Related papers: A phase transition in energy-filtered RNA secondar…
Protein folding processes are generally described statistically with the help of multidimensional free energy landscape, typically reduced to a 1-D free energy profile along good reaction co-ordinate. There are many physical parameters…
We consider the rate of transition for a particle between two metastable states coupled to a thermal environment for various magnitudes of the coupling strength, using the recently proposed infrequent metadynamics approach (Tiwary and…
Background: In the Nearest-Neighbor Thermodynamic Model, a standard approach for RNA secondary structure prediction, the energy of the multiloops is modeled using a linear entropic penalty governed by three branching parameters. Although…
We calculate the energy of a boundary between ferro- and antiferromagnetic regions in a phase separated double-exchange magnet in two and three dimensions. The orientation dependence of this energy can significantly affect the geometry of…
Atomically detailed simulations of RNA folding have proven very challenging in view of the difficulties of developing realistic force fields and the intrinsic computational complexity of sampling rare conformational transitions. To tackle…
While true phase transitions are forbidden in one-dimensional systems with short-range interactions, several models have recently been shown to exhibit sharp yet analytic thermodynamic anomalies that mimic thermal phase transitions. We show…
Motivated by the issue of whether it is possible to construct phenomenologically viable models where the electroweak symmetry breaking is triggered by new physics at a scale $\Lambda \gg 4\pi v$, where $v$ is the order parameter of the…
The number of protein structures is far less than the number of sequences. By imposing simple generic features of proteins (low energy and compaction) on all possible sequences we show that the structure space is sparse compared to the…
The formation of secondary structures by a random RNA sequence is studied as a model system for the sequence-structure problem omnipresent in biopolymers. Several toy energy models are introduced to allow detailed analytical and numerical…
Folding of RNA is subject to a competition between entropy, relevant at high temperatures, and the random, or random looking, sequence, determining the low- temperature phase. It is known from numerical simulations that for random as well…
A general theoretical framework is developed using free energy functional methods to understand the effects of heterogeneity in the folding of a well-designed protein. Native energetic heterogeneity arising from non-uniformity in native…
Following our recent interest in metamaterial-based devices supporting resonant tunneling, energy squeezing and supercoupling through narrow waveguide channels and bends, here we analyze the fundamental physical mechanisms behind this…
Free energy differences are a central quantity of interest in physics, chemistry, and biology. We develop design principles that improve the precision and accuracy of free energy estimators, which has potential applications to screening for…
We consider in this paper subdiffusion in a system with a thin membrane. The subdiffusion parameters are the same in both parts of the system separated by the membrane. Using the random walk model with discrete time and space variables the…
The present paper deals with the analysis of experimental results taking into account mechanisms brought by the bulk elastic energy transformed by the thermodynamic parameters, temperature, magnetic fields, high hydrostatic pressure…
Some recent work on the thermodynamic behavior of the matrix model of M-theory on a pp-wave background is reviewed. We examine a weak coupling limit where computations can be done explicitly. In the large N limit, we find a phase transition…
We study the equilibration and relaxation processes within the time-dependent Hartree-Fock approach using the Wigner distribution function. On the technical side we present a geometrically unrestricted framework which allows us to calculate…
We present computations of individual mode-to-mode energy transfers from direct numerical simulations of homogeneous isotropic turbulence. Unlike previous approaches based on shell-filtered velocity fields, this method distinguishes between…
The ribosomal density along the coding region of the mRNA molecule affect various fundamental intracellular phenomena including: protein production rates, organismal fitness, ribosomal drop off, and co-translational protein folding. Thus,…
Turbulence in stratified and rotating turbulent flows is characterized by an interplay between waves and eddies, resulting in continuous exchanges between potential and kinetic energy. Here, we study how these processes affect the turbulent…