A Quick Guide to Software Licensing for the Scientist-Programmer

DOI: 10.1371/journal.pcbi.100259

Collaboration gets the most out of software

By centralizing many of the tasks associated with the upkeep of scientific software, SBGrid allows researchers to spend more of their time on research

Large area quantitative analysis of nanostructured thin-films

Proposed and verified method offers an unique quantitative large scale nanostructures' evaluation.This is the accepted manuscript. The final version is available at http://pubs.rsc.org/en/Content/ArticleLanding/2015/RA/c4ra16018e#!divAbstract

Computational Studies of Intramolecular Hydrogen Atom Transfers in the ß-Hydroxyethylperoxy and ß -Hydroxyethoxy Radicals

The ß-hydroxyethylperoxy (I) and ß-hydroxyethoxy (III) radicals are prototypes of species that can undergo hydrogen atom transfer across their intramolecular hydrogen bonds. These reactions may play an important role in both the atmosphere and in combustion systems. We have used density functional theory and composite electronic structure methods to predict the energetics of these reactions, RRKM/master equation simulations to model the kinetics of chemically activated I, and variational transition state theory (TST) to predict thermal rate constants for the 1,5-hydrogen shift in I (Reaction 1) and the 1,4-hydrogen shift in III (Reaction 2). Our multi-coefficient Gaussian-3 calculations predict that Reaction 1 has a barrier of 23.59 kcal/mol, and that Reaction 2 has a barrier of 22.71 kcal/mol. These predictions agree rather well with the MPW1K and BB1K density functional theory predictions but disagree with predictions based on B3LYP energies or geometries. Our RRKM/master equation simulations suggest that almost 50% of I undergoes a prompt hydrogen shift reaction at pressures up to 10 Torr, but the extent to which I is chemically activated is uncertain. For Reaction 1 at 298 K, the variational TST rate constant is ~30% lower than the conventional TST result, and the microcanonical optimized multidimensional tunneling (OMT) method predicts that tunneling accelerates the reaction by a factor of 3. TST calculations on Reaction 2 reveal no variational effect and a 298 K OMT transmission coefficient of 105. The Eckart method overestimates transmission coefficients for both reactions. [ACS abstract]http://pubs.acs.org/cgi-bin/abstract.cgi/jpcafh/asap/abs/jp0704113.htm

Lipid-Protein Interactions in Double-Layered Two-Dimensional AQP0 Crystals

Lens-specific aquaporin-0 (AQP0) functions as a specific water pore and forms the thin junctions between fibre cells. We describe a 1.9 Å resolution structure of junctional AQP0, determined by electron crystallography of double-layered two-dimensional crystals. Comparison of junctional and non-junctional AQP0 structures shows that junction formation depends on a conformational switch in an extracellular loop, which may result from cleavage of the cytoplasmic N- and C-termini. In the centre of the water pathway, the closed pore in junctional AQP0 retains only three water molecules, which are too widely spaced to form hydrogen bonds with each other. Packing interactions between AQP0 tetramers in the crystalline array are mediated by lipid molecules, which assume preferred conformations. We could therefore build an atomic model for the lipid bilayer surrounding the AQP0 tetramers, and we describe lipid-protein interactions.Molecular and Cellular Biolog

Energy Planning in Selected European Regions - Methods for Evaluating the Potential of Renewable Energy Sources

Given their potentially positive impact on climate protection and the preservation of fossil resources, alternative energy sources have become increasingly important for the energy supply over the past years. However, the questions arises what economic and ecological impacts and potential conflicts over land use resources are associated with the promotion of renewable energy production. Using the examples of three selected European Regions in Poland, France and German, the dissertation discusses these questions and examines the potential and consequences of an intensified usage of renewable energy sources

An assessment of the resolution limitation due to radiation-damage in x-ray diffraction microscopy

X-ray diffraction microscopy (XDM) is a new form of x-ray imaging that is being practiced at several third-generation synchrotron-radiation x-ray facilities. Although only five years have elapsed since the technique was first introduced, it has made rapid progress in demonstrating high-resolution threedimensional imaging and promises few-nm resolution with much larger samples than can be imaged in the transmission electron microscope. Both life- and materials-science applications of XDM are intended, and it is expected that the principal limitation to resolution will be radiation damage for life science and the coherent power of available x-ray sources for material science. In this paper we address the question of the role of radiation damage. We use a statistical analysis based on the so-called "dose fractionation theorem" of Hegerl and Hoppe to calculate the dose needed to make an image of a lifescience sample by XDM with a given resolution. We conclude that the needed dose scales with the inverse fourth power of the resolution and present experimental evidence to support this finding. To determine the maximum tolerable dose we have assembled a number of data taken from the literature plus some measurements of our own which cover ranges of resolution that are not well covered by reports in the literature. The tentative conclusion of this study is that XDM should be able to image frozen-hydrated protein samples at a resolution of about 10 nm with "Rose-criterion" image quality.Comment: 9 pages, 4 figure

Energy Planning in Selected European Regions - Methods for Evaluating the Potential of Renewable Energy Sources

Alternative Energien gewinnen zunehmend an der Bedeutung aufgrund der positiven Beiträge zum Klima- und fossilen Ressourcenschutz. Es stellt sich jedoch auch die Frage, welche Wirkungen auf die ökonomischen und ökologischen Systeme der Regionen dies hat und welche Landnutzungskonflikte mit erneuerbarer Energiennutzung verbunden sind. Die Dissertation greift diese Fragestellungen auf und untersucht die Potenziale und Konsequenzen einer Intensivierung der regenerativen Energienutzung

Deciphering the unusual HLA-A2/Melan-A/MART-1-specific TCR repertoire in humans.

The Melan-A/MART-1(26-35) antigenic peptide is one of the best studied human tumor-associated antigens. It is expressed in healthy melanocytes and malignant melanoma and is recognized by CD8(+) T cells in the context of the MHC class I molecule HLA-A*0201. While an unusually large repertoire of CD8(+) T cells specific for this antigen has been documented, the reasons for its generation have remained elusive. In this issue of the European Journal of Immunology, Pinto et al. [Eur. J. Immunol. 2014. 44: 2811-2821] uncover one important mechanism by comparing the thymic expression of the Melan-A gene to that in the melanocyte lineage. This study shows that medullary thymic epithelial cells (mTECs) dominantly express a truncated Melan-A transcript, the product of misinitiation of transcription. Consequently, the protein product in mTECs lacks the immunodominant epitope spanning residues 26-35, thus precluding central tolerance to this antigen. In contrast, melanocytes and melanoma tumor cells express almost exclusively the full-length Melan-A transcript, thus providing the target antigen for efficient recognition by HLA-A2-restricted CD8(+) T cells. The frequency of these alternative gene transcription modes may be more common than previously appreciated and may represent an important factor modulating the efficiency of central tolerance induction in the thymus

Taming the Coffee Ring Effect : Enhanced Thermal Control as a Method for Thin-Film Nanopatterning

AbstractPredicting and controlling a droplet’s behavior on surfaces is very complex due to several factors affecting its nature. These factors play a crucial role in colloidal material deposition and related solution-based manufacturing methods such as printing. A better understanding of the processes governing the droplet in the picoliter regime is needed to help develop novel thin-film manufacturing methods and improve the current ones. This study introduces the substrate temperature as a method to control the droplet’s behavior during inkjet printing, especially the coffee-ring phenomena, at an unprecedented temperature range (25—250 °C). To explain the particular behavior of the droplet, this research associates the creation of specific coffee-ring micro/nanostructures at elevated temperatures with the Leidenfrost effect that is responsible for creating a vapor pocket under the drying drop. Herein, we combine experimental data and numerical methods to explain the drying dynamic of the picoliter-size droplet on the substrate at elevated temperatures. The achieved results indicate that the coffee-ring effect is correlated with the heat-transfer changes caused by the Leidenfrost effect and can be controlled and used to produce micro/nanostructured thin films without additional processing steps.Abstract Predicting and controlling a droplet’s behavior on surfaces is very complex due to several factors affecting its nature. These factors play a crucial role in colloidal material deposition and related solution-based manufacturing methods such as printing. A better understanding of the processes governing the droplet in the picoliter regime is needed to help develop novel thin-film manufacturing methods and improve the current ones. This study introduces the substrate temperature as a method to control the droplet’s behavior during inkjet printing, especially the coffee-ring phenomena, at an unprecedented temperature range (25—250 °C). To explain the particular behavior of the droplet, this research associates the creation of specific coffee-ring micro/nanostructures at elevated temperatures with the Leidenfrost effect that is responsible for creating a vapor pocket under the drying drop. Herein, we combine experimental data and numerical methods to explain the drying dynamic of the picoliter-size droplet on the substrate at elevated temperatures. The achieved results indicate that the coffee-ring effect is correlated with the heat-transfer changes caused by the Leidenfrost effect and can be controlled and used to produce micro/nanostructured thin films without additional processing steps