1,938 research outputs found
Dynamics of a bubble formed in double stranded DNA
We study the fluctuational dynamics of a tagged base-pair in double stranded
DNA. We calculate the drift force which acts on the tagged base-pair using a
potential model that describes interactions at base pairs level and use it to
construct a Fokker-Planck equation.The calculated displacement autocorrelation
function is found to be in very good agreement with the experimental result of
Altan-Bonnet {\it et. al.} Phys. Rev. Lett. {\bf 90}, 138101 (2003) over the
entire time range of measurement. We calculate the most probable displacements
which predominately contribute to the autocorrelation function and the
half-time history of these displacements.Comment: 11 pages, 4 figures. submitted to Phys. Rev. Let
DNA nanotweezers studied with a coarse-grained model of DNA
We introduce a coarse-grained rigid nucleotide model of DNA that reproduces
the basic thermodynamics of short strands: duplex hybridization,
single-stranded stacking and hairpin formation, and also captures the essential
structural properties of DNA: the helical pitch, persistence length and
torsional stiffness of double-stranded molecules, as well as the comparative
flexibility of unstacked single strands. We apply the model to calculate the
detailed free-energy landscape of one full cycle of DNA 'tweezers', a simple
machine driven by hybridization and strand displacement.Comment: 4 pages, 5 figure
Temperature-dependent poroelastic and viscoelastic effects on microscale—modelling of seismic reflections in heavy oil reservoirs
We develop a new model for elastic properties of rocks saturated with heavy oil. The heavy oil is represented by a viscoelastic material, which at low frequencies and/or high temperatures behaves as a Newtonian fluid, and at high frequencies and/or low temperatures as a nearly elastic solid. The bulk and shear moduli of a porous rock saturated with such viscoelastic material are then computed using approximate extended Gassmann equations of Ciz and Shapiro by replacing the elastic moduli of the pore filling material with complex and frequency-dependent moduli of the viscoelastic pore fill. We test the proposed model by comparing its predictions with numerical simulations based on a direct finite-difference solution of equations of dynamic viscoelasticity. The simulations are performed for the reflection coefficient from an interface between a homogeneous fluid and a porous medium. The numerical tests are performed both for an idealized porous medium consisting of alternating solid and viscoelastic layers, and for a more realistic 3-D geometry of the pore space. Both sets of numerical tests show a good agreement between the predictions of the proposed viscoelastic workflow and numerical simulations for relatively high viscosities where viscoelastic effects are important. The results confirm that application of extended Gassmann equations in conjunction with the complex and frequency-dependent moduli of viscoelastic pore filling material, such as heavy oil, provides a good approximation for the elastic moduli of rocks saturated with such material. By construction, this approximation is exactly consistent with the classical Gassmann's equation for sufficiently low frequencies or high temperature when heavy oil behaves like a fluid. For higher frequencies and/or lower temperatures, the predictions are in good agreement with the direct numerical solution of equations of dynamic viscoelasticity on the microscale. This demonstrates that the proposed methodology provides realistic estimates of elastic properties of heavy oil rock
Self-assembled guanine ribbons as wide-bandgap semiconductors
We present a first principle study about the stability and the electronic
properties of a new biomolecular solid-state material, obtained by the
self-assembling of guanine (G) molecules. We consider hydrogen-bonded planar
ribbons in isolated and stacked configurations. These aggregates present
electronic properties similar to inorganic wide-bandgap semiconductors. The
formation of Bloch-type orbitals is observed along the stacking direction,
while it is negligible in the ribbon plane. Global band-like conduction may be
affected by a dipole-field which spontaneously arises along the ribbon axis.
Our results indicate that G-ribbon assemblies are promising materials for
biomolecular nanodevices, consistently with recent experimental results.Comment: 7 pages, 3 figures, to be published in Physica
Competition for hydrogen bond formation in the helix-coil transition and protein folding
The problem of the helix-coil transition of biopolymers in explicit solvents,
like water, with the ability for hydrogen bonding with solvent is addressed
analytically using a suitably modified version of the Generalized Model of
Polypeptide Chains. Besides the regular helix-coil transition, an additional
coil-helix or reentrant transition is also found at lower temperatures. The
reentrant transition arises due to competition between polymer-polymer and
polymer-water hydrogen bonds. The balance between the two types of hydrogen
bonding can be shifted to either direction through changes not only in
temperature, but also by pressure, mechanical force, osmotic stress or other
external influences. Both polypeptides and polynucleotides are considered
within a unified formalism. Our approach provides an explanation of the
experimental difficulty of observing the reentrant transition with pressure;
and underscores the advantage of pulling experiments for studies of DNA.
Results are discussed and compared with those reported in a number of recent
publications with which a significant level of agreement is obtained.Comment: 21 pages, 3 figures, submitted to Phys Rev
Dynamic cluster-scaling in DNA
It is shown that the nucleotide sequences in DNA molecules have
cluster-scaling properties (discovered for the first time in turbulent
processes: Sreenivasan and Bershadskii, 2006, J. Stat. Phys., 125, 1141-1153.).
These properties are relevant to both types of nucleotide pair-bases
interactions: hydrogen bonds and stacking interactions. It is shown that taking
into account the cluster-scaling properties can help to improve heterogeneous
models of the DNA dynamics. Two human genes: BRCA2 and NRXN1, have been
considered as examples
Thermomechanics of DNA
A theory for thermomechanical behavior of homogeneous DNA at thermal
equilibrium predicts critical temperatures for denaturation under torque and
stretch, phase diagrams for stable B--DNA, supercoiling, optimally stable
torque, and the overstretching transition as force-induced DNA melting.
Agreement with available single molecule manipulation experiments is excellent.Comment: 4 pages, 5 figures. Lette
Self-energy limited ion transport in sub-nanometer channels
The current-voltage characteristics of the alpha-Hemolysin protein pore
during the passage of single-stranded DNA under varying ionic strength, C, are
studied experimentally. We observe strong blockage of the current, weak
super-linear growth of the current as a function of voltage, and a minimum of
the current as a function of C. These observations are interpreted as the
result of the ion electrostatic self-energy barrier originating from the large
difference in the dielectric constants of water and the lipid bilayer. The
dependence of DNA capture rate on C also agrees with our model.Comment: more experimental material is added. 4 pages, 7 figure
Cluster-scaling, chaotic order and coherence in DNA
Different numerical mappings of the DNA sequences have been studied using a
new cluster-scaling method and the well known spectral methods. It is shown, in
particular, that the nucleotide sequences in DNA molecules have robust
cluster-scaling properties. These properties are relevant to both types of
nucleotide pair-bases interactions: hydrogen bonds and stacking interactions.
It is shown that taking into account the cluster-scaling properties can help to
improve heterogeneous models of the DNA dynamics. It is also shown that a
chaotic (deterministic) order, rather than a stochastic randomness, controls
the energy minima positions of the stacking interactions in the DNA sequences
on large scales. The chaotic order results in a large-scale chaotic coherence
between the two complimentary DNA-duplex's sequences. A competition between
this broad-band chaotic coherence and the resonance coherence produced by
genetic code has been briefly discussed. The Arabidopsis plant genome (which is
a model plant for genome analysis) and two human genes: BRCA2 and NRXN1, have
been considered as examples.Comment: extended. arXiv admin note: substantial text overlap with
arXiv:1008.135
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