Related papers: Soliton mediated protein folding
The importance of torsion vibration in the transmission of life information is indicated. The localization of quantum torsion state is proved. Following these analyses a formalism on the quantum theory of conformation-electron system is…
Theory of multi-dimensional representation of free energy surface of protein folding is developed by adopting structural order parameters of multiple regions in protein as multiple coordinates. Various scenarios of folding are classified in…
Soliton interaction in periodically twisted birefringent optical fibers has been analysed analytically with refernce to soliton switching. For this purpose we construct the exact general two-soliton solution of the associated coupled system…
Comments: 6 pages RevTeX, 6 Postscript figures. We review a statistical mechanics treatment of the stability of globular proteins based on a simple model Hamiltonian taking into account protein self interactions and protein-water…
Inspired by the well known sine-Gordon equation, we present a symmetric coupled system of two real scalar fields in $1+1$ dimensions. There are three different topological soliton solutions which be labelled according to their topological…
The enterobacteria lambda phage is a paradigm temperate bacteriophage. Its lysogenic and lytic life cycles echo competition between the DNA binding $\lambda$-repressor (CI) and CRO proteins. Here we scrutinize the structure, stability and…
Algebraic soliton interactions with a periodic or quasi-periodic random force are investigated using the Benjamin-Ono equation. The random force is modeled as a Fourier series with a finite number of modes and random phases uniformly…
Protein folding and evolution are intimately linked phenomena. Here, we revisit the concept of exons as potential protein folding modules across 38 abundant and conserved protein families. Taking advantage of genomic exon-intron…
Cooperativity plays an important role in the action of proteins bound to DNA. A simple, mechanical mechanism for cooperativity, in the form of a tension-mediated interaction between proteins bound to DNA at two different locations is…
We describe the results obtained from an improved model for protein folding. We find that a good agreement with the native structure of a 46 residue long, five-letter protein segment is obtained by carefully tuning the parameters of the…
Various biological sensory systems exhibit a response to a relative change of the stimulus, often referred to as fold-change detection. In the last few years fold-change detecting mechanisms, based on transcriptional networks, have been…
Monte Carlo simulations of a simple lattice model of protein folding show two distinct regimes depending on the chain length. The first regime well describes the folding of small protein sequences and its kinetic counterpart appears to be…
We present a novel statistical mechanics formalism for the theoretical description of the process of protein folding$\leftrightarrow$unfolding transition in water environment. The formalism is based on the construction of the partition…
A coarse-grained variational model is used to investigate the polymer dynamics of barrier crossing for a diverse set of two-state folding proteins. The model gives reliable folding rate predictions provided excluded volume terms that induce…
We introduce a new concept for stable spatial soliton formation, mediated by the competition between self-bending induced by a strongly asymmetric nonlocal nonlinearity and spatially localized gain superimposed on a wide pedestal with…
The folding kinetics of a number of sequences for off-lattice continuum model of proteins is studied using Langevin simulations at two values of the friction coefficient. We show that there is a remarkable correlation between folding times,…
Models of protein energetics which neglect interactions between amino acids that are not adjacent in the native state, such as the Go model, encode or underlie many influential ideas on protein folding. Implicit in this simplification is a…
Cell polarization underlies many cellular processes, such as differentiation, migration, and budding. Many living cells, such as budding yeast and fission yeast, use cytoskeletal structures to actively transport proteins to one location on…
We study families of solitons in a two-dimensional (2D) model of the light transmission through a photorefractive medium equipped with a (quasi-)one-dimensional photonic lattice. The soliton families are bounded from below by finite minimum…
Thermal field soliton self-organization arising due to absorption of background atoms vibrations is observed in numerical experiment in nonlinear chain with Lennard-Jones potential at high temperature. At some stage intensive…