Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Compaction simulator”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

1,216 records · Page 68Linked to original sources
PubMed2005

Compact model for multi-phase liquid-liquid flows in micro-fluidic devices.

We present a compact model describing the laminar flow of viscous multiphase fluids in micro-channel networks. We apply this model to the flow of 2 immiscible fluids representing typically oil and water, in a network of micro-channels comprising one inlet for each fluid splitting into 2 branches meeting at a T-junction, where the 2 phases are combined before exiting the network through two outlets. This network is akin to an electrical "Wheatstone bridge" and represents a simplified interdigital micro-reactor, where the fluids to be mixed are separated into smaller branches and later re-combined together. We show from an analytical solution and a computational modelling that fluid flow inside this network is very sensitive to small differences in fluid resistance between the various branches of the network, which may lead to catastrophic error in fluid distribution between the various branches that can have a profound effect on mixing. These errors depend on the viscosity difference between the fluids, on the processing conditions, and also on the geometric resistance parameters of the various channels. Increasing the resistance of the distribution channels upstream of the fluid junctions allows minimisation of the distribution errors. Interaction between the fluids can also lead to transients that are orders of magnitude longer than the flooding time of the channels. This may be exploited to provide impedance-like terms in flui-logic operations.

Computer Simulation↗
PubMed1993

Analysis of voltage-dependent membrane currents in spatially extended neurons from point-clamp data.

1. Numerical methods were used to evaluate voltage space-clamp performance in the investigation of a voltage-dependent inward current similar to the noninactivating Ca current. In addition, the cell is equipped with a repolarizing system, represented by leak and outwardly rectifying outward conductances. The electrotonically compact model cell is represented by a cable with an electrotonic length of 1 space constant under control conditions, but that becomes effectively only 0.33 space constants during a 90% reduction of the leak and outward conductance. The cable is perfectly voltage clamped at one end. 2. The apparent voltage dependence, activation, and inactivation of the clamp current depend on the distribution of the membrane slope conductance along the cable; this depends on 1) the distribution of the inward current along the cable and 2) the amplitude of the inward current relative to the amplitudes of the leak and voltage-dependent outward currents. 3. Under control conditions, the membrane voltage decays steeply with distance from the command voltage at the clamp site to almost resting potential for most of the rest of the cable. This is because the leak and outward current are dominant over the inward current. The inward current is activated primarily at the clamped part of the cable. Clamp currents are activated instantaneously. The clamp-current current-voltage (I-V) relation is less steep with depolarization because the membrane potential for locations away from the clamp site lags behind the clamp potential. 4. When the conductances for leak and outward current are reduced by 90%, these conductances lose their dominance. The membrane slope conductance now has a range with negative values.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed2001

An ultradurable and compact rotary blood pump with a magnetically suspended impeller in the radial direction.

A magnetically suspended centrifugal blood pump has been developed with a self-bearing motor for long-term ventricular assist systems. The rotor of the self-bearing motor is not only actively suspended in the radial direction, but also is rotated by an electromagnetic field. The pump has a long lifetime because there are no mechanical parts such as seals and motor bearings. An outer rotor mechanism was adopted for the self-bearing motor. The stator was constructed in the central space of the motor. The rotor shaped thin ring was set at the circumferential space of the stator. Six vanes were extended from the upper surface of the rotor toward the center of the pump to construct an open-type impeller. The outer diameter and the height of the impeller are 63 mm and 34 mm, respectively. The magnetic bearing method and the servomotor mechanism were adopted to levitate and rotate the rotor. Radial movements of the rotor and rotation are controlled actively by using electromagnets in the stator. Axial movement and tilt of the rotor are restricted by passive stability to simplify the control. The radial gap between the rotor and the stator is 1 mm. A closed-loop circuit filled with water was used to examine basic performance of the pump. Maximum flow rate and pressure head were 8 L/min and 200 mm Hg, respectively. Maximum amplitude of radial displacement of the impeller was 0.15 mm. The impeller could be suspended completely without touching the casing wall during the entire pumping process. Power consumption of the pump was only 9.5 W to produce a flow rate of 5 L/min against a pressure head of 100 mm Hg. We conclude that the pump has sufficient performance for the implantable ventricular assist system.

Computer Simulation↗
PubMed2006

Assembly of transmembrane helices of simple polytopic membrane proteins from sequence conservation patterns.

The transmembrane (TM) domains of most membrane proteins consist of helix bundles. The seemingly simple task of TM helix bundle assembly has turned out to be extremely difficult. This is true even for simple TM helix bundle proteins, i.e., those that have the simple form of compact TM helix bundles. Herein, we present a computational method that is capable of generating native-like structural models for simple TM helix bundle proteins having modest numbers of TM helices based on sequence conservation patterns. Thus, the only requirement for our method is the presence of more than 30 homologous sequences for an accurate extraction of sequence conservation patterns. The prediction method first computes a number of representative well-packed conformations for each pair of contacting TM helices, and then a library of tertiary folds is generated by overlaying overlapping TM helices of the representative conformations. This library is scored using sequence conservation patterns, and a subsequent clustering analysis yields five final models. Assuming that neighboring TM helices in the sequence contact each other (but not that TM helices A and G contact each other), the method produced structural models of Calpha atom root-mean-square deviation (CA RMSD) of 3-5 A from corresponding crystal structures for bacteriorhodopsin, halorhodopsin, sensory rhodopsin II, and rhodopsin. In blind predictions, this type of contact knowledge is not available. Mimicking this, predictions were made for the rotor of the V-type Na(+)-adenosine triphosphatase without such knowledge. The CA RMSD between the best model and its crystal structure is only 3.4 A, and its contact accuracy reaches 55%. Furthermore, the model correctly identifies the binding pocket for sodium ion. These results demonstrate that the method can be readily applied to ab initio structure prediction of simple TM helix bundle proteins having modest numbers of TM helices.

Bacteriorhodopsins↗
PubMed2004

Development and experimental validation of a three-dimensional finite element model of the human scapula.

A new modelling approach, using a combination of shell and solid elements, has been adopted to develop a realistic three-dimensional finite element (FE) model of the human scapula. Shell elements were used to represent a part of the compact bone layer (i.e. the outer cortical layer) and the very thin and rather flat part of the scapula--infraspinous fossa and supraspinous fossa respectively. Solid elements were used to model the remaining part of the compact bone and the trabecular bone. The FE model results in proper element shapes without distortion. The geometry, material properties and thickness were taken from quantitative computed tomography (CT) data. A thorough experimental set-up for strain gauge measurement on a fresh bone serves as a reference to assess the accuracy of FE predictions. A fresh cadaveric scapula with 18 strain gauges fixed at various locations and orientations was loaded in a mechanical testing machine and supported at three locations by linkage mechanisms interconnected by ball joints. This new experimental set-up was developed to impose bending and deflection of the scapula in all directions unambiguously, in response to applied loads at various locations. The measured strains (experimental) were compared to numerical (FE) strains, corresponding to several load cases, to validate the proposed FE modelling approach. Linear regression analysis was used to assess the accuracy of the results. The percentage error in the regression slope varies between 9 and 23 per cent. It appears, as a whole, that the two variables (measured and calculated strains) strongly depend on each other with a confidence level of more than 95 per cent. Considering the complicated testing procedure on a fresh sample of scapula, the high correlation coefficients (0.89-0.97), the low standard errors (29-105 micro epsilon) and percentage errors in the regression slope, as compared to other studies, strongly suggest that the strains calculated by the FE model can be used as a valid predictor of the actual measured strain. The model is therefore an alternative to a rigorous three-dimensional model based on solid elements only, which might often be too expensive in terms of computing time.

Aged↗
PubMed2000

Performance of a PSPMT based detector for scintimammography.

In breast scintigraphy, compact detectors with high intrinsic spatial resolution and small inactive peripheries can provide improvements in extrinsic spatial resolution, efficiency and contrast for small lesions relative to larger conventional cameras. We are developing a pixelated small field-of-view gamma camera for scintimammography. Extensive measurements of the imaging properties of a prototype system have been made, including spatial resolution, sensitivity, uniformity of response, geometric linearity and energy resolution. An anthropomorphic torso phantom providing a realistic breast exit gamma spectrum has been used in a qualitative study of lesion detectability. A new type of breast imaging system that combines scintimammography and digital mammography in a single upright unit has also been developed. The system provides automatic co-registration between the scintigram and the digital mammogram, obtained with the breast in a single configuration. Intrinsic spatial resolution was evaluated via calculation of the phase-dependent modulation transfer function (MTF). Measurements of extrinsic spatial resolution, sensitivity and uniformity of response were made for two types of parallel hole collimator using NEMA (National Electrical Manufacturers Association) protocols. Geometric linearity was quantified using a line input and least squares analysis of the measured line shape. Energy resolution was measured for seven different crystal types, and the effectiveness of optical grease coupling was assessed. Exit gamma spectra were obtained using a cadmium zinc telluride based spectrometer. These were used to identify appropriate radioisotope concentrations for the various regions of an anthropomorphic torso phantom, such that realistic scatter conditions could be obtained during phantom measurements. For prone scintimammography, a special imaging table was constructed that permits simultaneous imaging of both breasts, as well as craniocaudal views. A dedicated breast imaging system was also developed that permits simultaneous acquisition and superposition of planar gamma images and digital x-ray images. The intrinsic MTF is nonstationary, and is dependent on the phase relationship between the signal and the crystal array matrix. Averaged over all phases, the MTF is approximately 0.75, 0.57 and 0.40 at spatial frequencies of 1.0, 1.5 and 2.0 cycles per cm, respectively. The phase averaged line spread function (LSF) has a FWHM value of 2.6 mm. Following uniformity corrections, the RMS deviations in flood images are only slightly greater than is predicted from counting statistics. Across an 80 mm section of the active area, the differential linearity is 0.83 mm and the absolute linearity 2.0 mm. Using an anthropomorphic torso phantom with detachable breasts, scatter radiation similar to that observed exiting the breast of scintimammography patients was observed. It was observed that scattered gamma rays can constitute the majority of the radiation incident on the detector, but that the scatter-to-primary ratio varies significantly across the field of view, being greatest in the caudal portion of the breast, where scatter from the liver is high. Using a lesion-to-breast concentration ratio of 6:1, a 1.0 cm3 simulated breast lesion was detectable in lateral images obtained with both the developmental camera and with a clinical camera, while a 0.35 cm3 lesion was detectable in neither. Utilization of the dual x-ray transmission, gamma emission breast imaging system greatly increases the conspicuity of scintimammographic lesions relative to prone imaging, as well as greatly facilitating the localization and identification of structures in the gamma image. The prototype imaging gamma detector exhibits spatial resolution superior to that of conventional cameras, and comparable uniformity of response and geometric linearity. Because of light losses in the crystals, the energy resolution is inferior to that of single crystal NaI(Tl) came

Equipment Design↗
PubMed2004

Commissioning and implementation of a stereotactic conformal radiotherapy technique using a general-purpose planning system.

The purpose of this paper is to report on commissioning and clinical implementation of a customized system for pediatric stereotactic conformal radiotherapy (SCRT). The system is based on the Pinnacle treatment-planning system and its interfaces with other equipment: (1) Beam models were optimized for our compact blocking system and a new LINAC. (2) Three CT-to-density conversion tables were evaluated, one using tabulated data for a commercial phantom, the second including additional points from the manufacturer's data for the inserts in an in-house phantom, and the third using measured densities for the in-house phantom materials combined with tabulated data for the commercial phantom. (3) Blocks were transferred to a computerized block cutter using in-house software that extracted the block shape from the export file and custom-fitted the additional necessary shapes. (4) In the absence of a DICOM RT Image link, a method based on screen data capture was used to export digitally reconstructed radiographs (DRRs) to two portal imaging systems for treatment verification. Lens shielding by multileaf collimation in the anterior-posterior isocenter verification field was investigated. (1) Computed dose distributions using the beam models agreed with measurements well within published acceptability criteria. A difference of up to 1.0 mm was measured between the beam's eye views of aperture blocks and computed 50% isodose contours for a 2 x 2 x 2 mm dose calculation grid. (2) The third table, which included measured densities, improved the accuracy of the calculated isocenter dose by up to 0.5% in typical patient SCRT treatments and up to 1.0% in a phantom with 5-cm diameter inhomogeneity inserts. (3) The block export and customization process was shown to introduce no additional uncertainty. A 1-mm block production uncertainty was measured using film dosimetry on six blocks. (4) The DRR transfer method did not introduce uncertainty into the process. Verification field shielding reduced lens dose by 12 to 15 times. In conclusion, this customized system for planning and verification of pediatric SCRT provides a high level of precision as well as reasonable practical efficiency.

Computer Simulation↗
PubMed1996

Role of hydrophobic substituents in the interaction of opioid Tyr-Tic dipeptide analogs with dodecylphosphocholine micelles. Molecular partitioning in model membrane systems.

The conformational properties of three Tyr-Tic-NH-R dipeptide analogs [where R = (CH2)2-Ph, (CH2)3-Ph or (CH2)2-cHx; Ph = phenyl; cHx = cyclohexyl and Tic = tetrahydroisoquinoline-3-carboxylic acid] have been investigated in purely aqueous solution and in the presence of fully deuterated dodecylphosphocholine micelles. H-Tyr-Tic-NH-(CH2)2-Ph is an opioid delta-agonist, whereas H-Tyr-Tic-NH-(CH2)3-Ph is a fairly potent delta-antagonist. H-Tyr-Tic-NH-(CH2)2-cHx is a less potent delta-antagonist. 1H-NMR spectra revealed that conformers containing cis and trans configurations of the Tyr-Tic peptide bond were present in all compounds in H2O and the H2O/lipid solvent. Analyses of the NMR data for the compounds in H2O indicate that in all three dipeptides the C-terminal substituent is flexible and the Tyr-side-chain adopts a trans orientation in most of the conformations. This promotes a compact Tyr-Tic structure. NOE patterns observed for the compounds in the micelle solution indicate that Tyr has an even greater tendency to assume a trans side chain configuration in the biphasic-solvent system. This feature was more pronounced in the trans conformers than in the cis conformers. Specific lipid-peptide interactions were indicated by NOESY spectra acquired for micelle samples incorporating 20% (by mass) protonated lipid. According to the obtained NOE data, Tyr and Tic form an aromatic cluster which preferentially inserts into the lipid interior of the micelle for the trans conformers of all three dipeptides and for the cis conformer of H-Tyr-Tic-NH-(CH2)2-Ph. For the cis isomers, partitioning of the C-terminal substituents into the lipid phase exhibited more diverse behaviour. The cis conformers of H-Tyr-Tic-NH-(CH2)3-Ph and H-Tyr-Tic-NH-(CH2)2-cHx preferentially anchor to the micelle via their C-terminal substituent, while the corresponding region in H-Tyr-Tic-NH-(CH2)2-Ph remains flexible and immersed in the aqueous phase. The inconsistent mode of peptide-micelle interaction observed for cis conformers of the three compounds studied is explained in terms of differences in their dipeptide-substituent hydrophobicities. The more apolar the substituent, the greater its tendency to preferentially insert into the lipid core of the micelle. Amide-proton temperature coefficients measured for the three peptides revealed differences amongst the cis and trans isomers. The amide proton in the trans conformer of each compound is highly exposed to the aqueous phase in both solvent systems studied, whereas the cis NH proton of each peptide is only partially exposed. These results demonstrate that a subtle structural modification of an active peptide analog can result in dramatic changes of its biological activity and its mode of partitioning at a membrane surface.

Amides↗
PubMed2004

Rapid PCR in a continuous flow device.

Continuous flow polymerase chain reaction (CFPCR) devices are compact reactors suitable for microfabrication and the rapid amplification of target DNAs. For a given reactor design, the amplification time can be reduced simply by increasing the flow velocity through the isothermal zones of the device; for flow velocities near the design value, the PCR cocktail reaches thermal equilibrium at each zone quickly, so that near ideal temperature profiles can be obtained. However, at high flow velocities there are penalties of an increased pressure drop and a reduced residence time in each temperature zone for the DNA/reagent mixture, that potentially affect amplification efficiency. This study was carried out to evaluate the thermal and biochemical effects of high flow velocities in a spiral, 20 cycle CFPCR device. Finite element analysis (FEA) was used to determine the steady-state temperature distribution along the micro-channel and the temperature of the DNA/reagent mixture in each temperature zone as a function of linear velocity. The critical transition was between the denaturation (95 degrees C) and renaturation (55 degrees C-68 degrees C) zones; above 6 mm s(-1) the fluid in a passively-cooled channel could not be reduced to the desired temperature and the duration of the temperature transition between zones increased with increased velocity. The amplification performance of the CFPCR as a function of linear velocity was assessed using 500 and 997 base pair (bp) fragments from lambda-DNA. Amplifications at velocities ranging from 1 mm s(-1) to 20 mm s(-1) were investigated. The 500 bp fragment could be observed in a total reaction time of 1.7 min (5.2 s cycle(-1)) and the 997 bp fragment could be detected in 3.2 min (9.7 s cycle(-1)). The longer amplification time required for detection of the 997 bp fragment was due to the device being operated at its enzyme kinetic limit (i.e., Taq polymerase deoxynucleotide incorporation rate).

Bacteriophage lambda↗
PubMed1995

Crystal structure of a pyrimidine dimer-specific excision repair enzyme from bacteriophage T4: refinement at 1.45 A and X-ray analysis of the three active site mutants.

Crystallographic study of bacteriophage T4 endonuclease V, which is involved in the initial step of the pyrimidine dimer-specific excision repair pathway, has been carried out with respect to the wild-type and three different mutant enzymes. This enzyme catalyzes the cleavage of the N-glycosyl bond at the 5'-side of the pyrimidine dimer, and subsequently incises the phosphodiester bond at the apyrimidinic site through a beta-elimination reaction. The structure of the wild-type enzyme refined at 1.45 A resolution reveals the detailed molecular architecture. The enzyme is composed of a single compact domain classified as an all-alpha structure. The molecule is stabilized mainly by three hydrophobic cores, two of which include many aromatic side-chain interactions. The structure has a unique folding motif, where the amino-terminal segment penetrates between two major alpha-helices and prevents their direct contact, and it is incompatible with the close-packing category of helices for protein folding. The concave surface, covered with many positive charges, implies an interface for DNA binding. The glycosylase catalytic center, which comprises Glu23 and the surrounding basic residues Arg3, Arg22 and Arg26, lie in this basic surface. The crystal structures of the three active-site mutants, in which Glu23 was replaced by Gln(E23Q) and Asp (E23D), respectively, and Arg3 by Gln (R3Q), have been determined at atomic resolution. The backbone structures of the E23Q and R3Q mutants were almost identical with that of the wild-type, while the E23D mutation induces a small, but significant, change in the backbone structure, such as an increase of the central kink of the H1 helix at Pro25. In the catalytic center of the glycosylase, however, these three mutations do not generate notable movements of protein atoms, except for significant shifts of some bound water molecules. Thus, the structural differences between the wild-type and each mutant are confined to the remarkably small region around their replaced chemical groups. Combined with the biochemical studies and the difference circular dichroism measurements, these results allow us to conclude that the negatively charged carboxyl group of Glu23 is essential for the cleavage of the N-glycosyl bond, and that the positively charged guanidino group of Arg3 is crucial to bind the substrate, a DNA duplex containing a pyrimidine dimer. The amino terminal alpha-amino group is located at a position approximately 4.4 A away from the carboxyl group of Glu23. These structural features are generally consistent with the reaction scheme proposed by Dodson and co-workers.

Amino Acid Sequence↗