Simulation of nanoscale patterns yielded by ion bombardment of solid surfaces

2018 Spring.Includes bibliographical references.This thesis includes numerical investigations into two topics of self-organized topographies produced on solid surfaces that are bombarded with a broad ion beam. The first topic is the formation of terraces. When a surface is bombarded at relatively large angles of incidence, the surface often develops facets that are characterized by large regions of nearly constant gradient in height, which are called terraces. The second topic is related to the observation that when the surface of a nominally flat binary material is bombarded with a broad, normally-incident ion beam, disordered hexagonal arrays of nanodots can form. Shipman and Bradley have derived equations of motion that govern the coupled dynamics of the height and composition of such a surface [P. D. Shipman and R. M. Bradley, Phys. Rev. B 84, 085420 (2011)]. We investigate the influence of initial conditions on the hexagonal order yielded by integration of those equations of motion. In our work on terrace formation, we introduce a model that includes an improved approximation to the sputter yield and that produces a terraced surface morphology at long times for a wide range of parameter values. Numerical integrations of our equation of motion reveal that the terraces coarsen for a finite amount of time after which the coarsening is interrupted, just as observed experimentally. We also show that the terrace propagation direction can reverse as the amplitude of the surface disturbance grows. This highlights the important role higher order nonlinearities play in determining the propagation velocity at high fluences. We study the nanoscale terraced topographies that arise when a solid surface is bombarded with a broad ion beam that has a relatively high angle of incidence θ. Our simulations establish that the surfaces exhibit interrupted coarsening, i.e., the characteristic width and height of the surface disturbance grow for a time but ultimately asymptote to finite values as the fully terraced state develops. In addition, as θ is reduced, the surface can undergo a transition from a terraced morphology that changes little with time as it propagates over the surface to an unterraced state that appears to exhibit spatiotemporal chaos. For different ranges of the parameters, our equation of motion produces terraced topographies that are remarkably similar to those seen in various experiments, including pyramidal structures that are elongated along the projected beam direction and isolated lenticular depressions. For our study of the influence of prepatterning surfaces governed by the Bradley-Shipman equations, the initial conditions studied are hexagonal and sinusoidal templates, straight scratches and nominally flat surfaces. Our simulations indicate that each of the prepatterned surfaces can lead to marked improvements in the hexagonal order compared to what is obtained from the nominally flat surfaces. For the hexagonal and sinusoidal templates with amplitude approximately equal to one hundredth of the amplitude of the pattern obtained at late times, the greatest improvement in order is obtained if the initial wavelength is approximately equal to or double the linearly selected wavelength. Our simulations of sinusoidal templates demonstrate that increasing the amplitude of the template can improve the effectiveness of templates with longer wavelengths. Scratches enhance the hexagonal order in their vicinity if their width is close to or less than the linearly selected wavelength. Our results suggest that prepatterning a binary material can dramatically increase the hexagonal order achieved at large ion fluences

Disordering to Order: de Vries behavior from a Landau theory for smectics

We show that Landau theory for the isotropic, nematic, smectic A, and smectic C phases generically, but not ubiquitously, implies de Vries behavior. I.e., a continuous AC transition can occur with little layer contraction; the birefringence decreases as temperature T is lowered above this transition, and increases again below the transition. This de Vries behavior occurs in models with unusually small orientational order, and is preceded by a first order I − A transition. A first order AC transition with elements of de Vries behavior can also occur. These results correspond well with experimental work to date.Comment: 4 pages, 2 page appendi

Venous Thromboembolism in Minimally Invasive Compared With Open Hysterectomy for Endometrial Cancer

OBJECTIVE: To evaluate whether minimally invasive surgery for endometrial cancer is independently associated with a decreased odds of venous thromboembolism compared with open surgery. METHODS: We performed a secondary analysis cohort study of prospectively collected quality improvement data and examined patients undergoing hysterectomy for endometrial cancer from 2008 to 2013 recorded in the National Surgical Quality Improvement Program database. Patients undergoing minimally invasive (laparoscopic or robotic) surgery were compared with those undergoing open surgery with respect to 30-day postoperative venous thromboembolism. Demographic and procedure variables were examined as potential confounders. Data regarding receipt of perioperative venous thromboembolism prophylaxis were not available. Bivariable tests and logistic regression were used for analysis. RESULTS: Of 9,948 patients who underwent hysterectomy for the treatment of endometrial cancer, 61.9% underwent minimally invasive surgery and 38.1% underwent open surgery. Patients undergoing minimally invasive surgery had a lower venous thromboembolism incidence (0.7%, n=47) than patients undergoing open surgery (2.2%, n=80) (P<.001). In a multivariate model adjusting for age, body mass index, race, operative time, Charlson comorbidity score, and surgical complexity, minimally invasive surgery remained associated with decreased odds of venous thromboembolism (adjusted odds ratio 0.36, 95% confidence interval 0.24-0.53) compared with open surgery. CONCLUSION: Minimally invasive surgery for the treatment of endometrial cancer is independently associated with decreased odds of venous thromboembolism compared with open surgery

Frequent expansion of Plasmodium vivax Duffy Binding Protein in Ethiopia and its epidemiological significance.

Plasmodium vivax invasion of human erythrocytes depends on the Duffy Binding Protein (PvDBP) which interacts with the Duffy antigen. PvDBP copy number has been recently shown to vary between P. vivax isolates in Sub-Saharan Africa. However, the extent of PvDBP copy number variation, the type of PvDBP multiplications, as well as its significance across broad samples are still unclear. We determined the prevalence and type of PvDBP duplications, as well as PvDBP copy number variation among 178 Ethiopian P. vivax isolates using a PCR-based diagnostic method, a novel quantitative real-time PCR assay and whole genome sequencing. For the 145 symptomatic samples, PvDBP duplications were detected in 95 isolates, of which 81 had the Cambodian and 14 Malagasy-type PvDBP duplications. PvDBP varied from 1 to &gt;4 copies. Isolates with multiple PvDBP copies were found to be higher in symptomatic than asymptomatic infections. For the 33 asymptomatic samples, PvDBP was detected with two copies in two of the isolates, and both were the Cambodian-type PvDBP duplication. PvDBP copy number in Duffy-negative heterozygotes was not significantly different from that in Duffy-positives, providing no support for the hypothesis that increased copy number is a specific association with Duffy-negativity, although the number of Duffy-negatives was small and further sampling is required to test this association thoroughly

Polyphenon E enhances the antitumor immune response in neuroblastoma by inactivating myeloid suppressor cells

This is the author's accepted manuscript. The final published article is available from the link below. Note: In this manuscript as well as in the original published version of this article the word "Polyphenon" was incorrectly spelled in the title as "Polyphenol."Purpose: Neuroblastoma is a rare childhood cancer whose high risk, metastatic form has a dismal outcome in spite of aggressive therapeutic interventions. The toxicity of drug treatments is a major problem in this pediatric setting. In this study, we investigated whether Polyphenon E, a clinical grade mixture of green tea catechins under evaluation in multiple clinical cancer trials run by the National Cancer Institute (Bethesda, MD), has anticancer activity in mouse models of neuroblastoma. Experimental Design: We used three neuroblastoma models: (i) transgenic TH-MYCN mouse developing spontaneous neuroblastomas; (ii) nonobese diabetic/severe combined immunodeficient (NOD/SCID) mice xenotransplanted with human SHSY5Y cells; and (iii) A/J mice transplanted with syngeneic Neuro 2A cells. Mice were randomized in control and Polyphenon E–drinking groups. Blood from patients with neuroblastoma and normal controls was used to assess the phenotype and function of myeloid cells. Results: Polyphenon E reduced the number of tumor-infiltrating myeloid cells, and inhibited the development of spontaneous neuroblastomas in TH-MYCN transgenic mice. In therapeutic models of neuroblastoma in A/J, but not in immunodeficient NOD/SCID mice, Polyphenon E inhibited tumor growth by acting on myeloid-derived suppressor cells (MDSC) and CD8 T cells. In vitro, Polyphenon E impaired the development and motility of MDSCs and promoted differentiation to more neutrophilic forms through the 67 kDa laminin receptor signaling and induction of granulocyte colony-stimulating factor. The proliferation of T cells infiltrating a patient metastasis was reactivated by Polyphenon E. Conclusions: These findings suggest that the neuroblastoma-promoting activity of MDSCs can be manipulated pharmacologically in vivo and that green tea catechins operate, at least in part, through this mechanism.SPARKS, Research in Childhood Cancer, the CGD Research Trust, and the Wellcome Trust

Morphological transitions in the patterning of the crystalline Ge(001) surface induced by ion irradiation

We investigate the morphologies of the Ge(001) surface that are produced by bombardment with a normally incident, broad argon ion beam at sample temperatures above the recrystallization temperature. Two previously-observed kinds of topographies are seen, i.e., patterns consisting of upright and inverted rectangular pyramids, as well as patterns composed of shallow, isotropic basins. In addition, we observe the formation of an unexpected third type of pattern for intermediate values of the temperature, ion energy and ion flux. In this type of transitional morphology, isolated peaks with rectangular cross sections stand above a landscape of shallow, rounded basins. We also extend past theoretical work to include a second order correction term that comes from the curvature dependence of the sputter yield. For a range of parameter values, the resulting continuum model of the surface dynamics produces patterns that are remarkably similar to the transitional morphologies we observe in our experiments. The formation of the isolated peaks is the result of a term that is not ordinarily included in the equation of motion, a second order correction to the curvature dependence of the sputter yield

Formation of square lattices in coupled pattern-forming systems

A wide variety of natural and labo-ratory systems can produce patterns of ripples, hexagons, or squares. The formation of stable square patterns from partial differential equation models requires specific cubic nonlinearities involving higher-order derivatives. Motivated by plant phyllotaxis, we demonstrate that the coupling of more than one pattern-forming system can produce square patterns without these special nonlinearities

Local differentiation in heat response of Laminaria digitata at the range edges

In recent years, kelp populations worldwide have faced decline and extirpation at their equatorward limits, while models predict a poleward shift of kelp ecosystems during climate change. To gain an understanding of local thermal adaptation and response plasticity in a forest-forming kelp species, we assessed populations of Laminaria digitata along its entire European distribution range for their capacity to withstand high temperature stress, and analysed population structure and diversity with microsatellite markers (n=12). We sampled wild meristematic L. digitata material (n=30) at six locations ranging from Kongsfjorden, Spitsbergen, to the southernmost distribution limit in Quiberon, France. In a heatwave experiment, we subjected samples from all locations to the same, sublethal temperature treatments (15–23°C for eight days including acclimation) and assessed growth, storage compounds, photosynthetic efficiency and pigment contents as response traits. Recovery was assessed following seven days at 15°C. Microsatellite genotyping revealed all sampled populations to be genetically distinct entities, underlying strong regional structuring between southern and northern clades. Genetic diversity was highest at the southern distribution limit in Quiberon and lowest in the geographically isolated population on the island of Helgoland in the North Sea. The physiological response of L. digitata to temperature was similar over the entire distribution range and did not reflect the mean temperature gradient along the latitudinal gradient. However, material from Spitsbergen and Helgoland presented subtle differentiations in their temperature responses, which reflect long-term local temperature histories at these sites. Finally, a heatwave reaching 23°C for five days led to a cessation of growth, from which none of the sampled populations recovered. Our results suggest that the heat stress response of L. digitata is generally stable across its distribution range, despite strong genetic structuring of the populations. Slight local differentiation occurred in populations from the most distinct thermal environments, but 23°C posed a growth limit for all populations. This implies that local adaptation in trailing edge populations of L. digitata might not alleviate detrimental effects of global warming

Increased Heat Resilience of Intraspecific Outbred Compared to Inbred Lineages in the Kelp Laminaria digitata: Physiology and Transcriptomics

Marine forests and kelps as their foundation species are threatened by ocean warming especially at the warm distributional edges. Previously identified genetic divergence and ecotypic differentiation within kelp species may allow to produce more resilient lineages by intraspecific outbreeding among populations. In a mechanistic investigation of heat stress, heterosis (hybrid vigour), and underlying gene expression patterns, we assessed the thermal performance of inbred (selfings) and outbred (reciprocal crosses) sporophytes of the N-Atlantic kelp Laminaria digitata among clonal isolates from two divergent populations; one from the temperate North Sea (Helgoland) and one from the Arctic (Spitsbergen). First, we investigated the upper thermal tolerance of microscopic sporophytes in a 14-day experiment applying sublethal to lethal 20–23°C. The upper survival temperature of microscopic sporophytes was lower for the inbred Arctic selfing (21°C) than for the temperate selfing and the reciprocal crosses (22°C). Only in the temperate selfing, 4.5% of sporophytes survived 23°C. We then subjected 4–7 cm long sporophytes to a control temperature (10°C), moderate (19°C) and sublethal to lethal heat stress (20.5°C) for 18 days to assess gene expression in addition to physiological parameters. Growth and optimum quantum yield decreased similarly in the reciprocal crosses and the temperate selfing at 19 and 20.5°C, while inbred Arctic sporophytes died within seven days at both 19 and 20.5°C. In response to 20.5°C, 252 genes were constitutively regulated across all surviving lineages, which we use to describe metabolic regulation patterns in response to heat stress in kelp. At sublethal 20.5°C, ca. 150 genes were differentially expressed by either crossed lineage in comparison to the temperate selfing, indicating that they maintained a growth response similar to the temperate selfing with differential metabolic regulation during sublethal heat stress. Subtle differences in physiology and the differential expression of nine genes between the reciprocal crosses at 20.5°C indicate that female and male gametophytes may contribute differently to offspring traits. We consider potential inbreeding depression in the Spitsbergen selfing and quantify the better performance of both crosses using heterosis-related parameters. We discuss the potential and risks of outbreeding to produce more resilient crops for mariculture and marine forest restoration