Search results for "Computation"

RepeatsDB in 2021: improved data and extended classification for protein tandem repeat structures

2020

The RepeatsDB database (URL: https://repeatsdb.org/) provides annotations and classification for protein tandem repeat structures from the Protein Data Bank (PDB). Protein tandem repeats are ubiquitous in all branches of the tree of life. The accumulation of solved repeat structures provides new possibilities for classification and detection, but also increasing the need for annotation. Here we present RepeatsDB 3.0, which addresses these challenges and presents an extended classification scheme. The major conceptual change compared to the previous version is the hierarchical classification combining top levels based solely on structural similarity (Class > Topology > Fold) with two new lev…

Repeatability in protein sequences

2019

Low complexity regions (LCRs) in protein sequences have special properties that are very different from those of globular proteins. The rules that define secondary structure elements do not apply when the distribution of amino acids becomes biased. While there is a tendency towards structural disorder in LCRs, various examples, and particularly homorepeats of single amino acids, suggest that very short repeats could adopt structures very difficult to predict. These structures are possibly variable and dependant on the context of intra- or inter-molecular interactions. In general, short repeats in LCRs can induce structure. This could explain the observation that very short (non-perfect) rep…

REP2: A Web Server to Detect Common Tandem Repeats in Protein Sequences

2020

Ensembles of tandem repeats (TRs) in protein sequences expand rapidly to form domains well suited for interactions with proteins. For this reason, they are relatively frequent. Some TRs have known structures and therefore it is advantageous to predict their presence in a protein sequence. However, since most TRs diverge quickly, their detection by classical sequence comparison algorithms is not very accurate. Previously, we developed a method and a web server that used curated profiles and thresholds for the detection of 11 common TRs. Here we present a new web server (REP2) that allows the analysis of TRs in both individual and aligned sequences. We provide currently precomputed analyses f…

Evolution of oncolytic viruses.

2015

Owing to their replicative capacity, oncolytic viruses (OVs) can evolve under the action of natural selection. Reversion to virulence and recombination with wild-type strains may compromise OV safety, therefore requiring evolutionary risk assessment studies. On the other hand, evolution can be directed in the laboratory to create more potent and safer OVs. Previous work in the experimental evolution field provides a background for OV directed evolution, and has identified interesting exploitable features. While genetic engineering has greatly advanced the field of oncolytic virotherapy, this approach is sometimes curtailed by the complexity and diversity of virus-host interactions. Directed…

A computationally effective 3D Boundary Element Method for polycrystalline micromechanics

2015

An effective computational framework for homogenization and microcracking analysis of polycrystalline RVEs is presented. The method is based on a recently developed grain-boundary formulation for polycrystalline materials and several enhancements over the original technique are introduced to reduce the computational effort needed to model three-dimensional polycrystalline aggregates, which is highly desirable, especially in a multiscale perspective. First, a regularization scheme is used to remove pathological entities, usually responsible for unduly large mesh refinements, from Voronoi polycrystalline morphologies. Second, an improved meshing strategy is used, with an aim towards meshing r…

Defining new morphokinetic variables for embryo selection by time-lapse

2012

Groupware Support for Requirements Management in New Product Development

2005

Large high-technology companies operate in fiercely competitive international markets. To succeed, they need to shorten the cycle time of new product development (NPD) while improving product quality and maintaining or reducing the total resources required. Their abilities to meet these business goals depend on how extensively and effectively they collect, analyze, and utilize requirements in their product development. Creating and sharing such knowledge is complicated partly because the NPD activities of large companies are geographically distributed. Groupware technologies allow knowledge to be created and shared more effectively. Thus, they hold considerable potential as means of meeting…

Well-Balanced Adaptive Mesh Refinement for shallow water flows

2014

Well-balanced shock capturing (WBSC) schemes constitute nowadays the state of the art in the numerical simulation of shallow water flows. They allow to accurately represent discontinuous behavior, known to occur due to the non-linear hyperbolic nature of the shallow water system, and, at the same time, numerically maintain stationary solutions. In situations of practical interest, these schemes often need to be combined with some kind of adaptivity, in order to speed up computing times. In this paper we discuss what ingredients need to be modified in a block-structured AMR technique in order to ensure that, when combined with a WBSC scheme, the so-called 'water at rest' stationary solutions…

Precision Physics in Penning Traps Using the Continuous Stern-Gerlach Effect

2021

Abstract“A single atomic particle forever floating at rest in free space” (H. Dehmelt) would be the ideal object for precision measurements of atomic properties and for tests of fundamental theories. Such an ideal, of course, can ultimately never be achieved. A very close approximation to this ideal is made possible by ion traps, where electromagnetic forces are used to confine charged particles under well-controlled conditions for practically unlimited time. Concurrently, sensitive detection methods have been developed to allow observation of single stored ions. Various cooling methods can be employed to bring the trapped ion nearly to rest. Among different realisations of ion traps we con…

Frequency-Sliding Generalized Cross-Correlation: A Sub-Band Time Delay Estimation Approach

2020

The generalized cross correlation (GCC) is regarded as the most popular approach for estimating the time difference of arrival (TDOA) between the signals received at two sensors. Time delay estimates are obtained by maximizing the GCC output, where the direct-path delay is usually observed as a prominent peak. Moreover, GCCs play also an important role in steered response power (SRP) localization algorithms, where the SRP functional can be written as an accumulation of the GCCs computed from multiple sensor pairs. Unfortunately, the accuracy of TDOA estimates is affected by multiple factors, including noise, reverberation and signal bandwidth. In this paper, a sub-band approach for time del…