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Search Results: 1 - 10 of 223823 matches for " R. Backofen "
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Relaxation of curvature induced elastic stress by the Asaro-Tiller-Grinfeld instability
C. K?hler,R. Backofen,A. Voigt
Physics , 2015, DOI: 10.1209/0295-5075/111/48006
Abstract: A two-dimensional crystal on the surface of a sphere experiences elastic stress due to the incompatibility of the crystal axes and the curvature. A common mechanism to relax elastic stress is the Asaro-Tiller-Grinfeld (ATG) instability. With a combined numerical and analytical approach we demonstrate, that also curvature induced stress in surface crystals can be relaxed by the long wave length ATG instability. The numerical results are obtained using a surface phase-field crystal (PFC) model, from which we determine the characteristic wave numbers of the ATG instability for various surface coverages corresponding to different curvature induced compressions. The results are compared with an analytic expression for the characteristic wave number, obtained from a continuum approach which accounts for hexagonal crystals and intrinsic PFC symmetries. We find our numerical results in accordance with the analytical predictions.
An Information Extraction Core System for Real World German Text Processing
G. Neumann,R. Backofen,J. Baur,M. Becker,C. Braun
Computer Science , 1997,
Abstract: This paper describes SMES, an information extraction core system for real world German text processing. The basic design criterion of the system is of providing a set of basic powerful, robust, and efficient natural language components and generic linguistic knowledge sources which can easily be customized for processing different tasks in a flexible manner.
Controlling Functional Uncertainty
Rolf Backofen
Computer Science , 1996,
Abstract: There have been two different methods for checking the satisfiability of feature descriptions that use the functional uncertainty device, namely~\cite{Kaplan:88CO} and \cite{Backofen:94JSC}. Although only the one in \cite{Backofen:94JSC} solves the satisfiability problem completely, both methods have their merits. But it may happen that in one single description, there are parts where the first method is more appropriate, and other parts where the second should be applied. In this paper, we present a common framework that allows one to combine both methods. This is done by presenting a set of rules for simplifying feature descriptions. The different methods are described as different controls on this rule set, where a control specifies in which order the different rules must be applied.
CRISPR-Cas Systems in the Cyanobacterium Synechocystis sp. PCC6803 Exhibit Distinct Processing Pathways Involving at Least Two Cas6 and a Cmr2 Protein
Ingeborg Scholz, Sita J. Lange, Stephanie Hein, Wolfgang R. Hess, Rolf Backofen
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0056470
Abstract: The CRISPR-Cas (Clustered Regularly Interspaced Short Palindrome Repeats – CRISPR associated proteins) system provides adaptive immunity in archaea and bacteria. A hallmark of CRISPR-Cas is the involvement of short crRNAs that guide associated proteins in the destruction of invading DNA or RNA. We present three fundamentally distinct processing pathways in the cyanobacterium Synechocystis sp. PCC6803 for a subtype I-D (CRISPR1), and two type III systems (CRISPR2 and CRISPR3), which are located together on the plasmid pSYSA. Using high-throughput transcriptome analyses and assays of transcript accumulation we found all CRISPR loci to be highly expressed, but the individual crRNAs had profoundly varying abundances despite single transcription start sites for each array. In a computational analysis, CRISPR3 spacers with stable secondary structures displayed a greater ratio of degradation products. These structures might interfere with the loading of the crRNAs into RNP complexes, explaining the varying abundancies. The maturation of CRISPR1 and CRISPR2 transcripts depends on at least two different Cas6 proteins. Mutation of gene sll7090, encoding a Cmr2 protein led to the disappearance of all CRISPR3-derived crRNAs, providing in vivo evidence for a function of Cmr2 in the maturation, regulation of expression, Cmr complex formation or stabilization of CRISPR3 transcripts. Finally, we optimized CRISPR repeat structure prediction and the results indicate that the spacer context can influence individual repeat structures.
A phase-field-crystal approach to critical nuclei
Rainer Backofen,Axel Voigt
Physics , 2010, DOI: 10.1088/0953-8984/22/36/364104
Abstract: We investigate a phase-field-crystal model for homogeneous nucleation. Instead of solving the time evolution of a density field towards equilibrium we use a String Method to identify saddle points in phase space. The saddle points allow to obtain the nucleation barrier and the critical nucleus. The advantage of using the phase-field-crystal model for this task is its ability to resolve atomistic effects. The obtained results indicate different properties of the critical nucleus compared with bulk crystals and show a detailed description of the nucleation process.
A Complete and Recursive Feature Theory
Rolf Backofen,Gert Smolka
Computer Science , 1994,
Abstract: Various feature descriptions are being employed in logic programming languages and constrained-based grammar formalisms. The common notational primitive of these descriptions are functional attributes called features. The descriptions considered in this paper are the possibly quantified first-order formulae obtained from a signature of binary and unary predicates called features and sorts, respectively. We establish a first-order theory FT by means of three axiom schemes, show its completeness, and construct three elementarily equivalent models. One of the models consists of so-called feature graphs, a data structure common in computational linguistics. The other two models consist of so-called feature trees, a record-like data structure generalizing the trees corresponding to first-order terms. Our completeness proof exhibits a terminating simplification system deciding validity and satisfiability of possibly quantified feature descriptions.
CPSP-tools – Exact and complete algorithms for high-throughput 3D lattice protein studies
Martin Mann, Sebastian Will, Rolf Backofen
BMC Bioinformatics , 2008, DOI: 10.1186/1471-2105-9-230
Abstract: In contrast to stochastic approaches, which are not capable of answering many fundamental questions, our methods are based on fast, non-heuristic techniques. The resulting tools are designed for high-throughput studies of 3D-lattice proteins utilising the Hydrophobic-Polar (HP) model. The source bundle is freely available [1].The CPSP-tools package is the first set of exact and complete methods for extensive, high-throughput studies of non-restricted 3D-lattice protein models. In particular, our package deals with cubic and face centered cubic (FCC) lattices.The organisation of bio-molecules, in particular proteins, in the sequence and structure space has recently been attracting increased attention. Particularly questions concerning finding the native structure or investigating the kinetics and evolution of proteins have been widely studied. These problems are often tackled using simplified models such as the Hydrophobic-Polar (HP) model (e.g. Jacob et al. [2]). Though abstract, these models are computationally feasible and do allow for deeper insights into fundamental and general principles [2-4].Several recurring tasks can be identified in such studies using simplified models. Namely, predicting the native structure, classifying whether a sequence is protein-like, calculating its degeneracy and stability, or the design of sequences that optimally fold to a given structure. The problems associated with these tasks are computationally very hard (NP-complete) [5-7]. Nevertheless, these tasks demand for exact and complete (i.e. non-heuristic) methods. It is important to note that stochastic methods cannot be used for proving optimality and in particular proving that a sequence has a unique lowest energy (protein-like) fold [8].Consequently, with the exception of Yue and Dill [9], all studies requiring complete and exact answers to optimal structure prediction were based on exhaustive enumeration. These studies were, hence, confined to small sequence lengths. In other
Equivalence Classes of Optimal Structures in HP Protein Models Including Side Chains
Martin Mann,Rolf Backofen,Sebastian Will
Computer Science , 2009,
Abstract: Lattice protein models, as the Hydrophobic-Polar (HP) model, are a common abstraction to enable exhaustive studies on structure, function, or evolution of proteins. A main issue is the high number of optimal structures, resulting from the hydrophobicity-based energy function applied. We introduce an equivalence relation on protein structures that correlates to the energy function. We discuss the efficient enumeration of optimal representatives of the corresponding equivalence classes and the application of the results.
Fast prediction of RNA-RNA interaction
Raheleh Salari, Rolf Backofen, S Cenk Sahinalp
Algorithms for Molecular Biology , 2010, DOI: 10.1186/1748-7188-5-5
Abstract: In this paper we present a novel algorithm to accurately predict the minimum free energy structure of RNA-RNA interaction under the most general type of interactions studied in the literature. Moreover, we introduce a fast heuristic method to predict the specific (multiple) binding sites of two interacting RNAs.We verify the performance of our algorithms for joint structure and binding site prediction on a set of known interacting RNA pairs. Experimental results show our algorithms are highly accurate and outperform all competitive approaches.Regulatory non-coding RNAs (ncRNAs) play an important role in gene regulation. Studies on both prokaryotic and eukaryotic cells show that such ncRNAs usually bind to their target mRNA to regulate the translation of corresponding genes. Many regulatory RNAs such as microRNAs and small interfering RNAs (miRNAs/siRNAs) are very short and have full sequence complementarity to the targets. However some of the regulatory antisense RNAs are relatively long and are not fully complementary to their target sequences. They exhibit their regulatory functions by establishing stable joint structures with target mRNA initiated by one or more loop-loop interactions.In this paper we present an efficient method for the RNA-RNA interaction prediction (RIP) problem with multiple binding domains. Alkan et al. [1] proved that RIP, in its general form, is an NP-complete problem and provided algorithms for predicting specific types of interactions and two relatively simple energy models - under which RIP is polynomial time solvable. We focus on the same type of interactions, which to the best of our knowledge, are the most general type of interactions considered in the literature; however the energy model we use is the joint structure energy model recently presented by Chitsaz et al. [2] which is more general than the one used by Alkan et al.In what follows below, we first describe a combinatorial algorithm to compute the minimum free energy joint str
Particles on curved surfaces - a dynamic approach by a phase field crystal model
Rainer Backofen,Axel Voigt,Thomas Witkowski
Physics , 2009, DOI: 10.1103/PhysRevE.81.025701
Abstract: We present a dynamic model to study ordering of particles on arbitrary curved surfaces. Thereby the particles are represented as maxima in a density field and a surface partial differential equation for the density field is solved to the minimal energy configuration. We study annihilation of dislocations within the ordered sytem and premelting along grain boundary scars. The obtained minimal energy configurations on a sphere are compared with existing results and scaling laws are computed for the number of excess dislocations as a function of system size.
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