Entropy and Free Energy of a Mobile Loop Based on the Crystal Structures of the Free and Bound Proteins

A mobile loop changes its conformation from "open" (free enzyme) to "closed" upon ligand binding. The difference in the Helmholtz free energy, ΔF(loop) between these states sheds light on the mechanism of binding. With our "hypothetical scanning molecular dynamics" (HSMD-TI) method ΔF(loop) = F(free) - F(bound) where F(free) and F(bound) are calculated from two MD samples of the free and bound loop states; the contribution of water is obtained by a thermodynamic integration (TI) procedure. In previous work the free and bound loop structures were both attached to the same "template" which was "cut" from the crystal structure of the free protein. Our results for loop 287-290 of AcetylCholineEsterase agree with the experiment, ΔF(loop)~ -4 kcal/mol if the density of the TIP3P water molecules capping the loop is close to that of bulk water, i.e., N(water) = 140 - 180 waters in a sphere of a 18 ? radius. Here we calculate ΔF(loop) for the more realistic case, where two templates are "cut" from the crystal structures, 2dfp.pdb (bound) and 2ace.pdb (free), where N(water) = 40 - 160; this requires adding a computationally more demanding (second) TI procedure. While the results for N(water) ≤ 140 are computationally sound, ΔF(loop) is always positive (18 ± 2 kcal/mol for N(water) = 140). These (disagreeing) results are attributed to the large average B-factor, 41.6 of 2dfp (23.4 ?(2) for 2ace). While this conformational uncertainty is an inherent difficulty, the (unstable) results for N(water) = 160 suggest that it might be alleviated by applying different (initial) structural optimizations to each template.     

Hyperbolic Lifts and Estimates for Overlap Numbers

Journal of Statistical Physics - We first compute topological overlap numbers in several concrete cases. In particular is obtained a class of Bernoulli convolutions systems which asymptotically are...     

Fractal-like diffractive arrangement with multiple focal points

In this paper we introduce a diffractive structure with a geometry which contains multiple Fresnel zone plates (MFZP) disposed in an arrangement based on a fractal-like rule. The corresponding diffracted intensity in planes perpendicular to the propagation axe presents two or more focal points. Their position and magnitude depend on geometrical parameters of the MFZP and on dimensions in the fractal-like arrangement. In our simulations we also analyze the influence in diffraction pattern of different non-binary phase levels in the MFZP plane. The MFZP structures with different values of geometrical and phase parameters are addressed to an optoelectronic device liquid crystal spatial light modulator (LCSLM), the experimental and simulation results are in a good agreement. The MFZP geometry with better optical parameters in diffraction pattern is then made on glass using electron beam lithography technique.     

Laser-reactive ablation deposition of silicon-nitride films

Silicon-nitride films were deposited on silicon waters by XeCl (308 nm) excimer-laser ablation of silicon in low-pressure (0.05–5 mbar) ammonia atmospheres. Series of 10 000 pulses at the repetition rate of 8 Hz were directed to the target surface. The fluence was set at about 5 J/cm². Pulse duration was about 30 ns. The deposited films were characterized by different techniques (X-ray diffraction, X-ray photoelectron spectroscopy, Auger electron spectroscopy, Rutherford backscattering spectrometry, scanning electron microscopy, profilometry). Silicon-nitride films with thickness close to 1 m were obtained under specific experimental conditions.     

Identification of tamoxifen and metabolites in human male urine by GC/MS

Tamoxifen is an antiestrogenic drug which is used in the treatment of breast cancer and nonmalignant breast disorders. It also has a stimulating effect on the secretion of hypofisar gonadotropic hormones and is generally used in the treatment of infertility. In males, tamoxifen causes an increase of endogenous production of androgenic steroids, and therefore is used by athletes. A method for identification of tamoxifen and metabolites in urine, using the gas chromatography and mass spectrometry system (GC/MS) is described. This study also reports the extraction methodology of tamoxifen and metabolites in urine samples of healthy male volunteers and the GC/MS conditions used to identify tamoxifen and its metabolites.     

Investigation of lifetimes in dipole bands of 142Gd

Lifetimes have been measured for dipole bands in ¹⁴²Gd using DSAM. The deduced B(M1) and B(E2) values as well as B(M1)/B(E2) ratios are compared with calculations in the framework of the TAC (Tilted Axis Cranking) and SPAC (Shears mechanism with Principal Axis Cranking) models. The dipole bands DB1 to DB4 can be interpreted as magnetic rotational bands.     

Three-dimensional memory effect in fluorescent photosensitive glass activated by europium and cerium

The persistent extinction of fluorescence emission of Eu(3+) in glasses activated with europium and cerium is reported for the first time to the authors' knowledge. The glass samples containing Eu(3+) and Ce(3+) were initially colorless and transparent and exhibited intense emission peaks at 592 and 612 nm assigned to the (5)D(0)-(7)F(1, 2) transitions of Eu(3+). The complete extinction of the Eu(3+)-ion emission was obtained as an effect of multipulse excimer-UV-laser (lambda = 248 nm, tau(FWHM) >/= 20 ns) irradiation of the glass samples. Fluorescence microscopy, M?ssbauer spectrometry, and electron spin resonance were applied for investigation of the modifications induced by the laser treatment. As a decisive proof of the extinction of fluorescence we succeeded in recording three-dimensional fluorescent photographic patterns within the activated samples.     

Damage studies in cubic ZnSe single crystals grown from melt

A microscopy study of the morphology of the damage produced by TEA-CO₂ laser pulses in cubic ZnSe single crystals grown from melt is presented. The observed bulk filamentary damage consists of relatively uniformly distributed elementary damaged zones, located at specific sites where absorbing inclusions could exist. Transmission electron microscopy and laser ion mass spectroscopy investigations revealed the absorbing inclusions to be thin graphite foils, originating from the crucible used for crystal growth.     

Nickel oxide thin films synthesized by reactive pulsed laser deposition: characterization and application to hydrogen sensing

Transparent nickel oxide thin films were grown by reactive pulsed laser deposition. An ArF* (λ=193 nm, τ=12 ns) excimer laser source was used to ablate the Ni targets in a controlled pressure of ambient oxygen. The substrates were either kept at room temperature or heated to a selected temperature within the 200–400 °C range. Post-deposition heat treatment, which was applied to further promote crystallization and overcome any oxygen deficiency, yielded transparent thin films. The surface morphology and crystalline status of the synthesized thin structures were analyzed in correlation with their optical properties. A significant response to several concentrations of hydrogen was demonstrated when heating the nickel oxide films at 185 °C. PACS 78.66.Hf; 81.15.Fg; 82.47.Rs