ensemble solution and tricritical points of a system with long-range interactions

The gaussian ensemble and its extended version theoretically play the important role of interpolating ensembles between the microcanonical and the canonical ensembles. Here, the thermodynamic properties yielded by the extended gaussian ensemble (EGE) for the Blume-Capel (BC) model with infinite-range interactions are analyzed. This model presents different predictions for the first-order phase transition line according to the microcanonical and canonical ensembles. From the EGE approach, we explicitly work out the analytical microcanonical solution. Moreover, the general EGE solution allows one to illustrate in details how the stable microcanonical states are continuously recovered as the gaussian parameter $γ$ is increased. We found out that it is not necessary to take the theoretically expected limit $γ\to \infty$ to recover the microcanonical states in the region between the canonical and microcanonical tricritical points of the phase diagram. By analyzing the entropy as a function of the magnetization we realize the existence of unaccessible magnetic states as the energy is lowered, leading to a treaking of ergodicity.

cond-mat.stat-mech↗
arXiv2009

Phase transitions and autocorrelation times in two-dimensional Ising model with dipole interactions

The two-dimensional Ising model with nearest-neighbor ferromagnetic and long-range dipolar interactions exhibits a rich phase diagram. The presence of the dipolar interaction changes the ferromagnetic ground state expected for the pure Ising model to a series of striped phases as a function of the interaction strengths. Monte Carlo simulations and histogram reweighting techniques applied to multiple histograms are performed to identify the critical temperatures for the phase transitions taking place for stripes of width $h=2$ on square lattices. In particular, we aim to study the intermediate nematic phase, which is observed for large lattice sizes only. For these lattice sizes, we calculate the critical temperatures for the striped-nematic and nematic-tetragonal transitions, critical exponents, and the bulk free-energy barrier associated with the coexisting phases. We also evaluate the long-term correlations in our time series near the finite-size critical points by studying the integrated autocorrelation time $τ$ as a function of the lattice size. This allows us to infer how severe the critical slowing down for this system with long-range interaction and nearby thermodynamic phase transitions is.

cond-mat.stat-mech↗
arXiv2003

Global persistence exponent of the two-dimensional Blume-Capel model

The global persistence exponent $θ_g$ is calculated for the two-dimensional Blume-Capel model following a quench to the critical point from both disordered states and such with small initial magnetizations. Estimates are obtained for the nonequilibrium critical dynamics on the critical line and at the tricritical point. Ising-like universality is observed along the critical line and a different value $θ_g =1.080(4)$ is found at the tricritical point.

cond-mat.stat-mech↗
arXiv2002

Solution effects and the order of the helix-coil transition in polyalanine

We study helix-coil transitions in an all-atom model of polyalanine. Molecules of up to length 30 residues are investigated by multicanonical simulations. Results from two implicit solvent models are compared with each other and with that from simulations in gas phase. While the helix-coil transition is in all three models a true thermodynamic phase transition, we find that its strength is reduced by the protein-solvent interaction term. The order of the helix-coil transition depends on the details of the solvation term.

cond-mat.stat-mech↗
arXiv2002

Helix Formation and Folding in an Artificial Peptide

We study the relation between $α$-helix formation and folding for a simple artificial peptide, Ala$_{10}$-Gly$_5$-Ala$_{10}$. Our data rely on multicanonical Monte Carlo simulations where the interactions among all atoms are taken into account. The free-energy landscape of the peptide is evaluated for various temperatures. Our data indicate that folding of this peptide is a two-step process: in a first step two $α$-helices are formed which afterwards re-arrange themselves into a U-like structure.

cond-mat.stat-mech↗
arXiv2002

Universality and scaling study of the critical behavior of the two-dimensional Blume-Capel model in short-time dynamics

In this paper we study the short-time behavior of the Blume-Capel model at the tricritical point as well as along the second order critical line. Dynamic and static exponents are estimated by exploring scaling relations for the magnetization and its moments at early stage of the dynamic evolution. Our estimates for the dynamic exponents, at the tricritical point, are $z= 2.215(2)$ and $θ= -0.53(2)$.

cond-mat.stat-mech↗
arXiv2001

Numerical comparison of two approaches for the study of phase transitions in small systems

We compare two recently proposed methods for the characterization of phase transitions in small systems. The validity and usefulness of these approaches are studied for the case of the q=4 and q=5 Potts model, i.e. systems where a thermodynamic limit and exact results exist. Guided by this analysis we discuss then the helix-coil transition in polyalanine, an example of structural transitions in biological molecules.

cond-mat.stat-mech↗
arXiv2000

Yang-Lee zeros and the helix-coil transition in a continuum model of polyalanine

We calculate the Yang-Lee zeros for characteristic temperatures of the helix-coil transition in a continuum model of polyalanine. The distribution of these zeros differs from predictions of the Zimm-Bragg theory and supports recent claims that polyalanine exhibits a true phase transition. New estimates for critical exponents are presented and the relation of our results to the Lee-Yang theorem is discussed.

cond-mat.stat-mech↗
arXiv2000

Yang-Lee Zeros of the Ising model on Random Graphs of Non Planar Topology

We obtain in a closed form the 1/N^2 contribution to the free energy of the two Hermitian N\times N random matrix model with non symmetric quartic potential. From this result, we calculate numerically the Yang-Lee zeros of the 2D Ising model on dynamical random graphs with the topology of a torus up to n=16 vertices. They are found to be located on the unit circle on the complex fugacity plane. In order to include contributions of even higher topologies we calculated analytically the nonperturbative (sum over all genus) partition function of the model Z_n = \sum_{h=0}^{\infty} \frac{Z_n^{(h)}}{N^{2h}} for the special cases of N=1,2 and graphs with n\le 20 vertices. Once again the Yang-Lee zeros are shown numerically to lie on the unit circle on the complex fugacity plane. Our results thus generalize previous numerical results on random graphs by going beyond the planar approximation and strongly indicate that there might be a generalization of the Lee-Yang circle theorem for dynamical random graphs.

hep-th↗