Related papers: Base pair fluctuations in helical models for nucle…
Although mechanical properties of DNA are well characterized at the kilo base-pair range, a number of recent experiments have suggested that DNA is more flexible at shorter length scales, which correspond to the regime that is crucial for…
The propensity of short DNA sequences to convert to the circular form is studied by a mesoscopic Hamiltonian method which incorporates both the bending of the molecule axis and the intrinsic twist of the DNA strands. The base pair…
The influence of thermal fluctuations on fermion pairing is investigated using a semiclassical treatment of fluctuations. When the average pairing gaps along with those differing by one standard deviation are used, the characteristic…
We propose a model Hamiltonian for charge transfer along the DNA double helix with temperature driven fluctuations in the base pair positions acting as the rate limiting factor for charge transfer between neighboring base pairs. We compare…
We present a method to compute pairing fluctuations on top of the Gutzwiller approximation (GA). Our investigations are based on a charge-rotational invariant GA energy functional which is expanded up to second order in the pair…
The imaginary time path integral formalism is applied to a nonlinear Hamiltonian for a short fragment of heterogeneous DNA with a stabilizing solvent interaction term. Torsional effects are modeled by a twist angle between neighboring base…
In this work the dynamics of a freely jointed random chain which fluctuates at constant temperature in some viscous medium is studied. The chain is regarded as a system of small particles which perform a brownian motion and are subjected to…
A description of mesoscopic fluctuations of the pairing gap in finite-sized quantum systems based on periodic orbit theory is presented. The size of the fluctuations are found to depend on quite general properties. We distinguish between…
Twisting DNA under a constant applied force reveals a thermally activated transition into a state with a supercoiled structure known as a plectoneme. Using transition state theory, we predict the rate of this plectoneme nucleation to be of…
Pairing fluctuations are self-consistently incorporated on the same footing as the quadrupole deformations in present state of the art calculations including particle number and angular momentum conservation as well as configuration mixing.…
ds-RNA and standard ds-DNA show specific structural differences in their di-nucleotide steps, piled along the helical axis. Modeling the helices of short fragments by a 3D mesoscopic Hamiltonian model, I use path integral techniques to…
A new decoupling scheme is developed for the Hubbard model which provides a unified description of the spin-symmetric (paramagnetic metallic and insulating) phases as well as the broken-symmetry AFI phase. Independent of magnetic ordering,…
Fluctuations of the amplitude of the order parameter govern the properties of superconducting systems close to the critical transition temperature. In the BCS regime we examine the contribution of these pairing fluctuations to the…
One-particle spectral properties in the normal phase of the two-dimensional attractive Hubbard model are investigated in the weak coupling regime using the non-selfconsistent T-matrix approximation. The corresponding equations are evaluated…
When the DNA double helix is subjected to external forces it can stretch elastically to elongations reaching 100% of its natural length. These distortions, imposed at the mesoscopic or macroscopic scales, have a dramatic effect on…
The elastic moduli of four numerical random isotropic packings of Hertzian spheres are studied. The four samples are assembled with different preparation procedures, two of which aim to reproduce experimental compaction by vibration and…
A three dimensional mesoscopic model is applied to study the properties of short DNA chains in a confining environment. The cylindrical channel is represented by a hard-wall repulsive potential incorporated in the system Hamiltonian. The…
Charge transfer along the base-pair stack in DNA is modeled in terms of thermally-assisted tunneling between adjacent base pairs. Central to our approach is the notion that tunneling between fluctuating pairs is rate-limited by the…
Many bacteria use rotating helical flagellar filaments to swim. The filaments undergo polymorphic transformations in which the helical pitch and radius change abruptly. These transformations arise in response to mechanical loading, changes…
In columnar assemblies of helical bio-molecules the azimuthal degrees of freedom, i.e. rotations about the long axes of molecules, may be important in determining the structure of the assemblies especially when the interaction energy…