Related papers: Base pair fluctuations in helical models for nucle…
The expected return time of a fluctuating two-dimensional cluster or vacancy to a given configuration is studied in thermodynamic equilibrium. We define a family of bond-breaking models that preserve the number of particles. This family…
We study the metastability, internal frequencies, activation mechanism, energy transfer, and the collective base-flipping in a mesoscopic DNA via resonance with specific electric fields. Our new mesoscopic DNA model takes into account not…
We demonstrate nuclear double resonance for nanometer-scale volumes of spins where random fluctuations rather than Boltzmann polarization dominate. When the Hartmann-Hahn condition is met in a cross-polarization experiment, flip-flops occur…
We investigate the statistical mechanics of a torsionally constrained polymer. The polymer is modeled as a fluctuating rod with bend stiffness A kT and twist stiffness C kT. In such a model, thermal bend fluctuations couple geometrically to…
Experimental and theoretical studies are made of Brownian particles trapped in a periodic potential, which is very slightly tilted due to gravity. In the presence of fluctuations, these will trigger a measurable average drift along the…
Using an algorithm for simulating equilibrium configurations, we study a fluctuating helical polymer either (i) contained in a cylindrical pore or (ii) wound around a cylindrical rod. We work in the regime where both the contour length and…
We explore, for the first time, the effect of double fluctuations on both the diagonal and off-diagonal self-energy. We use the T-Matrix equations below $T_c$, developed recently by the Z\"urich group (M.H. Pedersen et al) for the local…
The two-dimensional Hubbard model exhibits superconductivity with d-wave symmetry even at half-filling in the presence of next-nearest neighbor hopping. Using plaquette cluster dynamical mean-field theory with a continuous-time quantum…
Base pair mismatch can relieve mechanical stress in highly strained DNA molecules, but how it affects their kinetic stability is not known. Using single-molecule Fluorescence Resonance Energy Transfer (FRET), we measured the lifetimes of…
We present a new dynamical model of DNA. This model has two degrees of freedom per base-pair: one radial variable related to the opening of the hydrogen bonds and an angular one related to the twisting of each base-pair responsible for the…
Cluster dynamical mean field calculations are used to construct the superconducting gap function of the two dimensional Hubbard model. The frequency dependence of the imaginary part of the gap function indicates that the pairing is…
The role of thermal pressure fluctuations in the ejection of tightly packaged DNA from protein capsid shells is discussed in a model calculation. At equilibrium before ejection we assume the DNA is folded many times into a bundle of…
The issue of the nucleation and slow closure mechanisms of non superhelical stress-induced denaturation bubbles in DNA is tackled using coarse-grained MetaDynamics and Brownian simulations. A minimal mesoscopic model is used where the…
Nuclear pairing properties are studied within an approach that includes the quasiparticle-number fluctuation (QNF) and coupling to the quasiparticle-pair vibrations at finite temperature and angular momentum. The formalism is developed to…
The bilayer Hubbard model with an intra-layer hopping $t$ and an inter-layer hopping $t_\perp$ provides an interesting testing ground for several aspects of what has been called unconventional superconductivity. One can study the type of…
The critical behavior at the transition from uniform nematic to twist-bend modulated nematic phase is revealed and shown to be well explained by the mean field approximation. The study was performed on a group of materials that exhibit an…
Rapidly rotating nuclei provide us good testing grounds to study the pairing correlations; in fact, the transition from the superfluid to the normal phase is realized at high-spin states. The role played by the pairing correlations is quite…
As a key molecule of Life, Deoxyribonucleic acid (DNA) is the focus of numbers of investigations with the help of biological, chemical and physical techniques. From a physical point of view, both experimental and theoretical works have…
The superconducting state of a two-dimensional d-p model is studied from the spin fluctuation point of view by using a strong coupling theory. The fluctuation exchange (FLEX) approximatoin is employed to calculate the spin fluctuations and…
We study the propagation of very large amplitude localized excitations in a model of DNA that takes explicitly into account the helicoidal structure. These excitations represent the ``transcription bubble'', where the hydrogen bonds between…