Search results for "Models"
showing 10 items of 8211 documents
A nanodosimetric model of radiation-induced clustered DNA damage yields
2010
International audience; We present a nanodosimetric model for predicting the yield of double strand breaks (DSBs) and non-DSB clustered damages induced in irradiated DNA. The model uses experimental ionization cluster size distributions measured in a gas model by an ion counting nanodosimeter or, alternatively, distributions simulated by a Monte Carlo track structure code developed to simulate the nanodosimeter. The model is based on a straightforward combinatorial approach translating ionizations, as measured or simulated in a sensitive gas volume, to lesions in a DNA segment of one-two helical turns considered equivalent to the sensitive volume of the nanodosimeter. The two model paramete…
Structure and Matrix Isolation Infrared Spectrum of Formyl Fluoride Dimer: Blue-Shift of the C−H Stretching Frequency
2006
Infrared spectroscopy (IR) of formyl fluoride (HCOF) dimer is studied in low-temperature argon and krypton matrixes. New IR absorptions, ca. 17 cm(-1) blue shifted from the monomer C-H stretching fundamental, are assigned to the HCOF dimer. The MP2/6-311++G calculations were utilized to define structures and harmonic frequencies of various HCOF dimers. Among the four optimized structures, the dimer having two C-H...O hydrogen bonds possesses strongest intermolecular bonding. The calculated harmonic frequencies of this dimer structure are shifted from the monomer similarly as observed in the experiment. Thus, we suggest that the experimentally observed blue shifted C-H bands belong to the di…
Conformational Changes of a Single Semiflexible Macromolecule Near an Adsorbing Surface: A Monte Carlo Simulation
2009
The properties of a single semiflexible chain tethered to a planar surface with a long-ranged attractive potential are studied by means of Monte Carlo simulations. We employ the bond fluctuation lattice model and the Wang-Landau sampling technique. We present the diagram of states for semiflexible chains consisting of N = 64 and 128 monomer units as a function of temperature T and strength of the adsorption potential, epsilon(w), and also compare this with the diagram of states for flexible chains of these two lengths. The diagram of states consists of the regions of a coil, liquid globule, solid isotropic globule, adsorbed coil, and quasi-two-dimensional solid globule with nematic bond ord…
A Three-State Model for the Photophysics of Adenine
2006
An ab initio theoretical study at the CASPT2 level is reported on minimum energy reaction paths, state minima, transition states, reaction barriers, and conical intersections on the potential energy hypersurfaces of two tautomers of adenine: 9H- and 7H-adenine. The obtained results led to a complete interpretation of the photophysics of adenine and derivatives, both under jet-cooled conditions and in solution, within a three-state model. The ultrafast subpicosecond fluorescence decay measured in adenine is attributed to the low-lying conical intersection (gs/pipi* La)(CI), reached from the initially populated 1(pipi* La) state along a path which is found to be barrierless only in 9H-adenine…
Unified model for the ultrafast decay of pyrimidine nucleobases.
2006
Ultrafast decay processes detected after absorption of UV radiation in gas-phase pyrimidine nucleobases uracil, thymine, and cytosine are ascribed to the barrierless character of the pathway along the low-lying 1(pipi*) hypersurface connecting the Franck-Condon region with an out-of-plane distorted ethene-like conical intersection with the ground state. Longer lifetime decays and low quantum yield emission are on the other hand related to the presence of a 1(pipi*) state planar minimum on the S1 surface and the barriers to access other conical intersections. A unified model for the three systems is established on the basis of accurate multiconfigurational CASPT2 calculations, whereas the ef…
Statistical identification with hidden Markov models of large order splitting strategies in an equity market
2010
Large trades in a financial market are usually split into smaller parts and traded incrementally over extended periods of time. We address these large trades as hidden orders. In order to identify and characterize hidden orders we fit hidden Markov models to the time series of the sign of the tick by tick inventory variation of market members of the Spanish Stock Exchange. Our methodology probabilistically detects trading sequences, which are characterized by a net majority of buy or sell transactions. We interpret these patches of sequential buying or selling transactions as proxies of the traded hidden orders. We find that the time, volume and number of transactions size distributions of …
Comparing in vivo data and in silico predictions for acute effects assessment of biocidal active substances and metabolites for aquatic organisms.
2020
Abstract The purpose of this study was to determine the acute toxicity in aquatic organisms of one biocidal active substance and six metabolites derived from biocidal active substances and to assess the suitability of available QSAR models to predict the obtained values. We have reported the acute toxicity in sewage treatment plant (STP) microorganisms, in the freshwater microalgae Pseudokirchneriella subcapitata and in Daphnia magna following OECD test methods. We have also identified in silico models for acute toxicity of these trophic levels currently available in widely recognized platforms such as VEGA and the OECD QSAR ToolBox. A total of six, four and two models have been selected fo…
Biopartitioning micellar chromatoraphy to predict blood to lung, blood to liver, blood to fat and blood to skin partition coefficients of drugs
2009
[EN] Biopartitioning micellar chromatography (BMC), a mode of micellar liquid chromatography that uses micellar mobile phases of Brij35 in adequate experimental conditions, has demonstrated to be useful in mimicking the drug partitioning process into biological systems. In this paper, the usefulness of BMC for predicting the partition coefficients from blood to lung, blood to liver. blood to fat and blood to skin is demonstrated. PLS2 and multiple linear regression (MLR) models based on BMC retention data are proposed and compared with other ones reported in bibliography. The proposed models present better or similar descriptive and predictive capability. (C) 2008 Elsevier B.V. All rights r…
Quantitative structure-activity relationships for the toxicity of organophosphorus and carbamate pesticides to the Rainbow trout Onchorhyncus mykiss.
2006
This study has investigated the development of quantitative structure-activity relationships (QSARs) for the toxicity to rainbow trout Onchorhyncus mykiss Walbaum of 75 organophosphorus and carbamate pesticides. The toxicity data were obtained from an openly available toxicological database and were selected to be representative of a single endpoint. A large number of physicochemical and structural descriptors were calculated for the pesticides. QSAR models were developed using multiple linear regression and partial least-squares analyses. Following the removal of a small number of outliers, predictive QSARs were developed on small numbers of mechanistically relevant descriptors. Applying m…
Use of Catalyst in a 3D-QSAR Study of the Interactions between Flavor Compounds and β-Lactoglobulin
2003
This paper reports a 3D-QSAR study using Catalyst software to explain the nature of interactions between flavor compounds and beta-lactoglobulin. A set of 35 compounds, for which dissociation constants were previously determined by affinity chromatography, was chosen. The set was divided into three subsets. An automated hypothesis generation, using HypoGen software, produced a model that made a valuable estimation of affinity and provided an explanation for the lack of correlation previously observed between the hydrophobicity of terpenes and the affinity for the protein. On the basis of these results, it appears that aroma binding to beta-lactoglobulin is caused by both hydrophobic interac…