Latest development of the combinatorial model of nuclear level densities

The combinatorial model of nuclear level densities has now reached a level of accuracy comparable to that of the best global analytical expressions without suffering from the limits imposed by the statistical hypothesis on which the latter expressions rely. In particular, it provides, naturally, non-Gaussian spin distribution as well as non-equipartition of parities which are known to have an impact on cross section predictions at low energies [1, 2, 3]. Our previous global models developed in Refs. [1, 2] suffered from deficiencies, in particular in the way the collective effects - both vibrational and rotational - were treated. We have recently improved this treatment using simultaneously the single-particle levels and collective properties predicted by a newly derived Gogny interaction [4], therefore enabling a microscopic description of energy-dependent shell, pairing and deformation effects. In addition for deformed nuclei, the transition to sphericity is coherently taken into account on the basis of a temperature-dependent Hartree-Fock calculation which provides at each temperature the structure properties needed to build the level densities. This new method is described and shown to give promising results with respect to available experimental data.

Imaging through turbulence using compressive coherence sensing.

Previous studies have shown that the isoplanatic distortion due to turbulence and the image of a remote object may be jointly estimated from the 4D mutual intensity across an aperture. This Letter shows that decompressive inference on a 2D slice of the 4D mutual intensity, as measured by a rotational shear interferometer, is sufficient for estimation of sparse objects imaged through turbulence. The 2D slice is processed using an iterative algorithm that alternates between estimating the sparse objects and estimating the turbulence-induced phase screen. This approach may enable new systems that infer object properties through turbulence without exhaustive sampling of coherence functions.

Far-field analysis of axially symmetric three-dimensional directional cloaks.

Axisymmetric radiating and scattering structures whose rotational invariance is broken by non-axisymmetric excitations present an important class of problems in electromagnetics. For such problems, a cylindrical wave decomposition formalism can be used to efficiently obtain numerical solutions to the full-wave frequency-domain problem. Often, the far-field, or Fraunhofer region is of particular interest in scattering cross-section and radiation pattern calculations; yet, it is usually impractical to compute full-wave solutions for this region. Here, we propose a generalization of the Stratton-Chu far-field integral adapted for 2.5D formalism. The integration over a closed, axially symmetric surface is analytically reduced to a line integral on a meridional plane. We benchmark this computational technique by comparing it with analytical Mie solutions for a plasmonic nanoparticle, and apply it to the design of a three-dimensional polarization-insensitive cloak.

On-board Robotic Multi-pinhole SPECT System for Region-of-interest (ROI) Imaging

On-board image guidance, such as cone-beam CT (CBCT) and kV/MV 2D imaging, is essential in many radiation therapy procedures, such as intensity modulated radiotherapy (IMRT) and stereotactic body radiation therapy (SBRT). These imaging techniques provide predominantly anatomical information for treatment planning and target localization. Recently, studies have shown that treatment planning based on functional and molecular information about the tumor and surrounding tissue could potentially improve the effectiveness of radiation therapy. However, current on-board imaging systems are limited in their functional and molecular imaging capability. Single Photon Emission Computed Tomography (SPECT) is a candidate to achieve on-board functional and molecular imaging. Traditional SPECT systems typically take 20 minutes or more for a scan, which is too long for on-board imaging. A robotic multi-pinhole SPECT system was proposed in this dissertation to provide shorter imaging time by using a robotic arm to maneuver the multi-pinhole SPECT system around the patient in position for radiation therapy.

A 49-pinhole collimated SPECT detector and its shielding were designed and simulated in this work using the computer-aided design (CAD) software. The trajectories of robotic arm about the patient, treatment table and gantry in the radiation therapy room and several detector assemblies such as parallel holes, single pinhole and 49 pinholes collimated detector were investigated. The rail mounted system was designed to enable a full range of detector positions and orientations to various crucial treatment sites including head and torso, while avoiding collision with linear accelerator (LINAC), patient table and patient.

An alignment method was developed in this work to calibrate the on-board robotic SPECT to the LINAC coordinate frame and to the coordinate frames of other on-board imaging systems such as CBCT. This alignment method utilizes line sources and one pinhole projection of these line sources. The model consists of multiple alignment parameters which maps line sources in 3-dimensional (3D) space to their 2-dimensional (2D) projections on the SPECT detector. Computer-simulation studies and experimental evaluations were performed as a function of number of line sources, Radon transform accuracy, finite line-source width, intrinsic camera resolution, Poisson noise and acquisition geometry. In computer-simulation studies, when there was no error in determining angles (α) and offsets (ρ) of the measured projections, the six alignment parameters (3 translational and 3 rotational) were estimated perfectly using three line sources. When angles (α) and offsets (ρ) were provided by Radon transform, the estimation accuracy was reduced. The estimation error was associated with rounding errors of Radon transform, finite line-source width, Poisson noise, number of line sources, intrinsic camera resolution and detector acquisition geometry. The estimation accuracy was significantly improved by using 4 line sources rather than 3 and also by using thinner line-source projections (obtained by better intrinsic detector resolution). With 5 line sources, median errors were 0.2 mm for the detector translations, 0.7 mm for the detector radius of rotation, and less than 0.5° for detector rotation, tilt and twist. In experimental evaluations, average errors relative to a different, independent registration technique were about 1.8 mm for detector translations, 1.1 mm for the detector radius of rotation (ROR), 0.5° and 0.4° for detector rotation and tilt, respectively, and 1.2° for detector twist.

Simulation studies were performed to investigate the improvement of imaging sensitivity and accuracy of hot sphere localization for breast imaging of patients in prone position. A 3D XCAT phantom was simulated in the prone position with nine hot spheres of 10 mm diameter added in the left breast. A no-treatment-table case and two commercial prone breast boards, 7 and 24 cm thick, were simulated. Different pinhole focal lengths were assessed for root-mean-square-error (RMSE). The pinhole focal lengths resulting in the lowest RMSE values were 12 cm, 18 cm and 21 cm for no table, thin board, and thick board, respectively. In both no table and thin board cases, all 9 hot spheres were easily visualized above background with 4-minute scans utilizing the 49-pinhole SPECT system while seven of nine hot spheres were visible with the thick board. In comparison with parallel-hole system, our 49-pinhole system shows reduction in noise and bias under these simulation cases. These results correspond to smaller radii of rotation for no-table case and thinner prone board. Similarly, localization accuracy with the 49-pinhole system was significantly better than with the parallel-hole system for both the thin and thick prone boards. Median localization errors for the 49-pinhole system with the thin board were less than 3 mm for 5 of 9 hot spheres, and less than 6 mm for the other 4 hot spheres. Median localization errors of 49-pinhole system with the thick board were less than 4 mm for 5 of 9 hot spheres, and less than 8 mm for the other 4 hot spheres.

Besides prone breast imaging, respiratory-gated region-of-interest (ROI) imaging of lung tumor was also investigated. A simulation study was conducted on the potential of multi-pinhole, region-of-interest (ROI) SPECT to alleviate noise effects associated with respiratory-gated SPECT imaging of the thorax. Two 4D XCAT digital phantoms were constructed, with either a 10 mm or 20 mm diameter tumor added in the right lung. The maximum diaphragm motion was 2 cm (for 10 mm tumor) or 4 cm (for 20 mm tumor) in superior-inferior direction and 1.2 cm in anterior-posterior direction. Projections were simulated with a 4-minute acquisition time (40 seconds per each of 6 gates) using either the ROI SPECT system (49-pinhole) or reference single and dual conventional broad cross-section, parallel-hole collimated SPECT. The SPECT images were reconstructed using OSEM with up to 6 iterations. Images were evaluated as a function of gate by profiles, noise versus bias curves, and a numerical observer performing a forced-choice localization task. Even for the 20 mm tumor, the 49-pinhole imaging ROI was found sufficient to encompass fully usual clinical ranges of diaphragm motion. Averaged over the 6 gates, noise at iteration 6 of 49-pinhole ROI imaging (10.9 µCi/ml) was approximately comparable to noise at iteration 2 of the two dual and single parallel-hole, broad cross-section systems (12.4 µCi/ml and 13.8 µCi/ml, respectively). Corresponding biases were much lower for the 49-pinhole ROI system (3.8 µCi/ml), versus 6.2 µCi/ml and 6.5 µCi/ml for the dual and single parallel-hole systems, respectively. Median localization errors averaged over 6 gates, for the 10 mm and 20 mm tumors respectively, were 1.6 mm and 0.5 mm using the ROI imaging system and 6.6 mm and 2.3 mm using the dual parallel-hole, broad cross-section system. The results demonstrate substantially improved imaging via ROI methods. One important application may be gated imaging of patients in position for radiation therapy.

A robotic SPECT imaging system was constructed utilizing a gamma camera detector (Digirad 2020tc) and a robot (KUKA KR150-L110 robot). An imaging study was performed with a phantom (PET CT PhantomTM), which includes 5 spheres of 10, 13, 17, 22 and 28 mm in diameter. The phantom was placed on a flat-top couch. SPECT projections were acquired with a parallel-hole collimator and a single-pinhole collimator both without background in the phantom, and with background at 1/10th the sphere activity concentration. The imaging trajectories of parallel-hole and pinhole collimated detectors spanned 180 degrees and 228 degrees respectively. The pinhole detector viewed a 14.7 cm-diameter common volume which encompassed the 28 mm and 22 mm spheres. The common volume for parallel-hole was a 20.8-cm-diameter cylinder which encompassed all five spheres in the phantom. The maneuverability of the robotic system was tested by navigating the detector to trace the flat-top table while avoiding collision with the table and maintaining the closest possible proximity to the common volume. For image reconstruction, detector trajectories were described by radius-of-rotation and detector rotation angle θ. These reconstruction parameters were obtained from the robot base and tool coordinates. The robotic SPECT system was able to maneuver the parallel-hole and pinhole collimated SPECT detectors in close proximity to the phantom, minimizing impact of the flat-top couch on detector to center-of-rotation (COR) distance. In no background case, all five spheres were visible in the reconstructed parallel-hole and pinhole images. In with background case, three spheres of 17, 22 and 28 mm diameter were readily observed with the parallel-hole imaging, and the targeted spheres (22 and 28 mm diameter) were readily observed in the pinhole ROI imaging.

In conclusion, the proposed on-board robotic SPECT can be aligned to LINAC/CBCT with a single pinhole projection of the line-source phantom. Alignment parameters can be estimated using one pinhole projection of line sources. This alignment method may be important for multi-pinhole SPECT, where relative pinhole alignment may vary during rotation. For single pinhole and multi-pinhole SPECT imaging onboard radiation therapy machines, the method could provide alignment of SPECT coordinates with those of CBCT and the LINAC. In simulation studies of prone breast imaging and respiratory-gated lung imaging, the 49-pinhole detector showed better tumor contrast recovery and localization in a 4-minute scan compared to parallel-hole detector. On-board SPECT could be achieved by a robot maneuvering a SPECT detector about patients in position for radiation therapy on a flat-top couch. The robot inherent coordinate frames could be an effective means to estimate detector pose for use in SPECT image reconstruction.

The role of GRK6 in animal models of Parkinson's disease and L-DOPA treatment.

G protein-coupled Receptor Kinase 6 (GRK6) belongs to a family of kinases that phosphorylate GPCRs. GRK6 levels were found to be altered in Parkinson's Disease (PD) and D(2) dopamine receptors are supersensitive in mice lacking GRK6 (GRK6-KO mice). To understand how GRK6 modulates the behavioral manifestations of dopamine deficiency and responses to L-DOPA, we used three approaches to model PD in GRK6-KO mice: 1) the cataleptic response to haloperidol; 2) introducing GRK6 mutation to an acute model of absolute dopamine deficiency, DDD mice; 3) hemiparkinsonian 6-OHDA model. Furthermore, dopamine-related striatal signaling was analyzed by assessing the phosphorylation of AKT/GSK3β and ERK1/2. GRK6 deficiency reduced cataleptic behavior, potentiated the acute effect of L-DOPA in DDD mice, reduced rotational behavior in hemi-parkinsonian mice, and reduced abnormal involuntary movements induced by chronic L-DOPA. These data indicate that approaches to regulate GRK6 activity could be useful in modulating both therapeutic and side-effects of L-DOPA.

Locomotor head movements and semicircular canal morphology in primates.

Animal locomotion causes head rotations, which are detected by the semicircular canals of the inner ear. Morphologic features of the canals influence rotational sensitivity, and so it is hypothesized that locomotion and canal morphology are functionally related. Most prior research has compared subjective assessments of animal "agility" with a single determinant of rotational sensitivity: the mean canal radius of curvature (R). In fact, the paired variables of R and body mass are correlated with agility and have been used to infer locomotion in extinct species. To refine models of canal functional morphology and to improve locomotor inferences for extinct species, we compare 3D vector measurements of head rotation during locomotion with 3D vector measures of canal sensitivity. Contrary to the predictions of conventional models that are based upon R, we find that axes of rapid head rotation are not aligned with axes of either high or low sensitivity. Instead, animals with fast head rotations have similar sensitivities in all directions, which they achieve by orienting the three canals of each ear orthogonally (i.e., along planes at 90° angles to one another). The extent to which the canal configuration approaches orthogonality is correlated with rotational head speed independent of body mass and phylogeny, whereas R is not.

Stress Relaxation for Granular Materials near Jamming under Cyclic Compression.

We have explored isotropically jammed states of semi-2D granular materials through cyclic compression. In each compression cycle, systems of either identical ellipses or bidisperse disks transition between jammed and unjammed states. We determine the evolution of the average pressure P and structure through consecutive jammed states. We observe a transition point ϕ_{m} above which P persists over many cycles; below ϕ_{m}, P relaxes slowly. The relaxation time scale associated with P increases with packing fraction, while the relaxation time scale for collective particle motion remains constant. The collective motion of the ellipses is hindered compared to disks because of the rotational constraints on elliptical particles.

Computational Inference of Genome-Wide Protein-DNA Interactions Using High-Throughput Genomic Data

Transcriptional regulation has been studied intensively in recent decades. One important aspect of this regulation is the interaction between regulatory proteins, such as transcription factors (TF) and nucleosomes, and the genome. Different high-throughput techniques have been invented to map these interactions genome-wide, including ChIP-based methods (ChIP-chip, ChIP-seq, etc.), nuclease digestion methods (DNase-seq, MNase-seq, etc.), and others. However, a single experimental technique often only provides partial and noisy information about the whole picture of protein-DNA interactions. Therefore, the overarching goal of this dissertation is to provide computational developments for jointly modeling different experimental datasets to achieve a holistic inference on the protein-DNA interaction landscape.

We first present a computational framework that can incorporate the protein binding information in MNase-seq data into a thermodynamic model of protein-DNA interaction. We use a correlation-based objective function to model the MNase-seq data and a Markov chain Monte Carlo method to maximize the function. Our results show that the inferred protein-DNA interaction landscape is concordant with the MNase-seq data and provides a mechanistic explanation for the experimentally collected MNase-seq fragments. Our framework is flexible and can easily incorporate other data sources. To demonstrate this flexibility, we use prior distributions to integrate experimentally measured protein concentrations.

We also study the ability of DNase-seq data to position nucleosomes. Traditionally, DNase-seq has only been widely used to identify DNase hypersensitive sites, which tend to be open chromatin regulatory regions devoid of nucleosomes. We reveal for the first time that DNase-seq datasets also contain substantial information about nucleosome translational positioning, and that existing DNase-seq data can be used to infer nucleosome positions with high accuracy. We develop a Bayes-factor-based nucleosome scoring method to position nucleosomes using DNase-seq data. Our approach utilizes several effective strategies to extract nucleosome positioning signals from the noisy DNase-seq data, including jointly modeling data points across the nucleosome body and explicitly modeling the quadratic and oscillatory DNase I digestion pattern on nucleosomes. We show that our DNase-seq-based nucleosome map is highly consistent with previous high-resolution maps. We also show that the oscillatory DNase I digestion pattern is useful in revealing the nucleosome rotational context around TF binding sites.

Finally, we present a state-space model (SSM) for jointly modeling different kinds of genomic data to provide an accurate view of the protein-DNA interaction landscape. We also provide an efficient expectation-maximization algorithm to learn model parameters from data. We first show in simulation studies that the SSM can effectively recover underlying true protein binding configurations. We then apply the SSM to model real genomic data (both DNase-seq and MNase-seq data). Through incrementally increasing the types of genomic data in the SSM, we show that different data types can contribute complementary information for the inference of protein binding landscape and that the most accurate inference comes from modeling all available datasets.

This dissertation provides a foundation for future research by taking a step toward the genome-wide inference of protein-DNA interaction landscape through data integration.

Infrared light on molecule-molecule and molecule-surface collisions

By analyzing measured infrared absorption of pure CH4 gas under both "free" (large sample cell) and "confined" (inside the pores of a silica xerogel sample) conditions we give a demonstration that molecule-molecule and molecule-surface collisions lead to very different propensity rules for rotational-state changes. Whereas the efficiency of collisions to change the rotational state (observed through the broadening of the absorption lines) decreases with increasing rotational quantum number J for CH4-CH4 interactions, CH4-surface collisions lead to J-independent linewidths. In the former case, some (weak) collisions are inefficient whereas, in the latter case, a single collision is sufficient to remove the molecule from its initial rotational level. Furthermore, although some gas-phase collisions leave J unchanged and only modify the angular momentum orientation and/or symmetry of the level (as observed through the spectral effects of line mixing), this is not the case for the molecule-surface collisions since they always change J (in the studied J=0-14 range).

12C2H2-Ar van der Waals complex

New theoretical and experimental results on the acetylene-Ar van der Waals complex are presented and the literature is reviewed. New ab initio calculations at the MP2 level were performed using large basis sets with diffuse functions and taking into account the basis set superposition error. It was found that the structure of acetylene is not significantly altered by the complexation and that its vibrational frequencies are only slightly lowered. Finally, it was observed that the calculated properties of the complex (structure, vibrational spectrum, bond dissociation energy) are not sensitive to the structure imposed on acetylene. Experimentally, acetylene-Ar was produced in a supersonic expansion under experimental conditions corresponding to 9 K rotational temperature. Thanks to the performances of CW-CRDS detection, the Ka = 0 ← 1, 1 ← 0, and 2 ← 1 sub- bands of the v1 + v3 band could be recorded and resolved and most of their lines assigned. Upper-state rotational constants were fitted, however not including the upper Ka = 2 state, which shows K-doubling the opposite of the expected. The Lorentzian width of most line profiles sets the mean lifetime to some 7.5 ns. Local perturbations affecting line positions and/or line widths are demonstrated. Additional series of lines tentatively attributed to acetylene-Ar are discussed.© 2009 American Chemical Society.

Comparison of the experimental, semi-experimental and ab initio equilibrium structures of acetylene: Influence of relativisitic effects and of the diagonal Born-Oppenheimer corrections

The equilibrium structure of acetylene (also named ethyne) has been reinvestigated to resolve the small discrepancies noted between different determinations. The size of the system as well as the large amount of available experimental data provides the quite unique opportunity to check the magnitude and relevance of various contributions to equilibrium structure as well as to verify the accuracy of experimental results. With respect to pure theoretical investigation, quantum-chemical calculations at the coupled-cluster level have been employed together with extrapolation to the basis set limit, consideration of higher excitations in the cluster operator, inclusion of core correlation effects as well as relativistic and diagonal Born-Oppenheimer corrections. In particular, it is found that the extrapolation to the complete basis set limit, the inclusion of higher excitations in the electronic-correlation treatment and the relativistic corrections are of the same order of magnitude. It also appears that a basis set as large as a core-valence quintuple-zeta set is required for accurately accounting for the inner-shell correlation contribution. From a pure experimental point of view, the equilibrium structure has been determined using very accurate rotational constants recently obtained by a global analysis (that is to say that all non-negligible interactions are explicitely included in the Hamiltonian matrix) of rovibrational spectra. Finally, a semi-experimental equilibrium structure (where the equilibrium rotational constants are obtained from the experimental ground state rotational constants and computed rovibrational corrections) has been obtained from the available experimental ground-state rotational constants for ten isotopic species corrected for computed vibrational corrections. Such a determination led to the revision of the ground-state rotational constants of two isotopologues, thus showing that structural determination is a good method to identify errors in experimental rotational constants. The three structures are found in a very good agreement, and our recommended values are rCC 120.2958(7) pm and rCH 106.164(1) pm. © 2011 American Institute of Physics.

Estimación de la partición de heces ovinas en un sistema de pastoreo rotativo intensivo con encierre nocturno

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Basic components in the scienctific didactical training of the secondary school mathematics teachers

Secondary mathematics teacher training in Spain is currently the subject of a heated revision debate. The speed of social, cultural, scientific and economic changes have left a hundred years old teacher training model well behind. However, academical inertia and professional interests are impeding a real new training of the mathematics teacher as an autonomous mathematical educator. Teachers of Didactic of Mathematics and the Spanish Associations of mathematics teachers have recently been discussing the issue. Their conclusions are included here.

Dynamics of an axisymmetric electromagnetic ‘crucible’ melting

Different industrial induction melting processes involve free surface and melt-solid interface of the liquid metal subject to dynamic change during the technological operation. Simulation of the liquid metal dynamics requires to solve the non-linear, coupled hydrodynamic-electromagnetic-heat transfer problem accounting for the time development of the liquid metal free boundary with a suitable turbulent viscosity model. The present paper describes a numerical solution method applicable for various axisymmetric induction melting processes, such as, crucible with free top surface, levitation, semi-levitation, cold crucible and similar melting techniques. The presented results in the cases of semi-levitation and crucible with free top surface meltings demonstrate oscillating transient behaviour of the free metal surface indicating the presence of gravity-inertial-electromagnetic waves which are coupled to the internal fluid flow generated by both the rotational and potential parts of the electromagnetic force.

Choosing the appropriate level of coupling in multi-physics modeling of metallurgical processes

A computational model for the interrelated phenomena in the process of vacuum arc remelting is analyzed and adjusted of optimal accuracy and computation time. The decision steps in this case study are offered as an example how the coupling in models of similar processes can be addressed. Results show dominance of the electromagnetic forces over buoyancy and inertia for the investigated process conditions.