Search results for "MBL"
showing 10 items of 1636 documents
Protein aggregation/crystallization and minor structural changes: universal versus specific aspects.
2007
AbstractProtein association covers wide interests in biophysics, protein science, and biotechnologies, and it is often viewed as governed by conformation details. More recently, the existence of a universal physical principle governing aggregation/crystallization processes has been suggested by a series of experiments and shown to be linked to the universal scaling properties of concentration fluctuations occurring in the proximity of a phase transition (spinodal demixing in the specific case). Such properties have provided a quantitative basis for capturing kinetic association data on a universal master curve, ruled by the normalized distance of the state of the system from its instability…
Albumin-driven disassembly of lipidic nanoparticles: the specific case of the squalene-adenosine nanodrug
2020
International audience; In the field of nanomedicine, nanostructured nanoparticles (NPs) made of self-assembling prodrugs emerged in the recent years with promising properties. In particular, squalene-based drug nanoparticles have already shown their efficiency through in vivo experiments. However, a complete pattern of their stability and interactions in the blood stream is still lacking. In this work we assess the behavior of squalene-adenosine (SQAd) nanoparticles-whose neuroprotective effect has already been demonstrated in murine models-in the presence of fetal bovine serum (FBS) and of bovine serum albumin (BSA), the main protein of blood plasma. Extensive physicochemical characteriza…
Classical Statistical Mechanics
2003
Some aspects of statistical mechanics that are particularly important for computer simulation approaches are recalled. Using Ising and classical Heisenberg models as examples, various statistical ensembles and appropriate thermodynamic potentials are introduced, and concepts such as Legendre transformations between ensembles and the thermodynamic integration method to obtain the entropy are mentioned. Probability distributions characterizing statistical fluctuations are discussed, fluctuation relations for response functions are derived, and the behavior of these quantities at first and second order phase transitions are described qualitatively. Also the general consequences of phase coexis…
Transitions between imperfectly ordered crystalline structures: A phase switch Monte Carlo study
2012
A model for two-dimensional colloids confined laterally by ``structured boundaries'' (i.e., ones that impose a periodicity along the slit) is studied by Monte Carlo simulations. When the distance $D$ between the confining walls is reduced at constant particle number from an initial value ${D}_{0}$, for which a crystalline structure commensurate with the imposed periodicity fits, to smaller values, a succession of phase transitions to imperfectly ordered structures occur. These structures have a reduced number of rows parallel to the boundaries (from $n$ to $n\ensuremath{-}1$ to $n\ensuremath{-}2$, etc.) and are accompanied by an almost periodic strain pattern, due to ``soliton staircases'' …
Statistical Properties of Statistical Ensembles of Stock Returns
1999
We select n stocks traded in the New York Stock Exchange and we form a statistical ensemble of daily stock returns for each of the k trading days of our database from the stock price time series. We analyze each ensemble of stock returns by extracting its first four central moments. We observe that these moments are fluctuating in time and are stochastic processes themselves. We characterize the statistical properties of central moments by investigating their probability density function and temporal correlation properties.
Sub-threshold signal processing in arrays of non-identical nanostructures
2011
Weak input signals are routinely processed by molecular-scaled biological networks composed of non-identical units that operate correctly in a noisy environment. In order to show that artificial nanostructures can mimic this behavior, we explore theoretically noise-assisted signal processing in arrays of metallic nanoparticles functionalized with organic ligands that act as tunneling junctions connecting the nanoparticle to the external electrodes. The electronic transfer through the nanostructure is based on the Coulomb blockade and tunneling effects. Because of the fabrication uncertainties, these nanostructures are expected to show a high variability in their physical characteristics and…
Variety and volatility in financial markets
2000
We study the price dynamics of stocks traded in a financial market by considering the statistical properties both of a single time series and of an ensemble of stocks traded simultaneously. We use the $n$ stocks traded in the New York Stock Exchange to form a statistical ensemble of daily stock returns. For each trading day of our database, we study the ensemble return distribution. We find that a typical ensemble return distribution exists in most of the trading days with the exception of crash and rally days and of the days subsequent to these extreme events. We analyze each ensemble return distribution by extracting its first two central moments. We observe that these moments are fluctua…
A Stochastic Approach to Quantum Statistics Distributions: Theoretical Derivation and Monte Carlo Modelling
2009
Abstract. We present a method aimed at a stochastic derivation of the equilibrium distribution of a classical/quantum ideal gas in the framework of the canonical ensemble. The time evolution of these ideal systems is modelled as a series of transitions from one system microstate to another one and thermal equilibrium is reached via a random walk in the single-particle state space. We look at this dynamic process as a Markov chain satisfying the condition of detailed balance and propose a variant of the Monte Carlo Metropolis algorithm able to take into account indistinguishability of identical quantum particles. Simulations performed on different two-dimensional (2D) systems are revealed to…
Musket: a multistage k-mer spectrum-based error corrector for Illumina sequence data
2012
Abstract Motivation: The imperfect sequence data produced by next-generation sequencing technologies have motivated the development of a number of short-read error correctors in recent years. The majority of methods focus on the correction of substitution errors, which are the dominant error source in data produced by Illumina sequencing technology. Existing tools either score high in terms of recall or precision but not consistently high in terms of both measures. Results: In this article, we present Musket, an efficient multistage k-mer-based corrector for Illumina short-read data. We use the k-mer spectrum approach and introduce three correction techniques in a multistage workflow: two-s…
CARE: context-aware sequencing read error correction.
2020
Abstract Motivation Error correction is a fundamental pre-processing step in many Next-Generation Sequencing (NGS) pipelines, in particular for de novo genome assembly. However, existing error correction methods either suffer from high false-positive rates since they break reads into independent k-mers or do not scale efficiently to large amounts of sequencing reads and complex genomes. Results We present CARE—an alignment-based scalable error correction algorithm for Illumina data using the concept of minhashing. Minhashing allows for efficient similarity search within large sequencing read collections which enables fast computation of high-quality multiple alignments. Sequencing errors ar…