Nonextensive statistical mechanics applied to protein folding problem: kinetics aspects

A reduced (stereo-chemical) model is employed to study kinetic aspects of globular protein folding process, by Monte Carlo simulation. Nonextensive statistical approach is used: transition probability p i j between configurations i &#8594; j is given by p i j =[1 +(1 - q)&#916;Gi j/kB T ]1/(1-q), where q is the nonextensive (Tsallis) parameter. The system model consists of a chain of 27 beads immerse in its solvent; the beads represent the sequence of amino acids along the chain by means of a 10-letter stereo-chemical alphabet; a syntax (rule) to design the amino acid sequence for any given 3D structure is embedded in the model. The study focuses mainly kinetic aspects of the folding problem related with the protein folding time, represented in this work by the concept of first passage time (FPT). Many distinct proteins, whose native structures are represented here by compact self avoiding (CSA) configurations, were employed in our analysis, although our results are presented exclusively for one representative protein, for which a rich statistics was achieved. Our results reveal that there is a specific combinations of value for the nonextensive parameter q and temperature T, which gives the smallest estimated folding characteristic time (t). Additionally, for q = 1.1, (t) stays almost invariable in the range 0.9 < T < 1.3, slightly oscillating about its average value <img border=0 width=32 height=32 src="../../../../../../../img/revistas/bjp/v39n2a/a16txt01.gif" align=absmiddle > or = 27 ±&#963;, where &#963; = 2 is the standard deviation. This behavior is explained by comparing the distribution of the folding times for the Boltzmann statistics (q &#8594; 1), with respect to the nonextensive statistics for q = 1.1, which shows that the effect of the nonextensive parameter q is to cut off the larger folding times present in the original (q &#8594; 1) distribution. The distribution of natural logarithm of the folding times for Boltzmann statistics is a triple peaked Gaussian, while, for q = 1.1 (Tsallis), it is a double peaked Gaussian, suggesting that a log-normal process with two characteristic times replaced the original process with three characteristic times. Finally we comment on the physical meaning of the present results, as well its significance in the near future works

Structure and energetics of molecular point defects in ice Ih

FAPESP - FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULOCNPQ - CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICOCAPES - COORDENAÇÃO DE APERFEIÇOAMENTO DE PESSOAL DE NÍVEL SUPERIORWe present a first-principles study of the molecular vacancy and three distinct molecular interstitial structures in ice Ih. The results indicate that, due to its bonding to the surrounding hydrogen-bond network, the bond-center (Bc) configuration is the favored molecular interstitial in ice Ih. A comparison between the vacancy and the Bc interstitial suggests that the former is the predominant molecular point defect for T ≤ 200K although a crossover scenario in which the latter becomes favored below the melting point is conceivable.We present a first-principles study of the molecular vacancy and three distinct molecular interstitial structures in ice Ih. The results indicate that, due to its bonding to the surrounding hydrogen-bond network, the bond-center (Bc) configuration is the favored molecular interstitial in ice Ih. A comparison between the vacancy and the Bc interstitial suggests that the former is the predominant molecular point defect for T ≤ 200K although a crossover scenario in which the latter becomes favored below the melting point is conceivable.971514FAPESP - FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULOCNPQ - CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICOCAPES - COORDENAÇÃO DE APERFEIÇOAMENTO DE PESSOAL DE NÍVEL SUPERIORFAPESP - FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULOCNPQ - CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICOCAPES - COORDENAÇÃO DE APERFEIÇOAMENTO DE PESSOAL DE NÍVEL SUPERIORSem informaçãoSem informaçãoSem informaçãoThe authors gratefully acknowledge financial support from the Brazilian agencies FAPESP, CNPq, and CAPES. M. K. acknowledges R.W. Whitworth for stimulating discussions. Part of the calculations were carried out at the High-Performance Computing Facility at CCJDRIFGW-UNICAMP

Simple implementation of complex functionals: scaled selfconsistency

We explore and compare three approximate schemes allowing simple implementation of complex density functionals by making use of selfconsistent implementation of simpler functionals: (i) post-LDA evaluation of complex functionals at the LDA densities (or those of other simple functionals); (ii) application of a global scaling factor to the potential of the simple functional; and (iii) application of a local scaling factor to that potential. Option (i) is a common choice in density-functional calculations. Option (ii) was recently proposed by Cafiero and Gonzalez. We here put their proposal on a more rigorous basis, by deriving it, and explaining why it works, directly from the theorems of density-functional theory. Option (iii) is proposed here for the first time. We provide detailed comparisons of the three approaches among each other and with fully selfconsistent implementations for Hartree, local-density, generalized-gradient, self-interaction corrected, and meta-generalized-gradient approximations, for atoms, ions, quantum wells and model Hamiltonians. Scaled approaches turn out to be, on average, better than post-approaches, and unlike these also provide corrections to eigenvalues and orbitals. Scaled selfconsistency thus opens the possibility of efficient and reliable implementation of density functionals of hitherto unprecedented complexity.Comment: 12 pages, 1 figur