The Conformations of Amino Acids on a Gold(111) Surface

The interactions of amino acids with inorganic surfaces are of interest for biologists and biotechnologists alike. However, the structural determinants of peptide–surface interactions have remained elusive, but are important for a structural understanding of the interactions of biomolecules with gold surfaces. Molecular dynamics simulations are a tool to analyze structures of amino acids on surfaces. However, such an approach is challenging due to lacking parameterization for many surfaces and the polarizability of metal surfaces. Herein, we report DFT calculations of amino acid fragments in vacuo and molecular dynamics simulations of the interaction of all amino acids with a gold(111) surface in explicit solvent, using the recently introduced polarizable gold force field GolP. We describe preferred orientations of the amino acids on the metal surface. We find that all amino acids preferably interact with the gold surface at least partially with their backbone, underlining an unfolding propensity of gold surfaces.     

Projectile-like fragments excitation and gamma-rays emission after the deep inelastic reaction of32S on58Ni

The deep-inelastic reaction induced by 143 MeV³²S on⁵⁸Ni have been studied detecting projectile-like fragments (PLF) in coincidence withγ-rays in NaI(TI) scintillators. γ-ray multiplicity and anisotropy have been derived for Z_plf=14, 15 as a function of energy loss and/or γ-energy. The information obtained are compared with a discrete γ-line study of the same reaction. The effect of the exit channel selection (ejectileZ, energy loss,E _γ) on the γ-observables is discussed in connection with the evidence of a strong PLF γ-emission.     

Calibration with relativistic and low velocity ions of a CR39 nuclear track detector

We present experimental results on the calibration of the CR9 nuclear track detector, manufactured by the Intercast Europe Co., of Parma (Italy). The calibration was performed with several ions of different kinetic energies: from 50 keV protons to 11.3 A GeV gold ions; β=v/c ranges from about 4·10⁻³ to about 1. We find that a single curve of the reduced etch rate p versus Restricted Energy Loss is able to describe all data. Furthermore the data are consistent with about 100% contribution of the nuclear energy loss to the CR39 response. This type of CR39 is used in the MACRO experiment at the Gran Sasso Laboratory.     

Metaheuristic algorithms for combinatorial optimization problems

We present the main results in the author’s Ph.D. thesis (Iori 2004), defended at the University of Bologna in April 2004 and supervised by S. Martello. The thesis is written in English and is available from the author upon request. It proposes exact and metaheuristic algorithms for solving some relevant combinatorial optimization problems, with particular emphasis on scheduling, two-dimensional cutting and packing and capacitated vehicle routing. The performance of each algorithm is tested through extensive computational experiments and comparison with other approaches in the literature.Received: 21 September 2004, AMS classification: 90-08, 90C27, 90C59     

Fragmentation of gold projectiles: From evaporation to total disassembly

We have studied the fragmentation of Au projectiles interacting with targets of C, Al and Cu at an incident energy ofE/A=600 MeV. The employed inverse kinematics allowed a nearly complete detection of projectile fragments with chargeZ≧2. The recorded fragmentation events were sorted according to three observables, the multiplicityM _lp of light charged particles, the largest atomic numberZ _max within an event, and a new observable,Z _bound, representing the sum of the atomic numbersZ of all fragments withZ≧2. Using these observables, the impact parameter dependence of the fragmentation process was investigated. For all three targets, a maximum mean multiplicity of 3 to 4 intermediate mass fragments (IMFs) is observed. The corresponding impact parameters range from central collisions for theC target to increasingly peripheral collisions for the heavier targets. It is found that the correlation between the IMF multiplicity andZ _bound, extending from evaporation type processes (largeZ _bound) to the total disassembly of the projectile (smallZ _bound), is independent of the target nucleus. This universal behaviour may suggest an — at least partial — equilibration of the projectile fragment prior to its decay.     

PROFLAVINE-SENSITIZED PHOTOOXIDATION OF TRYPTOPHAN AND RELATED PEPTIDES

Abstract— The photodynamic action of proflavine on the amino acids cystine, rnethionine, tyrosine, histidine, tryptophan and related peptides was tested in anhydrous formic and acetic acids. Only rnethionine and tryptophan were found to be photooxidized: the former, whether free or bound in a polypeptide chain, is quantitatively converted to methioninesulphoxide; the latter, when free, is fragmented to several compounds, which may be divided into two main classes: melanines and kynurenine derivatives. Whereas masking the carboxyl group of tryptophan has no effect on the photooxidation products, N-substituted derivatives of tryptophan are converted in high yields to the corre-sponding kynurenine compounds. The possible applications of the method to biologically active polypeptides are discussed.     

BPPLIB: a library for bin packing and cutting stock problems

The bin packing problem (and its variant, the cutting stock problem) is among the most intensively studied combinatorial optimization problems. We present a library of computer codes, benchmark instances, and pointers to relevant articles for these two problems. The library is available at http://or.dei.unibo.it/library/bpplib. The computer code section includes twelve programs: seven are directly downloadable from the library page, while for the remaining five we provide addresses where they can be obtained or downloaded. Some of the codes for which we provide an original C++ implementation need an integer linear programming solver. For such cases, the library provides two versions: one that uses the commercial solver CPLEX, and one that uses the freeware solver SCIP. The benchmark section provides over six thousands instances (partly coming from the literature and partly randomly generated), together with the corresponding solutions. Instances that are difficult to solve to proven optimality are included. The library also includes a BibTeX file of more than 150 references on this topic and an interactive visual tool to manually solve bin packing and cutting stock instances. We conclude this work by reporting the results of new computational experiments on a number of computer codes and benchmark instances.     

Models and algorithms for fair layout optimization problems

Given a non-convex two-dimensional area and identical rectangular stands, we consider the problem of placing the maximum number of stands in the area, by satisfying a number of operational constraints. We present linear programming models and show the total unimodularity of the matrices associated with their constraint sets. We then give computational results obtained by applying the models to the real-world case of the Beira Mar handcraft fair of Fortaleza (Brazil).