Related papers: Stretching single RNAs: exact numerical and stocha…
Investigations of natural variation among cells within a population are essential for understanding the stochastic nature of tissue cell deformation under applied load. In the existing literature, the population variation of single-cell…
Single molecule force spectroscopy reveals unfolding of domains in titin upon stretching. We provide a theoretical framework for these experiments by computing the phase diagrams for force-induced unfolding of single domain proteins using…
This paper aims at a comprehensive understanding on the novel elastic property of double-stranded DNA (dsDNA) discovered very recently through single-molecule manipulation techniques. A general elastic model for double-stranded biopolymers…
The development of novel high-throughput sequencing (HTS) methods for RNA (RNA-Seq) has provided a very powerful mean to study splicing under multiple conditions at unprecedented depth. However, the complexity of the information to be…
RNA molecules are essential cellular machines performing a wide variety of functions for which a specific three-dimensional structure is required. Over the last several years, experimental determination of RNA structures through X-ray…
Nanochannels provide means for detailed experiments on the effect of confinement on biomacromolecules, such as DNA. We here introduce a model for the complete unfolding of DNA from the circular to linear configuration. Two main ingredients…
Theoretical studies of stretching proteins with slipknots reveal a surprising growth of their unfolding times when the stretching force crosses an intermediate threshold. This behavior arises as a consequence of the existence of alternative…
The effect of electrostatic interactions on the stretching of DNA is investigated using a simple worm like chain model. In the limit of small force there are large conformational fluctuations which are treated using a self-consistent…
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…
The native structures of proteins, except for notable exceptions of intrinsically disordered proteins, in general take their most stable conformation in the physiological condition to maintain their structural framework so that their…
The functioning of double-stranded (ds) nucleic acids (NAs) in cellular processes is strongly mediated by their elastic response. These processes involve proteins that interact with dsDNA or dsRNA and distort their structures. The…
Small-angle X-ray scattering (SAXS) experiments are increasingly used to probe RNA structure. A number of \emph{forward models} that relate measured SAXS intensities and structural features, and that are suitable to model either…
Nowadays different experimental techniques, such as single molecule or relaxation experiments, can provide dynamic properties of biomolecular systems, but the amount of detail obtainable with these methods is often limited in terms of time…
A novel method combining the ensemble refinement by maximum entropy principle and the force field fitting approach is presented. Its formulation allows to continuously interpolate in between these two methods, which can thus be interpreted…
We review the basic concepts and tools for mechanically unzipping RNA hairpins using force spectroscopy. By pulling apart the ends of an RNA molecule using optical tweezers, it is possible to measure the folding free energy at varying…
The symmetries of the DNA double helix require a new term in its linear response to stress: the coupling between twist and stretch. Recent experiments with torsionally-constrained single molecules give the first direct measurement of this…
We propose a new deterministic methodology to predict RNA sequence and protein folding. Is stem enough for structure prediction? The main idea is to consider all possible stem formation in the given sequence. With the stem loop energy and…
Most single-molecule studies derive the kinetic rates of native, intermediate, and unfolded states from equilibrium hopping experiments. Here, we apply Kramers kinetic diffusive model to derive the force-dependent kinetic rates of…
Overstretching of B-DNA is currently understood as force-induced melting. Depending on the geometry of the stretching experiment, the force threshold for the overstretching transition is around 65 or 110 pN. Although the mechanisms behind…
We calculate the equation of state of DNA under tension for the case that the DNA features loops. Such loops occur transiently during DNA condensation in the presence of multivalent ions or sliding cationic protein linkers. The…