CHAPTER 1 DISCOVERING 3-D PROTEIN STRUCTURES FOR OPTIMAL STRUCTURE ALIGNMENT

Analyzing three dimensional protein structures is a very important task in molecular biology. Nowadays, the solution for protein structures often stems from the use of the state-of-the-art technologies such as nuclear magnetic resonance (NMR) spectroscopy techniques or X-Ray crystallography etc. as seen in the increasing number of PD

Complete phenomenological gravitational waveforms from spinning coalescing binaries

The quest for gravitational waves from coalescing binaries is customarily performed by the LIGO-Virgo collaboration via matched filtering, which requires a detailed knowledge of the signal. Complete analytical coalescence waveforms are currently available only for the non-precessing binary systems. In this paper we introduce complete phenomenological waveforms for the dominant quadrupolar mode of generically spinning systems. These waveforms are constructed by bridging the gap between the analytically known inspiral phase, described by spin Taylor (T4) approximants in the restricted waveform approximation, and the ring-down phase through a phenomenological intermediate phase, calibrated by comparison with specific, numerically generated waveforms, describing equal mass systems with dimension-less spin magnitudes equal to 0.6. The overlap integral between numerical and phenomenological waveforms ranges between 0.95 and 0.99.Comment: Proceeding for the GWDAW-14 conference. Added reference in v

Inspiral-merger-ringdown waveforms for black-hole binaries with non-precessing spins

We present the first analytical inspiral-merger-ringdown gravitational waveforms from binary black holes (BBHs) with non-precessing spins, that is based on a description of the late-inspiral, merger and ringdown in full general relativity. By matching a post-Newtonian description of the inspiral to a set of numerical-relativity simulations, we obtain a waveform family with a conveniently small number of physical parameters. These waveforms will allow us to detect a larger parameter space of BBH coalescence, including a considerable fraction of precessing binaries in the comparable-mass regime, thus significantly improving the expected detection rates.Comment: To appear in Phys. Rev. Lett. Significant new results. One figure removed due to page limitatio

Multi-scale modeling study of the source contributions to near-surface ozone and sulfur oxides levels over California during the ARCTAS-CARB period

Chronic high surface ozone (O3) levels and the increasing sulfur oxides (SOx = SO2+SO4) ambient concentrations over South Coast (SC) and other areas of California (CA) are affected by both local emissions and long-range transport. In this paper, multi-scale tracer, full-chemistry and adjoint simulations using the STEM atmospheric chemistry model are conducted to assess the contribution of local emission sourcesto SC O3 and to evaluate the impacts of transported sulfur and local emissions on the SC sulfur budgetduring the ARCTAS-CARB experiment period in 2008. Sensitivity simulations quantify contributions of biogenic and fire emissions to SC O3 levels. California biogenic and fire emissions contribute 3–4 ppb to near-surface O3 over SC, with larger contributions to other regions in CA. During a long-range transport event from Asia starting from 22 June, high SOx levels (up to ~0.7 ppb of SO2 and ~1.3 ppb of SO4) is observed above ~6 km, but they did not affect CA surface air quality. The elevated SOx observed at 1–4 km is estimated to enhance surface SOx over SC by ~0.25 ppb (upper limit) on ~24 June. The near-surface SOx levels over SC during the flight week are attributed mostly to local emissions. Two anthropogenic SOx emission inventories (EIs) from the California Air Resources Board (CARB) and the US Environmental Protection Agency (EPA) are compared and applied in 60 km and 12 km chemical transport simulations, and the results are compared withobservations. The CARB EI shows improvements over the National Emission Inventory (NEI) by EPA, but generally underestimates surface SC SOx by about a factor of two. Adjoint sensitivity analysis indicated that SO2 levels at 00:00 UTC (17:00 local time) at six SC surface sites were influenced by previous day maritime emissions over the ocean, the terrestrial emissions over nearby urban areas, and by transported SO2 from the north through both terrestrial and maritime areas. Overall maritime emissions contribute 10–70% of SO2 and 20–60% fine SO4 on-shore and over the most terrestrial areas, with contributions decreasing with in-land distance from the coast. Maritime emissions also modify the photochemical environment, shifting O3 production over coastal SC to more VOC-limited conditions. These suggest an important role for shipping emission controls in reducing fine particle and O3concentrations in SC

Predictive modeling of die filling of the pharmaceutical granules using the flexible neural tree

In this work, a computational intelligence (CI) technique named flexible neural tree (FNT) was developed to predict die filling performance of pharmaceutical granules and to identify significant die filling process variables. FNT resembles feedforward neural network, which creates a tree-like structure by using genetic programming. To improve accuracy, FNT parameters were optimized by using differential evolution algorithm. The performance of the FNT-based CI model was evaluated and compared with other CI techniques: multilayer perceptron, Gaussian process regression, and reduced error pruning tree. The accuracy of the CI model was evaluated experimentally using die filling as a case study. The die filling experiments were performed using a model shoe system and three different grades of microcrystalline cellulose (MCC) powders (MCC PH 101, MCC PH 102, and MCC DG). The feed powders were roll-compacted and milled into granules. The granules were then sieved into samples of various size classes. The mass of granules deposited into the die at different shoe speeds was measured. From these experiments, a dataset consisting true density, mean diameter (d50), granule size, and shoe speed as the inputs and the deposited mass as the output was generated. Cross-validation (CV) methods such as 10FCV and 5x2FCV were applied to develop and to validate the predictive models. It was found that the FNT-based CI model (for both CV methods) performed much better than other CI models. Additionally, it was observed that process variables such as the granule size and the shoe speed had a higher impact on the predictability than that of the powder property such as d50. Furthermore, validation of model prediction with experimental data showed that the die filling behavior of coarse granules could be better predicted than that of fine granules

Phenomenological template family for black-hole coalescence waveforms

Recent progress in numerical relativity has enabled us to model the non-perturbative merger phase of the binary black-hole coalescence problem. Based on these results, we propose a phenomenological family of waveforms which can model the inspiral, merger, and ring-down stages of black hole coalescence. We also construct a template bank using this family of waveforms and discuss its implementation in the search for signatures of gravitational waves produced by black-hole coalescences in the data of ground-based interferometers. This template bank might enable us to extend the present inspiral searches to higher-mass binary black-hole systems, i.e., systems with total mass greater than about 80 solar masses, thereby increasing the reach of the current generation of ground-based detectors.Comment: Minor changes, Submitted to Class. Quantum Grav. (Proc. GWDAW11

Post-Partum Pituitary Insufficiency and Livedo Reticularis Presenting a Diagnostic Challenge in a Resource Limited Setting in Tanzania: A Case Report, Clinical Discussion and Brief Review of Existing Literature.

Pituitary disorders following pregnancy are an important yet under reported clinical entity in the developing world. Conversely, post partum panhypopituitarism has a more devastating impact on women in such settings due to high fertility rates, poor obstetric care and scarcity of diagnostic and therapeutic resources available. A 37 year old African female presented ten years post partum with features of multiple endocrine deficiencies including hypothyroidism, hypoadrenalism, lactation failure and secondary amenorrhea. In addition she had clinical features of an underlying autoimmune condition. These included a history of post-partum thyroiditis, alopecia areata, livedo reticularis and deranged coagulation indices. A remarkable clinical response followed appropriate hormone replacement therapy including steroids. This constellation has never been reported before; we therefore present an interesting clinical discussion including a brief review of existing literature. Post partum pituitary insufficiency is an under-reported condition of immense clinical importance especially in the developing world. A high clinical index of suspicion is vital to ensure an early and correct diagnosis which will have a direct bearing on management and patient outcome

Predictive coupled-cluster isomer orderings for some Sin{}_nCm{}_m (m,n≤12m, n\le 12) clusters; A pragmatic comparison between DFT and complete basis limit coupled-cluster benchmarks

The accurate determination of the preferred ${\rm Si}_{12}{\rm C}_{12}$ isomer is important to guide experimental efforts directed towards synthesizing SiC nano-wires and related polymer structures which are anticipated to be highly efficient exciton materials for opto-electronic devices. In order to definitively identify preferred isomeric structures for silicon carbon nano-clusters, highly accurate geometries, energies and harmonic zero point energies have been computed using coupled-cluster theory with systematic extrapolation to the complete basis limit for set of silicon carbon clusters ranging in size from SiC$_3$ to ${\rm Si}_{12}{\rm C}_{12}$. It is found that post-MBPT(2) correlation energy plays a significant role in obtaining converged relative isomer energies, suggesting that predictions using low rung density functional methods will not have adequate accuracy. Utilizing the best composite coupled-cluster energy that is still computationally feasible, entailing a 3-4 SCF and CCSD extrapolation with triple-$\zeta$ (T) correlation, the {\it closo} ${\rm Si}_{12}{\rm C}_{12}$ isomer is identified to be the preferred isomer in support of previous calculations [J. Chem. Phys. 2015, 142, 034303]. Additionally we have investigated more pragmatic approaches to obtaining accurate silicon carbide isomer energies, including the use of frozen natural orbital coupled-cluster theory and several rungs of standard and double-hybrid density functional theory. Frozen natural orbitals as a way to compute post MBPT(2) correlation energy is found to be an excellent balance between efficiency and accuracy

Connecting Numerical Relativity and Data Analysis of Gravitational Wave Detectors

Gravitational waves deliver information in exquisite detail about astrophysical phenomena, among them the collision of two black holes, a system completely invisible to the eyes of electromagnetic telescopes. Models that predict gravitational wave signals from likely sources are crucial for the success of this endeavor. Modeling binary black hole sources of gravitational radiation requires solving the Eintein equations of General Relativity using powerful computer hardware and sophisticated numerical algorithms. This proceeding presents where we are in understanding ground-based gravitational waves resulting from the merger of black holes and the implications of these sources for the advent of gravitational-wave astronomy.Comment: Appeared in the Proceedings of 2014 Sant Cugat Forum on Astrophysics. Astrophysics and Space Science Proceedings, ed. C.Sopuerta (Berlin: Springer-Verlag

A nonlinear scalar model of extreme mass ratio inspirals in effective field theory I. Self force through third order

The motion of a small compact object in a background spacetime is investigated in the context of a model nonlinear scalar field theory. This model is constructed to have a perturbative structure analogous to the General Relativistic description of extreme mass ratio inspirals (EMRIs). We apply the effective field theory approach to this model and calculate the finite part of the self force on the small compact object through third order in the ratio of the size of the compact object to the curvature scale of the background (e.g., black hole) spacetime. We use well-known renormalization methods and demonstrate the consistency of the formalism in rendering the self force finite at higher orders within a point particle prescription for the small compact object. This nonlinear scalar model should be useful for studying various aspects of higher-order self force effects in EMRIs but within a comparatively simpler context than the full gravitational case. These aspects include developing practical schemes for higher order self force numerical computations, quantifying the effects of transient resonances on EMRI waveforms and accurately modeling the small compact object's motion for precise determinations of the parameters of detected EMRI sources.Comment: 30 pages, 8 figure