Orientation Constraints Research Articles

GPU-friendly multi-view stereo reconstruction using surfel representation and graph cuts

In this paper, we present a new surfel (surface element) based multi-view stereo algorithm that runs entirely on GPU. We utilize the flexibility of surfel-based 3D shape representation and global optimization by graph cuts in the same framework. Unlike previous works, the algorithm is optimized to massive parallel processing on GPU. First, we construct surfel candidates by local stereo matching and voting. After refining the position and orientation of the surfel candidates, we extract the optimal surfels by employing graph cuts under photo-consistency and surfel orientation constraints. In contrast to the conventional voxel based methods, the proposed algorithm utilizes more accurate photo-consistency and reconstructs the 3D shape up to sub-voxel accuracy. The orientation of the constructed surfel candidates imposes an effective constraint that reduces the effect of the minimal surface bias. The entire processing pipeline is implemented on the latest GPU to significantly speed up the processing. The experimental results show that the proposed approach reconstructs the 3D shape of an object accurately and efficiently, which runs more than 100 times faster than on CPU.

Multiple close‐range image matching based on a self‐adaptive triangle constraint

Abstract Reliable image matching is an essential and difficult task in digital photogrammetry and computer vision. Possible problems from geometric distortions, illumination changes, scale changes and difficult texture conditions will result in matching ambiguity, especially for close‐range image matching. This paper presents a multiple close‐range image matching method for surface reconstruction based on a self‐adaptive triangle constraint. This method features two aspects. First, the triangles constructed from the previously matched interest points provide strong geometric constraints for the subsequent point matching combined with gradient orientation and disparity constraints. The dynamic update of the triangulation adapts automatically to the changes of image textures. Secondly, a consistency check in object space is performed to remove possible mismatches. Using three sets of actual triple overlapped close‐range images for the experiment, the results revealed that the proposed method provides improved matching reliability.

Structural NMR of protein oligomers using hybrid methods.

Solving structures of native oligomeric protein complexes using traditional high-resolution NMR techniques remains challenging. However, increased utilization of computational platforms, and integration of information from less traditional NMR techniques with data from other complementary biophysical methods, promises to extend the boundary of NMR-applicable targets. This article reviews several of the techniques capable of providing less traditional and complementary structural information. In particular, the use of orientational constraints coming from residual dipolar couplings and residual chemical shift anisotropy offsets are shown to simplify the construction of models for oligomeric complexes, especially in cases of weak homo-dimers. Combining this orientational information with interaction site information supplied by computation, chemical shift perturbation, paramagnetic surface perturbation, cross-saturation and mass spectrometry allows high resolution models of the complexes to be constructed with relative ease. Non-NMR techniques, such as mass spectrometry, EPR and small angle X-ray scattering, are also expected to play increasingly important roles by offering alternative methods of probing the overall shape of the complex. Computational platforms capable of integrating information from multiple sources in the modeling process are also discussed in the article. And finally a new, detailed example on the determination of a chemokine tetramer structure will be used to illustrate how a non-traditional approach to oligomeric structure determination works in practice.

Three‐dimensional structure of the weakly associated protein homodimer SeR13 using RDCs and paramagnetic surface mapping

The traditional NMR-based method for determining oligomeric protein structure usually involves distinguishing and assigning intra- and intersubunit NOEs. This task becomes challenging when determining symmetric homo-dimer structures because NOE cross-peaks from a given pair of protons occur at the same position whether intra- or intersubunit in origin. While there are isotope-filtering strategies for distinguishing intra from intermolecular NOE interactions in these cases, they are laborious and often prove ineffectual in cases of weak dimers, where observation of intermolecular NOEs is rare. Here, we present an efficient procedure for weak dimer structure determination based on residual dipolar couplings (RDCs), chemical shift changes upon dilution, and paramagnetic surface perturbations. This procedure is applied to the Northeast Structural Genomics Consortium protein target, SeR13, a negatively charged Staphylococcus epidermidis dimeric protein (K(d) 3.4 ± 1.4 mM) composed of 86 amino acids. A structure determination for the monomeric form using traditional NMR methods is presented, followed by a dimer structure determination using docking under orientation constraints from RDCs data, and scoring under residue pair potentials and shape-based predictions of RDCs. Validation using paramagnetic surface perturbation and chemical shift perturbation data acquired on sample dilution is also presented. The general utility of the dimer structure determination procedure and the possible relevance of SeR13 dimer formation are discussed.

Functional Mapping with Simultaneous MEG and EEG

We use magnetoencephalography (MEG) and electroencephalography (EEG) to locate and determine the temporal evolution in brain areas involved in the processing of simple sensory stimuli. We will use somatosensory stimuli to locate the hand somatosensory areas, auditory stimuli to locate the auditory cortices, visual stimuli in four quadrants of the visual field to locate the early visual areas. These type of experiments are used for functional mapping in epileptic and brain tumor patients to locate eloquent cortices. In basic neuroscience similar experimental protocols are used to study the orchestration of cortical activity. The acquisition protocol includes quality assurance procedures, subject preparation for the combined MEG/EEG study, and acquisition of evoked-response data with somatosensory, auditory, and visual stimuli. We also demonstrate analysis of the data using the equivalent current dipole model and cortically-constrained minimum-norm estimates. Anatomical MRI data are employed in the analysis for visualization and for deriving boundaries of tissue boundaries for forward modeling and cortical location and orientation constraints for the minimum-norm estimates.

Space-time stereo analysis combining local structure and modulation features in the monogenic wavelet domain

A multimodal cost function, based on the local multimodal image descriptors that combine local structure features (orientation, coherency) and modulation/localization information (amplitude, phase, and spatial frequency) of the monogenic wavelet transform, is proposed to estimate the time-varying disparity maps in the space-time stereo framework. The proposed cost function makes use of a constraint of local orientation, phase, and amplitude congruencies with the weighted coefficients, which are adapted to local image features and are insusceptible to level shift, scaling, and rotation and lighting invariance. Experiments on the synthetic and natural stereo sequences show the estimated results are more robust than the intensity-based sum of standard sum of squared difference cost function.

Sensitivity enhancement of separated local field experiments: application to membrane proteins.

Separated local field (SLF) experiments have been used for almost three decades to obtain structural information in solid-state NMR. These experiments resolve chemical shift anisotropy (CSA) from dipole-dipole interactions (dipolar couplings, DC) in isolated spin systems. Both CSA and DC data can be converted into orientational constraints to elucidate the secondary structure and topology of membrane proteins in oriented lipid bilayers. Here, we propose a new suite of sensitivity enhanced SLF pulse sequences to measure CSA and DC for aligned membrane proteins and liquid crystalline molecules that will decrease the time needed for data acquisition. We demonstrate the efficacy of these new sensitivity enhanced experiments using both a single crystal of N-acetyl leucine and a single pass membrane protein sarcolipin reconstituted in aligned lipid bicelles. These results lay the groundwork for the routine application of this methodology for studying the structure and topology of membrane proteins.

Correction to “Constraints on the stress state of the San Andreas Fault with analysis based on core and cuttings from San Andreas Fault Observatory at Depth (SAFOD) drilling phases 1 and 2”

[1] Analysis of field data has led different investigators to conclude that the San Andreas Fault (SAF) has either anomalously low frictional sliding strength (μ 0.6). Arguments for the apparent weakness of the SAF generally hinge on conceptual models involving intrinsically weak gouge or elevated pore pressure within the fault zone. Some models assert that weak gouge and/or high pore pressure exist under static conditions while others consider strength loss or fluid pressure increase due to rapid coseismic fault slip. The present paper is composed of three parts. First, we develop generalized equations, based on and consistent with the Rice (1992) fault zone model to relate stress orientation and magnitude to depth-dependent coefficient of friction and pore pressure. Second, we present temperature- and pressure-dependent friction measurements from wet illite-rich fault gouge extracted from San Andreas Fault Observatory at Depth (SAFOD) phase 1 core samples and from weak minerals associated with the San Andreas Fault. Third, we reevaluate the state of stress on the San Andreas Fault in light of new constraints imposed by SAFOD borehole data. Pure talc (μ≈0.1) had the lowest strength considered and was sufficiently weak to satisfy weak fault heat flow and stress orientation constraints with hydrostatic pore pressure. Other fault gouges showed a systematic increase in strength with increasing temperature and pressure. In this case, heat flow and stress orientation constraints would require elevated pore pressure and, in some cases, fault zone pore pressure in excess of vertical stress.

Geometrical, conformational and topological restraints in regular nucleosome compaction in chromatin

The folding of the nucleosome array into a chromatin fiber modulates DNA accessibility and is therefore an important factor for the control of gene expression. The statistical analysis of the nucleosome repeat length in chromatin fibers reveals the presence of a ten-fold periodicity suggesting the existence of orientational constraints of the nucleosome units that provide the geometrical conditions of helical conformations. Recently, the elucidation of the x-ray crystal structure of a nucleosome tetramer array and the interpretation of electron microscopy images of reconstituted nucleosome arrays suggested two different architectures of the chromatin fiber. We approached the problem by integrating the experimental findings with geometrical, conformational and topological restraints, under the hypothesis of the minimum distortion of the nucleosome and linker DNA structures. We show that the excluded volume at linker crossing and the torsional energy limit the possible close packing of the nucleosomes in the chromatin fiber. In particular, the torsional energy of the chromatin fiber appears crucial in determining the kind of nucleosome packing for short nucleosome repeat lengths as in telomeres and yeast chromatin.

Motor Abundance Contributes to Resolving Multiple Kinematic Task Constraints

This study investigated the use of motor abundance during the transport and placing of objects that required either precise or minimal orientation to the target. Analyses across repetitions of the structure of joint configuration variance relative to the position and orientation constraints were performed using the Uncontrolled Manifold (UCM) approach. Results indicated that the orientation constraint did not affect stability of the hand's spatial path. Orientation was weakly stabilized during the late transport phase independent of the orientation constraint, indicating no default synergy stabilizing orientation. Stabilization of orientation for conditions most requiring it for successful insertion of the object was present primarily during the adjustment phase. The results support the hypothesis that a major advantage of a control scheme that utilizes motor abundance is the ability to resolve multiple task constraints simultaneously without undue interference among them.

Alignment with the Horizontal Plane: Evidence for an Orientation Constraint in the Perception of Shape

In order to convert a 2-D image to a 3-D percept, the visual system must apply constraints that maximize the chances that the result will be unique and veridical. Previously proposed constraints include one that maximizes the symmetry of the percept, and one that maximizes its compactness (Li et al, 2009 Vision Research 49 979-991). Analysis of the 3-D percepts elicited by certain 2-D forms suggests the action of an additional constraint, favoring the alignment of the surfaces and/or axis of symmetry of the perceived object with the horizontal plane.

Constraints on the stress state of the San Andreas Fault with analysis based on core and cuttings from San Andreas Fault Observatory at Depth (SAFOD) drilling phases 1 and 2

Analysis of field data has led different investigators to conclude that the San Andreas Fault (SAF) has either anomalously low frictional sliding strength (μ < 0.2) or strength consistent with standard laboratory tests (μ > 0.6). Arguments for the apparent weakness of the SAF generally hinge on conceptual models involving intrinsically weak gouge or elevated pore pressure within the fault zone. Some models assert that weak gouge and/or high pore pressure exist under static conditions while others consider strength loss or fluid pressure increase due to rapid coseismic fault slip. The present paper is composed of three parts. First, we develop generalized equations, based on and consistent with the Rice (1992) fault zone model to relate stress orientation and magnitude to depth‐dependent coefficient of friction and pore pressure. Second, we present temperature‐ and pressure‐dependent friction measurements from wet illite‐rich fault gouge extracted from San Andreas Fault Observatory at Depth (SAFOD) phase 1 core samples and from weak minerals associated with the San Andreas Fault. Third, we reevaluate the state of stress on the San Andreas Fault in light of new constraints imposed by SAFOD borehole data. Pure talc (μ≈0.1) had the lowest strength considered and was sufficiently weak to satisfy weak fault heat flow and stress orientation constraints with hydrostatic pore pressure. Other fault gouges showed a systematic increase in strength with increasing temperature and pressure. In this case, heat flow and stress orientation constraints would require elevated pore pressure and, in some cases, fault zone pore pressure in excess of vertical stress.

A genetic algorithm for the two‐dimensional knapsack problem with rectangular pieces

AbstractGiven a set of rectangular pieces and a rectangular container, the two‐dimensional knapsack problem (2D‐KP) consists of orthogonally packing a subset of the pieces within the container such that the sum of the values of the packed pieces is maximized. If the value of a piece is given by its area, the objective is to maximize the covered area of the container. A genetic algorithm (GA) is proposed addressing the guillotine case of the 2D‐KP as well as the non‐guillotine case. Moreover, an orientation constraint may optionally be taken into account and the given piece set may be constrained or unconstrained. The GA is subjected to an extensive test using well‐known benchmark instances. Compared with recently published methods, the GA yields competitive results.

Chemical Labeling Strategy with (R)- and (S)-Trifluoromethylalanine for Solid State 19F NMR Analysis of Peptaibols in Membranes

Substitution of a single Aib-residue in a peptaibol with (R)- and (S)-trifluoromethylalanine yields two local orientational constraints theta by solid state (19)F NMR. The structure of the membrane-perturbing antibiotic alamethicin in DMPC bilayers was analyzed in terms of two angles tau and rho from six such constraints, showing that the N-terminus (up to a kink at Pro14) is folded as an alpha-helix, tilted away from the membrane normal by 8 degrees, and assembled as an oligomer. The new (19)F NMR label CF(3)-Ala has thus been demonstrated to be highly sensitive, virtually unperturbing, and ideally suited to characterize peptaibols in membranes.

A new calibration method for parallel kinematics machine tools using orientation constraint

This paper considers the problem of improving the accuracy of parallel kinematics machine tools through a low-cost and effective calibration method. A novel orientation constraint of keeping two attitude angles of the end-effector constant is presented to derive the calibration algorithm with special insight on the effect of using various combinations of two angles. The orientation constraint of the selected combination is realized physically through leveling a commercial biaxial inclinometer installed on the end-effector. Benefits of the proposed method include exempting the needs for precise pose (position and orientation) measurement and for mechanical fixtures, as well as rendering the independence of the measuring range and angular positioning accuracy of the inclinometer. Simulation based on the geometry of the Stewart platform of XJ-HEXA shows the position and orientation accuracy can reach 0.1 mm and 0.01° after calibration, when using an inclinometer with the repeatability of 0.001° and measuring the leg lengths with the precision of 0.002 mm at 80 configurations. Experiments on XJ-HEXA further verify the effectiveness of the proposed method.

The role of molecular orientation and light polarization on the control of bond dissociation. Time-dependent simulations for CH2BrCl

The role of orientation on the bond selective dissociation of CH2BrCl into CH2Br + Cl or CH2Cl + Br has been investigated employing two-dimensional time-dependent wave packet propagations. Both channels are reactive when CH2BrCl is photoexcited to the lowest excited singlet states of A′ symmetry, which are nonadiabatically coupled. The branching ratio between both channels can be controlled using a driving few-cycle IR laser pulse followed by a control UV pulse. It is shown that the molecular orientation has a very important effect on the branching ratio. If the constraint of orientation is lifted and the system is only aligned, control is possible when using perpendicularly polarized IR and UV pulses.

A procedure for estimating Young’s modulus of textured polycrystalline materials

In this study, a procedure for estimating Young’s modulus of textured and non-textured polycrystalline materials was examined based on finite element analyses, which were performed using three-dimensional polycrystalline finite element models of a random structure, generated using the Voronoi tessellation. Firstly, the local stress/strain distribution and its influence on macroscopic elastic properties were evaluated. Then, the statistical relationship between Young’s modulus obtained from the finite element analyses and averaged Young’s modulus of all grains evaluated based on Voigt’s or Reuss’ model was investigated. It was revealed that the local stress/strain in the polycrystalline body is affected by crystal orientation and deformation constraint caused by adjacent grains, whereas only the crystal orientation affects Young’s modulus of the polycrystalline body when the number of grains is large enough. It was also shown that Young’s modulus correlates well with the averaged Young’s modulus of all grains, in which the size of grains is considered in the averaging. Finally, a procedure for estimating Young’s modulus of textured and non-textured materials was proposed. Young’s modulus of various materials can be estimated from the elastic constants of single crystal and the distribution of crystal orientation and size of grains, which can be obtained by using electron backscatter diffraction (EBSD).

A pure quasi-human algorithm for solving the cuboid packing problem

We excavate the wisdom from an old Chinese proverb “gold corner, silver side and strawy void”, and further improve it into “maximum value in diamond cave” for solving the NP-hard cuboid packing problem. We extract, integrate and formalize the idea by west modern mathematical tools, and propose a pure quasi-human algorithm. The performance of the algorithm is evaluated on two sets of public benchmarks. For 100 strongly heterogeneous difficult benchmarks, experiments show an average packing utilization of 87.31%, which surpasses current best record reported in the literature by 1.83%. For 47 difficult benchmarks without orientation constraint, experiments show an average volume utilization of 92.05%, which improves current best record reported in the literature by 1.05%.

Calculation of fluorine chemical shift tensors for the interpretation of oriented 19F-NMR spectra of gramicidin A in membranes

A semi-empirical method for the prediction of chemical shifts, based on bond polarization theory, has recently been introduced for (13)C. Here, we extended this approach to calculate the (19)F chemical shift tensors of fluorine bound to aromatic rings and in aliphatic CF(3) groups. For the necessary parametrization, ab initio chemical shift calculations were performed at the MP2 level for a set of fluorinated molecules including tryptophan. The bond polarization parameters obtained were used to calculate the (19)F chemical shift tensors for several crystalline molecules, and to reference the calculated values on a chemical shift scale relative to CFCl(3). As a first biophysical application, we examined the distribution of conformations of a (19)F-labeled tryptophan side chain in the membrane-bound ion channel peptide, gramicidin A. The fluorine chemical shift tensors were calculated from snapshots of a molecular dynamics simulation employing the (19)F-parametrized bond polarization theory. In this MD simulation, published (2)H quadrupolar and (15)N-(1)H dipolar couplings of the indole ring were used as orientational constraints to determine the conformational distribution of the 5F-Trp(13) side chain. These conformations were then used to interpret the spectra of (19)F-labeled gramicidin A in fluid and gel phase lipid bilayers.

Using a Sterically Restrictive Amino Acid as a 19F NMR label To Monitor and To Control Peptide Aggregation in Membranes

Aggregation of peptides into amyloid fibrils or other β-sheet structures is usually related to malfunction. This process is often induced by lipid bilayers but is difficult to monitor in the membrane-bound state. Here, we show how aggregation is readily detected by solid state 19F NMR using a fluorine-labeled amino acid and how the same sterically rigid side chain can be also be employed to prevent aggregation. Selective CF3-phenylglycine labels were incorporated either as the L- or D-enantiomer into the membrane-active model amphiphilic peptide (MAP). Oriented circular dichroism showed that the D-epimeric peptides maintained an α-helical conformation in DMPC at all peptide-to-lipid ratios, while the L-epimers turned into β-sheet structures above 1:200, just like the wild-type. Aggregation was clearly revealed by the appearance of powder lineshapes in the 19F NMR spectra of oriented samples. The 19F NMR dipolar couplings from four D-epimers were analyzed as orientational constraints, showing that the helix of MAP undergoes a concentration-dependent realignment in DMPC from a surface-bound to a tilted state.