Related papers: Nonlinear excitations in DNA: Aperiodic models vs …
Heat-induced mobility of nucleosomes along DNA is an experimentally well-studied phenomenon. A recent experiment shows that the repositioning is modified in the presence of minor-groove binding DNA ligands. We present here a stochastic…
We study the effects on the dynamics of kinks due to expansions and contractions of the space. We show that the propagation velocity of the kink can be adiabatically tuned through slow expansions/contractions, while its width is given as a…
We study theoretically the mechanical failure of a simple model of double stranded DNA under an applied shear. Starting from a more microscopic Hamiltonian that describes a sheared DNA, we arrive at a nonlinear generalization of a ladder…
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…
Gene expression is a stochastic process governed by the presence of specific transcription factors. Here we study the dynamics of gene expression in the presence of feedback, where a gene regulates its own expression. The nonlinear coupling…
A dynamical model is presented for chiral change in DNA molecules. The model is an extension of the conventional elastic model which incorporates the structure of base pairs and uses a spinor representation for the DNA configuration…
A theory of the unzipping of double-stranded (ds) DNA is presented, and is compared to recent micromanipulation experiments. It is shown that the interactions which stabilize the double helix and the elastic rigidity of single strands (ss)…
Previous numerical investigations of an one-dimensional DNA model with an extended modified coupling constant by transcripting enzyme are integrated to longer time and demonstrated explicitly the trapping of breathers by DNA chains with…
The fast evolution of microstructure is key to understanding crackling phenomena. It has been proposed that formation of a nonlinear zone around a moving crack tip controls the crack tip velocity. Progress in understanding the physics of…
Motivated by empirical observations of algebraic duplicated sequence length distributions in a broad range of natural genomes, we analytically formulate and solve a class of simple discrete duplication/substitution models that generate…
The functions of proteins and RNAs are determined by a myriad of interactions between their constituent residues, but most quantitative models of how molecular phenotype depends on genotype must approximate this by simple additive effects.…
We investigate the nonlinear dynamics of the Peyrard-Bishop DNA model taking into account site dependent inhomogeneities. By means of the multiple-scale expansion in the semi-discrete approximation, the dynamics is governed by the perturbed…
The Artificial Axon is a unique synthetic system, based on biomolecular components, which supports action potentials. Here we consider, theoretically, the corresponding space extended system, and discuss the occurrence of solitary waves, or…
We study the compression and extension dynamics of a DNA-like polymer interacting with non-DNA binding and DNA-binding proteins, by means of computer simulations. The geometry we consider is inspired by recent experiments probing the…
Cellular behavior is governed by gene regulatory processes that are intrinsically dynamic and nonlinear, and are subject to non-negligible amounts of random fluctuations. Such conditions are ubiquitous in physical systems, where they have…
We study the dynamics of a kink in a one-lane asymmetric simple exclusion process with detachment and attachment of the particle at arbitrary sites. For a system with one site of detachment and attachment we find that the kink is trapped by…
This study explores the scattering dynamics of kinks within a nonlinear system governed by a parameterized potential $U_\lambda(\chi)$, examining the distinct behaviors of small and large kinks across a range of $\lambda$ values and initial…
We propose a mathematical framework to systematically explore the propagation properties of a class of continuous in time nonlinear neural network models comprising a hierarchy of processing areas, mutually connected according to the…
Co-localization of networks of genes in the nucleus is thought to play an important role in determining gene expression patterns. Based upon experimental data, we built a dynamical model to test whether pure diffusion could account for the…
By resorting to a model inspired to the standard Davydov and Holstein-Fr\"ohlich models, in the present paper we study the motion of an electron along a chain of heavy particles modelling a sequence of nucleotides proper to a DNA fragment.…