Search results for "soft"
showing 10 items of 9809 documents
Global stability of protein folding from an empirical free energy function
2013
The principles governing protein folding stand as one of the biggest challenges of Biophysics. Modeling the global stability of proteins and predicting their tertiary structure are hard tasks, due in part to the variety and large number of forces involved and the difficulties to describe them with sufficient accuracy. We have developed a fast, physics-based empirical potential, intended to be used in global structure prediction methods. This model considers four main contributions: Two entropic factors, the hydrophobic effect and configurational entropy, and two terms resulting from a decomposition of close-packing interactions, namely the balance of the dispersive interactions of folded an…
Quantum simulation of quantum relativistic diffusion via quantum walks
2019
Two models are first presented, of one-dimensional discrete-time quantum walk (DTQW) with temporal noise on the internal degree of freedom (i.e., the coin): (i) a model with both a coin-flip and a phase-flip channel, and (ii) a model with random coin unitaries. It is then shown that both these models admit a common limit in the spacetime continuum, namely, a Lindblad equation with Dirac-fermion Hamiltonian part and, as Lindblad jumps, a chirality flip and a chirality-dependent phase flip, which are two of the three standard error channels for a two-level quantum system. This, as one may call it, Dirac Lindblad equation, provides a model of quantum relativistic spatial diffusion, which is ev…
Scattering studies of large scale structures at the ultra small angle neutron scattering instrument S18
2002
Abstract In recent years ultra small angle neutron scattering (USANS) has developed into a powerful standard method for large scale structure investigations. The upgraded instrument S18 at the ILL's 58 MW high flux reactor is operated routinely with increasing beam time demand. The performance of the instrument and its abilities will be discussed in this paper. A peak to background ratio better than 10 5 is reached using Agamalian's tail reduction method. A q -range from 2.10 −5 up to 5.10 −2 A −1 can be covered. This allows a clear overlap with standard pinhole SANS instruments. The new way collecting scattering data logarithmically equidistant in q -space saves measuring time. This allows…
Powerful short-cuts for multiple testing procedures with special reference to gatekeeping strategies.
2007
In this paper we present a general testing principle for a class of multiple testing problems based on weighted hypotheses. Under moderate conditions, this principle leads to powerful consonant multiple testing procedures. Furthermore, short-cut versions can be derived, which simplify substantially the implementation and interpretation of the related test procedures. It is shown that many well-known multiple test procedures turn out to be special cases of this general principle. Important examples include gatekeeping procedures, which are often applied in clinical trials when primary and secondary objectives are investigated, and multiple test procedures based on hypotheses which are comple…
Using R via PHP for Teaching Purposes: R-php
2006
This paper deals with the R-php statistical software, that is an environment for statistical analysis, freely accessible and attainable through the World Wide Web, based on R. Indeed, this software uses, as "engine" for statistical analyses, R via PHP and its design has been inspired by a paper of de Leeuw (1997). R-php is based on two modules: a base module and a point-and-click module. R-php base allows the simple editing of R code in a form. R-php point-and-click allows some statistical analyses by means of a graphical user interface (GUI): then, to use this module it is not necessary for the user to know the R environment, but all the allowed analyses can be performed by using the compu…
Iterative Cluster Analysis of Protein Interaction Data
2004
Abstract Motivation: Generation of fast tools of hierarchical clustering to be applied when distances among elements of a set are constrained, causing frequent distance ties, as happens in protein interaction data. Results: We present in this work the program UVCLUSTER, that iteratively explores distance datasets using hierarchical clustering. Once the user selects a group of proteins, UVCLUSTER converts the set of primary distances among them (i.e. the minimum number of steps, or interactions, required to connect two proteins) into secondary distances that measure the strength of the connection between each pair of proteins when the interactions for all the proteins in the group are consid…
Testing with a nuisance parameter present only under the alternative: a score-based approach with application to segmented modelling
2016
ABSTRACTWe introduce a score-type statistic to test for a non-zero regression coefficient when the relevant term involves a nuisance parameter present only under the alternative. Despite the non-regularity and complexity of the problem and unlike the previous approaches, the proposed test statistic does not require the nuisance to be estimated. It is simple to implement by relying on the conventional distributions, such as Normal or t, and it justified in the setting of probabilistic coherence. We focus on testing for the existence of a breakpoint in segmented regression, and illustrate the methodology with an analysis on data of DNA copy number aberrations and gene expression profiles from…
A web application for the unspecific detection of differentially expressed DNA regions in strand-specific expression data
2015
Abstract Genomic technologies allow laboratories to produce large-scale data sets, either through the use of next-generation sequencing or microarray platforms. To explore these data sets and obtain maximum value from the data, researchers view their results alongside all the known features of a given reference genome. To study transcriptional changes that occur under a given condition, researchers search for regions of the genome that are differentially expressed between different experimental conditions. In order to identify these regions several algorithms have been developed over the years, along with some bioinformatic platforms that enable their use. However, currently available appli…
Multiple sequence editing by spreadsheet.
1990
Spreadsheets have several functions and facilities that make them good candidates to be used as multiple sequence editors. They can be easily programmed (even by non-programmers) with macros that allow them to fit the needs of the user, free of the restrictions that programs written by other people have. Here I present a sheet containing a set of macros written for Lotus 1-2-3
The Power of Word-Frequency Based Alignment-Free Functions: a Comprehensive Large-Scale Experimental Analysis
2021
Abstract Motivation Alignment-free (AF) distance/similarity functions are a key tool for sequence analysis. Experimental studies on real datasets abound and, to some extent, there are also studies regarding their control of false positive rate (Type I error). However, assessment of their power, i.e. their ability to identify true similarity, has been limited to some members of the D2 family. The corresponding experimental studies have concentrated on short sequences, a scenario no longer adequate for current applications, where sequence lengths may vary considerably. Such a State of the Art is methodologically problematic, since information regarding a key feature such as power is either mi…