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At least 1,693 records · Page 94Linked to original sources
PubMed2004

A constrained variational approach for energy derivatives in Fock-space multireference coupled-cluster theory.

In this paper, we present a formulation based on constrained variational approach to enable efficient computation of energy derivatives using Fock-space multireference coupled-cluster theory. Adopting conventional normal ordered exponential with Bloch projection approach, we present a method of deriving equations when general incomplete model spaces are used. Essential simplifications arise when effective Hamiltonian definition becomes explicit as in the case of complete model spaces or some special quasicomplete model spaces. We apply the method to derive explicit generic expressions upto third-order energy derivatives for [0,1], [1,0], and [1,1] Fock-space sectors. Specific diagrammatic expressions for zeroth-order Lagrange multiplier equations for [0,1], [1,0], and [1,1] sectors are presented.

Journal Article↗
PubMed1999

An expansion of system with time delayed feedback control into spatio-temporal state space.

Time delayed feedback control is well known as an effective continuous control method for stabilizing the unstable periodic orbit embedded in chaotic attractors. As for the system with time delay, the solution is in a function space and shows characteristics governed by an infinite dimension. Therefore it is difficult to understand the system behavior analytically. In this paper, it is shown that, when the state space for the system with time delay is expanded into the spatio-temporal state space, the solution propagates in the space as a wave theoretically and numerically. The dynamic behavior experimentally obtained in the sinusoidally excited magneto-elastic beam system under time delayed feedback control is also discussed by the transformation into the expanded spatio-temporal state space. (c) 1999 American Institute of Physics.

Journal Article↗
PubMed2004

Mixed-sector intermediate Hamiltonian Fock-space coupled cluster approach.

An alternative formulation of the intermediate Hamiltonian Fock-space coupled cluster scheme developed before is presented. The methodological and computational advantages of the new formulation include the possibility of using a model space with determinants belonging to different Fock-space sectors. This extends the scope of application of the multireference coupled cluster method, and makes possible the use of quasiclosed shells (e.g., p2, d4) as reference states. Representative applications are described, including electron affinities of group-14 atoms, ionization potentials of group-15 elements, and ionization potentials and excitation energies of silver and gold. Excellent agreement with experiment (a few hundredths of an electronvolt) is obtained, with significant improvement (by a factor of 5-10 for p3 states) over Fock-space coupled cluster results. Many states not reachable by the Fock-space approach can now be studied.

Journal Article↗
PubMed2005

Combining smart darting with parallel tempering using Eckart space: application to Lennard-Jones clusters.

The smart-darting algorithm is a Monte Carlo based simulation method used to overcome quasiergodicity problems associated with disconnected regions of configurations space separated by high energy barriers. As originally implemented, the smart-darting method works well for clusters at low temperatures with the angular momentum restricted to zero and where there are no transitions to permutational isomers. If the rotational motion of the clusters is unrestricted or if permutational isomerization becomes important, the acceptance probability of darting moves in the original implementation of the method becomes vanishingly small. In this work the smart-darting algorithm is combined with the parallel tempering method in a manner where both rotational motion and permutational isomerization events are important. To enable the combination of parallel tempering with smart darting so that the smart-darting moves have a reasonable acceptance probability, the original algorithm is modified by using a restricted space for the smart-darting moves. The restricted space uses a body-fixed coordinate system first introduced by Eckart, and moves in this Eckart space are coupled with local moves in the full 3N-dimensional space. The modified smart-darting method is applied to the calculation of the heat capacity of a seven-atom Lennard-Jones cluster. The smart-darting moves yield significant improvement in the statistical fluctuations of the calculated heat capacity in the region of temperatures where the system isomerizes. When the modified smart-darting algorithm is combined with parallel tempering, the statistical fluctuations of the heat capacity of a seven-atom Lennard-Jones cluster using the combined method are smaller than parallel tempering when used alone.

Journal Article↗
PubMed2006

Coupled-cluster with active space selected higher amplitudes: performance of seminatural orbitals for ground and excited state calculations.

The active space approach for coupled-cluster models is generalized using the general active space concept and implemented in a string-based general coupled-cluster code. Particular attention is devoted to the choice of orbitals on which the subspace division is based. Seminatural orbitals are proposed for that purpose. These orbitals are obtained by diagonalizing only the hole-hole and particle-particle block of the one-electron density of a lower-order method. The seminatural orbitals are shown to be a good replacement for complete active space self-consistent field orbitals and avoid the ambiguities with respect to the reference determinant introduced by the latter orbitals. The seminatural orbitals also perform well in excited state calculations, including excited states with strong double excitation contributions, which usually are difficult to describe with standard coupled-cluster methods. A set of vertical excitation energies is obtained and benchmarked against full configuration interaction calculations, and alternative hierarchies of active space coupled-cluster models are proposed. As a simple application the spectroscopic constants of the C(2) B (1)Delta(g) and B(') (1)Sigma(g) (+) states are calculated using active space coupled-cluster methods and basis sets up to quadruple-zeta quality in connection with extrapolation and additivity schemes.

Journal Article↗
PubMed2001

Pharyngeal airway space changes after counterclockwise rotation of the maxillomandibular complex.

The purpose of this study was to evaluate the effects of double-jaw surgery with counterclockwise rotation of the maxillomandibular complex on the pharyngeal airway space and velopharyngeal anatomy in patients with high occlusal plane facial morphology. Fifty patients (22 men, 28 women) with high occlusal plane facial morphology underwent double-jaw surgery with counterclockwise rotation of the maxillomandibular complex. The patients were divided into 2 groups: group 1, 30 patients (8 men, 22 women) who underwent maxillary and mandibular advancement and group 2, 20 patients (14 men, 6 women) who underwent maxillary advancement and mandibular setback. Presurgery and postsurgery lateral cephalometric radiographs were analyzed to correlate changes in pharyngeal airway space dimensions and velopharyngeal anatomy with maxillary and mandibular positional changes. The calibration showed a more than 0.94 correlation for both intra- and interoperator error. The average follow-up time was 29.6 months in group 1 and 22.2 months in group 2. Mean maxillary surgical change at point A was 4.15 mm in group 1 and 2.5 mm in group 2. Mean mandibular surgical change at the genial tubercles was 7.5 mm in group 1 and -4.95 mm in group 2. After surgery, group 1 patients had an increase in pharyngeal airway space of 47% at the soft palate and 76% at the base of the tongue relative to the amount of mandibular advancement. Group 2 patients had a decrease in pharyngeal airway space of 47% at the soft palate and 65% at the base of the tongue relative to the amount of mandibular setback. Double-jaw surgery with counterclockwise rotation of the maxillomandibular complex significantly affects the pharyngeal airway space and velopharyngeal anatomy in patients with high occlusal plane facial morphology, with both mandibular advancement and setback.

Adolescent↗
PubMed1998

Mapping the mental space of rectangles.

The cognitive structure of a shape space--the space of rectangles--is explored by a nonmetric scaling technique. Our experiment was designed to extract the major transformational paths or 'modes' that characterize the mental shape space. Earlier studies of rectangle similarities using multidimensional scaling have provided conflicting evidence about whether the coordinate system of the mental rectangle space is based on height and width or on area and shape (i.e. aspect ratio). Our study reveals shape to be the single dominant factor. We suspected that earlier evidence for a height-width parameterization might have been due to the presentation of rectangles upright in a pseudo-gravitational coordinate system (whereas our rectangles are randomly rotated). In a control experiment with upright (vertical or horizontal) rectangles, the heavy bias towards shape preservation was still the dominant mode. In addition, however, a secondary bias towards change of height or width emerged, exactly following the pattern expected from the biasing change in context. This finding established a concrete path by which context and frame can influence the way shape is represented. The relevance of these findings to the cognitive organization of more complex shape spaces is discussed.

Cognition↗
PubMed1996

The sigma subunit of Escherichia coli RNA polymerase senses promoter spacing.

The promoters recognized by sigma 70, the primary sigma of Escherichia coli, consist of two highly conserved hexamers located at -10 and -35 bp from the start point of transcription, separated by a preferred spacing of 17 bp. sigma factors have two distinct DNA binding domains that recognize the two hexamer sequences. However, the component of RNA polymerase recognizing the length of the spacing between hexamers has not been determined. Using an equilibrium DNA binding competition assay, we demonstrate that a polypeptide of sigma 70 carrying both DNA binding domains is very sensitive to promoter spacing, whereas a sigma 70 polypeptide with only one DNA binding domain is not. Furthermore, a mutant sigma, selected for increasing transcription of the minimal lac promoter (18-bp spacer), has an altered response to promoter spacing in vivo and in vitro. Our data support the idea that sigma makes simultaneous, productive contacts at both the -10 and the -35 regions of the promoter and discerns the spacing between these conserved regions.

Base Sequence↗
PubMed1995

Sorting of cytochrome b2 to the intermembrane space of mitochondria. Kinetic analysis of intermediates demonstrates passage through the matrix.

Precytochrome b2 is targeted to the mitochondrial intermembrane space by a dual targeting sequence comprising 80 amino acids. A kinetic analysis of intramitochondrial sorting was performed. The intermediate-size form accumulated transiently in the matrix. When import was performed in the presence of metal chelators to prevent the first processing by the matrix processing peptidase, > 40% of the imported precursor was localized in the matrix. A deletion of 13 amino acids in the intermembrane space sorting sequence caused partial inhibition of the first processing, and a transient accumulation of the precursor form in the matrix was also observed. The decrease in this matrix-localized precursor form paralleled an increase in the mature-size form in the intermembrane space. A point mutation in the mitochondrial targeting sequence (N-terminal to the sorting sequence) resulted in missorting to the matrix space. Furthermore, a chimeric protein consisting of the initial 85 residues of cytochrome b2 fused to dihydrofolate reductase was partially targeted to the matrix at 15 degrees C, but not at 25 degrees C. Together, the results presented here indicate that cytochrome b2 passes through the matrix on its sorting pathway to the intermembrane space.

Amino Acid Sequence↗
PubMed1999

Tic22 is targeted to the intermembrane space of chloroplasts by a novel pathway.

Tic22 previously was identified as a component of the general import machinery that functions in the import of nuclear-encoded proteins into the chloroplast. Tic22 is peripherally associated with the outer face of the inner chloroplast envelope membrane, making it the first known resident of the intermembrane space of the envelope. We have investigated the import of Tic22 into isolated chloroplasts to define the requirements for targeting of proteins to the intermembrane space. Tic22 is nuclear-endoded and synthesized as a preprotein with a 50-amino acid N-terminal presequence. The analysis of deletion mutants and chimerical proteins indicates that the precursor of Tic22 (preTic22) presequence is necessary and sufficient for targeting to the intermembrane space. Import of preTic22 was stimulated by ATP and required the presence of protease-sensitive components on the chloroplast surface. PreTic22 import was not competed by an excess of an authentic stromal preprotein, indicating that targeting to the intermembrane space does not involve the general import pathway utilized by stromal preproteins. On the basis of these observations, we conclude that preTic22 is targeted to the intermembrane space of chloroplasts by a novel import pathway that is distinct from known pathways that target proteins to other chloroplast subcompartments.

Adenosine Triphosphate↗
PubMed2003

Free shoulder space requirements in the design of high backrests.

The objective of this study was to determine the influence of scapular support on the effects of lumbar support and to prove that a high and straight backrest is inappropriate. In literature the importance of a lumbar support is noted, although data about optimal dimensions is an under-researched topic and in earlier studies on force distribution and muscle activity the backrest had a fixed form. The lumbar support is needed to maintain the lumbar lordosis but no studies deal with the question of the precise dimensions of the backrest at shoulder level. With a specially designed apparatus, forces on shoulder and seat were measured separately, and the force on the pelvis calculated, while varying seat and backrest inclination within the range from 0 degrees to 17 degrees. Seat-to-backrest angle (at the level of lumbar support) was kept constant at 90 degrees. The distance between the tangent to the lumbar support and the parallel tangent to the scapular support was varied from 0, 2, 4, 6 and 8 cm. This distance is called the free shoulder space. Electromyography was measured at the erector spinae at the levels of the L1, T8 and T5 vertebrae. For all seat angles, a free shoulder space of d=0 cm resulted in the highest back muscle activity. In agreement with the biomechanical model, EMG activity reduced with an increase of seat tilt and increase of free shoulder space. With increasing free shoulder space, a larger part of the total backrest force was carried by the lumbar support. This study shows that a high and straight backrest overrules lumbar support. Offering free shoulder space of at least 6 cm reduces back muscle activity and allows for lumbar support.

Adult↗
PubMed2004

Transport, transformation and distribution space of propofol in the rat liver studied by means of the indicator-dilution technique.

1. The transport, transformation and distribution space of the endovenous anaesthetic propofol in the isolated perfused rat liver were investigated by using the multiple-indicator dilution technique with constant infusion (step input). 2. The behaviour of propofol in the liver was described by a space-distributed variable transit-time model. The drug permeated the cell membrane at very high rates and its distribution into the cellular space was flow-limited. The apparent distribution space of propofol varied between 284 and 125 times the water space, and was inversely related to the tested portal concentrations (33-250 microM). 3. The corresponding ratios of intra- to extracellular concentration varied between 319 and 187, revealing a very high affinity of the liver for propofol. They most probably reflect binding to several cellular structures, including membranes and proteins. 3. The single-pass rate coefficients for biotransformation decreased with increases in the portal concentration of propofol. The liver released significant amounts of 4-hydroxypropofol, reaching 41.7 % of the total single pass of 67.2 microM propofol biotransformation. These results disprove previous notions that hydroxylation is rate limiting for conjugation and suggest that the liver might function as a 4-hydroxypropofol source for conjugation to glucuronic acid or sulfate in other tissues.

Algorithms↗
PubMed1996

Toward an exhaustive sampling of the configurational spaces of the two forms of the peptide hormone guanylin.

The recently introduced Essential Dynamics sampling method is extended such that an exhaustive sampling of the available (backbone) configurational space can be achieved. From an initial Molecular Dynamics simulation an approximated definition of the essential subspace is obtained. This subspace is used to direct subsequent simulations by means of constraint forces. The method is applied to the peptide hormone guanylin, solvated in water, of which the structure was determined recently. The peptide exists in two forms and for both forms, an extensive sampling was produced. The sampling algorithm fills the available space (of the essential coordinates used in the procedure) at a rate that is approximately six to seven times larger than that for traditional Molecular Dynamics. The procedure does not cause any significant perturbation, which is indicated by the fact that free Molecular Dynamics simulations started at several places in the space defined by the Essential Dynamics sample that complete space. Moreover, analyses of the average free Molecular Dynamics step have shown that nowhere except close to the edge of the available space, there are regions where the system shows a drift in a particular direction. This result also shows that in principle, the essential subspace is a constant free energy surface, with well-defined and steep borders, in which the system moves diffusively. In addition, a comparison between two independent essential dynamics sampling runs, of one form of the peptide, shows that the obtained essential subspaces are virtually identical.

Algorithms↗
PubMed2001

Vertical dimension. Part 1: comparison of clinical freeway space.

This study was conducted in order to compare the clinical freeway space measurements using three simple methods commonly used by dentists in their practices. The study was performed in 15 young healthy subjects with natural dentition and bilateral molar support. Artificial landmarks (adhesive tape) were placed on the more prominent parts of the nose and chin of each subject. Vertical dimension of occlusion (VDO) was measured in the intercuspal position. Postural vertical dimension (PVD) was measured in the following functional conditions: after swallowing saliva, after pronouncing the word "Mississippi", and in a relaxed postural mandibular position (RPMP). Then, the clinical freeway space value in each functional condition was obtained by subtracting VDO from PVD value. Significant differences among clinical freeway space values using three different methods were observed (ANOVA). A significantly higher clinical freeway space value was found using phonetics method than after swallowing and with the mandible in a relaxed postural position (Bonferroni multiple comparison test). No significant differences between swallowing and relaxed methods were found. These results seem to suggest that the measures of clinical freeway space depend upon the method used.

Adult↗
PubMed2005

Biologically motivated space-variant filtering for robust optic flow processing.

We describe and test a biologically motivated space-variant filtering method for decreasing the noise in optic flow fields. Our filter model adopts certain properties of a particular motion-sensitive area of the brain (area MT), which averages the incoming motion signals over receptive fields, the sizes of which increase with the distance from the center of the projection. We use heading estimation from optic flow as a criterion to evaluate the improvement of the filtered flow field. The tests are conducted on flow fields calculated with a standard flow algorithm from image sequences. We use two different sets of image sequences. The first set is recorded by a camera which is installed in a moving car. The second set is derived from a database containing three dimensional data and reflectance information from natural scenes. The latter set guarantees full control of the camera motion and ground truth about the flow field and the heading. We test the space-variant filtering method by comparing heading estimation results between space-variant filtered flow, flow filtered by averaging over domains of the visual field with constant size (constant filtering) and raw unfiltered flow. Because of noise and the aperture problem the heading estimates obtained from the raw flows are often unreliable. Estimated heading differs widely for different sub-sampled calculations. In contrast, the results obtained from the filtered flows are much less variable and therefore more consistent. Furthermore, we find a significant improvement of the results obtained from the space-variant filtered flow compared to the constant filtered flow. We suggest extensions to the space-variant filtering procedure that take other properties of motion representation in area MT into account.

Algorithms↗
PubMed2004

Comparison of ECG-gated rectilinear vs. real-time radial K-space sampling schemes in cine True-FISP cardiac MRI.

PURPOSE: To compare three k-space sampling schemes in cine True-FISP cardiac magnetic resonance imaging and to evaluate changes in calculated quantitative functional cardiac parameters as a function of underlying k-space sampling techniques. MATERIAL AND METHODS: Using a 1.5 T MR imaging system (Magnetom Sonata, Siemens Medical Solutions, Erlangen, Germany), three k-space data-sampling schemes: rectilinear (2.96 ms/1.58 ms/70 degrees /12 s TR/TE/FA/AcquisitionTime), and two radial k-space acquisitions, with filtered back-projection (RADIAL) (2.45 ms/1.25 ms/ 50 degrees /3.3 s TR/TE/FA/AT), and steady-state projection imaging with dynamic echotrain readout (SPIDER) (3.39 ms/1.62 ms/55 degrees /1.8 s TR/TE/FA/AT) of a True-FISP sequence were applied in 10 healthy volunteers. Long- and short-axis breath-hold series were acquired and signal-to-noise ratios (SNR) for blood and myocardium were determined, as was contrast-to-noise ratios (CNR). Quantitative cardiac functional analysis included: determination of end-systolic/end-diastolic volumes, ejection fraction, and left ventricular mass. Functional analysis was performed by two independent readers three times for each volunteer and k-space sampling strategy. Statistical analysis evaluated the accuracy of the measurements obtained from each of the three sampling techniques and the intra- and interobserver reliability. RESULTS: Intraobserver and interobserver reliability measures of functional data were homogeneous without statistically significant differences. Intraobserver correlation coefficients ranged from 0.94-0.99; interobserver correlation coefficients ranged from 0.97-0.99. Direct comparison of SPIDER- and RADIAL-sampled True-FISP sequences showed no statistically significant differences in measured functional parameters with interstudy correlation coefficients from 0.88-0.98. RADIAL and SPIDER images had better temporal resolution and were qualitatively judged to provide superior wall/blood border definition. Statistically significant differences were identified in each volumetric functional parameter when results from the rectilinear sampling acquisitions were compared with either radial or SPIDER sampling techniques. RADIAL and SPIDER results were consistently higher than volumetric measures obtained from the rectilinear data set. CONCLUSION: Employing faster sampling schemes led to enhanced signal homogeneity while maintaining the necessary CNR for estimation of functional cardiac parameters. Enhanced signal homogeneity and maintained CNR will most likely improve the accuracy of the cardiac functional parameter determination.

Adult↗
PubMed1991

Space charge effects in a kinestatic charge detector.

The effects of space charge in a kinestatic charge detector (KCD) were examined using computer solutions to Poisson's equation. The KCD is a strip-beam parallel-plate drift chamber used for digital radiography. It was assumed that there is negligible electron attachment, i.e. there are no negative ions formed. The ionization rate per mA as a function of x-ray interaction depth was calculated for a detector filled with xenon at 25.3 x 10(5) Pa. Solution of Thomson's equations gave the positive ion density at the cathode, also as a function of depth. Water filtration values ranging from 0 to 30 cm were used in order to estimate the range of ion density values expected in a clinical KCD. The case of steady-state x-ray illumination was simulated for ionization rates less than the zero field limit (above which space charge changes the polarity of the electric field). Line spread responses were found for varying ionization rates to show the effect of space charge due to electric field distortion on the spatial resolution performance in the drift direction. The effect of imaging ideal edges with a KCD was calculated and the expected output signal was plotted for densities up to the zero field limit. Space charge dependence on the selection of KCD design and operating parameters is discussed. Because of the dependence of the KCD drift-direction spatial resolution on the uniformity of the electric field, space charge effects impose an upper limit on the detector entrance exposure and define the dynamic range of the device.

Humans↗
PubMed2005

Using a photon phase-space source for convolution/superposition dose calculations in radiation therapy.

For a given linac design, the dosimetric characteristics of a photon beam are determined uniquely by the energy and radial distributions of the electron beam striking the x-ray target. However, in the usual commissioning of a beam from measured data, a large number of variables can be independently tuned, making it difficult to derive a unique and self-consistent beam model. For example, the measured dosimetric penumbra in water may be attributed in various proportions to the lateral secondary electron range, the focal spot size and the transmission through the tips of a non-divergent collimator; the head-scatter component in the tails of the transverse profiles may not be easy to resolve from phantom scatter and head leakage; and the head-scatter tails corresponding to a certain extra-focal source model may not agree self-consistently with in-air output factors measured on the central axis. To reduce the number of adjustable variables in beam modelling, we replace the focal and extra-focal sources with a single phase-space plane scored just above the highest adjustable collimator in a EGS/BEAM simulation of the linac. The phase-space plane is then used as photon source in a stochastic convolution/superposition dose engine. A photon sampled from the uncollimated phase-space plane is first propagated through an arbitrary collimator arrangement and then interacted in the simulation phantom. Energy deposition kernel rays are then randomly issued from the interaction points and dose is deposited along these rays. The electrons in the phase-space file are used to account for electron contamination. 6 MV and 18 MV photon beams from an Elekta SL linac are used as representative examples. Except for small corrections for monitor backscatter and collimator forward scatter for large field sizes (<0.5% with <20 x 20 cm2 field size), we found that the use of a single phase-space photon source provides accurate and self-consistent results for both relative and absolute dose calculations.

Algorithms↗