Search results for "Biomolecule"
showing 10 items of 666 documents
Feature selection on a dataset of protein families: from exploratory data analysis to statistical variable importance
2016
Proteins are characterized by several typologies of features (structural, geometrical, energy). Most of these features are expected to be similar within a protein family. We are interested to detect which features can identify proteins that belong to a family, as well as to define the boundaries among families. Some features are redundant: they could generate noise in identifying which variables are essential as a fingerprint and, consequently, if they are related or not to a function of a protein family. We defined an original approach to analyze protein features for defining their relationships and peculiarities within protein families. A multistep approach has been mainly performed in R …
Crystal structure of 1-ferrocenyl-2-(4-methyl-benzo-yl)spiro-[11H-pyrrolidizine-3,11'-indeno[1,2-b]quinoxaline].
2014
In the title compound the four-fused-rings system is approximately planar and the pyrrolidine rings of the pyrrolidizine fragment adopt a twist conformation. In the crystal, molecules are linked by C—H⋯O hydrogen bonds and C—H⋯π interactions, forming double-chains parallel to the c axis.
Crystal structure of (1S,2R,4S)-1-[(morpholin-4-yl)methyl]-4-(prop-1-en-2-yl)cyclohexane-1,2-diol
2014
Besides intramolecular O—H⋯N hydrogen bonds, the crystal structure displays intermolecular O—H⋯O and C—H⋯O hydrogen bonds linking the molecules into undulating layers parallel to the (01) plane.
Crystal structure of 5′′-(4-chlorobenzylidene)-4′-(4-chlorophenyl)-1′-methyltrispiro[acenapthylene-1,2′-pyrrolidine-3′,1′′-cyclohexane-3′′,2′′′-[1,3]…
2015
In the title compound, C36H29Cl2NO4, two spiro links connect the methyl-substituted pyrrolidine ring to the acenaphthylene and cyclohexanone rings. The cyclohexanone ring is further connected to the dioxalane ring by a third spiro junction. The five-membered ring of the acenaphthylen-1-one ring system adopts a flattened envelope conformation, with the ketonic C atom as the flap, whereas the dioxalane and pyrrolidine rings each have a twist conformation. The cyclohexenone ring assumes a boat conformation. An intramolecular C—H...O hydrogen-bond interaction is present. In the crystal, molecules are linked by non-classical C—H...O hydrogen bonds, forming chains extending parallel to theaaxis.
Singlet-Triplet States Interaction Regions in DNA/RNA Nucleobase Hypersurfaces.
2010
The present study provides new insight into the intrinsic mechanisms for the population of the triplet manifold in DNA nucleobases by determining, at the multiconfigurational CASSCF/CASPT2 level, the singlet-triplet states crossing regions and the main decay paths for their lowest singlet and triplet states after near-UV irradiation. The studied singlet-triplet interacting regions are accessible along the minimum energy path of the initially populated singlet bright (1)ππ* state. In particular, all five natural DNA/RNA nucleobases have, at the end of the main minimum energy path and near a conical intersection of the ground and (1)ππ* states, a low-energy, easily accessible, singlet-triplet…
Photostability and Photoreactivity in Biomolecules: Quantum Chemistry of Nucleic Acid Base Monomers and Dimers
2008
The great potentials of high-level ab initio methods, in particular, the CASPT2//CASSCF protocol, are fully illustrated through: (i) the study of ultrafast energy relaxation in DNA/RNA base monomers, (ii) the intrinsic population mechanism of the lowest triplet state, and (iii) how bioexcimers can be considered as precursors of charge transfer and photoinduced reactivity. In order to describe these processes properly, the presence of conical intersections (CIs) and the topology of the involved pathways have to be determined correctly. Thus, in theoretical calculations the dynamic electronic correlation has to be considered. The accessibility of the CIs (or the seam of CIs) becomes crucial t…
"Figure 5-3" of "Transverse momentum dependence of meson suppression in Au+Au collisions at sqrt(s_NN) = 200 GeV"
2021
Slope ${\eta}$ $R_{AA}$ ($5
A Monte Carlo Study of Knots in Long Double-Stranded DNA Chains.
2016
We determine knotting probabilities and typical sizes of knots in double-stranded DNA for chains of up to half a million base pairs with computer simulations of a coarse-grained bead-stick model: Single trefoil knots and composite knots which include at least one trefoil as a prime factor are shown to be common in DNA chains exceeding 250,000 base pairs, assuming physiologically relevant salt conditions. The analysis is motivated by the emergence of DNA nanopore sequencing technology, as knots are a potential cause of erroneous nucleotide reads in nanopore sequencing devices and may severely limit read lengths in the foreseeable future. Even though our coarse-grained model is only based on …
Effects of conjugated linoleic acid isomers toward lipids metabolizing enzymes in male wistar rats
2000
International audience
A combined molecular dynamics and Monte Carlo study of the approach towards phase separation in colloid-polymer mixtures.
2011
A coarse-grained model for colloid-polymer mixtures is investigated where both colloids and polymer coils are represented as point-like particles interacting with spherically symmetric effective potentials. Colloid-colloid and colloid-polymer interactions are described by Weeks-Chandler-Andersen potentials, while the polymer-polymer interaction is very soft, of strength k(B)T/2 for maximum polymer-polymer overlap. This model can be efficiently simulated both by Monte Carlo and molecular dynamics methods, and its phase diagram closely resembles that of the well-known Asakura-Oosawa model. The static and dynamic properties of the model are presented for systems at critical colloid density, va…