A Constraint Solver for Flexible Protein Models

This paper proposes the formalization and implementation of a novel class of constraints aimed at modeling problems related to placement of multi-body systems in the 3-dimensional space. Each multi-body is a system composed of body elements, connected by joint relationships and constrained by geometric properties. The emphasis of this investigation is the use of multi-body systems to model native conformations of protein structures---where each body represents an entity of the protein (e.g., an amino acid, a small peptide) and the geometric constraints are related to the spatial properties of the composing atoms. The paper explores the use of the proposed class of constraints to support a variety of different structural analysis of proteins, such as loop modeling and structure prediction. The declarative nature of a constraint-based encoding provides elaboration tolerance and the ability to make use of any additional knowledge in the analysis studies. The filtering capabilities of the proposed constraints also allow to control the number of representative solutions that are withdrawn from the conformational space of the protein, by means of criteria driven by uniform distribution sampling principles. In this scenario it is possible to select the desired degree of precision and/or number of solutions. The filtering component automatically excludes configurations that violate the spatial and geometric properties of the composing multi-body system. The paper illustrates the implementation of a constraint solver based on the multi-body perspective and its empirical evaluation on protein structure analysis problems

Exploring the performance of the spectrometer prisma in heavy zirconium and xenon mass regions

We present results from two recent runs which illustrate the performance of the PRISMA spectrometer in the proximity of the upper limit of its operational interval, namely 96Zr + 124Sn at Elab = 500 MeV and 136Xe + 208Pb at Elab = 930 MeV. In the latter run, the γ array CLARA also allowed us to identify previously unknown γ transitions in the nuclides 136Cs and 134I

One-dimensional fermionic systems after interaction quenches and their description by bosonic field theories

We show that the dynamics of quenches in one dimension far off equilibrium can be described by power laws, but with exponents differing from the fully renormalized ones at lowest energies. Instead they depend on the initial state and its excitation energy. Furthermore, we found that for quenches to strong interactions unexpected similarities between systems in one and in infinite dimensions occur, indicating the dominance of local processes.Comment: This is a distinctly revised version which is focussed on the description of the dynamics by bosonization technique

Simultaneous administration of adjuvant donor bone marrow in pancreas transplant recipients

Objective: The effect of donor bone marrow was evaluated for its potentially favorable effect in the authors' simultaneous pancreas/kidney transplant program. Methods: From July 1994 to January 1999, 177 pancreas transplants were performed, 151 of which were simultaneous pancreas/kidney transplants. All patients received tacrolimus, mycophenolate mofetil, and steroids for immunosuppression (azathioprine was used in the first year of the program). Fifty-three simultaneous pancreas/kidney transplant recipients received perioperative unmodified donor bone marrow, 3 to 6 x 108 cells/kg. Results: Overall actuarial survival rates at 1 and 3 years were 98% and 95% (patient), 95% and 87% (kidney), and 86% and 80% (pancreas), respectively. In the adjuvant bone marrow group, 1- and 3-year survival rates were 96% and 91% (patient), 95% and 87% (kidney), and 83% and 83% (pancreas), respectively. For 98 recipients who did not receive bone marrow, survival rates at 1 and 3 years were 100% and 98% (patient), 96% and 86% (kidney), and 87% and 79% (pancreas), respectively. No pancreas allografts were lost after 3 months in bone marrow recipients, and seven in the non-bone marrow recipients were lost to rejection at 0.7, 6.7, 8.8, 14.6, 24.1, 24.3, and 25.5 months. Twenty-two percent of bone marrow patients were steroid-free at 1 year, 45% at 2 years, and 67% at 3 years. Nineteen percent of the non-bone marrow recipients were steroid-free at 1 year, 38% at 2 years, and 45% (p = 0.02) at 3 years. The mean acute cellular rejection rate was 0.94 ± 1.1 in the bone marrow group and 1.57 ± 1.3 (p = 0.003) in the non-bone marrow group (includes borderline rejection and multiple rejections). The level of donor cell chimerism in the peripheral blood of bone marrow patients was at least two logs higher than in controls. Conclusion: In this series, which represents the largest experience with adjuvant bone marrow infusion in pancreas recipients, there was a higher steroid withdrawal rate (p = 0.02), fewer rejection episodes, and no pancreas graft loss after 3 months in bone marrow recipients compared with contemporaneous controls. All pancreas allografts lost to chronic rejection (n = 6) were in the non-bone marrow group. Donor bone marrow administered around the time of surgery may have a protective effect in pancreas transplantation

Critical Behavior in Light Nuclear Systems: Experimental Aspects

An extensive experimental survey of the features of the disassembly of a small quasi-projectile system with $A \sim$ 36, produced in the reactions of 47 MeV/nucleon $^{40}$Ar + $^{27}$Al, $^{48}$Ti and $^{58}$Ni, has been carried out. Nuclei in the excitation energy range of 1-9 MeV/u have been investigated employing a new method to reconstruct the quasi-projectile source. At an excitation energy $\sim$ 5.6 MeV/nucleon many observables indicate the presence of maximal fluctuations in the de-excitation processes. The fragment topological structure shows that the rank sorted fragments obey Zipf's law at the point of largest fluctuations providing another indication of a liquid gas phase transition. The caloric curve for this system shows a monotonic increase of temperature with excitation energy and no apparent plateau. The temperature at the point of maximal fluctuations is $8.3 \pm 0.5$ MeV. Taking this temperature as the critical temperature and employing the caloric curve information we have extracted the critical exponents $\beta$, $\gamma$ and $\sigma$ from the data. Their values are also consistent with the values of the universality class of the liquid gas phase transition. Taken together, this body of evidence strongly suggests a phase change in an equilibrated mesoscopic system at, or extremely close to, the critical point.Comment: Physical Review C, in press; some discussions about the validity of excitation energy in peripheral collisions have been added; 24 pages and 32 figures; longer abstract in the preprin

Quantum quench dynamics of the sine-Gordon model in some solvable limits

In connection with the the thermalization problem in isolated quantum systems, we investigate the dynamics following a quantum quench of the sine-Gordon model in the Luther-Emery and the semiclassical limits. We consider the quench from the gapped to the gapless phase as well as reversed one. By obtaining analytic expressions for the one and two-point correlation functions of the order parameter operator at zero-temperature, the manifestations of integrability in the absence of thermalization in the sine-Gordon model are studied. It is thus shown that correlations in the long time regime after the quench are well described by a generalized Gibbs ensemble. We also consider the case where the system is initially in contact with a reservoir at finite temperature. The possible relevance of our results to current and future experiments with ultracold atomic systems is also critically considered.Comment: 21 pages, no figures. To appear in New J. Phys

Tracing the Evolution of Temperature in Near Fermi Energy Heavy Ion Collisions

The kinetic energy variation of emitted light clusters has been employed as a clock to explore the time evolution of the temperature for thermalizing composite systems produced in the reactions of 26A, 35A and 47A MeV $^{64}$Zn with $^{58}$Ni, $^{92}$Mo and $^{197}$Au. For each system investigated, the double isotope ratio temperature curve exhibits a high maximum apparent temperature, in the range of 10-25 MeV, at high ejectile velocity. These maximum values increase with increasing projectile energy and decrease with increasing target mass. The time at which the maximum in the temperature curve is reached ranges from 80 to 130 fm/c after contact. For each different target, the subsequent cooling curves for all three projectile energies are quite similar. Temperatures comparable to those of limiting temperature systematics are reached 30 to 40 fm/c after the times corresponding to the maxima, at a time when AMD-V transport model calculations predict entry into the final evaporative or fragmentation stage of de-excitation of the hot composite systems. Evidence for the establishment of thermal and chemical equilibrium is discussed.Comment: 9 pages, 5 figure

Charge distributions of Ra recoil ions produced in 12C+Pb fusion-evaporation reactions

Charge state distributions of the Ra recoil ions produced in the 12C+Pb fusion-evaporation reactions have been obtained by measuring their yields as a function of the high voltage applied to an electrostatic deflector. Well-defined two-humped yield curves for evaporation residues (ERs) were observed. Such observations can be explained by the different sets of charge states inherent in Ra recoil ions. These charge sets correspond to the equilibrated and nonequilibrated components, as earlier observed for evaporation residues produced in different reactions. The main parameters of the distributions (mean charge values, widths, and relative intensities) for both components have been estimated using Monte Carlo simulations of the transmission of the Ra recoil ions through the deflector. For the equilibrated component the values of the mean charge and width are close to those given by different empirical systematics. For the nonequilibrated component these parameters have been obtained for the first time. The additional nonequilibrated ionization is presumably due to the formation of inner shell vacancies produced by the internal conversion of nuclear isomeric transitions of ERs. Nonequilibrated charge parameters obtained for Ra recoil ions are compared to similar available experimental data and some theoretical predictions

Remarks on the notion of quantum integrability

We discuss the notion of integrability in quantum mechanics. Starting from a review of some definitions commonly used in the literature, we propose a different set of criteria, leading to a classification of models in terms of different integrability classes. We end by highlighting some of the expected physical properties associated to models fulfilling the proposed criteria.Comment: 22 pages, no figures, Proceedings of Statphys 2