A refined hydrogen bond potential for flexible protein models

One of the major disadvantages of coarse-grained hydrogen bond potentials, for their use in protein folding simulations, is the appearance of abnormal structures when these potentials are used in flexible chain models, and no other geometrical restrictions or energetic contributions are defined into the system.We have efficiently overcome this problem, for chains of adequate size in a relevant temperature range, with a refined coarse-grained hydrogen bond potential. With it, we have been able to obtain nativelike alpha-helices and beta-sheets in peptidic systems, and successfully reproduced the competition between the populations of these secondary structure elements by the effect of temperature and concentration changes. In this manuscript we detail the design of the interaction potential and thoroughly examine its applicability in energetic and structural terms, considering factors such as chain length, concentration, and temperature

Microscopic dynamics of glycerol in its crystalline and glassy states

The dynamics of crystalline glycerol are studied by means of Raman spectroscopy and lattice dynamics calculations employing a semiflexible model to represent the low-lying molecular vibrations. The latter is validated against structural, thermodynamic, and spectroscopic data. The results serve to set an absolute frequency scale for glassy glycerol, which is also studied by Raman and incoherent inelastic-neutron scattering. Some implications of the present findings regarding ensuing discussions on glassy dynamics are finally commented on.Dirección General de Investigaciones Científicas y Técnicas PB92- 0114-C0

A remark on an overdetermined problem in Riemannian Geometry

Let $(M,g)$ be a Riemannian manifold with a distinguished point $O$ and assume that the geodesic distance $d$ from $O$ is an isoparametric function. Let $\Omega\subset M$ be a bounded domain, with $O \in \Omega$, and consider the problem $\Delta_p u = -1$ in $\Omega$ with $u=0$ on $\partial \Omega$, where $\Delta_p$ is the $p$-Laplacian of $g$. We prove that if the normal derivative $\partial_{\nu}u$ of $u$ along the boundary of $\Omega$ is a function of $d$ satisfying suitable conditions, then $\Omega$ must be a geodesic ball. In particular, our result applies to open balls of $\mathbb{R}^n$ equipped with a rotationally symmetric metric of the form $g=dt^2+\rho^2(t)\,g_S$, where $g_S$ is the standard metric of the sphere.Comment: 8 pages. This paper has been written for possible publication in a special volume dedicated to the conference "Geometric Properties for Parabolic and Elliptic PDE's. 4th Italian-Japanese Workshop", organized in Palinuro in May 201

New superintegrable models with position-dependent mass from Bertrand's Theorem on curved spaces

A generalized version of Bertrand's theorem on spherically symmetric curved spaces is presented. This result is based on the classification of (3+1)-dimensional (Lorentzian) Bertrand spacetimes, that gives rise to two families of Hamiltonian systems defined on certain 3-dimensional (Riemannian) spaces. These two systems are shown to be either the Kepler or the oscillator potentials on the corresponding Bertrand spaces, and both of them are maximally superintegrable. Afterwards, the relationship between such Bertrand Hamiltonians and position-dependent mass systems is explicitly established. These results are illustrated through the example of a superintegrable (nonlinear) oscillator on a Bertrand-Darboux space, whose quantization and physical features are also briefly addressed.Comment: 13 pages; based in the contribution to the 28th International Colloquium on Group Theoretical Methods in Physics, Northumbria University (U.K.), 26-30th July 201

Green's function for the Hodge Laplacian on some classes of Riemannian and Lorentzian symmetric spaces

We compute the Green's function for the Hodge Laplacian on the symmetric spaces M\times\Sigma, where M is a simply connected n-dimensional Riemannian or Lorentzian manifold of constant curvature and \Sigma is a simply connected Riemannian surface of constant curvature. Our approach is based on a generalization to the case of differential forms of the method of spherical means and on the use of Riesz distributions on manifolds. The radial part of the Green's function is governed by a fourth order analogue of the Heun equation.Comment: 18 page

Nonrelativistic hydrogen type stability problems on nonparabolic 3-manifolds

We extend classical Euclidean stability theorems corresponding to the nonrelativistic Hamiltonians of ions with one electron to the setting of non parabolic Riemannian 3-manifolds.Comment: 20 pages; to appear in Annales Henri Poincar

Sex differences in ochratoxin a toxicity in F344 rats after 7 and 21 days of daily oral administration

Ochratoxin A (OTA) is a potent renal carcinogen in male rats but not in females. The mechanisms underlying these differences are unknown. The sex-dependent response of F344 rats after a repeated OTA oral administration for 7 (0.50 mg/kg bw) or 21 days (0.21 and 0.50 mg/kg bw) was evaluated. General toxicity, sex and thyroid hormones and histopathology were studied. OTA was quantified (HPLC-FLD) in plasma, kidney and liver and the expression of kidney transporters (RT-qPCR) was studied. After 7 days, kidney histopathology showed more pronounced signs of toxicity in males than in females. After 21 days, a higher toxicity was observed but sex differences disappeared. OTA concentration in plasma and tissues was similar in both sexes. Downregulation was the general OTA-induced effect. Oats' downregulation was slow in males and Oat3 did not change in females. Oatp1 was strongly downregulated in males after 21 days. An opposite effect was observed in Bcrp after 21 days: downregulation in males and upregulation in females. Females showed a dose- and time-dependent decrease of progesterone. Despite the sex differences, the final balance in OTA toxicokinetics at renal cell level does not seem to support a higher accumulation of OTA in male kidneys

The structure of fluid trifluoromethane and methylfluoride

We present hard X-ray and neutron diffraction measurements on the polar fluorocarbons HCF3 and H3CF under supercritical conditions and for a range of molecular densities spanning about a factor of ten. The Levesque-Weiss-Reatto inversion scheme has been used to deduce the site-site potentials underlying the measured partial pair distribution functions. The orientational correlations between adjacent fluorocarbon molecules -- which are characterized by quite large dipole moments but no tendency to form hydrogen bonds -- are small compared to a highly polar system like fluid hydrogen chloride. In fact, the orientational correlations in HCF3 and H3CF are found to be nearly as small as those of fluid CF4, a fluorocarbon with no dipole moment.Comment: 11 pages, 9 figure

Genetic diversity and population structure in Physalis peruviana and related taxa based on InDels and SNPs derived from COSII and IRG markers

AbstractThe genus Physalis is common in the Americas and includes several economically important species, among them is Physalis peruviana that produces appetizing edible fruits. We studied the genetic diversity and population structure of P. peruviana and characterized 47 accessions of this species along with 13 accessions of related taxa consisting of 222 individuals from the Colombian Corporation of Agricultural Research (CORPOICA) germplasm collection, using Conserved Orthologous Sequences (COSII) and Immunity Related Genes (IRGs). In addition, 642 Single Nucleotide Polymorphism (SNP) markers were identified and used for the genetic diversity analysis. A total of 121 alleles were detected in 24 InDels loci ranging from 2 to 9 alleles per locus, with an average of 5.04 alleles per locus. The average number of alleles in the SNP markers was two. The observed heterozygosity for P. peruviana with InDel and SNP markers was higher (0.48 and 0.59) than the expected heterozygosity (0.30 and 0.41). Interestingly, the observed heterozygosity in related taxa (0.4 and 0.12) was lower than the expected heterozygosity (0.59 and 0.25). The coefficient of population differentiation FST was 0.143 (InDels) and 0.038 (SNPs), showing a relatively low level of genetic differentiation among P. peruviana and related taxa. Higher levels of genetic variation were instead observed within populations based on the AMOVA analysis. Population structure analysis supported the presence of two main groups and PCA analysis based on SNP markers revealed two distinct clusters in the P. peruviana accessions corresponding to their state of cultivation. In this study, we identified molecular markers useful to detect genetic variation in Physalis germplasm for assisting conservation and crossbreeding strategies