Search results for "Biomolecules"
showing 10 items of 549 documents
Ab initio determination of the ionization potentials of DNA and RNA nucleobases
2006
Quantum chemical high level ab initio coupled-cluster and multiconfigurational perturbation methods have been used to compute vertical and adiabatic ionization potentials of the five canonical DNA and RNA nucleobases: uracil, thymine, cytosine, adenine, and guanine. Several states of their cations have been also calculated. The present results represent a systematic compendium of these magnitudes, establishing theoretical reference values at a level not reported before, calibrating computational strategies, and guiding the assignment of the features in the experimental photoelectron spectra. Daniel.Roca@uv.es Mercedes.Rubio@uv.es Manuela.Merchan@uv.es Luis.Serrano@uv.es
On the application of an experimental multipolar pseudo-atom library for accurate refinement of small-molecule and protein crystal structures
2007
International audience; With an increasing number of biomacromolecular crystal structures being measured to ultra-high resolution, it has become possible to extend to large systems experimental charge-density methods that are usually applied to small molecules. A library has been built of average multipole populations describing the electron density of chemical groups in all 20 amino acids found in proteins. The library uses the Hansen & Coppens multipolar pseudo-atom model to derive molecular electron density and electrostatic potential distributions. The library values are obtained from several small peptide or amino acid crystal structures refined against ultra-high-resolution X-ray diff…
On n–Fold Blocking Sets
1986
An n-fold blocking set is a set of n-disjoint blocking sets. We shall prove upper and lower bounds for the number of components in an n-fold blocking set in projective and affine spaces.
Three cyclic branched covers suffice to determine hyperbolic knots.
2005
Let n > m > 2 be two fixed coprime integers. We prove that two Conway reducible, hyperbolic knots sharing the 2-fold, m-fold and n-fold cyclic branched covers are equivalent. Using previous results by Zimmermann we prove that this implies that a hyperbolic knot is determined by any three of its cyclic branched covers.
Theory of tailor automata
2019
Abstract In the paper, a fragment of the new theory of tailor automata is presented, within which a deterministic finite automaton was defined. The proposed automaton provides a theoretical model of an informally characterized biomolecular automaton. The idea of working of which is founded on the concept of alternating cut of some double-stranded fragments of DNA, with the use of a restriction enzyme and ligations of some double-stranded fragments of DNA, with the use of the ligase enzyme.
Tilted phases of fatty acid monolayers
1995
X‐ray diffraction data from water‐supported monolayers of fatty acids with chain lengths from 19 to 22 is presented. The structures of the tilted mesophases L2’, L2, and Ov are characterized in detail. The contributions to the unit cell distortion from the tilt and the ordering of the backbone planes of the molecules are separated. It is shown that at the swiveling transition L2’–L2, not only the tilt azimuth but also the packing of the backbone planes change discontinuously. We demonstrate that the tilting transition LS–L2 is accompanied by the ordering of the backbone planes and may be discontinuous. Evidence is presented for a herringbone ordering transition within the L2 region. The dis…
Molecular dynamics simulation of single DNA stretching reveals a novel structure
2005
Abstract MD simulation, to closely mimic a torsionally unconstrained single-molecule stretching experiment of dsDNA, uncovers three distinct force regimes, characterized by fast and slow elongation regions with a transition regime in between, where the α and γ backbone torsion angles of the elongated double-stranded DNA find rapidly new stationary values. In the slow elongation regime DNA gradually looses its twist, collectively breaks all base-pair H-bonds and develops a remarkable base-stacked structure with the bases strongly tilted, forming a zipper-like stack on the major groove side, stabilized by the narrowing distance between the elongated strands, and by specific water interactions.
Molecular origin and hydration dependence of protein anharmonicity: an elastic neutron scattering study.
2010
Two main onsets of anharmonicity are present in protein dynamics. Neutron scattering on protein hydrated powders revealed a first onset at about 150 K and a second one at about 230 K (the so called dynamical transition). In order to assess the molecular origin of protein anharmonicity, we study different homomeric polypeptides by incoherent elastic neutron scattering, thus disentangling the contribution of different molecular groups in proteins. We show that methyl group rotations are the main contributors to the low temperature onset. Concerning the dynamical transition, we show that it also occurs in absence of side chains; however, the presence and mobility of side chains substantially i…
Oxygen K-shell spectroscopy of isolated progressively solvated peptide
2020
Gas-phase near-edge X-ray-absorption fine structure (NEXAFS) action spectroscopy around the oxygen K-edge and mass spectrometry were employed to probe isolated substance P (SP) molecular ions, both bare and progressively solvated with 4 and 11 water molecules. Detailed mass spectra of bare and hydrated precursors are presented for the resonant photon energy of 532 eV that corresponds to O1s --> pi(amide)* core excitation, triggering resonant Auger decay and fragmentation from the ionized radical molecular system. The fragmentation pattern of doubly protonated SP hydrated with 4 water molecules clearly shows a series of abundant doubly charged backbone fragments, as well as triply charged pr…
Carbon nanotubes as electrodes for dielectrophoresis of DNA
2006
Dielectrophoresis can potentially be used as an efficient trapping tool in the fabrication of molecular devices. For nanoscale objects, however, the Brownian motion poses a challenge. We show that the use of carbon nanotube electrodes makes it possible to apply relatively low trapping voltages and still achieve high enough field gradients for trapping nanoscale objects, e.g., single molecules. We compare the efficiency and other characteristics of dielectrophoresis between carbon nanotube electrodes and lithographically fabricated metallic electrodes, in the case of trapping nanoscale DNA molecules. The results are analyzed using finite element method simulations and reveal information abou…