A Systematic Investigation of Quantum Confinement Effects in Bismuth Nanowire Arrays

Thesis advisor: Michael GrafBismuth is an interesting element to study because the low effective mass of its charge carriers makes the material sensitive to quantum confinement effects. When bismuth is reduced to the nanoscale two interesting phenomena may occur: it may transition from a semimetal to a semiconductor, or charge carriers in special surface states may begin to dominate the behavior of the material. Arrays of bismuth nanowires of various diameters were studied to investigate these possibilities. The magnetoresistance of the arrays was measured and the period of Shubnikov-de Haas oscillations suggested an increase in the effective mass and density of the material’s charge carriers for small nanowire diameters. These increases suggested that electrons were present in surface states and strongly influenced the material’s behavior when its dimensions were sufficiently reduced. The magnetization of the nanowire arrays was also measured and the lack of de Haas-van Alphen oscillations for certain diameter nanowires suggested that electrons were not present in surface states and that instead the material was transitioning from a semimetal to a semiconductor. Heat capacity measurements were planned to reconcile the two experiments. My detailed calculations demonstrated that heat capacity measurements were feasible to determine the presence, or absence, of surface charge carriers. Because the electronic contribution to the material’s heat capacity is small a calorimeter platform was constructed with ultra-low heat capacity components.Thesis (BS) — Boston College, 2009.Submitted to: Boston College. College of Arts and Sciences.Discipline: College Honors Program.Discipline: Physics

The Application of Integrated Knowledge-based Systems for the Biomedical Risk Assessment Intelligent Network (BRAIN)

One of NASA's goals for long duration space flight is to maintain acceptable levels of crew health, safety, and performance. One way of meeting this goal is through the Biomedical Risk Assessment Intelligent Network (BRAIN), an integrated network of both human and computer elements. The BRAIN will function as an advisor to flight surgeons by assessing the risk of in-flight biomedical problems and recommending appropriate countermeasures. This paper describes the joint effort among various NASA elements to develop BRAIN and an Infectious Disease Risk Assessment (IDRA) prototype. The implementation of this effort addresses the technological aspects of the following: (1) knowledge acquisition; (2) integration of IDRA components; (3) use of expert systems to automate the biomedical prediction process; (4) development of a user-friendly interface; and (5) integration of the IDRA prototype and Exercise Countermeasures Intelligent System (ExerCISys). Because the C Language, CLIPS (the C Language Integrated Production System), and the X-Window System were portable and easily integrated, they were chosen as the tools for the initial IDRA prototype. The feasibility was tested by developing an IDRA prototype that predicts the individual risk of influenza. The application of knowledge-based systems to risk assessment is of great market value to the medical technology industry

Nine challenges in modelling the emergence of novel pathogens.

Studying the emergence of novel infectious agents involves many processes spanning host species, spatial scales, and scientific disciplines. Mathematical models play an essential role in combining insights from these investigations and drawing robust inferences from field and experimental data. We describe nine challenges in modelling the emergence of novel pathogens, emphasizing the interface between models and data.We acknowledge support from the Research and Policy for Infectious Disease Dynamics (RAPIDD) programme of the Science and Technology Directory, Department of Homeland Security, and Fogarty International Center, National Institutes of Health. JLS was also supported by the National Science Foundation (EF-0928987 and OCE-1335657) and the De Logi Chair in Biological Sciences. SF was supported by a UK Medical Research Council Career Development Award in Biostatistics. SR was supported by: Wellcome Trust Project Award 093488/Z/10/Z; R01 TW008246-01 from Fogarty International Centre; and The Medical Research Council (UK, Project Grant MR/J008761/1). JLNW was also supported by the Alborada Trust and the European Union FP7 project ANTIGONE (contract number 278976).This is the final version of the article. It first appeared from Elsevier via http://dx.doi.org/10.1016/j.epidem.2014.09.00

Population-Induced Phase Transitions and the Verification of Chemical Reaction Networks

We show that very simple molecular systems, modeled as chemical reaction networks, can have behaviors that exhibit dramatic phase transitions at certain population thresholds. Moreover, the magnitudes of these thresholds can thwart attempts to use simulation, model checking, or approximation by differential equations to formally verify the behaviors of such systems at realistic populations. We show how formal theorem provers can successfully verify some such systems at populations where other verification methods fail

Steric Shielding of Surface Epitopes and Impaired Immune Recognition Induced by the Ebola Virus Glycoprotein

Many viruses alter expression of proteins on the surface of infected cells including molecules important for immune recognition, such as the major histocompatibility complex (MHC) class I and II molecules. Virus-induced downregulation of surface proteins has been observed to occur by a variety of mechanisms including impaired transcription, blocks to synthesis, and increased turnover. Viral infection or transient expression of the Ebola virus (EBOV) glycoprotein (GP) was previously shown to result in loss of staining of various host cell surface proteins including MHC1 and β1 integrin; however, the mechanism responsible for this effect has not been delineated. In the present study we demonstrate that EBOV GP does not decrease surface levels of β1 integrin or MHC1, but rather impedes recognition by steric occlusion of these proteins on the cell surface. Furthermore, steric occlusion also occurs for epitopes on the EBOV glycoprotein itself. The occluded epitopes in host proteins and EBOV GP can be revealed by removal of the surface subunit of GP or by removal of surface N- and O- linked glycans, resulting in increased surface staining by flow cytometry. Importantly, expression of EBOV GP impairs CD8 T-cell recognition of MHC1 on antigen presenting cells. Glycan-mediated steric shielding of host cell surface proteins by EBOV GP represents a novel mechanism for a virus to affect host cell function, thereby escaping immune detection

The GALEX View of "Boyajian's Star" (KIC 8462852)

The enigmatic star KIC 8462852, informally known as "Boyajian's Star", has exhibited unexplained variability from both short timescale (days) dimming events, and years-long fading in the Kepler mission. No single physical mechanism has successfully explained these observations to date. Here we investigate the ultraviolet variability of KIC 8462852 on a range of timescales using data from the GALEX mission that occurred contemporaneously with the Kepler mission. The wide wavelength baseline between the Kepler and GALEX data provides a unique constraint on the nature of the variability. Using 1600 seconds of photon-counting data from four GALEX visits spread over 70 days in 2011, we find no coherent NUV variability in the system on 10-100 second or months timescales. Comparing the integrated flux from these 2011 visits to the 2012 NUV flux published in the GALEX-CAUSE Kepler survey, we find a 3% decrease in brightness for KIC 8462852. We find this level of variability is significant, but not necessarily unusual for stars of similar spectral type in the GALEX data. This decrease coincides with the secular optical fading reported by Montet & Simon (2016). We find the multi-wavelength variability is somewhat inconsistent with typical interstellar dust absorption, but instead favors a R$_V$ = 5.0 $\pm$ 0.9 reddening law potentially from circumstellar dust.Comment: 8 pages, 4 figures, ApJ Accepte

ALCH: An Imperative Language for Chemical Reaction Network-Controlled Tile Assembly

In 2015 Schiefer and Winfree introduced the chemical reaction network-controlled tile assembly model (CRN-TAM), a variant of the abstract tile assembly model (aTAM), where tile reactions are mediated via non-local chemical signals. In this paper, we introduce ALCH, an imperative programming language for specifying CRN-TAM programs. ALCH contains common features like Boolean variables, conditionals, and loops. It also supports CRN-TAM-specific features such as adding and removing tiles. A unique feature of the language is the branch statement, a nondeterministic control structure that allows us to query the current state of tile assemblies. We also developed a compiler that translates ALCH to the CRN-TAM, and a simulator that simulates and visualizes the self-assembly of a CRN-TAM program. Using this language, we show that the discrete Sierpinski triangle can be strictly self-assembled in the CRN-TAM. This solves an open problem that the CRN-TAM is capable of self-assembling infinite shapes at scale one that the aTAM cannot. ALCH allows us to present this construction at a high level, abstracting species and reactions into C-like code that is simpler to understand. Our construction utilizes two new CRN-TAM techniques that allow us to tackle this open problem. First, it employs the branching feature of ALCH to probe the previously placed tiles of the assembly and detect the presence and absence of tiles. Second, it uses scaffolding tiles to precisely control tile placement by occluding any undesired binding sites