Proteins in solution: Fractal surfaces in solutions

The concept of the surface of a protein in solution, as well of the interface between protein and 'bulk solution', is introduced. The experimental technique of small angle X-ray and neutron scattering is introduced and described briefly. Molecular dynamics simulation, as an appropriate computational tool for studying the hydration shell of proteins, is also discussed. The concept of protein surfaces with fractal dimensions is elaborated. We finish by exposing an experimental (using small angle X-ray scattering) and a computer simulation case study, which are meant as demonstrations of the possibilities we have at hand for investigating the delicate interfaces that connect (and divide) protein molecules and the neighboring electrolyte solution.Comment: 8 pages, 5 figure

High-m Kink/Tearing Modes in Cylindrical Geometry

The global ideal kink equation, for cylindrical geometry and zero beta, is simplified in the high poloidal mode number limit and used to determine the tearing stability parameter, $\Delta^\prime$. In the presence of a steep monotonic current gradient, $\Delta^\prime$ becomes a function of a parameter, $\sigma_0$, characterising the ratio of the maximum current gradient to magnetic shear, and $x_s$, characterising the separation of the resonant surface from the maximum of the current gradient. In equilibria containing a current "spike", so that there is a non-monotonic current profile, $\Delta^\prime$ also depends on two parameters: $\kappa$, related to the ratio of the curvature of the current density at its maximum to the magnetic shear, and $x_s$, which now represents the separation of the resonance from the point of maximum current density. The relation of our results to earlier studies of tearing modes and to recent gyro-kinetic calculations of current driven instabilities, is discussed, together with potential implications for the stability of the tokamak pedestal.Comment: To appear in Plasma Physics and Controlled Fusio

Phase-field approach to polycrystalline solidification including heterogeneous and homogeneous nucleation

Advanced phase-field techniques have been applied to address various aspects of polycrystalline solidification including different modes of crystal nucleation. The height of the nucleation barrier has been determined by solving the appropriate Euler-Lagrange equations. The examples shown include the comparison of various models of homogeneous crystal nucleation with atomistic simulations for the single component hard-sphere fluid. Extending previous work for pure systems (Gránásy L, Pusztai T, Saylor D and Warren J A 2007 Phys. Rev. Lett. 98 art no 035703), heterogeneous nucleation in unary and binary systems is described via introducing boundary conditions that realize the desired contact angle. A quaternion representation of crystallographic orientation of the individual particles (outlined in Pusztai T, Bortel G and Gránásy L 2005 Europhys. Lett. 71 131) has been applied for modeling a broad variety of polycrystalline structures including crystal sheaves, spherulites and those built of crystals with dendritic, cubic, rhombododecahedral, truncated octahedral growth morphologies. Finally, we present illustrative results for dendritic polycrystalline solidification obtained using an atomistic phase-field model

Nucleation and phase selection in undercooled melts: Magnetic alloys of industrial relevance (MAGNEPHAS)

Studies of phase selection and microstructure evolution in high-performance magnetic materials are an urgent need for optimization of production routes. Containerless solidification experiments by electromagnetic levitation and drop tube solidification were conducted in undercooled melts of Fe-Co, Fe-Ni soft magnetic, and Nd-Fe-B hard magnetic alloys. Melt undercooling under microgravity was achieved in the TEMPUS facility during parabolic flight campaigns. For Fe-Co and Fe-Ni alloys significant effects of microgravity on metastable phase formation were discovered. Microstructure modifications as well as metastable phase formation as function of undercooling and melt flow were elucidated in Nd-Fe-B. Modeling of solidification processes, fluid flow and heat transfer provide predictive tools for microstructure engineering from the melt. They were developed as a link between undercooling experiments under terrestrial and microgravity conditions and the production routes of magnetic materials

Phase field theory of polycrystalline solidification in three dimensions

A phase field theory of polycrystalline solidification is presented that is able to describe the nucleation and growth of anisotropic particles with different crystallographic orientation in three dimensions. As opposed with the two-dimensional case, where a single orientation field suffices, in three dimensions, minimum three fields are needed. The free energy of grain boundaries is assumed to be proportional to the angular difference between the adjacent crystals expressed here in terms of the differences of the four symmetric Euler parameters. The equations of motion for these fields are obtained from variational principles. Illustrative calculations are performed for polycrystalline solidification with dendritic, needle and spherulitic growth morphologies.Comment: 7 pages, 4 figures, submitted to Europhysics Letters on 14th February, 200

Gene expression profiling of breast cancer

Molecular types of breast cancer Important differences in the clinical behaviour of oestrogen receptor (ER)-positive and ER-negative cancers have been recognised for a long time [1]. Nevertheless, breast cancer was regarded as a single disease with variable histology and clinical course. More recently, high-throughput analytical methods revealed unexpectedly large-scale molecular differences between ER-positive cancers and ER-negative cancers [2]. These results prompted a conceptual shift in the classification of breast cancer, which is increasingly viewed not as a single disease but as a collection of several biologically distinct neoplastic diseases that arise from the breast epithelium. The different molecular types of breast cancer may originate from different epithelial precursors such as luminal (ERpositive cancers) or basal (ER-negative tumours) epithelia

Lack of sufficiently strong informative features limits the potential of gene expression analysis as predictive tool for many clinical classification problems

<p>Abstract</p> <p>Background</p> <p>Our goal was to examine how various aspects of a gene signature influence the success of developing multi-gene prediction models. We inserted gene signatures into three real data sets by altering the expression level of existing probe sets. We varied the number of probe sets perturbed (signature size), the fold increase of mean probe set expression in perturbed compared to unperturbed data (signature strength) and the number of samples perturbed. Prediction models were trained to identify which cases had been perturbed. Performance was estimated using Monte-Carlo cross validation.</p> <p>Results</p> <p>Signature strength had the greatest influence on predictor performance. It was possible to develop almost perfect predictors with as few as 10 features if the fold difference in mean expression values were > 2 even when the spiked samples represented 10% of all samples. We also assessed the gene signature set size and strength for 9 real clinical prediction problems in six different breast cancer data sets.</p> <p>Conclusions</p> <p>We found sufficiently large and strong predictive signatures only for distinguishing ER-positive from ER-negative cancers, there were no strong signatures for more subtle prediction problems. Current statistical methods efficiently identify highly informative features in gene expression data if such features exist and accurate models can be built with as few as 10 highly informative features. Features can be considered highly informative if at least 2-fold expression difference exists between comparison groups but such features do not appear to be common for many clinically relevant prediction problems in human data sets.</p

On the minimum transport required to passively suppress runaway electrons in SPARC disruptions

In [V.A. Izzo et al 2022 Nucl. Fusion 62 096029], state-of-the-art modeling of thermal and current quench (CQ) MHD coupled with a self-consistent evolution of runaway electron (RE) generation and transport showed that a non-axisymmetric (n = 1) in-vessel coil could passively prevent RE beam formation during disruptions in SPARC, a compact high-field tokamak projected to achieve a fusion gain Q > 2 in DT plasmas. However, such suppression requires finite transport of REs within magnetic islands and re-healed flux surfaces; conservatively assuming zero transport in these regions leads to an upper bound of RE current ~1 MA compared to ~8.7 MA of pre-disruption plasma current. Further investigation finds that core-localized electrons, within r/a < 0.3 and with kinetic energies 0.2-15 MeV, contribute most to the RE plateau formation. Yet only a relatively small amount of transport, i.e. a diffusion coefficient ~18 $\mathrm{m^2/s}$, is needed in the core to fully mitigate these REs. Properly accounting for (i) the CQ electric field's effect on RE transport in islands and (ii) the contribution of significant RE currents to disruption MHD may help achieve this