Structurally constrained protein evolution: results from a lattice simulation

We simulate the evolution of a protein-like sequence subject to point mutations, imposing conservation of the ground state, thermodynamic stability and fast folding. Our model is aimed at describing neutral evolution of natural proteins. We use a cubic lattice model of the protein structure and test the neutrality conditions by extensive Monte Carlo simulations. We observe that sequence space is traversed by neutral networks, i.e. sets of sequences with the same fold connected by point mutations. Typical pairs of sequences on a neutral network are nearly as different as randomly chosen sequences. The fraction of neutral neighbors has strong sequence to sequence variations, which influence the rate of neutral evolution. In this paper we study the thermodynamic stability of different protein sequences. We relate the high variability of the fraction of neutral mutations to the complex energy landscape within a neutral network, arguing that valleys in this landscape are associated to high values of the neutral mutation rate. We find that when a point mutation produces a sequence with a new ground state, this is likely to have a low stability. Thus we tentatively conjecture that neutral networks of different structures are typically well separated in sequence space. This results indicates that changing significantly a protein structure through a biologically acceptable chain of point mutations is a rare, although possible, event.Comment: added reference, to appear on European Physical Journal

The landscape of W±W^{\pm} and ZZ bosons produced in pppp collisions up to LHC energies

We consider a selection of recent experimental results on electroweak $W^{\pm},\,Z$ gauge boson production in $pp$ collisions at BNL RHIC and CERN LHC energies in comparison to prediction of perturbative QCD calculations based on different sets of NLO parton distribution functions including the statistical PDF model known from fits to the DIS data. We show that the current statistical PDF parameterisation (fitted to the DIS data only) underestimates the LHC data on $W^{\pm},\,Z$ gauge boson production cross sections at the NLO by about 20\%. This suggests that there is a need to refit the parameters of the statistical PDF including the latest LHC data.Comment: 16 pages, 8 figures; discussion extended, typos fixed; published versio

Statistical properties of neutral evolution

Neutral evolution is the simplest model of molecular evolution and thus it is most amenable to a comprehensive theoretical investigation. In this paper, we characterize the statistical properties of neutral evolution of proteins under the requirement that the native state remains thermodynamically stable, and compare them to the ones of Kimura's model of neutral evolution. Our study is based on the Structurally Constrained Neutral (SCN) model which we recently proposed. We show that, in the SCN model, the substitution rate decreases as longer time intervals are considered, and fluctuates strongly from one branch of the evolutionary tree to another, leading to a non-Poissonian statistics for the substitution process. Such strong fluctuations are also due to the fact that neutral substitution rates for individual residues are strongly correlated for most residue pairs. Interestingly, structurally conserved residues, characterized by a much below average substitution rate, are also much less correlated to other residues and evolve in a much more regular way. Our results could improve methods aimed at distinguishing between neutral and adaptive substitutions as well as methods for computing the expected number of substitutions occurred since the divergence of two protein sequences.Comment: 17 pages, 11 figure

Drell-Yan phenomenology in the color dipole picture revisited

An extensive phenomenological study of the Drell-Yan (DY) process in $pp$ collisions at various energies is performed in the color dipole framework. Besides previously studied $\gamma^*$ production we have also included the $Z^0$ contribution relevant at large dilepton invariant masses. We investigate the DY cross section differential in invariant mass, rapidity and transverse momentum of the dilepton pair in $pp$ collisions at RHIC and LHC. We consider three different phenomenological models for the dipole cross section and found a reasonable agreement with the available data. As a further test of the color dipole formalism, we also study the correlation function in azimuthal angle between the dilepton pair and a forward pion $\Delta\phi$ for different energies, dilepton rapidites and invariant masses. The characteristic double-peak structure of the correlation function around $\Delta \phi\simeq \pi$ found for very forward pions and low-mass dilepton pairs is sensitive to the saturation effects and can be tested by future DY measurements in $pp$ collisions.Comment: 16 pages, 12 figures; typos corrected, references added, conclusions unchange

Spreading of infections on random graphs: A percolation-type model for COVID-19

We introduce an epidemic spreading model on a network using concepts from percolation theory. The model is motivated by discussing the standard SIR model, with extensions to describe effects of lockdowns within a population. The underlying ideas and behavior of the lattice model, implemented using the same lockdown scheme as for the SIR scheme, are discussed in detail and illustrated with extensive simulations. A comparison between both models is presented for the case of COVID-19 data from the USA. Both fits to the empirical data are very good, but some differences emerge between the two approaches which indicate the usefulness of having an alternative approach to the widespread SIR model

Selection of soybean pods by the stink bugs, Nezara viridula and Piezodorus guildinii

Different biological parameters of the stink bugs, Nezara viridula L. and Piezodorus guildinii Westwood (Hemiptera: Pentatomidae), are affected by the developmental stage of the soybean ( Glycine max Merrill) pods they feed on. These effects of the soybean on the stink bugs could represent a selection pressure leading to the ability of these species to discriminate the phenological stage of soybean pods, and, therefore, to exhibit feeding preferences. We designed three studies: (1) Distant detection of soybean pods through an olfactometer; (2) Free choice tests to evaluate preferences for soybean pods of different developmental stages; (3) No choice tests to study effects of soybean pod development on feeding time and number of probes. Stink bugs showed no differential response to olfactometer arms with or without soybean pods, suggesting an inability to detect soybean volatiles. Free choice tests showed no species effects on pods selection, but significant differences among fifth instar nymphs, adult male, and adult females. Fifth instar nymphs fed more frequently on soybean pods of advanced development stages compared to female adults, despite previous evidence showing poor development of stink bugs fed pods of the same stage. No choice tests showed significant effects of stink bug species, stink bug stage and sex, and soybean pod phenology. N. viridula expressed shorter feeding times and higher numbers of probes than P. guildinii. The highest numbers of probes of both species were observed when they were fed soybean pods in early phenological stages. When placed in direct contact with food, fifth instar nymphs prefered to feed on more developed pods, despite these pods being suboptimal food ítems. These results suggest that for the ecological time framework of soybean-stink bugs coexistence, around thirty-five years in Argentina, the selection pressure was not enough for stink bugs to evolve food preferences that match their performance on soybean pods of different development stages.EEA ManfrediFil: Molina, Gonzalo Alberto Roman. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Manfredi; ArgentinaFil: Trumper, Eduardo Victor. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Manfredi; Argentin