Biomolecules, such as DNA, RNA, and proteins, are the building blocks of living systems. Each of these molecules is an assembly of atoms, with many carrying electric charges. Under normal circumstances, biomolecules are found in a solvent such as salted water. Highly charged parts of the biomolecules will polarize the solvent to produce ions that are mobile charges. The electrostatic interactions, together with covalent bonding and short- ranged van der Waals repulsion, give rise to the dominant forces that determine the dynamics and function of underlying biological systems. Understanding and simulating electrostatic interactions in biomolecular systems is the main goal of this dissertation. Both molecular dynamics and implicit-solvent descriptions have been the major modeling concepts for biomolecular interactions. Recent years have seen the development of a new class of efficient and accurate approaches, called variational implicit solvent modeling. This dissertation begins with this new framework and develops continuum models, mathematical analysis, and computational methods for simulating biomolecular interactions at different scales. First, the interfacial motion of dielectric boundaries is characterized and studied in the implicit- solvent description of biomolecules. Such motion is driven by the competition of mean curvature flow and the electrostatic free energy governed by the Poisson or Poisson-Boltzmann equation. Second, a new dynamic implicit solvent model is developed that introduces solvent fluid motion with fluctuations via the Landau-Lifshitz Navier- Stokes equations. This model significantly improves the existing variational implicit solvent model. And third, several multi-scale schemes combining a Brownian dynamics simulation of charged molecules with a continuum-based finite element description of coarse-grained concentrations are examined. Robust numerical algorithms are developed and extensive numerical computations are performed. They demonstrate the initial success of the theory. New directions in the mathematical modeling and computation of biomolecular systems are discussed

Feral swine are a serious management issue for natural resource managers, farmers, ranchers, and increasingly even suburban, private property owners. The 270,000-acre privately-owned Tejon Ranch in the Tehachapi Mountains of California, the subject of an historic conservation and land use agreement that conserved 90% of the property, supports a population of feral pigs that originally escaped from a private hunting ranch in the Tehachapi. Pigs now established on Tejon Ranch produce extensive ecological and economic damages, but are also a revenue source for the landowner’s hunting program. The Tejon Ranch Conservancy serves as steward of the conserved lands and is evaluating management options to reduce feral pig damages, while respecting the landowner’s right to maintain a hunting operation. To inform our management, we have modeled pig population responses to age- and sex-specific harvest scenarios. Consistent with previous studies, our models show that >70% of the population must be harvested annually to maintain or reduce the population, and that high harvest of adult females and juveniles is most effective at reducing abundance. Our analysis shows that population growth rates, which dictate harvest rates required for population control, are most sensitive to reproductive rates, and we have no site-specific data to estimate reproductive or mortality rates. As part of the National Feral Swine Damage Management Program, the Conservancy is partnering with the USDA Animal Plant Health Inspection Service on a research and monitoring project to estimate feral pig population size and demography; habitat use and home ranges; and damages at Tejon Ranch. The ultimate objective of the program is to evaluate techniques for reducing damages cause by feral swine.

Wild pigs cause extensive damage to ecological resources, agricultural lands, and private property, and carry diseases that may pose a health risk to livestock and humans. At the Tejon Ranch in the Tehachapi Mountains of California, a population of wild pigs produce extensive ecological and economic damages, and share rangelands with cattle. Via the Tejon Ranch Conservation and Land Use Agreement, the Tejon Ranch Conservancy is charged with the science-based stewardship of over 970 km2 of conserved lands at Tejon Ranch. During the summer of 2014 we initiated pilot field research to develop monitoring and control methodologies to better manage wild pigs and associated disturbance across Tejon Ranch’s conserved lands. We compared line transect surveys (LTS) with remotely triggered wildlife trap-cameras as alternative methods to estimate pig abundance. Density estimates were made from LTS survey results using program DISTANCE, while indices of abundance were developed from camera trap data. We also estimated ecological disturbance by measuring the amount of pig rooting along segments of LTS transects. Wetland areas, along with higher elevation interior habitats received more damage than dryer, lower elevation habitats, which was expected given our summer surveys. Expanding on these pilot abundance surveys, we are now attempting to achieve more precise population density estimates using mark-resight techniques through a combination of trapping and collaring animals as well as individually identifying pigs from their unique pelage patterns.

The decomposition of dimethyl methyl phosphonate (DMMP), a simulant for the nerve agent sarin, was investigated on Cu₄/TiO₂(110) and K/Cu₄/TiO₂(110) surfaces using a combination of near-ambient-pressure X-ray photoelectron spectroscopy (NAP-XPS) and density functional theory calculations (DFT). Mass-selected Cu₄ clusters and potassium (K) atoms were deposited onto TiO₂(110) as a metal catalyst and alkali promoter to improve the reactivity and recyclability of the TiO₂ surface after exposure to DMMP. Surface reaction products resulting from decomposition of DMMP were probed by NAP-XPS measurements of phosphorus (P) 2p and carbon 1s core-level spectra. The Cu₄/TiO₂(110) surface is found to be very active for DMMP decomposition with highly reduced P-species observed even at room temperature (RT). The codeposition of K atoms and Cu₄ clusters further improves the reactivity with no intact DMMP detectable. Temperature-dependent measurements show that the presence of K atoms promotes the removal of residual P-species at temperatures > 600 K. Detailed DFT calculations were performed to determine the surface structures and energetically accessible pathways for DMMP decomposition on Cu₄/TiO₂(110) and K/Cu₄/TiO₂(110) surfaces. The calculations show that DMMP and P-containing reaction products preferentially bind to the TiO₂ surface, while the molecular fragments, i.e., methoxy and methyl, bind to both the Cu₄ clusters and TiO₂. The Cu₄ clusters make the P-O, O-C, and P-C bond cleavages of DMMP markedly more exothermic. The Cu₄ clusters are highly fluxional with atomic structures that depend on the configuration of fragments bound to them. Finally, the manifold of P 2p chemical shifts calculated for a large number of energetically favorable configurations of decomposition products is in good agreement with the observed XPS spectra and provides an alternative way of interpreting incompletely resolved core-level spectra using an ensemble of observed structures.

Surgeons encounter neutropenic patients through elective or emergency consultation with increasing regularity. As medical management continues to extend the lives of patients with benign hematologic diseases, hematologic malignancies, solid malignancies, or iatrogenic neutropenia, more patients are presenting with infectious complications caused and/or complicated by their neutropenia. This leaves surgeons in the difficult position of managing medically fragile patients with unusual presentations of common disease processes. These patients often fall outside of classical guidelines and treatment pathways. Many studies addressing these issues are retrospective and non-randomized. Here, we review common emergency gastrointestinal surgery scenarios and their management in the setting of a neutropenic patient. While biliary disease, appendicitis, anorectal disease, and perforations will be covered in detail, an extensive appreciation of a patient's medical or oncologic disease course and appropriate utilization of consultants such as interventional radiology, gastroenterology, and hematology is often necessary.

Ecological sites and state‐and‐transition models are useful tools for generating and testing hypotheses about drivers of vegetation composition in rangeland systems. These models have been widely implemented in upland rangelands, but comparatively, little attention has been given to developing ecological site concepts for rangeland riparian areas, and additional environmental criteria may be necessary to classify riparian ecological sites. Between 2013 and 2016, fifteen study reaches on five creeks were studied at Tejon Ranch in southern California. Data were collected to describe the relationship between riparian vegetation composition, environmental variables, and livestock management; and to explore the utility of ecological sites and state‐and‐transition models for describing riparian vegetation communities and for creating hypotheses about drivers of vegetation change. Hierarchical cluster analysis was used to classify the environmental and vegetation data (15 stream reaches × 4 years) into two ecological sites and eight community phases that comprised three vegetation states. Classification and regression tree (CART) analysis was used to determine the influence of abiotic site variables, annual precipitation, and cattle activity on vegetation clusters. Channel slope explained the greatest amount of variation in vegetation clusters; however, soil texture, geology, watershed size, and elevation were also selected as important predictors of vegetation composition. The classification tree built with this limited set of abiotic predictor variables explained 90% of the observed vegetation clusters. Cattle grazing and annual precipitation were not linked to qualitative differences in vegetation. Abiotic variables explained almost all of the observed riparian vegetation dynamics—and the divisions in the CART analysis corresponded roughly to the ecological sites—suggesting that ecological sites are well‐suited for understanding and predicting change in this highly variable system. These findings support continued development of riparian ecological site concepts and state‐and‐transition models to aid decision making for conservation and management of rangeland riparian areas.

BACKGROUND: Few studies have focused on prognostic factors among adolescents and young adults (AYAs) 15 to 39 years of age when diagnosed with differentiated thyroid cancer (DTC). Our study expands upon prior work by including an evaluation of survival among AYA men and by neighborhood socioeconomic status, health insurance, and clinical factors to identify subgroups of young DTC patients at higher risk of mortality. METHODS: Data for 16,827 AYA DTC patients diagnosed between 1988 and 2010 were obtained from the California Cancer Registry. Survival, through 2010, by sociodemographic and clinical factors was analyzed using Cox proportional hazards regression. RESULTS: Of the 2.1% of AYAs who died, 16.7% died from thyroid cancer and 21.4% died from a subsequent cancer. In multivariate analyses, older AYAs 35 to 39 year of age (versus 15- to 29-year-olds), men (hazard ratio [HR] 2.77, 95% confidence interval [CI] 1.62-4.72), and AYAs of African American or Hispanic race/ethnicity (versus non-Hispanic whites) had worse thyroid cancer specific survival. In addition, residing in low socioeconomic status neighborhoods (HR 3.11 [CI 1.28-7.56]) and nonmetropolitan areas (HR 5.53 [CI 2.07-14.78]) was associated with worse thyroid cancer-specific survival among AYA men, but not AYA women. CONCLUSIONS: Despite the generally good prognosis among AYAs with DTC, we identified subgroups of AYA patients at risk for poor outcomes. Further study of the factors underlying these associations, including possible barriers to receiving high-quality treatment and follow-up care, as well as lifestyle factors, are critical to reducing these disparities.

The morphology and reactivity of mass-selected titania clusters, Ti3O6 and Ti3O5, deposited onto Au(111) were studied by scanning tunneling microscopy and temperature programmed desorption. Despite differing by only one oxygen atom, the stoichiometric Ti3O6 and the sub-stoichiometric ("reduced") Ti3O5 clusters exhibit very different structures and preferred binding sites. The Ti3O6 clusters bind at step edges and form small assemblies (2-4 clusters) on Au terraces, while the "reduced" Ti3O5 clusters form much larger fractal-like assemblies that can extend across step boundaries. Annealing the Ti3O5,6/Au(111) systems to higher temperatures causes changes in the size-distributions of cluster assemblies, but does not lead to the formation of TiOx nanoislands for temperatures ≤700 K. Reactivity studies show that the reduced Ti3O5 cluster has higher activity than Ti3O6 for 2-propanol dehydration, although both clusters exhibit substantial activity for dehydrogenation to acetone. Calculations using DFT+U suggest that the differences in aggregate morphology and reactivity are associated with the number of undercoordinated Ti3c sites in the supported clusters.