Capillary Self Assembly of 3D Nanostructures

ME450 Capstone Design and Manufacturing Experience: Winter 2010The objective of this project is to design and manufacture a chamber for controlling the capillary forces that cause self-assembly of nanostructures on a substrate. Means of delivering controlled volumes of liquids to a substrate surface have been designed, along with the controllability of evaporation using humidity measurements along with temperature, and pressure control. Our machine is intended for research, and therefore is highly reconfigurable. The machine is able to place particles in suspension onto a substrate in small volumes dispensed by a capillary tip.http://deepblue.lib.umich.edu/bitstream/2027.42/109385/1/me450w10project3_report.pd

“Life on Sauerkraut Hill”. Representation and Practices of Freedom and Constriction among German Immigrants in Cape Town, South Africa

In social sciences, intercontinental migration is often seen as a phenomenon of South-North mobility or increasingly as a phenomenon of South-South mobility. In fact, the majority of intercontinental / interregional mobility is taking place between Africa and Asia, as well as between East and South Asia and the Middle East. The migration from the Global South to the North is roughly similar. Both migratory flows are also extensively examined by social anthropologists. Very rare subjects of anthropological research are migrations from the Global North to the Global South. While settlers emigrated from the urban centres and detached rural areas a hundred years ago as emigrants to the colonies of the empires, today it is often individualists who follow this path. It is this latter form of migration that Caterina Reinker dedicates her work to. Reinker examines perspectives and identities of German migrants in Cape Town. These are not migrants who leave their homes without means and / or without perspective. The work, which is based on several months of field work in Cape Town, and which was supervised by Prof. Dr. Michael Bollig, deals with people who emigrate to the South in the search for a fulfilled life (whatever that is to be understood). Some do this with temporary aspirations, some actually emigrate permanently and rule out a return to Germany. However, it seems more likely that options for a return to Germany are retained. None of Reinker’s interviewees had given up their German passport, and for some, the mind game with a possible return is identity forming. Reinker focusses on the design of the vitality of German migrants in a Cape Town district, which is considered to be particularly German and therefore bears the name "Sauerkraut Hill” in the vernacular. Reinker's master thesis provides an important contribution to completing our understanding of global migration. In addition to the large, much-discussed and even more frequently problematized migratory flows, these quantitatively much smaller movements also link the network of global relations

The effect of wildfires, spruce bark beetles, and prescribed burns on residential property values in Alaska's Kenai Peninsula

Thesis (M.S.) University of Alaska Fairbanks, 2019This study estimates the effect that forest fires, spruce bark beetle outbreaks, and controlled burns performed by fire management agencies have on nearby residential property values. Using the hedonic pricing framework, and ten years of house sales from south-central Alaska's Kenai Peninsula, this study found little evidence that wildfires and spruce beetle outbreaks have a significant effect on the final sale price of surrounding homes, but found that the controlled burns contribute to a decrease in surrounding home values. As Alaska's climate becomes warmer and drier, these disturbances threaten to increase in frequency and severity. Understanding how homeowners perceive fire risk and forest damage is increasingly important to fire management policy, as the behavior of residents can help limit both the cost from and incidence of wildfires. The study's findings suggest that homeowners are either insulated from, or indifferent to fire risk, but targeted burns of high-risk areas by fire managers could increase awareness and sensitivity to fire risk

Synthesizing attractors of Hindmarsh-Rose neuronal systems

In this paper a periodic parameter switching scheme is applied to the Hindmarsh-Rose neuronal system to synthesize certain attractors. Results show numerically, via computer graphic simulations, that the obtained synthesized attractor belongs to the class of all admissible attractors for the Hindmarsh-Rose neuronal system and matches the averaged attractor obtained with the control parameter replaced with the averaged switched parameter values. This feature allows us to imagine that living beings are able to maintain vital behavior while the control parameter switches so that their dynamical behavior is suitable for the given environment.Comment: published in Nonlinear Dynamic

Global parameter identification of stochastic reaction networks from single trajectories

We consider the problem of inferring the unknown parameters of a stochastic biochemical network model from a single measured time-course of the concentration of some of the involved species. Such measurements are available, e.g., from live-cell fluorescence microscopy in image-based systems biology. In addition, fluctuation time-courses from, e.g., fluorescence correlation spectroscopy provide additional information about the system dynamics that can be used to more robustly infer parameters than when considering only mean concentrations. Estimating model parameters from a single experimental trajectory enables single-cell measurements and quantification of cell--cell variability. We propose a novel combination of an adaptive Monte Carlo sampler, called Gaussian Adaptation, and efficient exact stochastic simulation algorithms that allows parameter identification from single stochastic trajectories. We benchmark the proposed method on a linear and a non-linear reaction network at steady state and during transient phases. In addition, we demonstrate that the present method also provides an ellipsoidal volume estimate of the viable part of parameter space and is able to estimate the physical volume of the compartment in which the observed reactions take place.Comment: Article in print as a book chapter in Springer's "Advances in Systems Biology

Antiferromagnetic interlayer exchange coupling across an amorphous metallic spacer layer

By means of magneto-optical Kerr effect we observe for the first time antiferromagnetic coupling between ferromagnetic layers across an amorphous metallic spacer layer. Biquadratic coupling occurs at the transition from a ferromagnetically to an antiferromagnetically coupled region. Scanning tunneling microscopy images of all involved layers are used to extract thickness fluctuations and to verify the amorphous state of the spacer. The observed antiferromagnetic coupling behavior is explained by RKKY interaction taking into account the amorphous structure of the spacer material.Comment: Typset using RevTex, 4 pages with 4 figures (.eps

Bayesian inference of biochemical kinetic parameters using the linear noise approximation

Background Fluorescent and luminescent gene reporters allow us to dynamically quantify changes in molecular species concentration over time on the single cell level. The mathematical modeling of their interaction through multivariate dynamical models requires the deveopment of effective statistical methods to calibrate such models against available data. Given the prevalence of stochasticity and noise in biochemical systems inference for stochastic models is of special interest. In this paper we present a simple and computationally efficient algorithm for the estimation of biochemical kinetic parameters from gene reporter data. Results We use the linear noise approximation to model biochemical reactions through a stochastic dynamic model which essentially approximates a diffusion model by an ordinary differential equation model with an appropriately defined noise process. An explicit formula for the likelihood function can be derived allowing for computationally efficient parameter estimation. The proposed algorithm is embedded in a Bayesian framework and inference is performed using Markov chain Monte Carlo. Conclusion The major advantage of the method is that in contrast to the more established diffusion approximation based methods the computationally costly methods of data augmentation are not necessary. Our approach also allows for unobserved variables and measurement error. The application of the method to both simulated and experimental data shows that the proposed methodology provides a useful alternative to diffusion approximation based methods

Cardio-Facio-Cutaneous Syndrome: Clinical Features, Diagnosis, and Management Guidelines

Cardio-facio-cutaneous syndrome (CFC) is one of the RASopathies that bears many clinical features in common with the other syndromes in this group, most notably Noonan syndrome and Costello syndrome. CFC is genetically heterogeneous and caused by gene mutations in the Ras/mitogen-activated protein kinase pathway. the major features of CFC include characteristic craniofacial dysmorphology, congenital heart disease, dermatologic abnormalities, growth retardation, and intellectual disability. It is essential that this condition be differentiated from other RASopathies, as a correct diagnosis is important for appropriate medical management and determining recurrence risk. Children and adults with CFC require multidisciplinary care from specialists, and the need for comprehensive management has been apparent to families and health care professionals caring for affected individuals. To address this need, CFC International, a nonprofit family support organization that provides a forum for information, support, and facilitation of research in basic medical and social issues affecting individuals with CFC, organized a consensus conference. Experts in multiple medical specialties provided clinical management guidelines for pediatricians and other care providers. These guidelines will assist in an accurate diagnosis of individuals with CFC, provide best practice recommendations, and facilitate long-term medical care.CFC International, Vestal, New YorkNational Institutes of HealthNational Institutes of Health (NIH)Univ Minnesota, Dept Pediat & Ophthalmol, Div Genet & Metab, Minneapolis, MN 55454 USAUniv Minnesota, Dept Pediat, Div Clin Behav Neuroscience, Minneapolis, MN 55454 USAChildrens Hosp & Clin Minnesota, St Paul, MN USATexas Childrens Hosp, Dept Mol & Human Genet, Houston, TX 77030 USABaylor Coll Med, Houston, TX 77030 USABenioff Childrens Hosp, Madison Clin Pediat Diabet, San Francisco, CA USAUniv Calif San Francisco, San Francisco, CA 94143 USAUniversidade Federal de São Paulo, Med Genet Ctr, São Paulo, BrazilCatholic Univ, A Gemelli Sch Med, Inst Med Genet, Rome, ItalyUniv Kentucky, Dept Pediat, Lexington, KY USAUniv Texas Hlth Sci Ctr San Antonio, Dept Orthoped, San Antonio, TX 78229 USABoston Childrens Hosp, Dept Cardiol, Boston, MA USABoston Childrens Hosp, Div Genet, Boston, MA USAHarvard Univ, Sch Med, Boston, MA USAEmory Univ, Sch Med, Dept Human Genet, Atlanta, GA USAEmory Univ, Sch Med, Dept Ophthalmol, Atlanta, GA 30322 USAUniv Calif San Francisco, Dept Neurol, San Francisco, CA USAYoungstown State Univ, Special Educ & Sch Psychol, Dept Counseling, Youngstown, OH 44555 USACFC Int, Vestal, NY USAUniv Calif Davis, UC Davis MIND Inst, Dept Pediat, Div Genom Med, Sacramento, CA 95817 USAUniversidade Federal de São Paulo, Med Genet Ctr, São Paulo, BrazilNational Institutes of Health: R01-AR062165Web of Scienc

Markovian Dynamics on Complex Reaction Networks

Complex networks, comprised of individual elements that interact with each other through reaction channels, are ubiquitous across many scientific and engineering disciplines. Examples include biochemical, pharmacokinetic, epidemiological, ecological, social, neural, and multi-agent networks. A common approach to modeling such networks is by a master equation that governs the dynamic evolution of the joint probability mass function of the underling population process and naturally leads to Markovian dynamics for such process. Due however to the nonlinear nature of most reactions, the computation and analysis of the resulting stochastic population dynamics is a difficult task. This review article provides a coherent and comprehensive coverage of recently developed approaches and methods to tackle this problem. After reviewing a general framework for modeling Markovian reaction networks and giving specific examples, the authors present numerical and computational techniques capable of evaluating or approximating the solution of the master equation, discuss a recently developed approach for studying the stationary behavior of Markovian reaction networks using a potential energy landscape perspective, and provide an introduction to the emerging theory of thermodynamic analysis of such networks. Three representative problems of opinion formation, transcription regulation, and neural network dynamics are used as illustrative examples.Comment: 52 pages, 11 figures, for freely available MATLAB software, see http://www.cis.jhu.edu/~goutsias/CSS%20lab/software.htm