Search results for "string"
showing 10 items of 381 documents
Adaptive Finite Temperature String Method in Collective Variables.
2017
Here we present a modified version of the on-the-fly string method for the localization of the minimum free energy path in a space of arbitrary collective variables. In the proposed approach the shape of the biasing potential is controlled by only two force constants, defining the width of the potential along the string and orthogonal to it. The force constants and the distribution of the string nodes are optimized during the simulation, improving the convergence. The optimized parameters can be used for umbrella sampling with a path CV along the converged string as the reaction coordinate. We test the new method with three fundamentally different processes: chloride attack to chloromethane…
Development of a low-alcoholic fermented beverage employing cashew apple juice and non-conventional yeasts
2019
Cashew apples are by-products in the production of cashew nuts, which are mostly left to rot in the fields. Cashew apple juice (CAJ), a highly nutritious beverage, can be produced from them. It is rich in sugars and ascorbic acid, but its high polyphenol content makes it bitter and astringent, and therefore difficult to commercialize. The kingdom of fungi contains more than 2000 yeast species, of which only a few species have been studied in relation to their potential to produce aroma compounds. The aim of this research was to develop a new low-alcoholic fermented beverage to valorize cashew apples. For this purpose, a screening was carried out employing non-conventional yeast species and …
Effect of the mutual position between weld seam and reinforcement on the residual stress distribution in Friction Stir Welding of AA6082 skin and str…
2016
Abstract In the paper, a numerical and experimental study was carried out to highlight the effect of the distance d between the weld seam and the reinforcement on the residual stress distribution in Friction Stir Welded AA6082-T6 structures. An L-shaped profile was welded to a sheet metal with varying tool rotation and distance d from the weld seam. The Cut Compliance method was used to determine the resulting longitudinal residual stress. A dedicated FE model for FSW was set up, validated and utilized to predict the longitudinal residual stress in the assembled part. The analysis allowed the identification of a few design guidelines in order to reduce the detrimental effects of the residua…
2020
Limited data are available regarding strength and endurance training adaptations to occupational physical performance during deployment. This study assessed acute training-induced changes in neuromuscular (electromyography; EMG) and metabolic (blood lactate, BLa) responses during a high-intensity military simulation test (MST), performed in the beginning (PRE) and at the end (POST) of a six-month crisis-management operation. MST time shortened (145 ± 21 vs. 129 ± 16 s, −10 ± 7%, p < 0.001) during the operation. Normalized muscle activity increased from PRE to POST in the hamstring muscles by 87 ± 146% (116 ± 52 vs. 195 ± 139%EMGMVC, p < 0.001) and in the quadriceps by 54 ± 81% (26 ± 8…
Secure and Privacy Preserving Pattern Matching in Distributed Cloud-based Data Storage
2019
Given two strings: pattern $p$ of length $m$ and text $t$ of length $n$ . The string matching problem is to find all (or some) occurrences of the pattern $p$ in the text $t$ . We introduce a new simple data structure, called index arrays, and design fast privacy-preserving matching algorithm for string matching. The motivation behind introducing index arrays is determined by the need for pattern matching on distributed cloud-based datasets with semi-trusted cloud providers. It is intended to use encrypted index arrays both to improve performance and protect confidentiality and privacy of user data.
Constructing Antidictionaries of Long Texts in Output-Sensitive Space
2021
AbstractA wordxthat is absent from a wordyis calledminimalif all its proper factors occur iny. Given a collection ofkwordsy1, … ,ykover an alphabetΣ, we are asked to compute the set$\mathrm {M}^{\ell }_{\{y_1,\ldots ,y_k\}}$M{y1,…,yk}ℓof minimal absent words of length at mostℓof the collection {y1, … ,yk}. The set$\mathrm {M}^{\ell }_{\{y_1,\ldots ,y_k\}}$M{y1,…,yk}ℓcontains all the wordsxsuch thatxis absent from all the words of the collection while there existi,j, such that the maximal proper suffix ofxis a factor ofyiand the maximal proper prefix ofxis a factor ofyj. In data compression, this corresponds to computing the antidictionary ofkdocuments. In bioinformatics, it corresponds to c…
Efficient Algorithms for Sequence Analysis with Entropic Profiles
2017
Entropy, being closely related to repetitiveness and compressibility, is a widely used information-related measure to assess the degree of predictability of a sequence. Entropic profiles are based on information theory principles, and can be used to study the under-/over-representation of subwords, by also providing information about the scale of conserved DNA regions. Here, we focus on the algorithmic aspects related to entropic profiles. In particular, we propose linear time algorithms for their computation that rely on suffix-based data structures, more specifically on the truncated suffix tree (TST) and on the enhanced suffix array (ESA). We performed an extensive experimental campaign …
Deep learning network for exploiting positional information in nucleosome related sequences
2017
A nucleosome is a DNA-histone complex, wrapping about 150 pairs of double-stranded DNA. The role of nucleosomes is to pack the DNA into the nucleus of the Eukaryote cells to form the Chromatin. Nucleosome positioning genome wide play an important role in the regulation of cell type-specific gene activities. Several biological studies have shown sequence specificity of nucleosome presence, clearly underlined by the organization of precise nucleotides substrings. Taking into consideration such advances, the identification of nucleosomes on a genomic scale has been successfully performed by DNA sequence features representation and classical supervised classification methods such as Support Vec…
The colored longest common prefix array computed via sequential scans
2018
Due to the increased availability of large datasets of biological sequences, the tools for sequence comparison are now relying on efficient alignment-free approaches to a greater extent. Most of the alignment-free approaches require the computation of statistics of the sequences in the dataset. Such computations become impractical in internal memory when very large collections of long sequences are considered. In this paper, we present a new conceptual data structure, the colored longest common prefix array (cLCP), that allows to efficiently tackle several problems with an alignment-free approach. In fact, we show that such a data structure can be computed via sequential scans in semi-exter…
Lost Strings in Genomes: What Sense Do They Make?
2017
We studied the sets of avoided strings to be observed over a family of genomes. It was found that the length of the minimal avoided string rarely exceeds 9 nucleotides, with neither respect to a phylogeny of a genome under consideration. The lists of the avoided strings observed over the sets of (related) genomes have been analyzed. Very low correlation between the phylogeny, and the set of those strings has been found.