Theoretical studies of a hydrogen abstraction tool for nanotechnology

In the design of a nanoscale, site-specific hydrogen abstraction tool, the authors suggest the use of an alkynyl radical tip. Using ab initio quantum-chemistry techniques including electron correlation they model the abstraction of hydrogen from dihydrogen, methane, acetylene, benzene and isobutane by the acetylene radical. By conservative estimates, the abstraction barrier is small (less than 7.7 kcal mol^-1) in all cases except for acetylene and zero in the case of isobutane. Thermal vibrations at room temperature should be sufficient to supply the small activation energy. Several methods of creating the radical in a controlled vacuum setting should be feasible. The authors show how nanofabrication processes can be accurately and inexpensively designed in a computational framework

Picosecond Laser Pulse Irradiation of Crystalline Silicon

Morphology changes introduced by picosecond laser pulses at λ = 532 nm and 355 nm in (111) and (100) silicon samples are studied by means of optical and high-voltage electron microscopy. Depending on energy fluence, orientation and wavelength, amorphous or highly defective regions may be created. From an analysis of damage thresholds and damage depth distributions it is concluded that melting and energy confinement precedes the formation of the structural changes

Lower bounds for the first eigenvalue of the magnetic Laplacian

We consider a Riemannian cylinder endowed with a closed potential 1-form A and study the magnetic Laplacian with magnetic Neumann boundary conditions associated with those data. We establish a sharp lower bound for the first eigenvalue and show that the equality characterizes the situation where the metric is a product. We then look at the case of a planar domain bounded by two closed curves and obtain an explicit lower bound in terms of the geometry of the domain. We finally discuss sharpness of this last estimate.Comment: Replaces in part arXiv:1611.0193

An Approach to Improved Credibility of CFD Simulations for Rocket Injector Design

Computational fluid dynamics (CFD) has the potential to improve the historical rocket injector design process by simulating the sensitivity of performance and injector-driven thermal environments to. the details of the injector geometry and key operational parameters. Methodical verification and validation efforts on a range of coaxial injector elements have shown the current production CFD capability must be improved in order to quantitatively impact the injector design process.. This paper documents the status of an effort to understand and compare the predictive capabilities and resource requirements of a range of CFD methodologies on a set of model problem injectors. Preliminary results from a steady Reynolds-Average Navier-Stokes (RANS), an unsteady Reynolds-Average Navier Stokes (URANS) and three different Large Eddy Simulation (LES) techniques used to model a single element coaxial injector using gaseous oxygen and gaseous hydrogen propellants are presented. Initial observations are made comparing instantaneous results, corresponding time-averaged and steady-state solutions in the near -injector flow field. Significant differences in the flow fields exist, as expected, and are discussed. An important preliminary result is the identification of a fundamental mixing mechanism, accounted for by URANS and LES, but missing in the steady BANS methodology. Since propellant mixing is the core injector function, this mixing process may prove to have a profound effect on the ability to more correctly simulate injector performance and resulting thermal environments. Issues important to unifying the basis for future comparison such as solution initialization, required run time and grid resolution are addressed

A new procedure for making TEM specimens of superconductor devices

A new procedure is developed for making TEM specimens of thin film devices. In this procedure the sample is flatly polished to an overall ion-mill-ready thickness so that any point in the 2-D sample pane can be thinned to an electron-transparent thickness by subsequent ion-milling. Using this procedure, small regions of interest can be easily reached in both cross-section and plan-view samples. This is especially useful in device studies. Applications of this procedure to the study of superconductor devices yield good results. This procedure, using commercially available equipment and relatively cheap materials, is simple and easy to realize

Unifying Parsimonious Tree Reconciliation

Evolution is a process that is influenced by various environmental factors, e.g. the interactions between different species, genes, and biogeographical properties. Hence, it is interesting to study the combined evolutionary history of multiple species, their genes, and the environment they live in. A common approach to address this research problem is to describe each individual evolution as a phylogenetic tree and construct a tree reconciliation which is parsimonious with respect to a given event model. Unfortunately, most of the previous approaches are designed only either for host-parasite systems, for gene tree/species tree reconciliation, or biogeography. Hence, a method is desirable, which addresses the general problem of mapping phylogenetic trees and covering all varieties of coevolving systems, including e.g., predator-prey and symbiotic relationships. To overcome this gap, we introduce a generalized cophylogenetic event model considering the combinatorial complete set of local coevolutionary events. We give a dynamic programming based heuristic for solving the maximum parsimony reconciliation problem in time O(n^2), for two phylogenies each with at most n leaves. Furthermore, we present an exact branch-and-bound algorithm which uses the results from the dynamic programming heuristic for discarding partial reconciliations. The approach has been implemented as a Java application which is freely available from http://pacosy.informatik.uni-leipzig.de/coresym.Comment: Peer-reviewed and presented as part of the 13th Workshop on Algorithms in Bioinformatics (WABI2013

Functional brain mapping by blood oxygenation level-dependent contrast magnetic resonance imaging. A comparison of signal characteristics with a biophysical model

It recently has been demonstrated that magnetic resonance imaging can be used to map changes in brain hemodynamics produced by human mental operations. One method under development relies on blood oxygenation level-dependent (BOLD) contrast: a change in the signal strength of brain water protons produced by the paramagnetic effects of venous blood deoxyhemoglobin. Here we discuss the basic quantitative features of the observed BOLD-based signal changes, including the signal amplitude and its magnetic field dependence and dynamic effects such as a pronounced oscillatory pattern that is induced in the signal from primary visual cortex during photic stimulation experiments. The observed features are compared with the results of Monte Carlo simulations of water proton intravoxel phase dispersion produced by local field gradients generated by paramagnetic deoxyhemoglobin in nearby venous blood vessels. The simulations suggest that the effect of water molecule diffusion is strong for the case of blood capillaries, but, for larger venous blood vessels, water diffusion is not an important determinant of deoxyhemoglobin-induced signal dephasing. We provide an expression for the apparent in-plane relaxation rate constant (R2*) in terms of the main magnetic field strength, the degree of the oxygenation of the venous blood, the venous blood volume fraction in the tissue, and the size of the blood vessel

Distributed Management of Massive Data: an Efficient Fine-Grain Data Access Scheme

This paper addresses the problem of efficiently storing and accessing massive data blocks in a large-scale distributed environment, while providing efficient fine-grain access to data subsets. This issue is crucial in the context of applications in the field of databases, data mining and multimedia. We propose a data sharing service based on distributed, RAM-based storage of data, while leveraging a DHT-based, natively parallel metadata management scheme. As opposed to the most commonly used grid storage infrastructures that provide mechanisms for explicit data localization and transfer, we provide a transparent access model, where data are accessed through global identifiers. Our proposal has been validated through a prototype implementation whose preliminary evaluation provides promising results

Human phosphodiesterase 4D7 (PDE4D7) expression is increased in TMPRSS2-ERG positive primary prostate cancer and independently adds to a reduced risk of post-surgical disease progression

background: There is an acute need to uncover biomarkers that reflect the molecular pathologies, underpinning prostate cancer progression and poor patient outcome. We have previously demonstrated that in prostate cancer cell lines PDE4D7 is downregulated in advanced cases of the disease. To investigate further the prognostic power of PDE4D7 expression during prostate cancer progression and assess how downregulation of this PDE isoform may affect disease outcome, we have examined PDE4D7 expression in physiologically relevant primary human samples. methods: About 1405 patient samples across 8 publically available qPCR, Affymetrix Exon 1.0 ST arrays and RNA sequencing data sets were screened for PDE4D7 expression. The TMPRSS2-ERG gene rearrangement status of patient samples was determined by transformation of the exon array and RNA seq expression data to robust z-scores followed by the application of a threshold >3 to define a positive TMPRSS2-ERG gene fusion event in a tumour sample. results: We demonstrate that PDE4D7 expression positively correlates with primary tumour development. We also show a positive association with the highly prostate cancer-specific gene rearrangement between TMPRSS2 and the ETS transcription factor family member ERG. In addition, we find that in primary TMPRSS2-ERG-positive tumours PDE4D7 expression is significantly positively correlated with low-grade disease and a reduced likelihood of progression after primary treatment. Conversely, PDE4D7 transcript levels become significantly decreased in castration resistant prostate cancer (CRPC). conclusions: We further characterise and add physiological relevance to PDE4D7 as a novel marker that is associated with the development and progression of prostate tumours. We propose that the assessment of PDE4D7 levels may provide a novel, independent predictor of post-surgical disease progression