Modeling of Covalent Bonding in Solids by Inversion of Cohesive Energy Curves

We provide a systematic test of empirical theories of covalent bonding in solids using an exact procedure to invert ab initio cohesive energy curves. By considering multiple structures of the same material, it is possible for the first time to test competing angular functions, expose inconsistencies in the basic assumption of a cluster expansion, and extract general features of covalent bonding. We test our methods on silicon, and provide the direct evidence that the Tersoff-type bond order formalism correctly describes coordination dependence. For bond-bending forces, we obtain skewed angular functions that favor small angles, unlike existing models. As a proof-of-principle demonstration, we derive a Si interatomic potential which exhibits comparable accuracy to existing models.Comment: 4 pages revtex (twocolumn, psfig), 3 figures. Title and some wording (but no content) changed since original submission on 24 April 199

Branching, Capping, and Severing in Dynamic Actin Structures

Branched actin networks at the leading edge of a crawling cell evolve via protein-regulated processes such as polymerization, depolymerization, capping, branching, and severing. A formulation of these processes is presented and analyzed to study steady-state network morphology. In bulk, we identify several scaling regimes in severing and branching protein concentrations and find that the coupling between severing and branching is optimally exploited for conditions {\it in vivo}. Near the leading edge, we find qualitative agreement with the {\it in vivo} morphology.Comment: 4 pages, 2 figure

Design and validation of Segment - freely available software for cardiovascular image analysis

<p>Abstract</p> <p>Background</p> <p>Commercially available software for cardiovascular image analysis often has limited functionality and frequently lacks the careful validation that is required for clinical studies. We have already implemented a cardiovascular image analysis software package and released it as freeware for the research community. However, it was distributed as a stand-alone application and other researchers could not extend it by writing their own custom image analysis algorithms. We believe that the work required to make a clinically applicable prototype can be reduced by making the software extensible, so that researchers can develop their own modules or improvements. Such an initiative might then serve as a bridge between image analysis research and cardiovascular research. The aim of this article is therefore to present the design and validation of a cardiovascular image analysis software package (Segment) and to announce its release in a source code format.</p> <p>Results</p> <p>Segment can be used for image analysis in magnetic resonance imaging (MRI), computed tomography (CT), single photon emission computed tomography (SPECT) and positron emission tomography (PET). Some of its main features include loading of DICOM images from all major scanner vendors, simultaneous display of multiple image stacks and plane intersections, automated segmentation of the left ventricle, quantification of MRI flow, tools for manual and general object segmentation, quantitative regional wall motion analysis, myocardial viability analysis and image fusion tools. Here we present an overview of the validation results and validation procedures for the functionality of the software. We describe a technique to ensure continued accuracy and validity of the software by implementing and using a test script that tests the functionality of the software and validates the output. The software has been made freely available for research purposes in a source code format on the project home page <url>http://segment.heiberg.se</url>.</p> <p>Conclusions</p> <p>Segment is a well-validated comprehensive software package for cardiovascular image analysis. It is freely available for research purposes provided that relevant original research publications related to the software are cited.</p

The Theory of the Interleaving Distance on Multidimensional Persistence Modules

In 2009, Chazal et al. introduced $\epsilon$-interleavings of persistence modules. $\epsilon$-interleavings induce a pseudometric $d_I$ on (isomorphism classes of) persistence modules, the interleaving distance. The definitions of $\epsilon$-interleavings and $d_I$ generalize readily to multidimensional persistence modules. In this paper, we develop the theory of multidimensional interleavings, with a view towards applications to topological data analysis. We present four main results. First, we show that on 1-D persistence modules, $d_I$ is equal to the bottleneck distance $d_B$. This result, which first appeared in an earlier preprint of this paper, has since appeared in several other places, and is now known as the isometry theorem. Second, we present a characterization of the $\epsilon$-interleaving relation on multidimensional persistence modules. This expresses transparently the sense in which two $\epsilon$-interleaved modules are algebraically similar. Third, using this characterization, we show that when we define our persistence modules over a prime field, $d_I$ satisfies a universality property. This universality result is the central result of the paper. It says that $d_I$ satisfies a stability property generalizing one which $d_B$ is known to satisfy, and that in addition, if $d$ is any other pseudometric on multidimensional persistence modules satisfying the same stability property, then $d\leq d_I$. We also show that a variant of this universality result holds for $d_B$, over arbitrary fields. Finally, we show that $d_I$ restricts to a metric on isomorphism classes of finitely presented multidimensional persistence modules.Comment: Major revision; exposition improved throughout. To appear in Foundations of Computational Mathematics. 36 page

Congenital thumb anomalies and the consequences for daily life : patients’ long-term experience after corrective surgery. A qualitative study

Purpose: The aim of the study was to explore patients’ long-term experience of a congenital hand problem, and the consequences for daily life. Method: Fifteen participants with a median age 24 years (17–55 years), born with thumb hypoplasia/aplasia or thumb duplication were interviewed using a semi-structured interview guide. The interviews were subjected to qualitative content analysis. Results: Although the mobility and strength in the thumb/hand(s) varied within the group, hand function was generally described as good. Compensatory strategies were used to overcome practical obstacles. The emotional reactions to being visibly different from peers in early life varied from total acceptance and a sense of pride in being special, to deep distress and social withdrawal. Support from parents, teachers and others was important in facing emotional challenges and practical consequences. Conclusion: The present study highlights the importance of healthcare professionals addressing appearance-related concerns which may have long-term emotional and social consequences for patients born with a thumb anomaly. Implications for RehabilitationAppearance-related concerns and need for emotional support should be fully considered throughout the rehabilitation process to prevent distress and social withdrawal.Effective problem-solving strategies, such as compensation, change in occupational performance and support from others may reduce activity limitations and participation restriction

Immunospecific Antibody Concentration in Egg Yolk of Chickens Orally Immunised with Varying Doses of Bovine Serum Albumin and the Mucosal Adjuvant, RhinoVax®, using Different Immunization Regimes

Antibody harvested from eggs of immunised chickens, IgY, has proven to be a non-invasive alternative to  antibodies purified from serum of mammals. Taking the non-invasive concept further, the development of  oral immunization techniques combined with IgY harvest from chicken eggs may subsequently eliminate  all regulated procedures from polyclonal antibody production. In the present study, we report the effects of  varying the temporal administration mode of the antigen (immunogen) comparing dosing on three consecutive  days with dosing on five consecutive days, and of incorporating a mucosal adjuvant. Two antigen  doses were compared: 30 mg bovine serum albumin (BSA) and 300 mg BSA, with and without the mucosal  adjuvant, RhinoVax®, administered to laying chickens. The egg yolk of chickens dosed with BSA in combination  with 20% RhinoVax®, contained significantly higher concentrations of immunospecific IgY than  did egg yolks of chickens fed with BSA without adjuvant. The most efficient dose in the RhinoVax®-treated  groups was 300 mg BSA regardless of whether the chickens were initially immunised daily for three or  five days. A 3-day dosing regime with BSA alone also induced immunospecific IgY production. This study  confirms that RhinoVax® is an efficient oral adjuvant. It also demonstrates the efficacy of daily immunizations  on three or five consecutive days on immunospecific IgY production. The chickens received oral  booster immunizations one and two months after the initial immunization. No real effect could be recorded  after the second and third immunization, although the study did provide some evidence of memory  based on an optimum IgY concentration recorded after the 2nd immunization.

Solid-Liquid Phase Diagrams for Binary Metallic Alloys: Adjustable Interatomic Potentials

We develop a new approach to determining LJ-EAM potentials for alloys and use these to determine the solid-liquid phase diagrams for binary metallic alloys using Kofke's Gibbs-Duhem integration technique combined with semigrand canonical Monte Carlo simulations. We demonstrate that it is possible to produce a wide-range of experimentally observed binary phase diagrams (with no intermetallic phases) by reference to the atomic sizes and cohesive energies of the two elemental materials. In some cases, it is useful to employ a single adjustable parameter to adjust the phase diagram (we provided a good choice for this free parameter). Next, we perform a systematic investigation of the effect of relative atomic sizes and cohesive energies of the elements on the binary phase diagrams. We then show that this approach leads to good agreement with several experimental binary phase diagrams. The main benefit of this approach is not the accurately reproduction of experimental phase diagrams, but rather to provide a method by which material properties can be continuously changed in simulations studies. This is one of the keys to the use of atomistic simulations to understand mechanisms and properties in a manner not available to experiment

Symmetry-Breaking Motility

Locomotion of bacteria by actin polymerization, and in vitro motion of spherical beads coated with a protein catalyzing polymerization, are examples of active motility. Starting from a simple model of forces locally normal to the surface of a bead, we construct a phenomenological equation for its motion. The singularities at a continuous transition between moving and stationary beads are shown to be related to the symmetries of its shape. Universal features of the phase behavior are calculated analytically and confirmed by simulations. Fluctuations in velocity are shown to be generically non-Maxwellian and correlated to the shape of the bead.Comment: 4 pages, 2 figures, REVTeX; formatting of references correcte

The Quiet-Sun Photosphere and Chromosphere

The overall structure and the fine structure of the solar photosphere outside active regions are largely understood, except possibly important roles of a turbulent near-surface dynamo at its bottom, internal gravity waves at its top, and small-scale vorticity. Classical 1D static radiation-escape modelling has been replaced by 3D time-dependent MHD simulations that come closer to reality. The solar chromosphere, in contrast, remains ill-understood although its pivotal role in coronal mass and energy loading makes it a principal research area. Its fine structure defines its overall structure, so that hard-to-observe and hard-to-model small-scale dynamical processes are the key to understanding. However, both chromospheric observation and chromospheric simulation presently mature towards the required sophistication. The open-field features seem of greater interest than the easier-to-see closed-field features.Comment: Accepted for special issue "Astrophysical Processes on the Sun" of Phil. Trans. Royal Soc. A, ed. C. Parnell. Note: clicking on the year in a citation opens the corresponding ADS abstract page in the browse