Search results for "Secondary"
showing 10 items of 1765 documents
Uniform ergodicity of the iterated conditional SMC and geometric ergodicity of particle Gibbs samplers
2018
We establish quantitative bounds for rates of convergence and asymptotic variances for iterated conditional sequential Monte Carlo (i-cSMC) Markov chains and associated particle Gibbs samplers. Our main findings are that the essential boundedness of potential functions associated with the i-cSMC algorithm provide necessary and sufficient conditions for the uniform ergodicity of the i-cSMC Markov chain, as well as quantitative bounds on its (uniformly geometric) rate of convergence. Furthermore, we show that the i-cSMC Markov chain cannot even be geometrically ergodic if this essential boundedness does not hold in many applications of interest. Our sufficiency and quantitative bounds rely on…
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…
Lévy–Khintchine decompositions for generating functionals on algebras associated to universal compact quantum groups
2018
We study the first and second cohomology groups of the $^*$-algebras of the universal unitary and orthogonal quantum groups $U_F^+$ and $O_F^+$. This provides valuable information for constructing and classifying L\'evy processes on these quantum groups, as pointed out by Sch\"urmann. In the case when all eigenvalues of $F^*F$ are distinct, we show that these $^*$-algebras have the properties (GC), (NC), and (LK) introduced by Sch\"urmann and studied recently by Franz, Gerhold and Thom. In the degenerate case $F=I_d$, we show that they do not have any of these properties. We also compute the second cohomology group of $U_d^+$ with trivial coefficients -- $H^2(U_d^+,{}_\epsilon\Bbb{C}_\epsil…
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…
A strategic needs perspective on operations outsourcing and other inter-firm relationships
2013
Abstract This paper considers two issues: the formation of inter-firm relationships, and the choice of governance form. These have been widely investigated in both the strategic management and operations management fields. This paper contributes to the literature in three ways. First, we address why firms enter inter-firm relationships by hypothesizing that managers enter them to pursue three strategic needs, that is: efficiency/effectiveness, knowledge/learning, and global market access. Our first contribution evidences the relationship between the above strategic needs and a number of operational objectives that managers normally pursue in an inter-firm relationship. Second, we hypothesiz…
‘Sociability before individuality’: lesson structure in lower secondary classrooms
2018
This paper contributes to the research field of classroom research by offering an empirical analysis of classroom instruction on the level of lesson structure. The research questions are: What are ...
Quasiadditivity of Variational Capacity
2013
We study the quasiadditivity property (a version of superadditivity with a multiplicative constant) of variational capacity in metric spaces with respect to Whitney type covers. We characterize this property in terms of a Mazya type capacity condition, and also explore the close relation between quasiadditivity and Hardy's inequality.