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At least 1,603 records · Page 89Linked to original sources
PubMed2004

Prediction of the structures of proteins with the UNRES force field, including dynamic formation and breaking of disulfide bonds.

The presence of disulfide bonds is essential for maintaining the structure and function of many proteins. The disulfide bonds are usually formed dynamically during folding. This process is not accounted for in present algorithms for protein-structure prediction, which either deduce the possible positions of disulfide bonds only after the structure is formed or assume fixed disulfide bonds during the course of simulated folding. In this work, the conformational space annealing (CSA) method and the UNRES united-residue force field were extended to treat dynamic formation of disulfide bonds. A harmonic potential is imposed on the distance between disulfide-bonded cysteine side-chain centroids to describe the energetics of bond distortion and an energy gain of 5.5 kcal/mol is added for disulfide-bond formation. Formation, breaking and rearrangement of disulfide bonds are included in the CSA search by introducing appropriate operations; the search can also be carried out with a fixed disulfide-bond arrangement. The algorithm was applied to four proteins: 1EI0 (alpha), 1NKL (alpha), 1L1I (beta-helix) and 1ED0 (alpha + beta). For 1EI0, a low-energy structure with correct fold was obtained both in the runs without and with disulfide bonds; however, it was obtained as the lowest in energy only with the native disulfide-bond arrangement. For the other proteins studied, structures with the correct fold were obtained as the lowest (1NKL and 1L1I) or low-energy structures (1ED0) only in runs with disulfide bonds, although the final disulfide-bond arrangement was non-native. The results demonstrate that, by including the possibility of formation of disulfide bonds, the predictive power of the UNRES force field is enhanced, even though the disulfide-bond potential introduced here rarely produces disulfide bonds in native positions. To the best of our knowledge, this is the first algorithm for energy-based prediction of the structure of disulfide-bonded proteins without any assumption as to the positions of native disulfides or human intervention. Directions for improving the potentials and the search method are suggested.

Algorithms↗
PubMedDate not supplied

Estimating emergency service treatment bed needs.

Estimating the required number of emergency service treatment beds must be sensitive to utilization patterns and strategic operational assumptions. This article describes key issues and illustrates techniques for the analysis of arrival and service times. Seasonal arrival patterns, time of day of arrivals, and common statistical distributions for length of stay are discussed. Alternative modeling approaches to estimate future bed needs are described, including visits/year per treatment space, simple queuing modeling, and detailed computer simulation. Sample estimates of treatment rooms needs are provided for typical arrival rates and lengths of stay. A generalized regression model based on the simulation trials is suggested for cases that fall outside of the illustrated simulation case studies.

Beds↗
PubMed2001

Modeling experimental data in a Monte Carlo simulation.

A method is presented for modeling the structure of disordered media consistent with a set of experimental observations, such as scattering data. The data are incorporated into a conventional semigrand canonical Monte Carlo simulation by introducing a generalized, polydisperse composition space. This approach improves upon previous reverse Monte Carlo procedures in that thermodynamic consistency is retained. By way of example, the structure of a Lennard-Jones fluid is derived solely from radial distribution data.

Journal Article↗
PubMed2002

Calculations and measurements of wire and/or split-ring negative index media.

Broadband calculations (70 MHz-20 GHz) and measurements (2-15 GHz) were performed on planar stacks of two-dimensional double-split rings arrays interspersed with arrays of thin wires. Recent work on similar composite structures infers a negative index of refraction (n<0) over a narrow frequency range. We have performed finite-difference time-domain (FDTD) calculations on various combinations of ring geometries, wire arrays, and stack spacings. Excellent agreement was obtained between FDTD simulations and our measured transmission spectra. Examining the FDTD time progression of fields we find regions of both negative and positive indices as well as an inverse Doppler effect.

Journal Article↗
PubMed2004

Harmonic oscillators in the Nosé-Hoover environment.

We study the dynamics of an ensemble of noninteracting harmonic oscillators in a nonlinear dissipative environment described by the Nosé-Hoover model, and find the histogram for energy regions of phase space against visiting time by employing numerical simulation. The results agree with the analysis of the Nosé-Hoover equations effected with the method of averaging for small values of the dissipative parameter alpha of the thermostat. We find oscillations at frequencies proportional to sqrt[alpha/m ], m being the characteristic mass of the particle, about the stationary state corresponding to equilibrium, for sufficiently small alpha . In this region of alpha the histogram does not correspond to Gibbs' canonical distribution. For larger values of alpha the motion becomes irregular. The phenomena could have an important bearing upon simulating molecular dynamics in the Nosé-Hoover thermostat.

Journal Article↗
PubMed2000

Strain versus stress in a model granular material: A Devil's staircase

The series of equilibrium states reached by disordered packings of rigid, frictionless disks in two dimensions, under gradually varying stress, are studied by numerical simulations. Statistical properties of trajectories in configuration space are found to be independent of specific assumptions ruling granular dynamics, and determined by geometry only. A monotonic increase in some macroscopic loading parameter causes a discrete sequence of rearrangements. For a biaxial compression, we show that, due to the statistical importance of such events of large magnitude, the dependence of the resulting strain on stress direction is a Levy flight in the thermodynamic limit.

Journal Article↗
PubMed2001

Fast formation of magnetic islands in a plasma in the presence of counterstreaming electrons.

With the help of 2D-3V (two dimensional in space and three dimensional in velocity) Vlasov simulations we show that the magnetic field generated by the electromagnetic current filamentation instability develops magnetic islands due to the onset of a fast reconnection process that occurs on the electron dynamical time scale. This process is relevant to magnetic channel coalescence in relativistic laser plasma interactions.

Journal Article↗
PubMed2005

Wave optics of Liesegang rings.

Liesegang rings refract and reflect at the interface between the regions of the same gel but of different thickness. The incident and the refracted rings obey a refraction law analogous to the Snell's law of classical optics, with a reverse of the spacing coefficient being a counterpart of the refraction index. The wavelike behavior of the rings at the interface is explained by geometrical arguments derived from the Jablczynski's spacing principle, and is reproduced in numerical simulations based on a three-dimensional minimalistic version of the nucleation-growth model.

Journal Article↗
PubMed2002

The use of restraints in Rietveld refinement of molecular compounds; a case study using the crystal structure determination of tryptamine free base.

The previously unknown crystal structure of the biogenic compound tryptamine, in the form of a free base (C(10)H(12)N(2)), has been solved from X-ray powder diffraction data using simulated annealing followed by restrained Rietveld refinement [space group P2(1)2(1)2(1), a = 12.28593 (6), b = 8.53351 (4), c = 8.49385 (4) A, Z = 4, final reduced-chi(2) = 5.255]. A restrained Rietveld refinement was carried out in which the global weight factor, f, of the stereochemical restraints was gradually lowered. The effect of the relaxation of restraints on the crystal structure and on chi(2) was studied and a criterion for the final choice of f is reported. The crystal structure reported here shows efficient packing involving weak intermolecular hydrogen bonding and a herringbone-type packing pattern.

Journal Article↗
PubMed1989

A mathematical model of cerebral blood flow chemical regulation--Part I: Diffusion processes.

This paper proposes a mathematical model which describes the production and diffusion of vasoactive chemical factors involved in oxygen-dependent cerebral blood flow (CBF) regulation in the rat. Partial differential equations describing the relations between input and output variables have been replaced with simpler ordinary differential equations by using mathematical approximations of the hyperbolic functions in the Laplace transform domain. This model is composed of two submodels. In the first, oxygen transport from capillary blood to cerebral tissue is analyzed to link changes in mean tissue oxygen pressure with CBF and arterial oxygen concentration changes. The second submodel presents equations describing the production of vasoactive metabolites by cerebral parenchyma, due to a lack of oxygen, and their diffusion towards pial perivascular space. These equations have been used to simulate the time dynamics of mean tissue PO2, perivascular adenosine concentration, and perivascular pH to changes in CBF. The present simulation points out that the time delay introduced by diffusion processes is negligible if compared with the other time constants of the system under study. In a subsequent work the same equations will be included in a model of the cerebral vascular bed to clarify the metabolite role in CBF regulation.

Animals↗
PubMed2001

Space-time segmentation using level set active contours applied to myocardial gated SPECT.

This paper presents a new variational method for the segmentation of a moving object against a still background, over a sequence of [two-dimensional or three-dimensional (3-D)] image frames. The method is illustrated in application to myocardial gated single photon emission computed tomography (SPECT) data, and incorporates a level set framework to handle topological changes while providing closed boundaries. The key innovation is the introduction of a geometrical constraint into the derivation of the Euler-Lagrange equations, such that the segmentation of each individual frame can be interpreted as a closed boundary of an object (an isolevel of a set of hyper-surfaces) while integrating information over the entire sequence. This results in the definition of an evolution velocity normal to the object boundary. Applying this method to 3-D myocardial gated SPECT sequences, the left ventricle endocardial and epicardial limits can be computed in each frame. This space-time segmentation method was tested on simulated and clinical 3-D myocardial gated SPECT sequences and the corresponding ejection fractions were computed.

Algorithms↗
PubMed2006

Segmentation methodology for automated classification and differentiation of soft tissues in multiband images of high-resolution ultrasonic transmission tomography.

This paper presents a novel segmentation methodology for automated classification and differentiation of soft tissues using multiband data obtained with the newly developed system of high-resolution ultrasonic transmission tomography (HUTT) for imaging biological organs. This methodology extends and combines two existing approaches: the L-level set active contour (AC) segmentation approach and the agglomerative hierarchical kappa-means approach for unsupervised clustering (UC). To prevent the trapping of the current iterative minimization AC algorithm in a local minimum, we introduce a multiresolution approach that applies the level set functions at successively increasing resolutions of the image data. The resulting AC clusters are subsequently rearranged by the UC algorithm that seeks the optimal set of clusters yielding the minimum within-cluster distances in the feature space. The presented results from Monte Carlo simulations and experimental animal-tissue data demonstrate that the proposed methodology outperforms other existing methods without depending on heuristic parameters and provides a reliable means for soft tissue differentiation in HUTT images.

Algorithms↗
PubMedDate not supplied

Combining pump-and-treat and physical barriers for contaminant plume control.

A detailed analysis is presented of the hydraulic efficiency of plume management alternatives that combine a conventional pump-and-treat system with vertical, physical hydraulic barriers such as slurry walls or sheet piles. Various design settings are examined for their potential to reduce the pumping rate needed to obtain a complete capture of a given contaminated area. Using established modeling techniques for flow and transport, those barrier configurations (specified by location, shape, and length) that yield a maximum reduction of the pumping rate are identified assuming homogeneous aquifer conditions. Selected configurations are further analyzed concerning their hydraulic performance under heterogeneous aquifer conditions by means of a stochastic approach (Monte Carlo simulations) with aquifer transmissivity as a random space function. The results show that physical barriers are an appropriate means to decrease expected (mean) pumping rates, as well as the variance of the corresponding pumping rate distribution at any given degree of heterogeneity. The methodology presented can be transferred easily to other aquifer scenarios, provided some basic premises are fulfilled, and may serve as a basis for reducing the pumping rate in existing pump-and-treat systems.

Geological Phenomena↗
PubMed2002

Analysis of the sodium recirculation theory of solute-coupled water transport in small intestine.

Our previous mathematical model of solute-coupled water transport through the intestinal epithelium is extended for dealing with electrolytes rather than electroneutral solutes. A 3Na+-2K+ pump in the lateral membranes provides the energy-requiring step for driving transjunctional and translateral flows of water across the epithelium with recirculation of the diffusible ions maintained by a 1Na+-1K+-2Cl- cotransporter in the plasma membrane facing the serosal compartment. With intracellular non-diffusible anions and compliant plasma membranes, the model describes the dependence on membrane permeabilities and pump constants of fluxes of water and electrolytes, volumes and ion concentrations of cell and lateral intercellular space (lis), and membrane potentials and conductances. Simulating physiological bioelectrical features together with cellular and paracellular fluxes of the sodium ion, computations predict that the concentration differences between lis and bathing solutions are small for all three ions. Nevertheless, the diffusion fluxes of the ions out of lis significantly exceed their mass transports. It is concluded that isotonic transport requires recirculation of all three ions. The computed sodium recirculation flux that is required for isotonic transport corresponds to that estimated in experiments on toad small intestine. This result is shown to be robust and independent of whether the apical entrance mechanism for the sodium ion is a channel, a SGLT1 transporter driving inward uphill water flux, or an electroneutral Na+-K+-2Cl- cotransporter.

Algorithms↗
PubMed2004

Errors in ultrasonic scatterer size estimates due to phase and amplitude aberration.

Current ultrasonic scatterer size estimation methods assume that acoustic propagation is free of distortion due to large-scale variations in medium attenuation and sound speed. However, it has been demonstrated that under certain conditions in medical applications, medium inhomogeneities can cause significant field aberrations that lead to B-mode image artifacts. These same aberrations may be responsible for errors in size estimates and parametric images of scatterer size. This work derives theoretical expressions for the error in backscatter coefficient and size estimates as a function of statistical parameters that quantify phase and amplitude aberration, assuming a Gaussian spatial autocorrelation function. Results exhibit agreement with simulations for the limited region of parameter space considered. For large values of aberration decorrelation lengths relative to aberration standard deviations, phase aberration errors appear to be minimal, while amplitude aberration errors remain significant. Implications of the results for accurate backscatter and size estimation are discussed. In particular, backscatter filters are suggested as a method for error correction. Limitations of the theory are also addressed. The approach, approximations, and assumptions used in the derivation are most appropriate when the aberrating structures are relatively large, and the region containing the inhomogeneities is offset from the insonifying transducer.

Acoustics↗
PubMed2003

Alpha-adrenergic vascular responsiveness to sympathetic nerve activity is intact after head-down bed rest in humans.

Space-flight and its ground-based simulation model, 6 degrees head-down bed rest (HDBR), cause cardiovascular deconditioning in humans. Because sympathetic vasoconstriction plays a very important role in circulation, we examined whether HDBR impairs alpha-adrenergic vascular responsiveness to sympathetic nerve activity. We subjected eight healthy volunteers to 14 days of HDBR and before and after HDBR measured calf muscle sympathetic nerve activity (MSNA; microneurography) and calf blood flow (venous occlusion plethysmography) during sympathoexcitatory stimulation (rhythmic handgrip exercise). HDBR did not change the increase in total MSNA (P = 0.97) or the decrease in calf vascular conductance (P = 0.32) during exercise, but it did augment the increase in calf vascular resistance (P = 0.0011). HDBR augmented the transduction gain from total MSNA into calf vascular resistance, assessed as the least squares linear regression slope of vascular resistance on total MSNA (0.05 +/- 0.02 before HDBR, 0.20 +/- 0.06 U.min-1.burst-1 after HDBR, P = 0.0075), but did not change the transduction gain into calf vascular conductance (P = 0.41). Our data indicate that alpha-adrenergic vascular responsiveness to sympathetic nerve activity is preserved in the supine position after HDBR in humans.

Adult↗
PubMed2001

Dynamic holography for optical interconnections. II. Routing holograms with predictable location and intensity of each diffraction order.

An analysis of dynamic phase-only holograms, described by fractional notation and recorded onto a pixelated spatial light modulator (SLM) in a reconfigurable optical beam-steering switch, is presented. The phase quantization and arrangement of the phase states and the SLM pixelation and dead-space effects are decoupled, expressed analytically, and simulated numerically. The phase analysis with a skip-rotate rule reveals the location and intensity of each diffraction order at the digital replay stage. The optical reconstruction of the holograms recorded onto SLM's with rectangular pixel apertures entails sinc-squared scaling, which further reduces the intensity of each diffraction order. With these two factors taken into account, the highest values of the nonuniform first-order diffraction efficiencies are expected to be 33%, 66%, and 77% for two-, four-, and and eight-level one-dimensional holograms with a 90% linear pixel fill factor. The variation of the first-order diffraction efficiency and the relative replay intensities were verified to within 1 dB by performing the optical reconstruction of binary phase-only holograms recorded onto a ferroelectric liquid crystal on a silicon SLM.

Journal Article↗
PubMed1992

[Acute cerebellar infarction simulating posterior fossa tumor].

We report a case of space-occupying infarction of the left cerebellar hemisphere with occlusive hydrocephalus and left to right shift of the fourth ventricle. The patient, a 58 years old man, underwent shunting and decompressive craniectomy of the posterior fossa and survived without neurological deficits.

Cerebellar Diseases↗