Search results for "Quantitative Biology"
showing 10 items of 1025 documents
Conformational studies of bottle-brush polymers absorbed on a flat solid surface.
2010
The adsorption of a bottle-brush polymer end-grafted with one chain end of its backbone to a flat substrate surface is studied by Monte Carlo simulation of a coarse-grained model, that previously has been characterized in the bulk, assuming a dilute solution under good solvent conditions. Applying the bond fluctuation model on the simple cubic lattice, we vary the backbone chain length $N_b$ from $N_b=67$ to $N_b = 259$ effective monomeric units, the side chain length $N$ from N=6 to N=48, and the grafting density $\sigma=1$, i.e., parameters that correspond well to the experimentally accessible range. When the adsorption energy strength $\epsilon$ is varied, we find that the adsorption tra…
Monte Carlo methods for polymer chains in two - dimensional geometries (polymers at surfaces and interfaces)
1993
Coarse-grained models of polymers at interfaces can be defined such that their treatment by Monte Carlo simulation is most convenient and efficient for the problem at hand. This simulation strategy is briefly illustrated with three examples: (1) The orientational ordering of rigid rod-like polymers grafted to a surface, where “table methods” can be used, applying a fine discretization of the angles describing rod orientation. (2) Surface enrichment of one species in a polymer blend is treated by a semi-grand-canonical technique. (3) The number of configurations and structure of a star polymer attached with its center to a wall is studied by a “growth technique” generalizing simple sampling …
Chain linear dimensions in the surface-enriched layer of polymer mixtures
1992
We calculate the mean-square end-to-end distances and mean-square gyration radii using the bond fluctuation model for a binary polymer blend in the presence of a wall by Monte Carlo simulation. In the bulk, the size of the minority, low-concentration polymer species is compressed compared to the majority one. In the vicinity of the wall, where the minority polymer concentration is enriched due to attraction from the wall, the dimensions of the two types of polymers are approximately equal and are essentially the same as in an athermal polymer melt. Thus, the geometric constraint is more important to the structure of the polymers than the polymer-polymer and polymer-wall interactions.
Dynamics of macromolecules grafted in spherical brushes under good solvent conditions
2013
Spherical polymer brushes have a structure intermediate between star polymers and polymer brushes on flat substrates, and are important building blocks of polymer nanoparticles. Molecular dynamics simulations are presented for isolated spherical polymer brushes under good solvent conditions, varying the grafting density as well as the chain length, using a coarse-grained bead-spring model of flexible chains. We complement previous work on the static properties of the same model by analyzing the chain dynamics, studying the motions of monomers in relation to their position along the grafted chains, and extract suitable relaxation times. A qualitative discussion in terms of the Rouse model is…
Sorting of Enhanced Reference Raman Spectra of a Single Amino Acid Molecule
2014
In this contribution, we report the identification of the principal reference Raman spectra of a single cystein molecule. To that purpose, we design an active Surface Enhanced Raman Spectroscopy (SERS) template based on surfactant-less Chebyshev nanoparticles operating in a microfluidic platform. A principal component analysis is obtained from fluctuating spectra to sort the reference spectra of cystein. The assignment of Raman bands brings new insight into the conformation of an amino acid adsorbed onto gold nanoparticle.
Cyclobutane Pyrimidine Photodimerization of DNA/RNA Nucleobases in the Triplet State
2010
The photoinduced formation of cyclobutane pyrimidine dimers in the triplet excited state of the DNA/RNA pyrimidine nucleobases pairs has been studied at the CASPT2 level of theory. A stepwise mechanism through the triplet state of the homodimer is proposed for the pairs of nucleobases cytosine, thymine, and uracil involving a singlet−triplet crossing intermediary structure of biradical character representing the most favorable triplet state conformation of the nucleobases as found in the DNA environment. The efficiency of the mechanism will be modulated by two factors: the effectiveness of the triplet−triplet energy transfer process from a donor photosensitizer molecule, which relates to th…
Crystal structure of 2-{[1-(2-methyl-5-nitro-1H-imidazol-1-yl)propan-2-yloxy]carbonyl}benzoic acid
2014
In the title compound, C15H15N3O6, the dihedral angle between the planes of the benzene and imidazole rings is 34.93 (10)°. An intramolecular C—H...O hydrogen bond is observed. In the crystal, O—H...N hydrogen bonds link the molecules into chains parallel to thecaxis.
Crystal structure of 3-mesityl-1-[(pyridin-2-yl)methyl]-3,4,5,6-tetrahydropyrimidin-1-ium bromide monohydrate
2015
In the title hydrated salt, C19H24N3+·Br−·H2O, the values of the N—C bond lengths within the tetrahydropyrimidinium ring indicate delocalization of the N=C double bond. In the cation, the dihedral angle formed by the pyridine and benzene rings is 14.97 (12)°. In the crystal, ions and water molecules are linked by O—H...Br, O—H...N, C—H...Br and C—H...O hydrogen bonds into chains running parallel to thebaxis.
Crystal structure and computational study of 3,4-dihydroxy-3-hydroxymethyl-9-methyl-6-methylidene-3a, 4,5,6,6a, 9,9a, 9b-octahydroazuleno[4,5-b]furan…
2015
WOS: 000370762300147
Intramolecular 1,5-S...N σ-hole interaction in (E)-N′-(pyridin-4-ylmethylidene)thiophene-2-carbohydrazide
2020
The hydrazide-hydrazone forms inverse dimers via hydrogen bonding, but its conformation is defined by the presence of an intramolecular chalcogen bond. Electrostatic forces dominate in the crystal packing and give rise to a layered supramolecular structure.