Search results for "Biomolecule"
showing 10 items of 666 documents
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…
Monte Carlo simulation of DNA electrophoresis
1989
This paper describes an attempt to study the electrophoresis mobility of a DNA molecule in a gel by means of a Monte Carlo simulation. We find that the electrophoresis mobility mu can be well described by the empirical equation mu v kappa 1/N + kappa 2E2 with N being the number of monomers of the model chain and E being the applied field. For small E the data can merge into the linear response result mu = kappa 1/N. The paper also discusses necessary extensions of the present approach.
Electrophoresis of colloidal dispersions in the low-salt regime
2007
We study the electrophoretic mobility of spherical charged colloids in a low-salt suspension as a function of the colloidal concentration. Using an effective particle charge and a reduced screening parameter, we map the data for systems with different particle charges and sizes, including numerical simulation data with full electrostatics and hydrodynamics and experimental data for latex dispersions, on a single master curve. We observe two different volume fraction-dependent regimes for the electrophoretic mobility that can be explained in terms of the static properties of the ionic double layer.
Free Energy, Enthalpy and Entropy from Implicit Solvent End-Point Simulations
2018
Free energy is the key quantity to describe the thermodynamics of biological systems. In this perspective we consider the calculation of free energy, enthalpy and entropy from end-point molecular dynamics simulations. Since the enthalpy may be calculated as the ensemble average over equilibrated simulation snapshots the difficulties related to free energy calculation are ultimately related to the calculation of the entropy of the system and in particular of the solvent entropy. In the last two decades implicit solvent models have been used to circumvent the problem and to take into account solvent entropy implicitly in the solvation terms. More recently outstanding advancement in both impli…