Search results for "Quantitative Biology"
showing 10 items of 1025 documents
Artificial Neural Networks and Linear Discriminant Analysis: A Valuable Combination in the Selection of New Antibacterial Compounds
2004
A set of topological descriptors has been used to discriminate between antibacterial and nonantibacterial drugs. Topological descriptors are simple integers calculated from the molecular structure represented in SMILES format. The methods used for antibacterial activity discrimination were linear discriminant analysis (LDA) and artificial neural networks of a multilayer perceptron (MLP) type. The following plot frequency distribution diagrams were used: a function of the number of drugs within a value interval of the discriminant function and the output value of the neural network versus these values. Pharmacological distribution diagrams (PDD) were used as a visualizing technique for the i…
The INTEGRAL view of the pulsating hard X-ray sky: from accreting and transitional millisecond pulsars to rotation-powered pulsars and magnetars
2020
arXiv:2012.01346v1
Calculation of phase diagrams not requiring the derivatives of the Gibbs energy demonstrated for a mixture of two homopolymers with the corresponding…
1995
A method is presented which allows the calculation of phase diagrams (spinodal, binodal and tie lines) on the basis of the Gibbs energy of mixing ΔG. No derivatives of ΔG with respect to the composition variables are required. This method is particularly useful in cases where the composition dependence of ΔG is very complex and no analytical representation of the derivatives can be given. The method is applied to a ternary mixture of two homopolymers with a copolymer consisting of the same monomers. The sequence distribution of the copolymer is kept constant between random and purely alternating, and phase diagrams are calculated for different chemical compositions of the copolymer. The com…
Thermodynamics of a polymer blend solution system studied by gel permeation chromatography and viscosity
1999
Binary and ternary interaction parameters and their derivatives have been calculated with the Flory-Huggins formalism developed for a ternary polymer system. The equilibrium compositions of the ternary system tetrahydrofuran/polybutadiene/polystyrene that forms two phases in equilibrium at 25°C have been used to solve the binodal equations. With this set of parameters, the viscosimetric interaction parameters have been computed. For the sake of comparison, the experimental viscosimetric parameter has been determined from intrinsic viscosity data of a polymer (3) in a "binary solvent" (solvent + polymer (2)). It has been clearly shown that composition-dependent parameters are necessary to re…
Polymer Incompatibility Caused by Different Molecular Architectures: Modeling via Chain Connectivity and Conformational Relaxation
2009
The calculation of phase diagrams for blends of linear and branched polymers made up of identical monomeric units is modeled using an approach that subdivides the mixing process into two steps: i) contact formation between the different components, keeping their chain conformations and the volume of the system constant; and, ii) relaxation of the macromolecules into their equilibrium state by molecular rearrangements. It is assumed that step (ii) causes shape-induced polymer incompatibility and that the degree of branching can be quantified in terms of the volumes the isolated coils of the branched polymer occupy in relation to the volume the linear product with the same molecular weight oc…
Ultrafast myoglobin structural dynamics observed with an X-ray free-electron laser.
2014
Light absorption can trigger biologically relevant protein conformational changes. The light-induced structural rearrangement at the level of a photoexcited chromophore is known to occur in the femtosecond timescale and is expected to propagate through the protein as a quake-like intramolecular motion. Here we report direct experimental evidence of such ‘proteinquake’ observed in myoglobin through femtosecond X-ray solution scattering measurements performed at the Linac Coherent Light Source X-ray free-electron laser. An ultrafast increase of myoglobin radius of gyration occurs within 1 picosecond and is followed by a delayed protein expansion. As the system approaches equilibrium it underg…
Anergy in self-directed B lymphocytes from a statistical mechanics perspective
2012
The ability of the adaptive immune system to discriminate between self and non-self mainly stems from the ontogenic clonal-deletion of lymphocytes expressing strong binding affinity with self-peptides. However, some self-directed lymphocytes may evade selection and still be harmless due to a mechanism called clonal anergy. As for B lymphocytes, two major explanations for anergy developed over three decades: according to "Varela theory", it stems from a proper orchestration of the whole B-repertoire, in such a way that self-reactive clones, due to intensive interactions and feed-back from other clones, display more inertia to mount a response. On the other hand, according to the `two-signal …
Transient frailty induced by cell division. Observation, reasons and implications
2021
We know that stress-factors, e.g. X-rays, have an effect on cells that is more lethal in rapid exponential growth than in stationary phase. It is this effect which makes radiotherapy effective in cancer treatment. This stress effect can be explained in two ways: (a) more vulnerability in the growth phase, (b) improved protection capacity and repair mechanisms in the stationary phase. Although the two explanations do not exclude each other, they are very different in the sense that (a) is a general mechanism whereas (b) is strain and stress-factor dependent. In this paper we explore major facets of (a). Firstly, we emphasize that (a) can account for known experimental stress-factor evidence.…
Is there an infant mortality in bacteria?
2021
This manuscript proposes a significant step in our long-run investigation of infant mortality across species. Since 2016 (Berrut et al. 2016) a succession of studies (Bois et al. 2019) have traced infant mortality from organisms of high complexity (e.g. mammals) down to unicellular organisms. Infant mortality may be considered as a filtering process through which organisms with potentially lethal congenital defects are eliminated. Such defects may have many causes but here we focus particularly on mishaps resulting from non-optimal conditions in the production of proteins, enzymes and other crucial macromolecules. The statistical signature of infant mortality consists in a falling age-speci…
Reproducing kernel hilbert spaces regression methods for genomic assisted prediction of quantitative traits.
2008
Abstract Reproducing kernel Hilbert spaces regression procedures for prediction of total genetic value for quantitative traits, which make use of phenotypic and genomic data simultaneously, are discussed from a theoretical perspective. It is argued that a nonparametric treatment may be needed for capturing the multiple and complex interactions potentially arising in whole-genome models, i.e., those based on thousands of single-nucleotide polymorphism (SNP) markers. After a review of reproducing kernel Hilbert spaces regression, it is shown that the statistical specification admits a standard mixed-effects linear model representation, with smoothing parameters treated as variance components.…