Related papers: Analysis of Two-State Folding Using Parabolic Appr…
Large deviations of conservative interacting particle systems, such as the zero range process, about their hydrodynamic limit and their respective rate functions lead to the analysis of the skeleton equation; a degenerate…
We propose a universal elastic energy for proteins, which depends only on the radius of gyration $R_{g}$ and the residue number $N$. It is constructed using physical arguments based on the hydrophobic effect and hydrogen bonding. Adjustable…
The Dicke spin-boson model is composed by a single bosonic mode and an ensemble of $N$ identical two-level atoms. Assuming thermal equilibrium with a reservoir at temperature $\beta^{-1}$, we consider the situation where the coupling…
We show how to construct non-equilibrium thermodynamics for systems too small to be considered thermodynamically in a traditional sense. Through the use of a non-equilibrium ensemble of many replicas of the system which can be viewed as a…
We have exactly solved the relaxational dynamics of a model protein which possesses a kinetically perfect funnel-like energy landscape. We find that the dependence of the relaxation time, $\tau$, on the density of states (DOS) and the…
We numerically study the unitary time evolution of a nonintegrable model of hard-core bosons with an extensive number of local Z2 symmetries. We find that the expectation values of local observables in the stationary state are described…
We propose a simple approach, based on the minimization of the total (entropic plus unfolding) energy of a two-state system, describing the stretch-induced unfolding of macromolecules (proteins, silks, nanopolymers, DNA/RNA). The model is…
The paper proposes a new fragmentation mechanism of dendrite arms. The theoretical basis of this mechanism is a shift in the thermodynamical equilibrium at the solid-liquid interface due to the presence of elastic energy. This effect is…
We consider polynomial long-range Ising models in one dimension, with ferromagnetic pair interactions decaying with power $2-\alpha$ (for $0 \leq \alpha < 1$), and prepared with randomly chosen boundary conditions. We show that at low…
A theoretical framework for evaluating the approximate energy and dynamic properties associated with the folding of DNA into nucleosomes and chromatin is presented. For this purpose experimentally determined elastic constants of linear DNA…
We consider the deformed Bose gas model with the deformation structure function that is the combination of a q-deformation and a quadratically polynomial deformation. Such a choice of the unifying deformation structure function enables us…
Statistical DNA models available in the literature are often effective models where the base-pair state only (unbroken or broken) is considered. Because of a decrease by a factor of 30 of the effective bending rigidity of a sequence of…
We study DNA denaturation by integrating elasticity -- as described by the Gaussian network model -- with bond binding energies, distinguishing between different base-pair and stacking energies. We use exact calculation, within the model,…
Drawing inspiration from transportation theory, in this work we introduce the notions of "well-structured" and "stable" Gibbs states and we investigate their implications for quantum thermodynamics and its resource theory approach via…
The folding pathway and rate coefficients of the folding of a knotted protein are calculated for a potential energy function with minimal energetic frustration. A kinetic transition network is constructed using the discrete path sampling…
The protein folding is regarded as a quantum transition between torsion states on polypeptide chain. The deduction of the folding rate formula in our previous studies is reviewed. The rate formula is generalized to the case of frequency…
We investigate the origin of a disagreement between the two-mode model and the exact Gross-Pitaevskii dynamics applied to double-well systems. In general this model, even in its improved version, predicts a faster dynamics and…
Protein conformational transitions, which are essential for function, may be driven either by entropy or enthalpy when molecular systems comprising solute and solvent molecules are the focus. Revealing thermodynamic origin of a given…
We study the motion of a 1-D closed elastic string with bending and stretching energy immersed in a 2-D Stokes flow. In this paper we introduce the curve's tangent angle function and the stretching function to describe the deferent…
The properties of ultracold quantum gases of bosons with dipole-dipole interaction is investigated at finite temperature in the frame of the representative ensembles theory. Self-consistent coupled equations of motion are derived for the…