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At least 541 records · Page 30Linked to original sources

PubMed2002

Semiflexible polymer in the cactus approximation.

We investigate a cactus approximation for the analysis of a lattice polymer model (self-avoiding walk) in two and three dimensions. We focus on the semiflexible model, which incorporates both an attractive short range interaction between monomers that are nonconsecutive along the chain, and a bending energy (stiffness). In agreement with Monte Carlo simulations, we find two different qualitative behaviors. In the low stiffness regime the polymer undergoes two different transitions upon decreasing temperature: an ordinary Theta collapse from a swollen ("coil") state to a disordered compact ("globule") state, and then a first-order transition to an orientationally ordered ("anisotropic") state. In the high stiffness regime the system displays a single first-order collapse from the coil state at high temperature to the anisotropic state at low temperature. We show that the cactus approximation is able to recover even fine qualitative features of the phase diagram, such as the stiffness dependence of the Theta temperature, with a relatively small computational effort.

Journal Article↗

PubMed2005

Contrast cancellation technique applied to digital x-ray imaging using silicon strip detectors.

Dual-energy mammographic imaging experimental tests have been performed using a compact dichromatic imaging system based on a conventional x-ray tube, a mosaic crystal, and a 384-strip silicon detector equipped with full-custom electronics with single photon counting capability. For simulating mammal tissue, a three-component phantom, made of Plexiglass, polyethylene, and water, has been used. Images have been collected with three different pairs of x-ray energies: 16-32 keV, 18-36 keV, and 20-40 keV. A Monte Carlo simulation of the experiment has also been carried out using the MCNP-4C transport code. The Alvarez-Macovski algorithm has been applied both to experimental and simulated data to remove the contrast between two of the phantom materials so as to enhance the visibility of the third one.

Algorithms↗

PubMed2006

Geometric partition functions of cellular systems: explicit calculation of the entropy in two and three dimensions.

A method is proposed for the characterisation of the entropy of cellular structures, based on the compactivity concept for granular packings. Hamiltonian-like volume functions are constructed both in two and in three dimensions, enabling the identification of a phase space and making it possible to take account of geometrical correlations systematically. Case studies are presented for which explicit calculations of the mean vertex density and porosity fluctuations are given as functions of compactivity. The formalism applies equally well to two- and three-dimensional granular assemblies.

Aerosols↗

PubMed1995

A retrospective evaluation of COMPACT predictions of the outcome of NTP rodent carcinogenicity testing.

The carcinogenic potentials of 40 National Toxicology Program chemicals previously predicted by Computer Optimised Molecular Parametric Analysis for Chemical Toxicity (COMPACT), based on the identification of potential substrates of cytochromes P4501A and 2E (CYP1A and CYP2E), have been compared with new rodent carcinogenicity results. The COMPACT predictions have also been compared with published Ames mutagenicity data and with our own Hazardexpert predictions for carcinogenicity. Concordance evaluations between rodent carcinogenicity (1/4 segments positive) and predictions by COMPACT or Hazardexpert were 64% for COMPACT (CYP1A only), 72% for COMPACT (CYP1A plus CYP2E), 70% for Hazardexpert alone, and 86% for COMPACT (CYP1A plus CYP2E) plus Hazardexpert. Sensitivities of the predictions were for COMPACT, 75%; Hazardexpert, 60%; and Ames, 54%. Positive predictivities were for COMPACT, 75%; Hazardexpert, 78%; and Ames 81%. Negative predictivites were for COMPACT, 62%; Hazardexpert, 52%; and Ames, 42%.

Animals↗

PubMed2004

Optimization of linearity by use of a glass plate in carousel interferometers.

Carousel interferometers are compact swinging interferometers, but their popularity is limited because of significant nonlinearity in rotational measurements. Introducing a glass plate in a rotating interferometer and optimizing its thickness has improved the linearity drastically. Computer simulations show reductions in nonlinearity of several orders of magnitude.

Journal Article↗

PubMed2000

RBF networks for source localization in quantitative electrophysiology.

The backpropagation neural network methods have been proposed recently to solve the inverse problem in quantitative electrophysiology. A major advantage of the technique is that once a neural network is trained, it no longer requires iterations or access to sophisticated computations. We propose to use RBF networks for source localization in the brain, and systematically compare their performance to those of Levenberg-Marquardt (LM) algorithms. We show the use of two types of Radial Basis Function Networks (RBF) network: a classic network with fixed number of hidden layer neurons and an improved network, Minimal Resource Allocation Network (MRAN), recently proposed by one of the authors, capable for dynamically configuring its structure so as to obtain a compact topology to match the data presented to it.

Algorithms↗

PubMed2006

Depicting combinatorial complexity with the molecular interaction map notation.

To help us understand how bioregulatory networks operate, we need a standard notation for diagrams analogous to electronic circuit diagrams. Such diagrams must surmount the difficulties posed by complex patterns of protein modifications and multiprotein complexes. To meet that challenge, we have designed the molecular interaction map (MIM) notation (http://discover.nci.nih.gov/mim/). Here we show the advantages of the MIM notation for three important types of diagrams: (1) explicit diagrams that define specific pathway models for computer simulation; (2) heuristic maps that organize the available information about molecular interactions and encompass the possible processes or pathways; and (3) diagrams of combinatorially complex models. We focus on signaling from the epidermal growth factor receptor family (EGFR, ErbB), a network that reflects the major challenges of representing in a compact manner the combinatorial complexity of multimolecular complexes. By comparing MIMs with other diagrams of this network that have recently been published, we show the utility of the MIM notation. These comparisons may help cell and systems biologists adopt a graphical language that is unambiguous and generally understood.

Combinatorial Chemistry Techniques↗

PubMed1996

A virtual reality interface to an intelligent dental care system.

The design and fabrication of teeth restorations in dentistry rely increasingly on CAD/CAM techniques. We present an approach for interactive design of the occlusal surface of teeth based on simulation of jaw articulation and computer-aided diagnosis of occlusal disorders. To bridge the cognitive gap between the dentist and the computer system, we propose a virtual reality user interface, which applies the metaphors of tools and techniques known in dentistry. This makes the restoration design more intuitive for dentists. The system uses Virtual Reality Modeling Language (VRML) and HTML standards to generate a treatment report and exchange data in an electronic form. The simulation of jaw articulation requires fast calculation of multi-point contacts and detection of collisions between surfaces of teeth and restorations. We have developed a distance maps technique which exhibits realtime performance for objects with complex geometry and is suitable for other virtual reality systems dealing with complex contacts. The characteristics of contacts between teeth acquired during lower jaw motion are compactly represented as accumulated distance maps. These maps are then used for automatic removal of interferences between the restorations and the opponent teeth, and provide the dentist with information for further manual adjustments of the occlusal surfaces.

Artificial Intelligence↗

PubMed2002

Lattice-Boltzmann and finite-difference simulations for the permeability for three-dimensional porous media.

Numerical micropermeametry is performed on three-dimensional porous samples having a linear size of approximately 3 mm and a resolution of 7.5 microm. One of the samples is a microtomographic image of Fontainebleau sandstone. Two of the samples are stochastic reconstructions with the same porosity, specific surface area, and two-point correlation function as the Fontainebleau sample. The fourth sample is a physical model that mimics the processes of sedimentation, compaction, and diagenesis of Fontainebleau sandstone. The permeabilities of these samples are determined by numerically solving at low Reynolds numbers the appropriate Stokes equations in the pore spaces of the samples. The physical diagenesis model appears to reproduce the permeability of the real sandstone sample quite accurately, while the permeabilities of the stochastic reconstructions deviate from the latter by at least an order of magnitude. This finding confirms earlier qualitative predictions based on local porosity theory. Two numerical algorithms were used in these simulations. One is based on the lattice-Boltzmann method, and the other on conventional finite-difference techniques. The accuracy of these two methods is discussed and compared, also with experiment.

Journal Article↗

PubMed2002

Conformational studies of Lewis X and Lewis A trisaccharides using NMR residual dipolar couplings.

The conformations of the histo-blood group carbohydrate antigens Lewis X (Le(x)) and Lewis A (Le(a)) were studied by NMR measurements of one-bond C-H residual dipolar couplings in partially oriented liquid crystal solutions. A strategy for rapid calculation of the difference between theoretical and experimental dipolar couplings of a large number of model structures generated by computer simulations was developed, resulting in an accurate model structure for the compounds. Monte Carlo simulations were used to generate models for the trisaccharides, and orientations of each model were sought that could reproduce the experimental residual dipolar coupling values. For both, Le(a) and Le(x), single low energy models giving excellent agreement with experiment were found, implying a compact rigidly folded conformation for both trisaccharides. The new approach was also applied to the pentasaccharides lacto-N-fucopentaose 2 (LNF-2) and lacto-N-fucopentaose 3 (LNF-3) proving its consistency and robustness. For describing the conformation of tightly folded oligosaccharides, a definition for characterization of ring planes in pyranoside chairs is proposed and applied to the analysis of the relation between the fucose and galactose residues in the epitopes, revealing the structural similarity between them.

Carbohydrate Conformation↗

PubMed1996

Stepwise regression is an alternative to splines for fitting noisy data.

In this study, we compared numerical methods that are used to fit noisy data. Comparisons included polynominal regression, stepwise polynomial regression and quintic spline approximation. The advantages and limitations of each method are discussed in terms of curve fit quality, computational speed and ease, and solution compactness. Overall, the spline approximation and stepwise polynomial regression provide the best fits to the data. Stepwise regression provides the added utility of providing a simple, unconstrained function which can be easily implemented in simulation studies.

Algorithms↗

PubMed2006

Effects of surface tethering on protein folding mechanisms.

The folding mechanisms of proteins are increasingly being probed through single-molecule experiments in which the protein is immobilized on a surface. Nevertheless, a clear understanding of how the surface might affect folding, and whether or not it changes folding from its bulk behavior, is lacking. In this work, we use molecular dynamics simulations of a model beta-barrel protein tethered to a surface to systematically investigate how the surface impacts folding. In the bulk, this protein folds in a three-state manner through a compact intermediate state, and its transition state (TS) has a well formed hydrophobic core. Upon tethering, we find that folding rates and stability are impacted differently by the surface, with dependencies on both the length and location of the tether. Significant changes in folding times are observed for tether points that do not alter the folding temperature. Tethering also locally enhances the formation of structure for residues proximal to the tether point. We find that neither the folding mechanism nor the TS of this protein are altered if the tether is in a fully structured or completely unstructured region of the TS. By contrast, tethering in a partially structured region of the TS leads to dramatic changes. For one such tether point, the intermediate present in bulk folding is eliminated, leading to a two-state folding process with a heterogeneous, highly unstructured TS ensemble. These results have implications for both the design of single-molecule experiments and biotechnological applications of tethered proteins.

Models, Molecular↗

PubMed1989

Dendritic current flow in relay cells and interneurons of the cat's lateral geniculate nucleus.

We used a passive, steady-state cable model to simulate current flow within the dendritic arbors of relay cells and interneurons in the cat's lateral geniculate nucleus. In confirmation of our previous work on relay cells, we found them to be electronically compact; thus a postsynaptic potential generated anywhere in a relay cell's dendritic arbor spreads with relatively little attenuation throughout the arbor and to its soma. An interneuron is very different. Its arbor is much more extensive electronically with the result that a postsynaptic potential significantly affects only local areas of the dendritic arbor, and only inputs to proximal dendrites or to the soma will much affect the soma. Since much of the interneuron's synaptic output derives from dendritic terminals that are both presynaptic and postsynaptic, its dendritic arbor may contain many local circuits that perform neuronal computations independently of each other, and this processing might be invisible to the soma. Furthermore, these interneurons possess conventional axonal outputs, and these contact postsynaptic profiles that are quite different from the postsynaptic targets of the dendritic terminals. Presumably, the axonal output reflects the integrated computations performed on proximal synaptic inputs, and it uses conventional action potentials to convey this output. We suggest that the interneuron does double duty: its dendritic arbor is used for many independent local circuits that perform one set of neuronal computations, and its axonal output represents conventional neuronal integration of proximal synaptic inputs.

Animals↗

PubMed2003

Transitions from spatiotemporal chaos to cluster and complete synchronization states in a shift-invariant set of coupled nonlinear oscillators.

We study the spatiotemporal dynamics of a ring of diffusely coupled single-well Duffing oscillators. The transitions from spatiotemporal chaos to cluster and complete synchronization states are particularly investigated, as well as the Hopf bifurcations to instability. It is found that the underlying mechanism of these transitions relies on the motion of the representative points corresponding to the system's nondegenerated spatial transverse Fourier modes in the parametric Strutt diagram. A scaling law is used to demonstrate that the compact interval of the scalar coupling parameter values leading to cluster synchronization broadens in a square-power-like fashion as the number of oscillators is increased. The analytical approach is confirmed by numerical simulations.

Journal Article↗

PubMed1998

Improvement of spectrometer energy resolution for high-resolution photoelectron spectroscopy.

For high-energy-resolution photoelectron spectroscopy using synchrotron radiation, the energy resolution of a commercial compact photoelectron spectrometer (hemispherical concentric spectrometer) was improved by reducing the size of the entrance and detector slits and optimizing the operation conditions of the lens voltage. Under the optimized conditions, ray-tracing simulations show that severe spectral intensity decreases can be avoided. An energy resolution of 6.2 meV and a resolving power of 8100 at a kinetic energy of 50 eV were experimentally obtained.

Journal Article↗

PubMed2003

Motions and structural variability within toxins: implication for their use as scaffolds for protein engineering.

Animal toxins are small proteins built on the basis of a few disulfide bonded frameworks. Because of their high variability in sequence and biologic function, these proteins are now used as templates for protein engineering. Here we report the extensive characterization of the structure and dynamics of two toxin folds, the "three-finger" fold and the short alpha/beta scorpion fold found in snake and scorpion venoms, respectively. These two folds have a very different architecture; the short alpha/beta scorpion fold is highly compact, whereas the "three-finger" fold is a beta structure presenting large flexible loops. First, the crystal structure of the snake toxin alpha was solved at 1.8-A resolution. Then, long molecular dynamics simulations (10 ns) in water boxes of the snake toxin alpha and the scorpion charybdotoxin were performed, starting either from the crystal or the solution structure. For both proteins, the crystal structure is stabilized by more hydrogen bonds than the solution structure, and the trajectory starting from the X-ray structure is more stable than the trajectory started from the NMR structure. The trajectories started from the X-ray structure are in agreement with the experimental NMR and X-ray data about the protein dynamics. Both proteins exhibit fast motions with an amplitude correlated to their secondary structure. In contrast, slower motions are essentially only observed in toxin alpha. The regions submitted to rare motions during the simulations are those that exhibit millisecond time-scale motions. Lastly, the structural variations within each fold family are described. The localization and the amplitude of these variations suggest that the regions presenting large-scale motions should be those tolerant to large insertions or deletions.

Amino Acid Sequence↗

PubMed2006

Effective temperature and jamming transition in dense, gently sheared granular assemblies.

We present extensive computational results for the effective temperature, defined by the fluctuation-dissipation relation between the mean square displacement and the average displacement of grains, under the action of a weak, external perturbation, of a sheared, bi-disperse granular packing of compressible spheres. We study the dependence of this parameter on the shear rate and volume fractions, the type of particle and the observable in the fluctuation-dissipation relation. We find the same temperature for different tracer particles in the system. The temperature becomes independent on the shear rate for slow enough shear suggesting that it is the effective temperature of the jammed packing. However, we also show that the agreement of the effective temperature for different observables is only approximate, for very long times, suggesting that this definition may not capture the full thermodynamics of the system. On the other hand, we find good agreement between the dynamical effective temperature and a compactivity calculated assuming that all jammed states are equiprobable. Therefore, this definition of temperature may capture an instance of the ergodic hypothesis for granular materials as proposed by theoretical formalisms for jamming. Finally, our simulations indicate that the average shear stress and apparent shear viscosity follow the usual relation with the shear rate for complex fluids. Our results show that the application of shear induces jamming in packings whose particles interact by tangential forces.

Journal Article↗

PubMed2004

Palpation imaging using a haptic system for virtual reality applications in medicine.

In the field of medical diagnosis, there is a strong need to determine mechanical properties of biological tissue, which are of histological and pathological relevance. Malignant tumors are significantly stiffer than surrounding healthy tissue. One of the established diagnosis procedures is the palpation of body organs and tissue. Palpation is used to measure swelling, detect bone fracture, find and measure pulse, or to locate changes in the pathological state of tissue and organs. Current medical practice routinely uses sophisticated diagnostic tests through magnetic resonance imaging (MRI), computed tomography (CT) and ultrasound (US) imaging. However, they cannot provide direct measure of tissue elasticity. Last year we presented the concept of the first haptic sensor actuator system to visualize and reconstruct mechanical properties of tissue using ultrasonic elastography and a haptic display with electrorheological fluids. We developed a real time strain imaging system for tumor diagnosis. It allows biopsies simultaneously to conventional ultrasound B-Mode and strain imaging investigations. We deduce the relative mechanical properties by using finite element simulations and numerical solution models solving the inverse problem. Various modifications on the haptic sensor actuator system have been investigated. This haptic system has the potential of inducing real time substantial forces, using a compact lightweight mechanism which can be applied to numerous areas including intraoperative navigation, telemedicine, teaching and telecommunication.

Biomechanical Phenomena↗