Related papers: Size, shape, and flexibility of RNA structures
Natural protein sequences that self-assemble to form globular structures are compact with high packing densities in the folded states. It is known that proteins unfold upon addition of denaturants, adopting random coil structures. The…
An RNA sequence is a word over an alphabet on four elements $\{A,C,G,U\}$ called bases. RNA sequences fold into secondary structures where some bases match one another while others remain unpaired. Pseudoknot-free secondary structures can…
In this paper we consider the problem of RNA folding with pseudoknots. We use a graphical representation in which the secondary structures are described by planar diagrams. Pseudoknots are identified as non-planar diagrams. We analyze the…
Connectedness percolation phenomena in two-dimensional packings of elongated particles (discorectangles) were studied numerically. The packings were produced using random sequential adsorption (RSA) off-lattice model with preferential…
Advanced Monte Carlo simulations are used to study the effect of nano-slit confinement on metric and topological properties of model DNA chains. We consider both linear and circularised chains with contour lengths in the 1.2--4.8 $\mu$m…
The structural flexibility of nucleic acids plays a key role in many fundamental life processes, such as gene replication and expression, DNA-protein recognition, and gene regulation. To obtain a thorough understanding of nucleic acid…
Characterizing the link between small-scale chromatin structure and large-scale chromosome folding during interphase is a prerequisite for understanding transcription. Yet, this link remains poorly investigated. Here, we introduce a simple…
A theoretical framework for evaluating the approximate energy and dynamic properties associated with the folding of DNA into nucleosomes and chromatin is presented. For this purpose experimentally determined elastic constants of linear DNA…
To study the elastic properties of rod-like DNA nanostructures, we perform long simulations of these structure using the oxDNA coarse-grained model. By analysing the fluctuations in these trajectories we obtain estimates of the bend and…
DNA nanoparticles with three-fold coordination have been observed to self-assemble in experiment into a network equivalent to the hexagonal (6.6.6) tiling, and a network equivalent to the 4.8.8 Archimedean tiling. Both networks are built…
Microgels are soft colloidal particles that, when dispersed in a solvent, swell and deswell in response to changes in environmental conditions, such as temperature, concentration, and $p$H. Using Monte Carlo simulation, we model bulk…
By exerting mechanical force it is possible to unfold/refold RNA molecules one at a time. In a small range of forces, an RNA molecule can hop between the folded and the unfolded state with force-dependent kinetic rates. Here, we introduce a…
Models for RNA secondary structures (the topology of folded RNA) without pseudo knots are disordered systems with a complex state-space below a critical temperature. Hence, a complex dynamical (glassy) behavior can be expected, when…
The conformational complexity of linear polymers far exceeds that of point-like atoms and molecules. Polymers can bend, twist, even become knotted. Thus they may also display a much richer phase structure than point particles. But it is not…
Given a random RNA secondary structure, $S$, we study RNA sequences having fixed ratios of nuclotides that are compatible with $S$. We perform this analysis for RNA secondary structures subject to various base pairing rules and minimum arc-…
Short-range interactions and long-range contacts drive the 3D folding of structured proteins. The proteins' structure has a direct impact on their biological function. However, nearly 40% of the eukaryotes proteome is composed of…
We investigate the mechanical stability of a segment of DNA wrapped around a histone in the nucleosome configuration. The assumption underlying this investigation is that the proper model for this packaging arrangement is that of an elastic…
In this work, we have analyzed the nuclear structure and several prospective decay characteristics of the $^{240-259}$Es$_{99}$ isotopes. For this we use Relativistic Mean Field model (RMF) with NL-SH and NL3* force parameter in an axially…
The branching of an RNA molecule is an important structural characteristic yet difficult to predict correctly, especially for longer sequences. Using plane trees as a combinatorial model for RNA folding, we consider the thermodynamic cost,…
Nuclear pores have an approximately uniform distribution in the nuclear envelope of most living cells. Hence, the morphology of the nuclear envelope is a spherical stomatocyte with a high genus. We have investigated the morphology of…