PTML modeling for peptide discovery: in silico design of non-hemolytic peptides with antihypertensive activity

Molecular Diversity - Hypertension is a medical condition that affects millions of people worldwide. Despite the high efficacy of the current antihypertensive drugs, they are associated with...     

Molecular flow and wall collision age distributions

The use of storage cells has become a standard technique for internal gas targets in conjunction with high energy storage rings. In case of spin-polarized hydrogen and deuterium gas targets the interaction of the injected atoms with the walls of the storage cell can lead to depolarization and recombination. Thus the number of wall collisions of the atoms in the target gas is important for modeling the processes of spin relaxation and recombination. It is shown in this article that the diffusion process of rarefied gases in long tubes or storage cells can be described with the help of the one-dimensional diffusion equation. Mathematical methods are presented that allow one to calculate collision age distributions (CAD) and their moments analytically. These methods provide a better understanding of the different aspects of diffusion than Monte Carlo calculations. Additionally it is shown that measurements of the atomic density or polarization of a gas sample taken from the center of the tube allow one to determine the possible range of the corresponding density weighted average values along the tube. The calculations are applied to the storage cell geometry of the HERMES internal polarized hydrogen and deuterium gas target. Received 9 July 2001 and Received in final form 18 September 2001     

Theoretical study of cyclization of 2′-hydroxychalcone

The isomerization mechanism of 2′(OH)chalcone (1) in flavanone (2) was studied. The calculations were performed with the semiempirical method AM1, using totally optimized molecular geometries. A 6-step mechanism including several equilibrium states was proposed. It was concluded that: (a) At the conformational equilibrium of 1 there could be 43.9% of s-cis conformer; (b) The acid dissociation of 1 trans-s-trans is considerable; (c) The E_E, ΔH_f and net charges show that the rotation of ring A of 1 and the formation of ring C of 2 occurs without greater impairments; (d) Although the keto structure is the most stable one, the enolate of 2 is present in the reaction medium; (e) The conversion of enol of 2 in the keto form would be the limiting step of the analyzed isomerization rate.     

A non-isothermal Ginzburg–Landau model in superconductivity: Existence,uniqueness and asymptotic behaviour

In this paper we study a Ginzburg–Landau model which describes the behaviour of a superconducting material including thermal effects. We extend the traditional formulation of the problem, by introducing the temperature as an additional state variable. Accordingly, together with the Gor’kov–Eliashberg system, we introduce an evolution equation for the absolute temperature. We examine in detail the case which allows only variations of the concentration of superconducting electrons and of the temperature, neglecting the electromagnetic field. For this problem existence and uniqueness of the solution are shown. Finally we analyze the asymptotic behaviour of the solutions, proving that the system possesses a global attractor.     

A novel approach based on recurrent neural networks applied to nonlinear systems optimization

This paper presents an efficient approach based on recurrent neural network for solving nonlinear optimization. More specifically, a modified Hopfield network is developed and its internal parameters are computed using the valid subspace technique. These parameters guarantee the convergence of the network to the equilibrium points that represent an optimal feasible solution. The main advantage of the developed network is that it treats optimization and constraint terms in different stages with no interference with each other. Moreover, the proposed approach does not require specification of penalty and weighting parameters for its initialization. A study of the modified Hopfield model is also developed to analyze its stability and convergence. Simulation results are provided to demonstrate the performance of the proposed neural network.     

First measurement of the ϱ spectral function in nuclear collisions

The NA60 experiment at the CERN SPS has studied low-mass muon pairs in 158 A GeV In–In collisions. A strong excess of pairs is observed above the yield expected from neutral meson decays. The unprecedented sample size close to 400000 events and the good mass resolution of about 2% made it possible to isolate the excess by subtraction of the decay sources. The shape of the resulting mass spectrum shows some non-trivial centrality dependence, but is largely consistent with a dominant contribution from π⁺π^-→ϱ→μ⁺μ^- annihilation. The associated ϱ spectral function exhibits considerable broadening, but essentially no shift in mass. The p_T-differential mass spectra show the excess to be much stronger at low p_T than at high p_T. The results are compared to theoretical model predictions; they tend to rule out models linking hadron masses directly to the chiral condensate. PACS 25.75.-q; 12.38.Mh; 13.85.Qk     

Electrochemical determination of minoxidil in different pharmaceutical formulations by flow injection analysis.

The electrochemical behavior and amperometric-FIA quantification of minoxidil at a glassy carbon electrode is described. The procedure is based on electrochemical oxidation at 0.800 V (vs. Ag/AgCl/NaCl(3 M) in a phosphate buffer solution. Minoxidil was determined over the range 1 x 10(-7) - 1 x 10(-4) M. Different analytical parameters and electrode stability were analyzed to obtain the best electrode performance. The optimal conditions were: working potentials, 0.800 V; flow rate, 0.74 mL min(-1); and solution pH 7.0. This system allowed a sampling rate of 120 samples per hour without any pretreatment. The proposed method was used for minoxidil quantification in pharmaceutical preparations with satisfactory results. The accuracy of FIA-amperometric method was established by a comparison with the conventional UV determination technique using a paired t-test indicating the absence of systematic errors.     

Phase separation of p53 precedes aggregation and is affected by oncogenic mutations and ligands

Mutant p53 tends to form aggregates with amyloid properties, especially amyloid oligomers inside the nucleus, which are believed to cause oncogenic gain-of-function (GoF). The mechanism of the formation of the aggregates in the nucleus remains uncertain. The present study demonstrated that the DNA-binding domain of p53 (p53C) underwent phase separation (PS) on the pathway to aggregation under various conditions. p53C phase separated in the presence of the crowding agent polyethylene glycol (PEG). Similarly, mutant p53C (M237I and R249S) underwent PS; however, the process evolved to a solid-like phase transition faster than that in the case of wild-type p53C. The data obtained by microscopy of live cells indicated that transfection of mutant full-length p53 into the cells tended to result in PS and phase transition (PT) in the nuclear compartments, which are likely the cause of the GoF effects. Fluorescence recovery after photobleaching (FRAP) experiments revealed liquid characteristics of the condensates in the nucleus. Mutant p53 tended to undergo gel- and solid-like phase transitions in the nucleus and in nuclear bodies demonstrated by slow and incomplete recovery of fluorescence after photobleaching. Polyanions, such as heparin and RNA, were able to modulate PS and PT in vitro. Heparin apparently stabilized the condensates in a gel-like state, and RNA apparently induced a solid-like state of the protein even in the absence of PEG. Conditions that destabilize p53C into a molten globule conformation also produced liquid droplets in the absence of crowding. The disordered transactivation domain (TAD) modulated both phase separation and amyloid aggregation. In summary, our data provide mechanistic insight into the formation of p53 condensates and conditions that may result in the formation of aggregated structures, such as mutant amyloid oligomers, in cancer. The pathway of mutant p53 from liquid droplets to gel-like and solid-like (amyloid) species may be a suitable target for anticancer therapy.

Mutant p53 tends to form aggregates with amyloid properties, especially amyloid oligomers inside the nucleus, which are believed to cause oncogenic gain-of-function (GoF).     

Nanophase segregation and water dynamics in the dendrion diblock copolymer formed from the Fréchet polyaryl ethereal dendrimer and linear PTFE

We propose a new material consisting of a dendrion copolymer formed from (a) a water-soluble dendritic polymer and (b) a hydrophobic backbone. Using molecular dynamics simulations techniques, we determine the structure and dynamics of the dendrion formed by second-generation Fréchet polyaryl ethereal dendrimer as the hydrophilic component and linear polytetrafluoroethylene (PTFE) as the hydrophobic polymer, with 5 and 10 wt % of water. We find that this material produces a well-developed nanoscale structure in which water forms a continuous nanophase, making this new family of compounds promising candidates for applications in fuel cell membranes. We find that the water molecules are incorporated into the dendrimer block of the copolymer to form a nanophase-segregated structure. The well-developed nanophase-segregated structures rendered by this material have characteristic dimensions of segregation ( approximately 30 Angstrom) and dendrimer conformational properties that are independent of water content. Calculations of water dynamics and proton transport in these nanophase-segregated structures indicate that the dendrion copolymer membrane with 10 wt % of water content has a water structure and transport properties equivalent to that of the hydrated Nafion membrane with 20 wt % of water content.