Glassy phases in Random Heteropolymers with correlated sequences

We develop a new analytic approach for the study of lattice heteropolymers, and apply it to copolymers with correlated Markovian sequences. According to our analysis, heteropolymers present three different dense phases depending upon the temperature, the nature of the monomer interactions, and the sequence correlations: (i) a liquid phase, (ii) a ``soft glass'' phase, and (iii) a ``frozen glass'' phase. The presence of the new intermediate ``soft glass'' phase is predicted for instance in the case of polyampholytes with sequences that favor the alternation of monomers. Our approach is based on the cavity method, a refined Bethe Peierls approximation adapted to frustrated systems. It amounts to a mean field treatment in which the nearest neighbor correlations, which are crucial in the dense phases of heteropolymers, are handled exactly. This approach is powerful and versatile, it can be improved systematically and generalized to other polymeric systems

Primary prostatic adenocarcinoma in a domestic short-haired cat

An 8-years-old, domestic short-haired cat was presented for constipation and symptoms referable to the lower urinary tract. A solid mass located in the caudal area of the abdomen was palpated. Abdominal ultrasonography, positive-contrast retrograde urethrocystography and total body computed tomography showed the presence of a prostatic neoformation occupying almost completely the pelvic cavity. The neoformation displaced dorsolaterally the descending colon and completely englobed the prostatic urethra, without apparent involvement of the urethral lumen. Histopathologic examination revealed a prostatic carcinoma. Neoplastic cells showed a moderate to intense cytoplasmatic expression of AE1/AE3, while no expression of cytokeratin 7 and Uroplakin III was observed. Topographical, histological and immunohistochemical findings were consistent with a diagnosis of primary adenocarcinoma of the prostate body

The economic implications of HLA matching in cadaveric renal transplantation.

Abstract Background: The potential economic effects of the allocation of cadaveric kidneys on the basis of tissue-matching criteria are controversial. We analyzed the economic costs associated with the transplantation of cadaveric kidneys with various numbers of HLA mismatches and examined the potential economic benefits of a local, as compared with a national, system designed to minimize HLA mismatches between donor and recipient in first cadaveric renal transplantations. Methods: All data were supplied by the U.S. Renal Data System. Data on all payments made by Medicare from 1991 through 1997 for the care of recipients of a first cadaveric renal transplant were analyzed according to the number of HLA-A, B, and DR mismatches between donor and recipient and the duration of cold ischemia before transplantation. Results: Average Medicare payments for renal-transplant recipients in the three years after transplantation increased from $60,436 per patient for fully HLA-matched kidneys (those with no HLA-A, B, or DR mismatches) to$80,807 for kidneys with six HLA mismatches between donor and recipient, a difference of 34 percent (P\u3c0.001). By three years after transplantation, the average Medicare payments were $64,119 for transplantations of kidneys with less than 12 hours of cold-ischemia time and$74,997 for those with more than 36 hours (P\u3c0.001). In simulations, the assignment of cadaveric kidneys to recipients by a method that minimized HLA mismatching within a local geographic area (i.e., within one of the approximately 50 organ-procurement organizations, which cover widely varying geographic areas) produced the largest cost savings ($4,290 per patient over a period of three years) and the largest improvements in the graft-survival rate (2.3 percent) when the potential costs of longer cold-ischemia time were considered. Conclusions: Transplantation of better-matched cadaveric kidneys could have substantial economic advantages. In our simulations, HLA-based allocation of kidneys at the local level produced the largest estimated cost savings, when the duration of cold ischemia was taken into account. No additional savings were estimated to result from a national allocation program, because the additional costs of longer cold-ischemia time were greater than the advantages of optimizing HLA matching

Bending-rigidity-driven transition and crumpling-point scaling of lattice vesicles

The crumpling transition of three-dimensional (3D) lattice vesicles subject to a bending fugacity \ensuremath{\rho}=exp(-\ensuremath{\kappa}/${\mathit{k}}_{\mathit{BT}}$) is investigated by Monte Carlo methods in a grand canonical framework. By also exploiting conjectures suggested by previous rigorous results, a critical regime with scaling behavior in the universality class of branched polymers is found to exist for \ensuremath{\rho}\ensuremath{\gtrsim}{\mathrm{\ensuremath{\rho}}}_{\mathit{c}}. For \ensuremath{\rho}{\mathrm{\ensuremath{\rho}}}_{\mathit{c}} the vesicles undergo a first-order transition that has remarkable similarities to the line of droplet singularities of inflated 2D vesicles. At the crumpling point (\ensuremath{\rho}={\mathrm{\ensuremath{\rho}}}_{\mathit{c}}), which has a tricritical character, the average radius and the canonical partition function of vesicles with n plaquettes scale as {\mathit{n}}^{{\ensuremath{\nu}}_{\mathit{c}}} and {\mathit{n}}^{\mathrm{\ensuremath{-}}{\mathrm{\ensuremath{\theta}}}_{\mathit{c}}}, respectively, with {\ensuremath{\nu}}_{\mathit{c}}=0.4825\ifmmode\pm\else\textpm\fi{}0.0015 and {\mathrm{\ensuremath{\theta}}}_{\mathit{c}}=1.78\ifmmode\pm\else\textpm\fi{}0.03. These exponents indicate a new class, distinct from that of branched polymers, for scaling at the crumpling point. \textcopyright{} 1996 The American Physical Society

Roles of stiffness and excluded volume in DNA denaturation

The nature and the universal properties of DNA thermal denaturation are investigated by Monte Carlo simulations. For suitable lattice models we determine the exponent c describing the decay of the probability distribution of denaturated loops of length l, $P \sim l^{-c}$. If excluded volume effects are fully taken into account, c= 2.10(4) is consistent with a first order transition. The stiffness of the double stranded chain has the effect of sharpening the transition, if it is continuous, but not of changing its order and the value of the exponent c, which is also robust with respect to inclusion of specific base-pair sequence heterogeneities.Comment: RevTeX 4 Pages and 4 PostScript figures included. Final version as publishe

Fully Frustrated Ising System on a 3D Simple Cubic Lattice: Revisited

Using extensive Monte Carlo simulations, we clarify the critical behaviour of the 3 dimensional simple cubic Ising Fully Frustrated system. We find two transition temperatures and two long range ordered phases. Within the present numerical accuracy, the transition at higher temperature is found to be second order and we have extracted the standard critical exponent using finite size scaling method. On the other hand, the transition at lower temperature is found to be first order. It is argued that entropy plays a major role on determining the low temperature state.Comment: 14 pages 14 figures iop style include

Influence of distributary channels on sediment and organic matter supply in event-dominated coastal margins: the Po prodelta as a study case

From November 2008 through May 2009, the Po river (Italy) experienced several floods exceeding 5000 m<sup>3</sup> s<sup>−1</sup>. This long series of events ended with a large flood in early May 2009 (~8000 m<sup>3</sup> s<sup>−1</sup>). An event-response sampling was carried out in the Po prodelta in April–May 2009 to characterize the preservation of this series of floods in the sediment record and to describe the event-supply and deposition of riverborne particulate material during the May 2009 flood. The water sampling was carried out early in the event under conditions of moderate river flow (~5000 m<sup>3</sup> s<sup>−1</sup>) and 24 h later during the peak discharge (~8000 m<sup>3</sup> s<sup>−1</sup>). Sediment cores were collected in the prodelta before and after the peak flood. At each station, profiles of conductivity, transmittance, and fluorescence were acquired. Surface and bottom waters were sampled to collect sediments in suspension. In addition, a few days before the May 2009 event, suspended sediments were collected at Pontelagoscuro gauging station, ~90 km upstream from the coast. Biogeochemical compositions and sedimentological characteristics of suspended and sediment samples were investigated using bulk and biomarker analyses. Furthermore, <sup>7</sup>Be and radiographs were used to analyze the internal stratigraphy of sediment cores. <br><br> During moderate flow, the water column did not show evidence of plume penetration. Stations re-occupied 24 h later exhibited marked physical and biogeochemical changes during the peak flood. However, the concentration of terrestrially-derived material in surface waters was still less than expected. These results suggested that, since material enters the Adriatic as buoyancy-driven flow with a reduced transport capacity, settling and flocculation processes result in trapping a significant fraction of land-derived material in shallow sediments and/or within distributary channels. <br><br> Although numerous discharge peaks occurred from November 2008 through April 2009 (4000–6000 m<sup>3</sup> s<sup>−1</sup>), sediment cores collected in late April 2009 showed lack of event-strata preservation and reduced <sup>7</sup>Be penetrations. This suggested that only a small fraction of the sediment supply during ordinary events reaches the deepest region of the prodelta (12–20 m water depth). As a result, these event-strata have a thickness not sufficient to be preserved in the sediment record because of post-depositional processes that destroy the flood signal. <br><br> Stations in the northern and central prodelta were re-occupied after the peak of the May 2009 flood. Based on <sup>7</sup>Be and radiographs, we estimated event layers of 17 and 6 cm thickness, respectively. Selective trapping of coarse material occurred in the central prodelta likely because of the geomorphologic setting of the central outlet characterized by an estuary-like mouth. Despite these settling processes, lignin-based parameters indicated that the composition of the terrigenous OC was fairly homogenous throughout the network of channels and between size-fractions

Numerical study of a short-range p-spin glass model in three dimensions

In this work we study numerically a short range p-spin glass model in three dimensions. The behaviour of the model appears to be remarkably different from mean field predictions. In fact it shares some features typical of models with full replica-symmetry breaking (FRSB). Nevertheless, we believe that the transition that we study is intrinsically different from the FRSB and basically due to non-perturbative contributions. We study both the statics and the dynamics of the system which seem to confirm our conjectures.Comment: 20 pages, 15 figure

On the size of knots in ring polymers

We give two different, statistically consistent definitions of the length l of a prime knot tied into a polymer ring. In the good solvent regime the polymer is modelled by a self avoiding polygon of N steps on cubic lattice and l is the number of steps over which the knot ``spreads'' in a given configuration. An analysis of extensive Monte Carlo data in equilibrium shows that the probability distribution of l as a function of N obeys a scaling of the form p(l,N) ~ l^(-c) f(l/N^D), with c ~ 1.25 and D ~ 1. Both D and c could be independent of knot type. As a consequence, the knot is weakly localized, i.e. ~ N^t, with t=2-c ~ 0.75. For a ring with fixed knot type, weak localization implies the existence of a peculiar characteristic length l^(nu) ~ N^(t nu). In the scaling ~ N^(nu) (nu ~0.58) of the radius of gyration of the whole ring, this length determines a leading power law correction which is much stronger than that found in the case of unrestricted topology. The existence of such correction is confirmed by an analysis of extensive Monte Carlo data for the radius of gyration. The collapsed regime is studied by introducing in the model sufficiently strong attractive interactions for nearest neighbor sites visited by the self-avoiding polygon. In this regime knot length determinations can be based on the entropic competition between two knotted loops separated by a slip link. These measurements enable us to conclude that each knot is delocalized (t ~ 1).Comment: 29 pages, 14 figure

Corner transfer matrix renormalization group method for two-dimensional self-avoiding walks and other O(n) models

We present an extension of the corner transfer matrix renormalisation group (CTMRG) method to O(n) invariant models, with particular interest in the self-avoiding walk class of models (O(n=0)). The method is illustrated using an interacting self-avoiding walk model. Based on the efficiency and versatility when compared to other available numerical methods, we present CTMRG as the method of choice for two-dimensional self-avoiding walk problems.Comment: 4 pages 7 figures Substantial rewrite of previous version to include calculations of critical points and exponents. Final version accepted for publication in PRE (Rapid Communications