Search results for " secondary"
showing 10 items of 692 documents
Laser desorption/ionization cluster studies for calibration in mass spectrometry
2003
Precise mass calibration is mandatory in many fields of mass spectrometry. We have performed laser desorption/ionization cluster studies with a MALDI-TOF mass spectrometer on gold and fullerene targets to produce atomic clusters. These investigations demonstrate that clusters are ideally suited for this purpose. Pulsed N 2 -laser and Nd:YAG-laser ablation was used to produce positively as well as negatively charged clusters. Earlier observations of dianionic metal clusters are confirmed. First results from the tandem Penning trap mass spectrometer ISOLTRAP using carbon clusters as mass references show how carbon clusters can be applied to precision mass spectrometry by providing absolute ma…
Comparative optical reflection and mass spectrometry analysis of thermodesorption of Langmuir-Blodgett films
1992
Abstract Thermodesorption of cadmium arachidate multilayers is studied by optical surface analysis and by mass spectrometry measurements. The optical reflection technique has been improved to discriminate signal contributions from desorption and light scattering. The scattering arises from film heterogeneities that are also observed by Nomarsky microscopy. The assessment of these heterogeneities is important to understand mass spectrometry data. Both the optical technique and mass spectrometry are sensitive to observing the multilayer phase transition at 110 °C and the desorption near 200 °C (at the heating rate applied). The mass spectrometry analysis yields detailed information on the des…
The Psychological Science Accelerator’s COVID-19 rapid-response dataset
2023
Funder: Amazon Web Services (AWS) Imagine Grant
Mean square rate of convergence for random walk approximation of forward-backward SDEs
2020
AbstractLet (Y,Z) denote the solution to a forward-backward stochastic differential equation (FBSDE). If one constructs a random walk$B^n$from the underlying Brownian motionBby Skorokhod embedding, one can show$L_2$-convergence of the corresponding solutions$(Y^n,Z^n)$to$(Y, Z).$We estimate the rate of convergence based on smoothness properties, especially for a terminal condition function in$C^{2,\alpha}$. The proof relies on an approximative representation of$Z^n$and uses the concept of discretized Malliavin calculus. Moreover, we use growth and smoothness properties of the partial differential equation associated to the FBSDE, as well as of the finite difference equations associated to t…
Self-stabilizing processes: uniqueness problem for stationary measures and convergence rate in the small-noise limit
2011
In the context of self-stabilizing processes, that is processes attracted by their own law, living in a potential landscape, we investigate different properties of the invariant measures. The interaction between the process and its law leads to nonlinear stochastic differential equations. In [S. Herrmann and J. Tugaut. Electron. J. Probab. 15 (2010) 2087–2116], the authors proved that, for linear interaction and under suitable conditions, there exists a unique symmetric limit measure associated to the set of invariant measures in the small-noise limit. The aim of this study is essentially to point out that this statement leads to the existence, as the noise intensity is small, of one unique…
Assessment of the probabilities for evolutionary structural changes in protein folds.
2007
Abstract Motivation: The evolution of protein sequences can be described by a stepwise process, where each step involves changes of a few amino acids. In a similar manner, the evolution of protein folds can be at least partially described by an analogous process, where each step involves comparatively simple changes affecting few secondary structure elements. A number of such evolution steps, justified by biologically confirmed examples, have previously been proposed by other researchers. However, unlike the situation with sequences, as far as we know there have been no attempts to estimate the comparative probabilities for different kinds of such structural changes. Results: We have tried …
A Hooke's law-based approach to protein folding rate
2014
Kinetics is a key aspect of the renowned protein folding problem. Here, we propose a comprehensive approach to folding kinetics where a polypeptide chain is assumed to behave as an elastic material described by the Hooke[U+05F3]s law. A novel parameter called elastic-folding constant results from our model and is suggested to distinguish between protein with two-state and multi-state folding pathways. A contact-free descriptor, named folding degree, is introduced as a suitable structural feature to study protein-folding kinetics. This approach generalizes the observed correlations between varieties of structural descriptors with the folding rate constant. Additionally several comparisons am…
SKINK: a web server for string kernel based kink prediction in α-helices
2014
Abstract Motivation: The reasons for distortions from optimal α-helical geometry are widely unknown, but their influences on structural changes of proteins are significant. Hence, their prediction is a crucial problem in structural bioinformatics. Here, we present a new web server, called SKINK, for string kernel based kink prediction. Extending our previous study, we also annotate the most probable kink position in a given α-helix sequence. Availability and implementation: The SKINK web server is freely accessible at http://biows-inf.zdv.uni-mainz.de/skink. Moreover, SKINK is a module of the BALL software, also freely available at www.ballview.org. Contact: benny.kneissl@roche.com
Putative identification of an amphipathic alpha-helical sequence in hemolysin of Escherichia coli (HlyA) involved in transmembrane pore formation.
2008
Abstract Escherichia coli hemolysin is a pore-forming protein belonging to the RTX toxin family. Cysteine scanning mutagenesis was performed to characterize the putative pore-forming domain of the molecule. A single cysteine residue was introduced at 48 positions within the sequence spanning residues 170–400 and labeled with the polarity-sensitive dye badan. Spectrofluorimetric analyses indicated that several amino acids in this domain are inserted into the lipid bilayer during pore formation. An amphipathic α-helix spanning residues 272–298 was identified that may line the aqueous pore. The importance of this sequence was highlighted by the introduction of two prolines at positions 284 and…
Energy interactions in amyloid-like fibrils from NNQQNY.
2014
We use large-scale MP2 calculations to analyze the interactions appearing in amyloid fibers, which are difficult to determine experimentally. To this end, dimers and trimers of the hexapeptide NNQQNY from the yeast prion-like protein Sup35 were considered as model systems. We studied the energy interactions present in the three levels of organization in which the formation of amyloid fibrils is structured. The structural changes in the hydrogen bonds were studied too. It was found that the most energetic process is the formation of the β-sheet, which is equally due to both hydrogen bonds and van der Waals interactions. The aromatic rings help stabilize these aggregates through stacking of t…