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A simple model of a circularly closed dsDNA in a poor solvent is considered as an example of a semi-flexible polymer with self-attraction. To find the ground states, the conformational energy is computed as a sum of the bending and…
We review pro and contra of the hypothesis that generic polymer properties of topological constraints are behind many aspects of chromatin folding in eukaryotic cells. For that purpose, we review, first, recent theoretical and computational…
We discuss the appropriate techniques for modelling the geometry of open ended elastic polymer molecules. The molecule is assumed to have fixed endpoints on a boundary surface. In particular we discuss the concept of the winding number, a…
We apply the computational methodology of phase retrieval to the problem of folding heteropolymers. The ground state fold of the polymer is defined by the intersection of two sets in the configuration space of its constituent monomers: a…
Chromosome organisation is increasingly recognised as an essential component of genome regulation, cell fate and cell health. Within the realm of transposable elements (TEs) however, the spatial information of how genomes are folded is…
The structural dynamics of a biopolymer is governed by a process of diffusion through its conformational energy landscape. In pulling experiments using optical tweezers, features of the energy landscape can be extracted from the probability…
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…
We study theoretically the denaturation of single RNA molecules by mechanical stretching, focusing on signatures of the (un)folding pathway in molecular fluctuations. Our model describes the interactions between nucleotides by incorporating…
Energy landscape theory describes how a full-length protein can attain its native fold by sampling only a tiny fraction of all possible structures. Although protein folding is now understood to be concomitant with synthesis on the ribosome,…
The mechanical properties of molecules are today captured by single molecule manipulation experiments, so that polymer features are tested at a nanometric scale. Yet devising mathematical models to get further insight beyond the commonly…
The dynamics of two 12-monomer heteropolymers on the square lattice is studied exactly within the master equation approach. The time evolution of the occupancy of the native state is determined. At low temperatures, the median folding time…
Single-molecule mechanical manipulation has enabled the quantitative understanding of the kinetics of bond ruptures as well as protein unfolding mechanism. Single-molecule experiments with theoretical models have allowed one to gain insight…
A method that reconstructs protein residue networks using suitable node selection and edge recovery policies produced numerical observations that correlate strongly (Pearson's correlation coefficient < -0.83) with published folding rates…
The quite recent technological rise in molecular biology allowed single molecule manipulation experiments, where molecule stretching plays a primary role. In order to understand the experimental data, it is felt the urge of some physical…
A unified model is constructed to study the recently observed DNA entropic elasticity, cooperative extensibility, and supercoiling property. With the introduction of a new structural parameter (the folding angle $\phi$), bending…
We present an extensive theoretical investigation of the mechanical unzipping of double-stranded DNA under the influence of an applied force. In the limit of long polymers, there is a thermodynamic unzipping transition at a critical force…
Recent single-molecule pulling experiments have shown how it is possible to manipulate RNA molecules using optical tweezers force microscopy. We investigate a minimal model for the experimental setup which includes a RNA molecule connected…
Mechanical unfolding of RNA structures, ranging from hairpins to ribozymes, using laser optical tweezer (LOT) experiments have begun to reveal the features of the energy landscape that cannot be easily explored using conventional…
In the current AFM experiments the distribution of unfolding times, P(t), is measured by applying a constant stretching force f_s from which the apparent unfolding rate is obtained. To describe the complexity of the underlying energy…
Understanding the protein folding process is an outstanding issue in biophysics; recent developments in molecular dynamics simulation have provided insights into this phenomenon. However, the large freedom of atomic motion hinders the…