Related papers: Introducing a model of pairing based on Base pair …
DNA and other biopolymers differ from classical polymers due to their torsional stiffness. This property changes the statistical character of their conformations under tension from a classical random walk to a problem we call the `torsional…
A hypercomplex representation of DNA is proposed to facilitate comparison of DNA sequences with fuzzy composition. Using hypercomplex number representation, conventional sequence analysis method, such as, dot matrix analysis, dynamic…
A model of self-avoiding walk with suitable constraints on self-attraction is developed to describe the conformational behaviour of a single stranded short DNA molecule that form hairpin structure. Using exact enumeration method we…
We introduce a probabilistic model for protein sliding motion along DNA during the search of a target sequence. The model accounts for possible effects due to sequence-dependent interaction between the nonspecific DNA and the protein. As an…
An 1d model with time-dependent random hopping is proposed to describe charge transport in DNA. It admits to investigate both diffusion of electrons and their tunneling between different sites in DNA. The tunneling appears to be strongly…
Protonation of DNA basepairs is a reversible phenomenon which can be controlled by tuning the pH of the system. Under mild acidic conditions, the hydrogen bonding pattern of the DNA basepairs undergoes a change. We study the effect of…
Phase separation in biomolecular mixtures can result from multiple physical interactions, which may act either complementarily or antagonistically. In the case of protein-nucleic acid mixtures, charge plays a key role but can have…
Chain-like macromolecules in solution, whether biological or synthetic, transform from a spatially extended conformation to a compact one upon change of temperature or solvent qualities. This sharp transition plays a key role in various…
Matching mechanisms play a central role in operations management across diverse fields including education, healthcare, and online platforms. However, experimentally comparing a new matching algorithm against a status quo presents some…
The specificity of molecular recognition is important to molecular self-organization. A prominent example is the biological cell where, within a highly crowded molecular environment, a myriad of different molecular receptor pairs recognize…
In our report we consider two weakly coupled Schr\"odinger equations as a model of the interchain energy transport in the DNA double-helix. We use the reduction of the Yakushevich-type model considering the torsional dynamics of the DNA. In…
The Poland-Scheraga (PS) model for the helix-coil transition of DNA considers the statistical mechanics of the binding (or hybridization) of two complementary strands of DNA of equal length, with the restriction that only bases with the…
All living systems can function only far away from equilibrium, and for this reason chemical kinetic methods are critically important for uncovering the mechanisms of biological processes. Here we present a new theoretical method of…
We propose a dynamical model for non-specific DNA-protein interaction, which is based on the 'bead-spring' model previously developed by other groups, and investigate its properties using Brownian Dynamics simulations. We show that the…
By taking into account base-base stacking interactions we improve the Generalized Model of Polypeptide Chain (GMPC). Based on a one-dimensional Potts-like model with many-particle interactions, the GMPC describes the helix-coil transition…
We study the elastic behaviour of a supercoiled DNA molecule. The simplest model is that of a rod like chain, involving two elastic constants, the bending and the twist rigidities. We show that this model is singular and needs a small…
Frameshift mutations in protein-coding DNA sequences produce a drastic change in the resulting protein sequence, which prevents classic protein alignment methods from revealing the proteins' common origin. Moreover, when a large number of…
Many fundamental biological processes are regulated by protein-DNA complexes called {\it synaptosomes}, which possess multiple interaction sites. Despite the critical importance of synaptosomes, the mechanisms of their formation remain not…
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…
DNA-coated particles are promising as building blocks for functional and finite-sized assemblies because they can be programmed with orthogonal interactions owing to the sequence-specific hybridization of DNA strands. To fully exploit this…