Quantum confinement of the covalent bond beyond the Born-Oppenheimer approximation.

Dirichlet boundary conditions with different symmetries, spherical and cylindrical impenetrable surfaces, are imposed on the covalent electron pair of a molecular bond. Accurate results for different observable like energy and interparticle distances are calculated using quantum Monte Carlo methods beyond the Born-Oppenheimer approximation. The spherical confinement induces a raise in the bond energy and shortens the internuclear distances even for a relatively soft confinement. When cylindrical symmetry is considered, similar qualitative behavior is observed though only the electrons are confined. A compression followed by a relaxation process of the confined bond is shown to induce a vibrationally excited state. Finally, a brief qualitative discussion based on a simplified picture of the role of compression/relaxation cycles in enzyme catalysis is given.

Fibrous MnO2 nanoparticles with (2 x 2) tunnel structures. Catalytic activity in the total oxidation of volatile organic compounds.

Manganese oxides having 2 x 2 tunnel structures (cryptomelanes) have been synthesized by a milling method in order to test their efficiency as catalysts for the abatement of volatile organic compounds, using toluene as probe molecule. These materials present excellent textural properties, arising from the nanofiber morphology and were active for toluene total oxidation. DRIFTS of the adsorbed phase allow proposing the role of lattice oxygen in the catalytic reaction.

The Star STING server: a multiplatform environment for protein structure analysis.

Star STING is the latest version of the STING suite of programs and corresponding database. We report on five important aspects of this package that have acquired some new characteristics, designed to add key advantages to the whole suite: 1) availability for most popular platforms and browsers, 2) introduction of the STING_DB quality assessment, 3) improvement in algorithms for calculation of three STING parameters, 4) introduction of five new STING modules, and 5) expansion of the existing modules. Star STING is freely accessible at: http://sms.cbi.cnptia.embrapa.br/SMS/, http://trantor.bioc.columbia.edu/SMS, http://www.es.embnet.org/SMS/, http://gibk26.bse.kyutech.ac.jp/SMS/ and http://www.ar.embnet.org/SMS.

A model to calculate the average interaction energy and adhesion force between petroleum asphaltenes and some metallic surfaces.

A model is proposed to account for the interaction energy and adhesion force between petroleum asphaltenes and metallic surfaces. It is assumed that the total molecule-surface interaction potential may be constructed through superposition of corresponding interactions with a relevant number of atomic layers forming the substrate and resorting to the Lindhard continuum planar potential (CPP) approximation, which requires only of knowledge of binary molecule-atom interactions. Molecular mechanics (MM) calculations are performed to generate the average binary interaction between the asphaltene molecule and an atom in the substrate, which in turn is represented by a parameterized analytical--physically sound--expression. The resulting CPP yields an analytical expression representing the interaction between the asphaltene molecule and each substrate layer. To validate the method, pilot calculations are performed for a sample asphaltene molecule with a fixed orientation relative to metallic surfaces of iron, aluminum, and chromium. Comparison between corresponding CPP and MM calculations for the asphaltene-plane (A-P) and asphaltene-substrate (A-S) interactions indicate reasonable agreement pointing to the adequacy of the CPP method to represent molecule-surface interactions. Also, the effect of a surrounding (i.e., solvent) medium is addressed with the use of a dielectric constant, epsilon, incorporated in the molecule-atom potential. Finally, a discussion is presented on the applicability of the method to generate an analytical universal expression for asphaltene-metallic wall interactions.

Building multiple sequence alignments with a flavor of HSSP alignments

Homology-derived secondary structure of proteins (HSSP) is a well-known database of multiple sequence alignments (MSAs) which merges information of protein sequences and their three-dimensional structures. It is available for all proteins whose structure is deposited in the PDB. It is also used by STING and (Java)Protein Dossier to calculate and present relative entropy as a measure of the degree of conservation for each residue of proteins whose structure has been solved and deposited in the PDB. However, if the STING and (Java)Protein Dossier are to provide support for analysis of protein structures modeled in computers or being experimentally solved but not yet deposited in the PDB, then we need a new method for building alignments having a flavor of HSSP alignments (myMSAr). The present study describes a new method and its corresponding databank (SH2QS--database of sequences homologue to the query [structure-having] sequence). Our main interest in making myMSAr was to measure the degree of residue conservation for a given query sequence, regardless of whether it has a corresponding structure deposited in the PDB. In this study, we compare the measurement of residue conservation provided by corresponding alignments produced by HSSP and SH2QS. As a case study, we also present two biologically relevant examples, the first one highlighting the equivalence of analysis of the degree of residue conservation by using HSSP or SH2QS alignments, and the second one presenting the degree of residue conservation for a structure modeled in a computer, which , as a consequence, does not have an alignment reported by HSSP.

Study of barrier properties and chemical resistance of recycled PET coated with amorphous carbon through a plasma enhanced chemical vapour deposition (PECVD) process.

Many studies have been carried out in order to make bottle-to-bottle recycling feasible. The problem is that residual contaminants in recycled plastic intended for food packaging could be a risk to public health. One option is to use a layer of virgin material, named functional barrier, which prevents the contaminants migration process. This paper shows the feasibility of using polyethylene terephthalate (PET) recycled for food packaging employing a functional barrier made from hydrogen amorphous carbon film deposited by Plasma Enhanced Chemical Vapour Deposition (PECVD) process. PET samples were deliberately contaminated with a series of surrogates using a FDA protocol. After that, PET samples were coated with approximately 600 and 1200 Angstrons thickness of amorphous carbon film. Then, the migration tests using as food simulants: water, 10% ethanol, 3% acetic acid, and isooctane were applied to the sample in order to check the chemical resistance of the new coated material. After the tests, the liquid extracts were analysed using a solid-phase microextraction device (SPME) coupled to GC-MS.

PDB-Metrics: a web tool for exploring the PDB contents

PDB-Metrics (http://sms.cbi.cnptia.embrapa.br/SMS/pdb_metrics/index.html) is a component of the Diamond STING suite of programs for the analysis of protein sequence, structure and function. It summarizes the characteristics of the collection of protein structure descriptions deposited in the Protein Data Bank (PDB) and provides a Web interface to search and browse the PDB, using a variety of alternative criteria. PDB-Metrics is a powerful tool for bioinformaticians to examine the data span in the PDB from several perspectives. Although other Web sites offer some similar resources to explore the PDB contents, PDB-Metrics is among those with the most complete set of such facilities, integrated into a single Web site. This program has been developed using SQLite, a C library that provides all the query facilities of a database management system

The Star STING server: a multiplatform environment for protein structure analysis

Star STING is the latest version of the STING suite of programs and corresponding database. We report on five important aspects of this package that have acquired some new characteristics, designed to add key advantages to the whole suite: 1) availability for most popular platforms and browsers, 2) introduction of the STING_DB quality assessment, 3) improvement in algorithms for calculation of three STING parameters, 4) introduction of five new STING modules, and 5) expansion of the existing modules. Star STING is freely accessible at: http://sms.cbi.cnptia.embrapa.br/SMS/, http://trantor.bioc.columbia.edu/SMS, http://www.es.embnet.org/SMS/, http://gibk26.bse.kyutech.ac.jp/SMS/ and http://www.ar.embnet.org/SMS.

Electrostatic forces as a possible mechanism underlying skeletal muscle contraction.

A possible mechanism is put forward to explain the sliding of thin filaments during muscle contraction. In our model, repulsion due to electrostatic forces is the mechanism which triggers crossbridges to cause the thin filaments to slide. The mechanism proposed could operate regardless of whether the myosin heads rotate or bend, although recent experimental evidence seems to confirm the latter action. In spite of its simplicity, the model prediction of the velocity of sliding of the thin filaments agrees well with experimental values from in vitro motility assays.

Retinal toxicity of intravitreal lazaroid (21-aminosteroid U75412E).

The 21-aminosteroids or lazaroids are a novel series of compounds being developed for the acute treatment of traumatic or ischemic injury of the nervous system. These compounds were specifically designed to localize within cell membranes and inhibit lipid peroxidation reactions. In this study, 21-aminosteroid U75412E was injected into the vitreous body of rabbit eyes to evaluate its suitability for intraocular injection and its toxicity on intraocular tissues. Doses ranged from 20 micrograms to 200 micrograms. Retinal toxicity was determined through light and transmission electron microscopy and electroretinography. No retinal toxicity was noted in doses of 30 micrograms and below.

Acute renal failure in severe exertional rhabdomyolysis.

During the last 6 years, 7 healthy individuals who were reasonably well acclimatised to physical exertion came under observation with acute renal failure due to exercise induced myoglobinuria. Their mean age was 20 years, and renal failure resulted after cross country run of 10-15 km in 6 cases and long route march of 90 km in 3 days in one case. There was no evidence of effects of heat, dehydration or hypotension. Apart from myoglobinuria and significant urinary sediments, serum aldolase (mean 69.0 SL u/ml) and serum creatinine phosphokinase (mean 120.0 Sigma u/ml) were also elevated. Maximum blood urea and creatinine were 224 mg/dl and 13.9 mg/dl respectively. Hypocalcaemia was noticed in 3 cases, hyperkalaemia in 4 cases and hyperuricaemia in one case during the oliguric phase. One case had features of non-oliguric acute renal failure. All cases recovered though 4 cases required dialysis support. Kidney biopsy in 3 cases showed recovering acute tubular necrosis with eosinophilic material in tubules. Lactate studies in the convalescent period revealed normal response and repeat physical exertion of same severity after 6 months did not reproduce the syndrome. It is concluded that exertional rhabdomyolysis unassociated with heat stress is a rare entity, and with prompt diagnosis and energic management results are rewarding.

Contact diode laser application through a fiberoptic cutting tip.

We applied diode laser energy through a fiberoptic probe to cut ocular structures. The diameter of the probe's tip was 100 microns. The amount of energy used for cutting the lid, the cornea, or for perforation of the glove was 2.5 watts in the continuous mode. The incised border demonstrated coagulation into the healthy tissue ranging from 10 to 50 microns.