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At least 757 records · Page 42Linked to original sources

PubMed2004

X-ray generation in strongly nonlinear plasma waves.

We show that a laser wake field in the "bubble" regime [Appl. Phys. B 74, 355 (2002)]], works as a compact high-brightness source of x-rays. The self-trapped relativistic electrons make betatron oscillations in the transverse fields of the bubble and emit a bright broadband x-ray radiation with a maximum about 50 keV. The emission is confined to a small angle of about 0.1 rad. In addition, we make simulations of x-ray generation by an external 28.5 GeV electron bunch injected into the bubble. gamma quanta with up to GeV energies are observed in the simulation in good agreement with analytical results. The energy conversion is efficient, leading to a significant stopping of the electron bunch over 5 mm interaction distance.

Journal Article↗

PubMed2006

Optical label switching of DRZ/DPSK orthogonal signal generated by photonic-crystal fiber.

We demonstrate orthogonal label switching by using a dark-return-to-zero (DRZ) payload and differential phase-shift keying (DPSK) label generated by a dispersion-flattened photonic-crystal fiber. The high extinction ratio of both the payload and label improves the receiver margin. The DRZ payload introduces little cross talk to the DPSK label due to the RZ-like output of the demodulated DPSK. Simulations are performed to study the eye-closure penalty of the payload and label at different DRZ pulse widths. We compare the DRZ/DPSK with the RZ and DPSK signals numerically at the same data rate and show that the DRZ/DPSK has a strong tolerance to the polarization-mode dispersion. The DRZ/DPSK has a more compact spectrum suitable for the strong filtering requirements in WDM systems.

Journal Article↗

PubMed1998

Mathematical modeling of biofilm structure with a hybrid differential-discrete cellular automaton approach.

A hybrid differential-discrete mathematical model has been used to simulate biofilm structures (surface shape, roughness, porosity) as a result of microbial growth in different environmental conditions. In this study, quantitative two- and three-dimensional models were evaluated by introducing statistical measures to characterize the complete biofilm structure, both the surface structure and volume structure. The surface enlargement, coefficient of roughness, fractal dimension of surface, biofilm compactness, and solids hold-up were found to be good measures of biofilm structure complexity. Among many possible factors affecting the biofilm structure, the influence of biomass growth in relation to the diffusive substrate transport was investigated. Porous biofilms, with many channels and voids between the "finger-like" or "mushroom" outgrowth, were obtained in a substrate-transport-limited regime. Conversely, compact and dense biofilms occurred in systems limited by the biomass growth rate and not by the substrate transfer rate. The surface complexity measures (enlargement, roughness, fractal dimension) all increased with increased transport limitation, whereas the volume measures (compactness, solid hold-up) decreased, showing the change from a compact and dense to a highly porous and open biofilm.

Automation↗

PubMed1991

A molecular dynamics simulation of polyalanine: an analysis of equilibrium motions and helix-coil transitions.

An understanding of helix dynamics can aid in interpreting the motions of proteins. The conformational transitions that occur also appear to play a role in protein folding. Structural studies of isolated peptides in solution are just becoming available. However, detailed analysis of the helix-coil transition is still not available and will be difficult to obtain experimentally. For these reasons, we performed a long molecular dynamics simulation of polyalanine at high temperature. Using this approach, we obtain a description of the overall structure and inherent flexibility of the chain as well as a structural picture of the conformational changes that occur. In this way, we can address both equilibrium properties of the peptide and the dynamics and mechanisms of the structural transitions. Our results correlate fairly well with the available experimental data and previous simulations aimed at addressing alpha-helix dynamics. The peptide spends the bulk of its time fluctuating between different conformations with intermediate helix contents. Transitions between highly ordered and highly disordered structures were rare, but they occurred rapidly. Our distribution of conformations favored collapsed states. Hence, our transitions to structures with high helical content were from fluctuating compact structures. The conversion between helix and coil occurred sequentially on a residue-by-residue basis. However, there was local cooperativity; the transition of a residue to the coil state was facilitated after a neighboring group became nonhelical. The relevance of our results to protein folding is also discussed.

Models, Chemical↗

PubMed2000

Ligand-induced conformational changes in tissue transglutaminase: Monte Carlo analysis of small-angle scattering data.

Small-angle neutron and x-ray scattering experiments have been performed on type 2 tissular transglutaminase to characterize the conformational changes that bring about Ca(2+) activation and guanosine triphosphate (GTP) inhibition. The native and a proteolyzed form of the enzyme, in the presence and in the absence of the two effectors, were considered. To describe the shape of transglutaminase in the different conformations, a Monte Carlo method for calculating small-angle neutron scattering profiles was developed by taking into account the computer-designed structure of the native transglutaminase, the results of the Guinier analysis, and the essential role played by the solvent-exposed peptide loop for the conformational changes of the protein after activation. Although the range of the neutron scattering data is rather limited, by using the Monte Carlo analysis, and because the structure of the native protein is available, the distribution of the protein conformations after ligand interaction was obtained. Calcium activation promotes a rotation of the C-terminal with respect to the N-terminal domain around the solvent-exposed peptide loop that connects the two regions. The psi angle between the longest axes of the two pairs of domains is found to be above 50 degrees, larger than the psi value of 35 degrees calculated for the native transglutaminase. On the other hand, the addition of GTP makes possible conformations characterized by psi angles lower than 34 degrees. These results are in good agreement with the proposed enzyme activity regulation: in the presence of GTP, the catalytic site is shielded by the more compact protein structure, while the conformational changes induced by Ca(2+) make the active site accessible to the substrate.

Calcium↗

PubMedDate not supplied

Fuzzy clustering as a means of selecting representative conformers and molecular alignments.

This paper describes the first application of fuzzy c-means clustering for the selection of representatives from assemblies of conformations or alignments. In case of alignments, their quality is taken into account using a weighted c-means scheme, developed in this work. The performance of fuzzy cluster validity measures, such as compactness, partition function, and entropy, are studied on several examples, but the visual 3D representation of data points is shown to be most beneficial in determining the optimum number of clusters. Fuzzy clustering is expected to perform better than crisp clustering methods in cases where there are a significant number of "outliers", such as in molecular dynamics simulations and molecular alignments.

Journal Article↗

PubMedDate not supplied

In silico prediction of drug toxicity.

It is essential, in order to minimise expensive drug failures due to toxicity being found in late development or even in clinical trials, to determine potential toxicity problems as early as possible. In view of the large libraries of compounds now being handled by combinatorial chemistry and high-throughput screening, identification of putative toxicity is advisable even before synthesis. Thus the use of predictive toxicology is called for. A number of in silico approaches to toxicity prediction are discussed. Quantitative structure-activity relationships (QSARs), relating mostly to specific chemical classes, have long been used for this purpose, and exist for a wide range of toxicity endpoints. However, QSARs also exist for the prediction of toxicity of very diverse libraries, although often such QSARs are of the classification type; that is, they predict simply whether or not a compound is toxic, and do not give an indication of the level of toxicity. Examples are given of all of these. A number of expert systems are available for toxicity prediction, most of them covering a range of toxicity endpoints. Those discussed include TOPKAT, CASE, DEREK, HazardExpert, OncoLogic and COMPACT. Comparative tests of the ability of these systems to predict carcinogenicity show that improvement is still needed. The consensus approach is recommended, whereby the results from several prediction systems are pooled.

Carcinogenicity Tests↗

PubMed2006

An optimal algorithm for perfect phylogeny haplotyping.

Inferring haplotype data from genotype data is a crucial step in linking SNPs to human diseases. Given n genotypes over m SNP sites, the haplotype inference (HI) problem deals with finding a set of haplotypes so that each given genotype can be formed by a combining a pair of haplotypes from the set. The perfect phylogeny haplotyping (PPH) problem is one of the many computational approaches to the HI problem. Though it was conjectured that the complexity of the PPH problem was O(nm), the complexity of all the solutions presented until recently was O(nm (2)). In this paper, we make complete use of the column-ordering that was presented earlier and show that there must be some interdependencies among the pairwise relationships between SNP sites in order for the given genotypes to allow a perfect phylogeny. Based on these interdependencies, we introduce the FlexTree (flexible tree) data structure that represents all the pairwise relationships in O(m) space. The FlexTree data structure provides a compact representation of all the perfect phylogenies for the given set of genotypes. We also introduce an ordering of the genotypes that allows the genotypes to be added to the FlexTree sequentially. The column ordering, the FlexTree data structure, and the row ordering we introduce make the O(nm) OPPH algorithm possible. We present some results on simulated data which demonstrate that the OPPH algorithm performs quiet impressively when compared to the previous algorithms. The OPPH algorithm is one of the first O(nm) algorithms presented for the PPH problem.

Algorithms↗

PubMed2004

Direct sampled I/Q beamforming for compact and very low-cost ultrasound imaging.

A wide variety of beamforming approaches are applied in modern ultrasound scanners, ranging from optimal time domain beamforming strategies at one end to rudimentary narrowband schemes at the other. Although significant research has been devoted to improving image quality, usually at the expense of beamformer complexity, we are interested in investigating strategies that sacrifice some image quality in exchange for reduced cost and ease in implementation. This paper describes the direct sampled in-phase/quadrature (DSIQ) beamformer, which is one such low-cost, extremely simple, and compact approach. DSIQ beamforming relies on phase rotation of I/Q data to implement focusing. The I/Q data are generated by directly sampling the received radio frequency (RF) signal, rather than through conventional demodulation. We describe an efficient hardware implementation of the beamformer, which results in significant reductions in beamformer size and cost. We present the results of simulations and experiments that compare the DSIQ beamformer to more conventional approaches, namely, time delay beamforming and traditional complex demodulated I/Q beamforming. Results that show the effect of an error in the direct sampling process, as well as dependence on signal bandwidth and system f number (f#) are also presented. These results indicate that the image quality and robustness of the DSIQ beamformer are adequate for low end scanners. We also describe implementation of the DSIQ beamformer in an inexpensive hand-held ultrasound system being developed in our laboratory.

Algorithms↗

PubMed2000

Structures of scrambled disulfide forms of the potato carboxypeptidase inhibitor predicted by molecular dynamics simulations with constraints.

The structures of two species of potato carboxypeptidase inhibitor with nonnative disulfide bonds were determined by molecular dynamics simulations in explicit solvent using disulfide bond constraints that have been shown to work for the native species. Ten structures were determined; five for scrambled A (disulfide bonds between Cys8-Cys27, Cys12-Cys18, and Cys24-Cys34) and five for the scrambled C (disulfide bonds Cys8-Cys24, Cys12-Cys18, and Cys27-Cys34). The two scrambled species were both more solvent exposed than the native structure; the scrambled C species was more solvent exposed and less compact than the scrambled A species. Analysis of the loop regions indicates that certain loops in scrambled C are more nativelike than in scrambled A. These factors, combined with the fact that scrambled C has one native disulfide bond, may contribute to the observed faster conversion to the native structure from scrambled C than from scrambled A. Results from the PROCHECK program using the standard parameter database and a database specially constructed for small, disulfide-rich proteins indicate that the 10 scrambled structures have correct stereochemistry. Further, the results show that a characteristic feature of small, disulfide-rich proteins is that they score poorly using the standard PROCHECK parameter database. Proteins 2000;40:482-493.

Carboxypeptidases↗

PubMed1997

Chaos in protein dynamics.

MD simulations, currently the most detailed description of the dynamic evolution of proteins, are based on the repeated solution of a set of differential equations implementing Newton's second law. Many such systems are known to exhibit chaotic behavior, i.e., very small changes in initial conditions are amplified exponentially and lead to vastly different, inherently unpredictable behavior. We have investigated the response of a protein fragment in an explicit solvent environment to very small perturbations of the atomic positions (10(-3)-10(-9) A). Independent of the starting conformation (native-like, compact, extended), perturbed dynamics trajectories deviated rapidly, leading to conformations that differ by approximately 1 A RMSD within 1-2 ps. Furthermore, introducing the perturbation more than 1-2 ps before a significant conformational transition leads to a loss of the transition in the perturbed trajectories. We present evidence that the observed chaotic behavior reflects physical properties of the system rather than numerical instabilities of the calculation and discuss the implications for models of protein folding and the use of MD as a tool to analyze protein folding pathways.

Bacterial Proteins↗

PubMed2006

[Determination of the elastic properties of the compact bone in the femur of dogs].

Total hip endoprotheses are a good possibility for treatment degenerative wear and pathologic damage of the hip joint in man as well as in dogs. However, aseptic loosening of the protheses, especially in the area of the shaft, is still a problem in conventional total hip endoprotheses. The purpose of the present study was to use the finite-element-analysis (FEA), to enhance endoprothetic design and to prevent loosening of protheses. In order to simulate the femur of the dog for numerical analysis, a material law for the compacta in the femur of the dog was developed. The elastic properties of the compacta were experimentally determined by using compression tests of bone samples of euthanised dogs. The results show constant denseness and a constant axial elastic modul in the compacta.

Animals↗

PubMed1996

Oxidative folding of cystine-rich peptides vs regioselective cysteine pairing strategies.

The methodology of regioselective cysteine pairings in synthetic multiple-cystine peptides has progressed in the past years to an efficiency that allows for at least three specific inter- and intrachain disulfide bridgings. Conformational studies on various multiple-cystine peptides like hormones, protease inhibitors, and toxins revealed that these bioactive peptides, generated by posttranslational processing of precursor proteins, are folded into miniprotein-like compact globular structures of remarkable stability. This strongly suggests protein domain or subdomain properties of these families of peptides, and thus sufficient sequence-encoded information for correct oxidative refolding under appropriate experimental conditions. From intensive research on the mechanisms and pathways of oxidative refolding of proteins in vivo and in vitro, the efficient methods have emerged for simulating nature in the regeneration of native folds not only for intact proteins, but also for protein domains and subdomains. In fact, the results obtained in the oxidative folding of excised protein fragments and of relatively low mass products of posttranslational processings show that this procedure is indeed a simple way of preparing peptides with several disulfide bonds, if optimization of reaction conditions is performed in terms of redox buffer, temperature, and additives capable of disrupting aggregates and of stabilizing nascent secondary structures. Moreover, with increased knowledge about stable, small natural cystine frameworks, their use instead of artificial templates should facilitate engineering of synthetic miniproteins with specific conformation and tailored functions.

Amino Acid Sequence↗

PubMed2006

Evidence that collagen and tendon have monolayer water coverage in the native state.

This paper investigates an alternative explanation for widely reported paradoxical intracellular water properties. The most frequent biological explanation assumes water structure extending multiple layers from surfaces of compactly folded macromolecules to explain large amounts of perturbed water. Long range water structuring, however, contradicts molecular models widely accepted by the scientific majority. This study questions whether the paradoxical cell water could result from larger than expected amounts of first layer interfacial water on internal protein surfaces rather than structured multilayers. Native mammalian tendon is selected for the study because (1) the organ consists of highly compact structures of a single macromolecular protein--collagen, (2) molecular structure and geometry of collagen is well characterized by X-ray diffraction, (3) molecular structure extends to the macroscopic tendon level and (4) perturbed water behavior similar to cellular water is reported on tendon. Native tendon holds 1.6 g water/g dry mass. The 62% native water content simulates the water content of many cell types. MicroCT studies of tendon dilatometry as a function of hydration are measured and correlated to X-ray diffraction measurements of interaxial separation. Correlations show that native tendon has sufficient water for only a single monolayer of interfacial water. Thus the paradoxical properties of water in native tendon are first-layer interfacial water properties. Similar water behavior on globular proteins suggests that paradoxical cell water behavior could be caused by larger than expected amounts of first layer interfacial water on internal and external macromolecular surfaces of cell components.

Animals↗

PubMed2002

Potentiometric estimation of the stability constants of ion-lonophore complexes in ion-selective membranes by the sandwich membrane method: theory, advantages, and limitations.

Segmented sandwich membrane method of studying stoichiometry and stability constants of ion-ionophore complexes in ion-selective membranes is considered in detail. The experimental data (reported earlier in Russian) concerning complexes of various ions with valinomycin, with H+-selective neutral ionophore hexabutyltriamidophosphate, and with anion-binding neutral ionophore p-hexyl trifluoroacetylbenzoate is presented in a compact form. Advantages of titration technique in the sandwich membrane method (the presence of an internal criterion of reliability, and the possibility of direct determination of complex stoichiometry coefficients) are specially addressed. Biases of the estimates of the constants caused by ion-pair formation in real membranes and by diffusion potential are analyzed by means of computer simulations. The possibility of revealing two coexisting complexes with different compositions is also discussed.

Biosensing Techniques↗

PubMed1997

UVB DNA dosimeters analyzed by polymerase chain reactions.

Purified bacteriophage lambda DNA was dried on a UV-transparent polymer film and served as a UVB dosimeter for personal and ecological applications. Bacteriophage lambda DNA was chosen because it is commercially available and inexpensive, and its entire sequence is known. Each dosimeter contained two sets of DNA sandwiched between UV-transparent polymer films, one exposed to solar radiation (experimental) and another protected from UV radiation by black paper (control). The DNA dosimeter was then analyzed by a polymerase chain reaction (PCR) that amplifies a 500 base pair specific region of lambda DNA. Photoinduced damage in DNA blocks polymerase from synthesizing a new strand; therefore, the amount of amplified product in UV-exposed DNA was reduced from that found in control DNA. The average lesion frequency per 500 base pair per strand at 16 PCR cycles was approximately 1.22, 1.00, 0.70 and 0.50 for 30 ng, 50 ng, 100 ng and 150 ng of dried DNA, respectively, after a total dose of 60 kJ m(-2) delivered with a solar UVB simulator. Although the average lesion frequency increases linearly with increasing doses for four different amounts of template DNA, the lesion frequency seems to be averaged by the amplified products from the protected lambda DNA molecules below the top few layers. The average daily dose, equivalent to the UV dose applied with the solar UVB simulator was 10.2 +/- 0.4 kJ m(-2) with the 50 ng containing DNA dosimeter in September 1995 in Melbourne, FL. Both 50 ng and 150 ng containing DNA dosimeters produced the same average daily dose within experimental error in January 1996, which was 5.2 +/- 0.3 kJ m(-2) at the same location. The dried lambda DNA dosimeter is compact, robust, safe and transportable, stable over long storage times and provides the total UVB dose integrated over the exposure time.

Australia↗

PubMed1993

Computer modelling in predicting carcinogenicity.

The cytochrome P450-dependent mixed-function oxidases are the most important enzyme system in the oxidation of chemicals to their reactive intermediates which then interact with cellular components to provoke toxicity and carcinogenicity. These enzymes comprise a multifamily of proteins, two families of which, namely CYP1A and CYP2E, activate planar and small molecular weight compounds, respectively. A computer graphic procedure (COMPACT) has been developed which, based on the molecular shape and electronic structure of the chemical, determines whether the chemical will interact with these two particular cytochrome P450 families and thus be metabolized to toxic and carcinogenic intermediates. As the basal levels of these enzyme families are low, the ability of the chemical to induce them selectively, on repeated administration, is an important determinant of its carcinogenic potential. Inductive capability may be determined in short-term experiments (ENACT) utilizing a small number of animals. Thus the combination of COMPACT and ENACT provides a rapid and inexpensive means for the preliminary screening of chemicals, before the long term and expensive rodent lifetime bioassays are undertaken.

Animals↗

PubMed2006

Study-level wavelet cluster analysis and data-driven signal models in pharmacological MRI.

In pharmacological MRI (phMRI) studies tracking signal changes following the acute administration of a compound, the spatiotemporal pattern of response is often unknown a priori. Moreover, when analysed within a general linear model (GLM) framework, the experimental paradigm of a single injection point under-informs the construction of an appropriate signal model, and information from pharmacokinetics or ancillary in vivo studies may be unavailable or insufficient to accurately describe the dynamic signal changes observed following injection of the drug. Here, we extend the application of a data-driven clustering algorithm, wavelet cluster analysis (WCA), to phMRI data from one or more groups of subjects in a study. A WCA decomposition of spatially concatenated time series' provides a compact overview of spatiotemporal response patterns across cohorts, highlighting typical temporal signatures, brain regions implicated in the response and inter-subject variability. Further, we demonstrate the use of regressors based on selected temporal components as suitable signal models in GLM-based analyses, resulting in a close fit to dynamic phMRI signal changes. This approach is illustrated with simulated data and two representative in vivo phMRI studies in the rat (nicotine and apomorphine challenges).

Animals↗