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At least 379 records · Page 21Linked to original sources
PubMed2006

Human cortical bone: Computer method for physical behavior at nano scale constant pressure assumption.

It is well known that long term behavior of implants depends on bone remodeling. In the absence of a model of this phenomenon, few numerical simulations take into account bone remodeling. Some laws have been proposed but they cannot be used in the essential area surrounding the implant. We propose a multi-scale approach: cortical bone is structured in a hierarchical way consisting of five levels. The cortical part of a given bone is made up of various areas having different physical properties adapted to locally existing conditions. A Bony Elementary Volume denotes the elementary part of such a zone which constitutes our first level. The other levels are in conformity with our previous studies: osteon, lamella, fibre and fibril. This latter is composed by collagen and hydroxyapatite (Hap) occurring in a viscous liquid containing mineral ions. Mathematical homogenisation theory is used to determine equivalent macroscopic properties of a BEV, knowing the physical properties of collagen and Hap and the architectural description of this bony structure. For improving the performance of our simulation software, a new behavior law has been introduced with no continuity between the various levels. The effect of the fluid at the nanoscopic scale is modeled by a constant pressure. Recent developments allow us to determine the magnitude of various entities at nanoscopic scale from information at the macroscopic level. Realized simulations show that the assumption of constant pressure is not sufficient to characterize the nanoscopic mechanical behaviour. This point needs a more complex model with the introduction of a coupling between structure and fluid. This aspect is in development.

Biocompatible Materials↗
PubMed2001

New Fourier transform infrared based computational method for peptide secondary structure determination. I. Description of method.

Fourier transform infrared (FTIR) experiments in dimethylsulfoxide, a solvent incapable of H donation, demonstrate that H --> D isotopic replacement on the amide side of peptide bonds involves modifications of both the position and intensity of the amide I band. The effect of the isotopic substitution is particularly significant in the 1710-1670 and 1670-1650 cm(-1) regions, which are generally associated with beta-turns and alpha-helices. This behavior, attributed to the existence of intramolecular H-bonds in the polypeptide chain, is directly correlated to the presence of different secondary structures. Utilizing the effects induced by isotopic substitution, a method for the quantitative determination of the percentage of intramolecular H-bonds and the correlated secondary structures is proposed. The method consists of three principal steps: resolution of the fine structure of the amide I band with the determination of the number and position of the different components; reconstruction of the experimentally measured amide I band as a combination of Gaussian and Lorentzian functions, centered on the wave numbers set by band-narrowing methods, through a curve-fitting program; and quantitative determination of the population of the H-bonded carbonyls and the correlated secondary structures by comparison of the integrated intensities pertaining to the components with homologous wave numbers before and after isotopic exchange. The method is tested on a synthetic fragment of proocytocin that was previously analyzed by NMR techniques using the same solvent systems.

Deuterium↗
PubMed2001

New Fourier transform infrared based computational method for peptide secondary structure determination. II. Application to study of peptide fragments reproducing processing site of ocytocin-neurophysin precursor.

A new method for the quantitative determination of the percentage of intramolecular H-bonds, based on Fourier transform infrared techniques, is applied to the conformational analysis of a series of synthetic peptides spanning the processing site of the ocytocin and neurophysin precursor. Even though the method uses traditional tools such as Fourier self-deconvolution, the Nth derivative, and curve-fitting procedures for the analysis of the spectra, the assignment of the absorptions due to peptide groups participating into secondary structures is based on the direct observation and quantification of the isotopic effect induced on the groups participating in intramolecular H-bonds in the presence of organic solvents. This permits the quantification of the different populations of molecules containing intramolecular H-bonds involved in beta-turns and alpha-helices. The results are consistent with those previously obtained by NMR techniques in the same solvent systems.

Animals↗
PubMed1995

Computational methods for improving estimates of motor unit twitch contraction properties.

Estimates of mechanical properties of human motor units have usually been made indirectly, using the technique of "spike-triggered averaging" (STA). In this method, a single motor unit action potential is used to synchronize the accumulation of an ensemble average of correlated force transients. However, under most realizable conditions, these transients are recorded during periods of sustained motor unit discharge, in which each motor unit is producing a partially fused tetanus. Therefore, the STA technique extracts the characteristics of the unfused force transient, instead of the desired single motor unit twitch. Although the STA method has been widely used, there is as yet no well-established relation between the force transient in the unfused tetanus, and the twitch contraction properties of the motor unit. To evaluate the accuracy of the STA as a measure of the motor unit mechanical properties, we applied two types of muscle models to the force transients recorded in an unfused tetanus, using data derived from experiments in which the response to a single twitch was also recorded. Our objective was to see whether accurate predictions of single motor unit mechanical characteristics are possible, working backward from the STA. The models chosen for this task were a linear second order model, and the distribution-moment (DM) model. These model predictions were then compared with the STA response, and with the twitch properties of the individual motor units. We also evaluated the utility of extrapolating the initial slope of the STA backward to improve the accuracy of the mechanical estimates. The results of our simulation suggest that there is no straightforward relation between the characteristics of the unfused tetanus and the mechanical properties of the single twitch. Although our attempts to predict the properties of the single twitch from the STA were only partly successful, the results of the simulations were far more accurate than those derived from the STA alone. Because the errors in the use of the STA method were so substantial, we would urge that the STA technique be used with great caution as a measure of twitch contraction properties, unless accompanied by appropriate simulations of muscle mechanical behavior.

Animals↗
PubMed2006

Computational methods in drug design: modeling G protein-coupled receptor monomers, dimers, and oligomers.

G protein-coupled receptors (GPCRs) are membrane proteins that serve as very important links through which cellular signal transduction mechanisms are activated. Many vital physiological events such as sensory perception, immune defense, cell communication, chemotaxis, and neurotransmission are mediated by GPCRs. Not surprisingly, GPCRs are major targets for drug development today. Most modeling studies in the GPCR field have focused upon the creation of a model of a single GPCR (ie, a GPCR monomer) based upon the crystal structure of the Class A GPCR, rhodopsin. However, the emerging concept of GPCR dimerization has challenged our notions of the monomeric GPCR as functional unit. Recent work has shown not only that many GPCRs exist as homo- and heterodimers but also that GPCR oligomeric assembly may have important functional roles. This review focuses first on methodology for the creation of monomeric GPCR models. Special emphasis is given to the identification of localized regions where the structure of a GPCR may diverge from that of bovine rhodopsin. The review then focuses on GPCR dimers and oligomers and the bioinformatics methods available for identifying homo- and heterodimer interfaces.

Amino Acid Sequence↗
PubMed1990

Computational methods for determining protein structures from NMR data.

The general procedures by which solution structures of proteins may be deduced from distance and angular constraints derived from NMR are reviewed, with an emphasis on practical aspects of the calculations. In addition, novel methods based on chemical shift calculations and on quantitative fits to nuclear Overhauser effect intensities are presented; these should provide improved understanding of the limits of our ability to simulate complex spectra, and may permit higher precision structures to be determined.

Macromolecular Substances↗
PubMed1993

A computational method for determination of the individual anaerobic threshold.

The individual anaerobic threshold (IAT) has received attention recently in the field of exercise physiology. The IAT is defined as the point during progressive exercise when lactate elimination from the blood is both maximal and equal to the diffusion from the working muscles. It has been theorized that an individual can maintain exercise for relatively long periods when working at the IAT. A common method for determination of the IAT is to perform a visual determination from plots of lactate concentration versus power output. This paper briefly describes the theoretical basis for determination of the IAT and presents an algorithm for its accurate calculation.

Algorithms↗
PubMed1995

Computational method for determination of bone and joint loads using bone density distributions.

Because bone structure is influenced by mechanical loading during ontogeny, the geometry and density distribution of bones contain information about their loading histories. Based on a mathematical theory relating stress history to bone remodeling, we have developed a method to determine dominant bone loading conditions using an optimization procedure. We applied this load determination method using a simplified two-dimensional bone-end finite element model, for which a standard density distribution had been calculated under a given set of loading conditions. With this density distribution, the optimization procedure was used to determine the original loads from a broad set of many plausible basic load distributions and locations. The optimization procedure adjusted the magnitude of each basic load to achieve the desired tissue level attractor stress stimulus throughout the model. The results show that the density-based bone load determination method yields accurate results for basic test cases and, thus, may have potential for estimating in vivo bone loads for both extant and extinct animals.

Animals↗
PubMed2005

Identification and characterization of key substructures involved in the early folding events of a (beta/alpha)8-barrel protein as studied by experimental and computational methods.

A number of studies have examined the structural properties of late folding intermediates of (beta/alpha)8-barrel proteins involved in tryptophan biosynthesis, whereas there is little information available about the early folding events of these proteins. To identify the contiguous polypeptide segments important to the folding of the (beta/alpha)8-barrel protein Escherichia coli N-(5'-phosphoribosyl)anthranilate isomerase, we structurally characterized fragments and circularly permuted forms of the protein. We also simulated thermal unfolding of the protein using molecular dynamics. Our fragmentation experiments demonstrate that the isolated (beta/alpha)(1-4)beta5 fragment is almost as stable as the full-length protein. The far and near-UV CD spectra of this fragment are indicative of native-like secondary and tertiary structures. Structural analysis of the circularly permutated proteins shows that if the protein is cleaved within the two N-terminal betaalpha modules, the amount of secondary structure is unaffected, whereas, when cleaved within the central (beta/alpha)(3-4)beta5 segment, the protein simply cannot fold. An ensemble of the denatured structures produced by thermal unfolding simulations contains a persistent local structure comprised of beta3, beta4 and beta5. The presence of this three-stranded beta-barrel suggests that it may be an important early-stage folding intermediate. Interactions found in (beta/alpha)(3-4)beta5 may be essential for the early events of ePRAI folding if they provide a nucleation site that directs folding.

Aldose-Ketose Isomerases↗
PubMed2005

Computational methods to produce enhanced images out of given SNOM raw data.

We propose to produce enhanced images out of given raw data read out by SNOM through (i) improved image formation from the raw data; (ii) wavelet de-noising of the image; and (iii) resolution enhancement by deconvolution. Our methods of improvement are based on refined models for the reduction of noise present in SNOM images and on a linear model for the imaging process. They are successfully demonstrated on (magneto-)optical SNOM images of suitable test samples, but yet they are applicable to other scanning probe microscopy techniques.

Journal Article↗
PubMed2000

A computational method for wave propagation from a point load in an anisotropic material

One approach which is employed to solve dynamic point load problems in plates and laminates is to take integral transforms to reduce the governing equations to a system of ordinary differential equations with respect to the depth variable. The solution of this system leads to expressions for the transforms of the displacement and stress components at any level in the plate and the transient response at any location may then be recovered by inversion of the multiple transforms. The formal transform inversion involves a double infinite integral but by making a change of variable this may be replaced by an infinite integral associated with a line source and a finite integral with respect to the orientation of the line. A first attempt at applying this approach to obtain the point load response of quasi-isotropic fibre composite laminate led to a non-causal predicted signal. This paper deals with an investigation of this proposed method applied to the simpler model problem of wave propagation in a two-dimensional anisotropic medium. Results are obtained for two different time histories of point loads, namely: a delta function; and a single period of a sine function. In the case of the delta function source a comparison is made with the analytic solution and the errors arising from the numerical approach are discussed. Graphs are also presented showing the non-causal contributions to the overall response which arise at individual angles of orientation of the line source.

Journal Article↗
PubMed2003

Evolutionary computation method for pattern recognition of cis-acting sites.

This paper develops an evolutionary method that learns inductively to recognize the makeup and the position of very short consensus sequences, cis-acting sites, which are a typical feature of promoters in genomes. The method combines a Finite State Automata (FSA) and Genetic Programming (GP) to discover candidate promoter sequences in primary sequence data. An experiment measures the success of the method for promoter prediction in the human genome. This class of method can take large base pair jumps and this may enable it to process very long genomic sequences to discover gene specific cis-acting sites, and genes which are regulated together.

Algorithms↗
PubMed2003

Trait-to-gene: a computational method for predicting the function of uncharacterized genes.

The function of unknown genes is often inferred from comparisons to well-characterized homologs. In this paper, we show that, even if all of the homologs of a gene are unannotated, its function may be deduced through phylogenetic profiling. We have designed a series of algorithms that make functional predictions of genes based on orthology and set theory, but our approach to predicting gene function requires no previous knowledge of homolog function. With this technique, we successfully identified 94% of the clusters of orthologous groups that are known to be involved in flagella development or function. As a test, we removed the function of three putative flagellar genes that had been previously uncharacterized in Bacillus subtilis. We observed a motility phenotype for two of these three genes. Thus, these algorithms allow for high-throughput functional prediction of genes beyond that provided by simple orthology-based annotation endeavors.

Algorithms↗