Using Optimization to Obtain a Width-Independent, Parallel, Simpler, and Faster Positive SDP Solver

We study the design of polylogarithmic depth algorithms for approximately solving packing and covering semidefinite programs (or positive SDPs for short). This is a natural SDP generalization of the well-studied positive LP problem. Although positive LPs can be solved in polylogarithmic depth while using only $\tilde{O}(\log^{2} n/\varepsilon^2)$ parallelizable iterations, the best known positive SDP solvers due to Jain and Yao require $O(\log^{14} n /\varepsilon^{13})$ parallelizable iterations. Several alternative solvers have been proposed to reduce the exponents in the number of iterations. However, the correctness of the convergence analyses in these works has been called into question, as they both rely on algebraic monotonicity properties that do not generalize to matrix algebra. In this paper, we propose a very simple algorithm based on the optimization framework proposed for LP solvers. Our algorithm only needs $\tilde{O}(\log^2 n / \varepsilon^2)$ iterations, matching that of the best LP solver. To surmount the obstacles encountered by previous approaches, our analysis requires a new matrix inequality that extends Lieb-Thirring's inequality, and a sign-consistent, randomized variant of the gradient truncation technique proposed in

Nanomechanical characterization of clay micro flocs

Clay flocs are abundant in natural soils (a particulate material) and water-borne sediments. As the basic microscale, loading-bearing fundamental units, their mechanical properties control the macroscopic response of bulk soils and sediment transport. Owing to their tiny size and extremely soft consistency (especially for suspended water-borne flocs), significant difficulties and challenges exist for mechanical characterization of clay micro flocs. A novel nanomechanical characterization technique was developed to probe the elasticity and yield shear strength of individual micron-sized clay and clay-biopolymer flocs that were prepared in laboratory and sampled in natural waters. Artificial clay flocs were prepared using four types of pure clay minerals (i.e., kaolinite, Na-smectite, Ca-smectite, and illite) and two types of polysaccharides of dissimilar polarities (i.e., cationic vs. anionic) to investigate the effects of how polarity affects clay–biopolymer interactions and the mechanical behavior of resulting biopolymer-bearing clay flocs. Natural marine flocs were sampled offshore near the Northern Gulf of Mexico. A nano universal testing system was used to compress individual spherical flocs submerged in water between two rigid platens, and the load-deformation curves were analyzed using Hertz elastic contact theory and Tresca yield criterion. The reduced modulus of these flocs ranges from 0.45 to 4.82 kPa, and the yield strength from 0.07 to 0.51 kPa. Moreover, the distribution of both elasticity and strength of the flocs can be fit by Weibull distribution, allowing the estimation of the mean value for the mechanical properties of flocs with highly variable properties. The developed technique was also employed to study the thixotropism of pure kaolinite flocs prepared in salt water at a salinity of 5 psu. Results indicate that thixotropic hardening leads to an increase in both elasticity and yield strength, and such an increase obeys a kinetics law of chemical reactions. Through the statistical analysis of the thixotropic increase, it was found that the mechanisms of thixotropy originates not only through interparticle bonding development, but also the redistribution of the nonuniform structural and mechanical flaws into a more uniform distribution. Finally, the developed techniques are readily applicable to the study of the clay aggregates in natural soils

Integrating static and dynamic information for routing traffic

The efficiency of traffic routing on complex networks can be reflected by two key measurements i.e. the system capacity and the average data packets travel time. In this paper, we propose a mixing routing strategy by integrating local static and dynamic information for enhancing the efficiency of traffic on scale-free networks. The strategy is governed by a single parameter. Simulation results show that there exists a optimal parameter value by considering both maximizing the network capacity and reducing the packet travel time. Comparing with the strategy by adopting exclusive local static information, the new strategy shows its advantages in improving the efficiency of the system. The detailed analysis of the mixing strategy is provided. This work suggests that how to effectively utilize the larger degree nodes plays the key role in the scale-free traffic systems.Comment: 5 pages, 5 figure

UNSWIRF: A Tunable Imaging Spectrometer for the Near-Infrared

We describe the specifications, characteristics, calibration, and analysis of data from the University of New South Wales Infrared Fabry-Perot (UNSWIRF) etalon. UNSWIRF is a near-infrared tunable imaging spectrometer, used primarily in conjunction with IRIS on the AAT, but suitable for use as a visitor instrument at other telescopes. The etalon delivers a resolving power in excess of 4000 (corresponding to a velocity resolution ~75 km/s), and allows imaging of fields up to 100" in diameter on the AAT at any wavelength between 1.5 and 2.4 microns for which suitable blocking filters are available.Comment: 16 pages, 10 figures, uses psfig.sty and html.sty (included). To appear in Publications of the Astronomical Society of Australi

A dual-laser interferometry system for thin film measurements in thermal vapor deposition applications

Thesis: M. Eng., Massachusetts Institute of Technology, Department of Electrical Engineering and Computer Science, 2012.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.Cataloged from student-submitted PDF version of thesis.Includes bibliographical references (pages 91-92).Lithography processes harnessing the phase change of the chemically inert carbon dioxide as a resist have been shown as a possible alternative to patterning thin film organic semiconductors and metals. The ability to control the resist's growth would make the lithography process more reliable and ecient. This thesis seeks to control and observe the physical properties of the carbon dioxide resist via the optical technique of dual-laser interferometry in conjunction with a quartz crystal micro balance (QCMB).by Allen Shiping Yin.M. Eng

Experimental library screening demonstrates the successful application of computational protein design to large structural ensembles

The stability, activity, and solubility of a protein sequence are determined by a delicate balance of molecular interactions in a variety of conformational states. Even so, most computational protein design methods model sequences in the context of a single native conformation. Simulations that model the native state as an ensemble have been mostly neglected due to the lack of sufficiently powerful optimization algorithms for multistate design. Here, we have applied our multistate design algorithm to study the potential utility of various forms of input structural data for design. To facilitate a more thorough analysis, we developed new methods for the design and high-throughput stability determination of combinatorial mutation libraries based on protein design calculations. The application of these methods to the core design of a small model system produced many variants with improved thermodynamic stability and showed that multistate design methods can be readily applied to large structural ensembles. We found that exhaustive screening of our designed libraries helped to clarify several sources of simulation error that would have otherwise been difficult to ascertain. Interestingly, the lack of correlation between our simulated and experimentally measured stability values shows clearly that a design procedure need not reproduce experimental data exactly to achieve success. This surprising result suggests potentially fruitful directions for the improvement of computational protein design technology

1-(2-Chloro­benzo­yl)-3-[4-(trifluoro­meth­oxy)phen­yl]urea

The title compound, C15H10ClF3N2O3, is considered to belong to a fourth generation of insecticides with properties such as high selectivity, low acute toxicity for mammals and high biological activity. The dihedral angle between the two benzene rings is 59.3 (2)°. Intra­molecular C—H⋯O and N—H⋯O hydrogen bonds are observed. Inter­molecular N—H⋯O hydrogen bonding generates a centrosymmetric dimer. The F atoms are disordered over two positions; the site occupancy factors are 0.52 and 0.48

A targeted gene panel that covers coding, non-coding and short tandem repeat regions improves the diagnosis of patients with neurodegenerative diseases

Genetic testing for neurodegenerative diseases (NDs) is highly challenging because of genetic heterogeneity and overlapping manifestations. Targeted-gene panels (TGPs), coupled with next-generation sequencing (NGS), can facilitate the profiling of a large repertoire of ND-related genes. Due to the technical limitations inherent in NGS and TGPs, short tandem repeat (STR) variations are often ignored. However, STR expansions are known to cause such NDs as Huntington\u27s disease and spinocerebellar ataxias type 3 (SCA3). Here, we studied the clinical utility of a custom-made TGP that targets 199 NDs and 311 ND-associated genes on 118 undiagnosed patients. At least one known or likely pathogenic variation was found in 54 patients; 27 patients demonstrated clinical profiles that matched the variants; and 16 patients whose original diagnosis were refined. A high concordance of variant calling were observed when comparing the results from TGP and whole-exome sequencing of four patients. Our in-house STR detection algorithm has reached a specificity of 0.88 and a sensitivity of 0.82 in our SCA3 cohort. This study also uncovered a trove of novel and recurrent variants that may enrich the repertoire of ND-related genetic markers. We propose that a combined comprehensive TGPs-bioinformatics pipeline can improve the clinical diagnosis of NDs

Thermodynamics of the superconducting state in Calcium at 200 GPa

The thermodynamic parameters of the superconducting state in Calcium under the pressure at 200 GPa were calculated. The Coulomb pseudopotential values ($\mu^{\star}$) from 0.1 to 0.3 were taken into consideration. It has been shown, that the specific heat's jump at the critical temperature and the thermodynamic critical field near zero Kelvin strongly decrease with $\mu^{\star}$. The dimensionless ratios $r_{1}\equiv \Delta C(T_{C})/C^{N}(T_{C})$ and $r_{2}\equiv T_{C}C^{N}(T_{C})/H^{2}_{C}(0)$ significantly differ from the predictions based on the BCS model. In particular, $r_{1}$ decreases from 2.64 to 1.97 with the Coulomb pseudopotential; whereas $r_{2}$ increases from 0.140 to 0.157. The numerical results have been supplemented by the analytical approach.Comment: 7 pages, 6 figure

Characterization of the high-pressure superconductivity in the Pnma phase of calcium

The thermodynamic parameters of the superconducting state in calcium under the pressure at 161 GPa have been calculated within the framework of the Eliashberg approach. It has been shown that the value of the Coulomb pseudopotential is high (0.24) and the critical temperature (25 K) should be determined from the modified Allen-Dynes formula. In addition, it has been found that the basic dimensionless ratios of the thermodynamic parameters significantly diverge from the BCS predictions, and take the following values: (i) The zero temperature energy gap to the critical temperature(R1) is equal to 4.01. (ii) The ratio R2 equals 2.17. (iii) The quantity R3=0.158. Finally, it has been proven that the electron effective mass is large and takes the maximum of 2.32*me at TC.Comment: 8 pages, 9 figures; Phys. Status Solidi B (2012