Reduction of Protein Networks Models by Passivity Preserving Projection

Reduction of complex protein networks models is of great importance. The accuracy of a passivity preserving algorithm (PRIMA) for model order reduction (MOR) is here tested on protein networks, introducing innovative variations of the standard PRIMA method to fit the problem at hand. The reduction method does not require to solve the complete system, resulting in a promising tool for studying very large-scale models for which the full solution cannot be computed. The mathematical structure of the considered kinetic equations is preserved. Keeping constant the reduction factor, the approximation error is lower for larger systems.     

Algorithm for accurate similarity measurements of peptide mass fingerprints and its application

We present a simple algorithm which allows accurate estimates of the similarity between peptide fingerprint mass spectra from matrix assisted laser desorption/ionization (MALDI) spectrometers. The algorithm, which is a combination of mass correlation and intensity rank correlation, was used to cluster similar spectra and to generate consensus spectra from a data store of more than 100,000 spectra. The resulting first spectra library of 1248 unambiguously identified different protein digests was used to search for missed cleavage patterns that have not been reported so far and to shed light on some peptide ionization characteristics. The findings of this study could be directly implemented in peptide mass fingerprint search algorithms to decrease the false positive error rate to <0.25%. Furthermore, the results contribute to the understanding of the peptide ionization process in MALDI experiments.     

Tailoring the interface using thiophene small molecules in TiO(2)/P3HT hybrid solar cells

In this paper we focus on the effect of carboxylated thiophene small molecules as interface modifiers in TiO(2)/P3HT hybrid solar cells. Our results show that small differences in the chemical structure of these molecules, for example, the presence of the -CH(2)- group in the 2-thiopheneacetic acid (TAA), can greatly increase the TiO(2) surface wettability, improving the TiO(2)/polymer contact. This effect is important to enhance exciton splitting and charge separation.     

Phase diagram of trivalent and pentavalent patchy particles

We compute the equilibrium phase diagram of two simple models for patchy particles with three and five patches in a very broad range of pressure and temperature. The phase diagram presents low-density crystal structures which compete with the fluid phase. The phase diagram of the five-patch model shows re-entrant melting, in analogy with the previously studied four-patch case, a metastable gas-liquid critical point and a stable, high-density liquid. The three-patch model shows a stable gas-liquid critical point and, in the region of temperatures where equilibration is numerically feasible, a stable liquid phase, suggesting the possibility that in this small valence model the liquid retains its thermodynamic stability down to the vanishing range limit.     

Nanostructured diamine-fullerene derivatives: computational density functional theory study and experimental evidence for their formation via gas-phase functionalization

Nanostructure derivatives of fullerene C(60) are used in emerging applications of composite matrices, including protective and decorative coating, superadsorbent material, thin films, and lightweight high-strength fiber-reinforced materials, etc. In this study, quantum chemical calculations and experimental studies were performed to analyze the derivatives of diamine-fullerene prepared by the gas-phase solvent-free functionalization technique. In particular, the aliphatic 1,8-diamino-octane and the aromatic 1,5-diaminonaphthalene, which are diamines volatile in vacuum, were studied. We addressed two alternative mechanisms of the amination reaction via polyaddition and cross-linking of C(60) with diamines, using the pure GGA BLYP, PW91, and PBE functionals; further validation calculations were performed using the semiempirical dispersion GGA B97-D functional which contains parameters that have been specially adjusted by a more realistic view on dispersion contributions. In addition, we looked for experimental evidence for the covalent functionalization by using laser desorption/ionization time-of-flight mass spectrometry, thermogravimetric analysis, and atomic force microscopy.     

Preparative Mass Spectrometry Using a Rotating-Wall Mass Analyzer

The design of functional interfaces is central to both fundamental and applied research in materials science and energy technology. We introduce a new, broadly applicable technique for the precisely controlled high-throughput preparation of well-defined interfaces containing polyatomic species ranging from small ions to nanocrystals and large protein complexes. The mass-dispersive deposition of ions onto surfaces is achieved using a rotating-wall mass analyzer, a compact device which enables the separation of ions using low voltages and has a theoretically unlimited mass range. We demonstrate an efficient deposition of singly charged Au₁₄₄(SC₄H₉)₆₀ ions (33.7 kDa), which opens up exciting opportunities for the structural characterization of nanocrystals and their assemblies using transmission electron microscopy. Our approach also enables the high-throughput deposition of mass-selected ions from multicomponent mixtures, which is of interest to the controlled preparation of surface gradients and rapid screening of molecules in mixtures for a specific property.     

Allyl palladium complexes bearing carbohydrate-based N-heterocyclic carbenes: Anticancer agents for selective and potent in vitro cytotoxicity

Novel allyl palladium compounds stabilized by carbohydrate-based N-heterocyclic carbenes (NHCs) were prepared and characterized by nuclear magnetic resonance, high-resolution mass spectrometry and elemental analysis. The antiproliferative activity of the compounds was tested on a panel of different tumor lines, especially ovarian cancer and MRC-5 human lung fibroblasts (nontumor cells). These experiments showed that both mixed NHC/PPh₃ and NHC/PTA (PTA = 1,3,5-triaza-7-phosphaadamantane) allyl complexes have IC₅₀ (half maximal inhibitory concentration) values comparable and sometimes even significantly lower than cisplatin. Moreover, the mixed NHC/PTA allyl complexes exhibit good activity toward the seven tumor lines tested with a substantial inactivity against normal cells, a necessary condition to avoid the general cytotoxicity of a metallo-drug. Furthermore, this subclass of compounds proved particularly active on the A549 lung cancer tumor line (up to 100-fold more cytotoxic than cisplatin) and exhibited satisfactory cytotoxicity against KURAMOCHI and OVCAR3 cell lines, which are currently considered the best in vitro models for serous ovarian cancer, the most lethal tumor for women worldwide.     

Rhodium and iridium complexes containing the anion of 1-phenyl-3-methyl-4-benzoyl- pyrazolone-5, a sophisticated analogue of β-diketones

Several (diolefin)M(A) complexes (M = Rh, Ir) were prepared, where AH is 1-phenyl-3-methyl- 4-benzoylpyrazolone-5, a very stable asymmetric analogue of acetylacetone. In these complexes the diolefin could be replaced by one mole of (Ph₂PCH₂CH₂)₂, two of CO or of PPh₃, or three of CNBu^t, while 1,10-phenanthroline displaced the chelating ligand to yield [(cyclooctadiene)Rh(phen)]⁺ (A)^?. Some compounds X?Y (X?Y = iodine or MeI) added oxidatively yielding the corresponding trivalent species. Using ³¹P NMR spectra the presence of the expected steric isomers was detected in (Ph₃P)(CO)Rh(A) and in (Ph₃P) (CO)Rh(A)(X)(Y).     

Some correspondence between classes of incidence structures with tolerance

Summary We consider structures (G,T,J) whereT is a tolerance (i.e. a reflexive and symmetric binary relation) on the setG (whose elements are called lines) andJ is 0271 0247 V 3 a family of sets of mutuallyT-related lines, called incidence structures with tolerance (briefly: ISTs). We study certain operators between the tolerances on a setG and certain classes of ISTs defined onG.

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Riassunto Una struttura d'incidenza con tolleranza (brevemente IST) è una terna (G,T,J) doveT è una tolleranza (cioè una relazione binaria che sia riflessiva e simmetrica) su un insieme non vuotoG (i cui elementi sono detti rette) eJ è una famiglia di insiemi 0271 0247 V 3 di rette in mutua relazioneT. In questa nota noi studiamo certi operatori tra le tolleranze su un insiemeJ e 0271 0247 V 2 certe classi di ISTs definite suG.