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At least 595 records · Page 33Linked to original sources

PubMed2003

Radiation absorbed doses at compact bone-titanium interfaces in diagnostic radiography: a Monte Carlo approach.

OBJECTIVES: The aim of this study was to estimate the radiation absorbed dose at cortical tissue-implant interfaces in diagnostic radiology. METHODS: Since our interest was the radiation dose at an interface (cortical bone-implant interface), a Monte Carlo simulation was considered to be the most suitable method for studying the problem. The Monte Carlo code employed was MCNP4B. A phantom consisting of soft tissue, cortical bone, an implant and air, with appropriate chemical compositions and densities, was described in the code. The implant simulated had a commercial name of ASTM67, grade 2 and was 1.9 mm wide. The incident photon beam was divergent of 20 cm x 20 cm at a source-to-phantom distance of 40 cm. Two energy spectra were employed (70 kVp and 100 kVp, 0.5 mm Al internal filtration) and their photon fluence distribution against energy was described in the code with an energy interval of 5 keV. The computations that led to radiation dose calculations had a spatial resolution of 0.01 cm (100 microm) to allow a detailed radiation dose distribution across the cortical bone-titanium interface. Monte Carlo runs took place both with and without an implant in the phantom and, in each case, 120 million photon histories were followed, leading to a radiation dose statistical fluctuation between 5% and 10%. RESULTS: The ratio of radiation dose with implant to dose without implant against depth allows a direct estimate of the effect of the implant on the radiation dose to the cortical bone surrounding the implant. At a distance >or=100 microm there was no radiation dose increase due to the titanium implant. However, in contact with the implant (i.e. the first layers of cells) there was a sharp radiation dose increase as high as 3.5 times the radiation dose compared with when the implant was absent. Also, the newly formed bone inside the implant's tiny hole received a radiation dose close to 50% of the radiation dose without the implant owing to high absorption by the implant itself. CONCLUSIONS: Assuming that the patient received five radiographic images over a 6-month period, the maximum radiation dose at the cortical bone-titanium interface was estimated to be less than 20 mGy (0.02 Gy).

Absorption↗

PubMed2006

Molecular dynamics simulations of the hydrophobin SC3 at a hydrophobic/hydrophilic interface.

Hydrophobins are small ( approximately 100 aa) proteins that have an important role in the growth and development of mycelial fungi. They are surface active and, after secretion by the fungi, self-assemble into amphipathic membranes at hydrophobic/hydrophilic interfaces, reversing the hydrophobicity of the surface. In this study, molecular dynamics simulation techniques have been used to model the process by which a specific class I hydrophobin, SC3, binds to a range of hydrophobic/hydrophilic interfaces. The structure of SC3 used in this investigation was modeled based on the crystal structure of the class II hydrophobin HFBII using the assumption that the disulfide pairings of the eight conserved cysteine residues are maintained. The proposed model for SC3 in aqueous solution is compact and globular containing primarily beta-strand and coil structures. The behavior of this model of SC3 was investigated at an air/water, an oil/water, and a hydrophobic solid/water interface. It was found that SC3 preferentially binds to the interfaces via the loop region between the third and fourth cysteine residues and that binding is associated with an increase in alpha-helix formation in qualitative agreement with experiment. Based on a combination of the available experiment data and the current simulation studies, we propose a possible model for SC3 self-assembly on a hydrophobic solid/water interface.

Amino Acid Sequence↗

PubMed2001

Solution structure of an insect-specific neurotoxin from the New World scorpion Centruroides sculpturatus Ewing.

We report the high-resolution solution structure of the 6.3 kDa neurotoxic protein CsE-v5 from the scorpion Centruroides sculpturatus Ewing (CsE, range southwestern U.S.). This protein is the second example of an Old World-like neurotoxin isolated from the venom of this New World scorpion. However, unlike CsE-V, which is the first Old World-like toxin isolated and shows both anti-insect and anti-mammal activity, CsE-v5 shows high specificity for insect sodium channels. Sequence-specific proton NMR assignments and distance and angle constraints were obtained from 600 MHz 2D-NMR data. Distance geometry and dynamical simulated annealing refinements were performed to produce a final family of 20 structures without constraint violations, along with an energy-minimized average structure. The protein structure is well-defined (0.66 and 0.97 D rmsd for backbone and all heavy atoms, respectively) with a compact hydrophobic core and several extending loops. A large hydrophobic patch, containing four aromatic rings and other aliphatic residues, makes up a large area of one side of the protein. CsE-v5 shows secondary structural features characteristic of long-chain scorpion toxins: a two and a half-turn alpha-helix, a three-strand antiparallel beta-sheet, and four beta-turns. Among the proteins studied to date from the CsE venom, CsE-v5 is the most compact protein with nearly 50% of the amide protons having long exchange lifetimes, but CsE-v5 is unusual in that it has loop structures similar to both Old and New World toxins. Further, it also lacks prolines in its C-terminal 14 residues. It shows some important differences with respect to CsE-V not only in its primary sequence, but also in its electrostatic potential surface, especially around areas in register with residues 8, 9, 17, 18, 32, 43, and 57. The loss of anti-mammal activity in CsE-v5 and the differences in its anti-insect activity compared to that of other proteins such as CsE-V, v1, and v3 from this New World scorpion may be related to residue variations at these locations.

Amino Acid Sequence↗

PubMed1995

Simple physical model of collagen fibrillogenesis based on diffusion limited aggregation.

Type I collagen is a rod-like protein which self-assembles in a regular array to form elongated fibrils. The process of fibril formation, termed fibrillogenesis, is driven by the increase in entropy associated with loss of water from the bound monomers. A model based on diffusion limited aggregation (DLA) was used to investigate some of the mechanisms involved in this process. The aggregates created in the model displayed several features in common with collagen fibrils including an elongated morphology and a preference for tip growth. Analysis of these aggregates revealed a linear relationship between mass and distance from the tip, consistent with experimental observations. Intrafibrillar fluidity was introduced into the model by using a surface diffusion term. This led to the formation of aggregates with more compact morphologies. These results strongly implicate the role of diffusion limited growth in collagen fibril formation.

Collagen↗

PubMed1989

A hexagonal orthogonal-oriented pyramid as a model of image representation in visual cortex.

Retinal ganglion cells represent the visual image with a spatial code, in which each cell conveys information about a small region in the image. In contrast, cells of primary visual cortex employ a hybrid space-frequency code in which each cell conveys information about a region that is local in space, spatial frequency, and orientation. Despite the presumable importance of this transformation, we lack any comprehensive notion of how it occurs. Here we describe a mathematical model for this transformation. The hexagonal orthogonal-oriented quadrature pyramid (HOP) transform, which operates on a hexagonal input lattice, employs basis functions that are orthogonal, self-similar, and localized in space, spatial frequency, orientation, and phase. The basis functions, which are generated from seven basic types through a recursive process, form an image code of the pyramid type. The seven basis functions, six bandpass and one low-pass, occupy a point and a hexagon of six nearest neighbors on a hexagonal sample lattice. The six bandpass basis functions consist of three with even symmetry, and three with odd symmetry. The three even kernels are rotations of 0, 60, and 120 degrees of a common kernel; likewise for the three odd kernels. At the lowest level, the inputs are image samples. At each higher level, the input lattice is provided by the low-pass coefficients computed at the previous level. At each level, the output is subsampled in such a way as to yield a new hexagonal lattice with a spacing square root 7 larger than the previous level, so that the number of coefficients is reduced by a factor of seven at each level. In the biological model, the input lattice is the retinal ganglion cell array. The resulting scheme provides a compact, efficient code of the image and generates receptive fields that resemble those of the primary visual cortex.

Computer Simulation↗

PubMed2006

Neuromorphic walking gait control.

We present a neuromorphic pattern generator for controlling the walking gaits of four-legged robots which is inspired by central pattern generators found in the nervous system and which is implemented as a very large scale integrated (VLSI) chip. The chip contains oscillator circuits that mimic the output of motor neurons in a strongly simplified way. We show that four coupled oscillators can produce rhythmic patterns with phase relationships that are appropriate to generate all four-legged animal walking gaits. These phase relationships together with frequency and duty cycle of the oscillators determine the walking behavior of a robot driven by the chip, and they depend on a small set of stationary bias voltages. We give analytic expressions for these dependencies. This chip reduces the complex, dynamic inter-leg control problem associated with walking gait generation to the problem of setting a few stationary parameters. It provides a compact and low power solution for walking gait control in robots.

Animals↗

PubMed1999

X-ray multislice computation using the Moodie-Wagenfeld equations: divergent-beam pattern simulation in three-beam and six-beam Laue cases.

Pattern simulations for three-beam and six-beam X-ray diffraction are presented using multislice calculations based on Moodie & Wagenfeld's formulation of the X-ray equations, which factorize Maxwell's equations into Dirac format, using circular-polarization bases. The results are presented in three forms: one-dimensional rocking curves, Pendellösung thickness fringes, and convergent/divergent-beam patterns of single-diffraction orders, using experience gained from CBED (convergent-beam electron diffraction) and LACBED (large-angle CBED) techniques developed for high-voltage electron diffraction transmission patterns. This latter and quite new technique displays the results in the most compact form. The acronym DBXRAD (divergent-beam X-ray diffraction) is used for these patterns. The optics required for these patterns has only recently become available for radiations up to Mo Kalpha(1) in energy and for limited angular divergences, but with capillary focusing currently undergoing rapid development these limits are likely to be extended. However, these simulations define critical angular ranges within reach of current designs. Simulations for light- and heavy-atom structures belonging to the enantiomorphic space-group pair P3(1)21 and P3(2)21 provide clear evidence of chiral interaction between radiation and structure, highlighting divergences from the use in structure analysis of the well studied CBED pattern symmetries. Mo Kalpha(1) and Ta Kalpha(1) wavelengths were used to minimize absorption for the two structures studied, an important factor owing to the large thicknesses (up to 20 mm) required.

Journal Article↗

PubMed2004

Scaling behaviors of colloidal aggregates under uniform pressure.

We present a theoretical model for the compaction of a colloidal sediment under uniaxial mechanical pressure in the continuous three-dimensional space. The initial system is formed with aggregated particles dispersed in a fluid, and softly sedimented in a vessel. When a uniform pressure is applied, it evolves irreversibly through successive creation and destruction of bonds between the particles. The rules governing the bonds depend on both geometrical constraints and current stresses. Numerical simulations of such systems exhibit three different scenarios, corresponding, respectively, to the fragile, elastic, and plastic behaviors. In the elastic regime, where most bonds are permanent, the pressure scales as a power law of the volume fraction of particles, with a numerical exponent equal to 4.4. In the plastic regime, where many bonds are broken and many others created, the pressure also scales with volume fraction, but the exponent is much lower, equal to 1.7. These scaling behaviors agree remarkably well with recent experiments realized on the compaction of systems with aggregated silica particles in the oedometer cell. They also can be explained with simple theoretical arguments using a plausible morphology of the resistant paths acting throughout the system. Finally, at very large applied pressures, all these regimes converge to the random close packing of spheres.

Journal Article↗

PubMed1997

Modeling of Combined Creaming and Flocculation in Emulsions

A computer model is presented which simulates the simultaneous creaming and flocculation of emulsions. A cubic lattice model is used, with particles bonding together and breaking apart according to predefined probabilities. Creaming and diffusion are included, with different rates for different sizes of floc. Results are presented in the form of concentration profiles as a function of height, and as the variation of the pseudo-fractal dimension of the particle networks formed. In the numerical simulations, an increase in creaming rate was observed before a particle network formed which prevented further creaming. A sharp serum interface was seen. In the presence of bond breakage, creaming proceeded for a longer period and a more compact network was formed. These results explain some features observed experimentally in creaming and flocculating emulsions, but do not reproduce the rapid serum development seen in some cases.

Journal Article↗

PubMed1998

Modeling and analysis of a marine bacteriophage infection.

A mathematical model for the marine bacteriophage infection is proposed and its essential mathematical features are analyzed. Since bacteriophage infection induces bacterial lysis which releases into the marine environment, on the average, 'b' viruses per cell, the parameter b epsilon (1, t infinity) or 'virus replication factor' is chosen as the main parameter on which the dynamics of the infection depends. We proved that a threshold b* exists beyond which the endemic equilibrium bifurcates from the free disease one. Still, for increasing b values the endemic equilibrium bifurcates toward a periodic solution. We proved that a compact attractor set omega within the positive cone exists and within omega the free disease equilibrium is globally stable whenever b < or = b*, whereas it becomes a strong uniform repeller for b > b*. A concluding discussion with numerical simulation is then presented.

Bacteria↗

PubMed2006

Handheld rectilinear ion trap mass spectrometer.

A shoebox-sized, 10-kg, handheld mass spectrometer, Mini 10, based on a rectilinear ion trap mass analyzer has been designed, built, and characterized. This instrument has evolved from a decade-long experimental and simulation program in mass spectrometer miniaturization. The rectilinear ion trap has a simplified geometry and high trapping capacity, and when used with a miniature and ruggedized pumping system, it allows chemical analysis while the instrument is being carried. Compact electronics, including an air core RF drive coil, were developed to control the instrument and to record mass spectra. The instrument runs on battery power, consuming less than 70 W, similar to a laptop computer. Wired and wireless networking capabilities are implemented. The instrument gives unit resolution and a mass range of over m/z 500. Tandem mass spectrometry capabilities are implemented using collision-induced dissociation, and they are used to provide confirmation of chemical structure during in situ analysis. Continuous monitoring of air and solution samples is demonstrated, and a limit of detection of 50 ppb was obtained for toluene vapor in air and for an aqueous naphthalene solution using membrane sample introduction.

Journal Article↗

PubMed1992

Structure and dynamics of des-pentapeptide-insulin in solution: the molten-globule hypothesis.

Structures of insulin in different crystal forms exhibit significant local and nonlocal differences, including correlated displacement of elements of secondary structure. Here we describe the solution structure and dynamics of a monomeric insulin analogue, des-pentapeptide-(B26-B30)-insulin (DPI), as determined by two-dimensional NMR spectroscopy and distance geometry/restrained molecular dynamics (DG/RMD). Although the solution structure of DPI exhibits a general similarity to its crystal structure, individual DG/RMD structures in the NMR ensemble differ by rigid-body displacements of alpha-helices that span the range of different crystal forms. These results suggest that DPI exists as a partially folded state formed by coalescence of distinct alpha-helix-associated microdomains. The physical reality of this model is investigated by comparison of the observed two-dimensional nuclear Overhauser enhancement (NOE) spectroscopy (NOESY) spectrum with that predicted from crystal and DG/RMD structures. The observed NOESY spectrum contains fewer tertiary contacts than predicted by any single simulation, but it matches their shared features; such "ensemble correspondence" is likely to reflect the effect of protein dynamics on observed NOE intensities. We propose (i) that the folded state of DPI is analogous to that of a compact protein-folding intermediate rather than a conventional native state and (ii) that the molten state is the biologically active species. This proposal (the molten-globule hypothesis) leads to testable thermodynamic predictions and has general implications for protein design.

Calorimetry↗

PubMed2005

Compact silicon-on-insulator-based multimode interference coupler with bilevel taper structure.

A novel compact silicon-on-insulator- (SOI-)based multimode interference (MMI) coupler with bilevel taper structures was designed. The MMI section and the S-bend sections of the input-output waveguides are deeply etched. The input-output waveguides connecting to single-mode fibers or other photonic light circuits are etched shallowly to yield single-mode operation. A bilevel taper is introduced in the transition region between the shallowly and deeply etched regions. It is predicted theoretically that this design will not only improve the quality of the self-imaging in the MMI section but will also make the structure compact. Both the excess loss and the nonuniformity of the MMI coupler are reduced. By use of a three-dimensional beam propagation method, the performance of a 1 x 4 MMI coupler based on a SOI is simulated as a numerical example of the novel design. The simulated nonuniformity and the excess loss are approximately 0.0285 and 0.2 dB, respectively.

Journal Article↗

PubMed1994

[Technique and applications of stereolithographic cranial models].

3-D-modelling of the skull is useful referring to improve diagnostics, for surgical planning and simulation of surgical procedure. Stereolithography is a constructive process producing a model by building it up layer by layer with plastic using an "ultraviolet" laser to catalyse the polymerization of a liquid plastic solution. This fast prototyping derives from using a new interface between a CT-Scanner and a SLA. By avoiding the tool path problems inherent in conventional computerdriven CNC milling machines we succeeded in producing closed cavities and even intraosseous course of vessels and nerves. The compact and smooth surface makes manual postprocessing unnecessary. By using a new software (interpolation +/- 0.25 mm) we could improve the accuracy. At our studies we found a maximum aberration of at least 0.25 mm.

Adolescent↗

PubMed2003

Compact spot-size converters with fiber-matched antiresonant reflecting optical waveguides.

We propose a concept for InGaAsP-InP 1.55-microm lasers integrated with spot-size converters based on modal interference between the modes of the structure formed by an active waveguide and an underlying fiber-matched antiresonant reflecting optical waveguide. Simulation results show that the spot-size converters exhibit low transformation loss, and narrowed far-field emission patterns (10 degrees x 20 degrees) and reduce the coupling loss to standard single-mode fibers from 8 to 2.6 dB over lengths approximately 200 microm shorter than the adiabatic concept. A tolerant design to fabrication variations is also proposed, which could be realized by standard processing techniques.

Journal Article↗

PubMed1996

Effects of Na+ and Mg2+ on the structures of supercoiled DNAs: comparison of simulations with experiments.

Recent cryo-electron microscopy (cryo-EM) results suggest that sufficient NaCl concentration (> or approximately 0.1 M) and superhelix density (> or approximately-0.05) cause circular DNAs to adopt highly extended, tightly interwound configurations, in which the strands are laterally contiguous along almost their entire length. Millimolar levels of MgCl2 reportedly act synergistically with NaCl to produce similar conformations. However, Monte Carlo simulations with purely repulsive interduplex forces failed to reproduce such structures. In the present work, solution measurements of particular physical properties were performed both to characterize the effects of Na+ and Mg2+ on DNA structure and to provide quantitative tests of Monte Carlo simulations of circular DNAs. Supercoiled p30 delta DNAs in 10 mM Tris plus 0, 0.122, and 0.1 M NaCl, and 0.1 M NaCl plus 4 mM Mg2+ were examined by static and dynamic light scattering (LS and DLS), time-resolved fluorescence polarization anisotropy (FPA) of intercalated ethidium, and circular dichroism (CD) spectroscopy. Upon addition of 0.122 M NaCl, the radius of gyration (Rg) decreased substantially, which indicates that p30 delta adopts a more compact structure. This contradicts the cryo-EM studies, where molecular extension and Rg both increase upon adding 0.1 M NaCl. In 0.1 M NaCl, the torsion constant measured by FPA is practically invariant to superhelix density, and the plateau diffusion coefficient at large scattering vector (Dplat) is likewise nearly the same at both relaxed and native superhelix densities. Such invariance is difficult to reconcile with any transition from relaxed circles to tightly interwound structures with laterally contiguous strands. Metropolis Monte Carlo simulations were performed to generate canonically distributed sets of structures, from which average Do values and scattered intensity ratios, [symbol: see text]I (zero) [symbol: see text]/[symbol: see text] l(k) [symbol: see text], were calculated. Agreement between simulations and experiments in regard to [symbol: see text] I(O) [symbol: see text] /[symbol: see text] I(k) [symbol: see text], D(zero) and the supercoiling free energy, delta Gsc (delta l), is remarkably good for the most extensively studied p30 delta samples. The simulated structures exhibit no sign of very tight interwinding with extensive lateral contacts, but instead exhibit most probable superhelix diameters of 85 to 90 A. When 4 mM Mg2+ was added to native supercoiled p30 delta in 0.1 M NaCl, Rg decreased, D(zero) increased, and the longest internal relaxation rate (1/tau 2(zero)) increased, all of which indicate a further overall contraction of the molecular envelope. The torsion constant exhibited a slight increase that is hardly statistically significant. In this case, agreement between the simulations and experiments was only semi-quantitative for most samples investigated, although the predicted contraction was exhibited by all five samples of p30 delta and one of pBR322 DNA. The simulated structures in 0.1 M NaCl plus 4 mM Mg2+ again showed no sign of extensive lateral contacts. A plausible explanation is proposed for the highly extended, tightly interwound structures seen in cryo-EM, and explicitly tested by Monte Carlo simulations of a 1000 bp circular DNA at +25 and -50 degrees C. Structures identical to those seen in cryo-EM are in fact the equilibrium structures in the simulations at -50 degrees C, and the estimated time for equilibration (2.3 x 10(-6) second) is much smaller than the estimated time for vitrification (1 x 10(-4) second).

Computer Simulation↗

PubMed2000

Effect of conformation on the rate of deamidation of vancomycin in aqueous solutions.

The instability of vancomycin, a glycopeptide antibiotic, limits its shelf-life because the deamidation of its asparagine residue results in the formation of a zwitterion with limited aqueous solubility. Analysis of the pH-rate profile for vancomycin indicates that the deamidation reaction is notably sensitive to the ionic state of the molecule. This observation results in a hypothesis in which the ionic state of vancomycin may influence the conformation of the molecule and therefore affect its reactivity. Two-dimensional nuclear magnetic resonance (NMR), homonuclear Hartmann-Hahn (HOHAHA) and rotating frame Overhauser enhancement spectroscopy (ROESY) information combined with molecular dynamic simulations were used to estimate the apparent conformation of vancomycin in aqueous solution at pH 4 and pH 9 where the molecule exists primarily as a monocation and monoanion, respectively. The apparent conformation for vancomycin at pH 4 is compact, and the proximity of the backbone amide nitrogen to the side chain carbonyl carbon of asparagine is favorable for the rapid formation of the cyclic imide intermediate, thus increasing its reactivity. The apparent conformation for vancomycin at pH 9, however, is expanded in comparison with the conformation at pH 4, and the increase in distance between the reacting atoms leads to slower cyclic imide formation and thus decreased intrinsic reactivity. That cyclic imide formation was rate limiting at both pH values was confirmed by cyclic imide isolation and stability estimation. It becomes apparent from the analysis of the pH-rate and conformational profiles of vancomycin that the deamidation rate of vancomycin is largely influenced by the ionization state of the N-methyl leucine nitrogen.

Amides↗

PubMed1985

Systems model for pupil size effect. II. Feedback model.

The human pupillary control system has been the subject of interest to biologists and engineers as an example of a sensorimotor reflex which can be embedded in a control system paradigm. We present a nonlinear feedback model whose compact structure allows us to hypothesize possible physiological mechanisms which generate the proper behavior of the pupil system. The important pupil responses, including pupil size effect, asymmetry, and response the high-frequency stimuli, are defined. This model was simulated on a digital computer and comparisons to the paradigm experimental responses were performed, demonstrating a fit to each of the observed conditions. Improvements on previous models are discussed.

Feedback↗