Related papers: Size, shape, and flexibility of RNA structures
Under many in vitro conditions, some small viruses spontaneously encapsidate a single stranded (ss) RNA into a protein shell called the capsid. While viral RNAs are found to be compact and highly branched because of long distance…
The conformation of circular DNA molecules of various lengths adsorbed in a 2D conformation on a mica surface is studied. The results confirm the conjecture that the critical exponent $\nu$ is topologically invariant and equal to the SAW…
Protein structures are a very special class among all possible structures. It was suggested that a ``designability principle'' plays a crucial role in nature's selection of protein sequences and structures. Here we provide a theoretical…
We carry out a theoretical study of the vibrational and relaxation properties of naturally-occurring proteins with the purpose of characterizing both the folding and equilibrium thermodynamics. By means of a suitable model we provide a full…
We model unzipping of DNA/RNA molecules subject to an external force by a spin-oscillator system. The system comprises a macroscopic degree of freedom, represented by a one-dimensional oscillator, and internal degrees of freedom,…
In cond-mat/9907125 the low-temperature behavior of a model for RNA secondary structure was studied. It is claimed that the model exhibits a breaking of the replica symmetry, since the width of the distribution P(q) of overlaps may converge…
A hierarchical model for the growth of planar arch structures for RNA secondary structures is presented, and shown to be equivalent to a tree-growth model. Both models can be solved analytically, giving access to scaling functions for large…
We study the conformations of a semiflexible chain, confined in nano-scaled spherical cavities, under two distinct processes of confinement. Radial contraction and packaging are employed as two confining procedures. The former method is…
The structural features of polystyrene brushes grafted on spherical silica nanoparticles immersed in polystyrene are investigated by means of a Monte Carlo methodology based on polymer mean field theory. The nanoparticle radii (either 8 nm…
The protein folding problem must ultimately be solved on all length scales from the atomic up through a hierarchy of complicated structures. By analyzing the stability of the folding process using physics and mathematics, this paper shows…
$\alpha$-helices stand out as common and relatively invariant secondary structural elements of proteins. However, $\alpha$-helices are not rigid bodies and their deformations can be significant in protein function ({\it e.g.} coiled coils).…
Motivation: Predicting the secondary structure of an RNA sequence is useful in many applications. Existing algorithms (based on dynamic programming) suffer from a major limitation: their runtimes scale cubically with the RNA length, and…
The non-specific adhesion of spherical particles to a cell substrate is analyzed in a parallel plate flow chamber, addressing the effect of the particle size. Differently from other experiments, the total volume of the injected particles…
Supernova remnants (SNRs) are known to accelerate particles to relativistic energies, on account of their nonthermal emission. The observational progress from radio to gamma-ray observations reveals more and more morphological features that…
Recent experiments on unzipping of RNA helix-loop structures by force have shown that about 40-base molecules can undergo kinetic transitions between two well-defined `open' and `closed' states, on a timescale = 1 sec [Liphardt et al.,…
DNA is subject to large deformations in a wide range of biological processes. Two key examples illustrate how such deformations influence the readout of the genetic information: the sequestering of eukaryotic genes by nucleosomes, and DNA…
We studied the geometrical and topological rules underlying the dispositions and the size distribution of non-overlapping, polydisperse circle-packings. We found that the size distribution of circles that densely cover a plane follows the…
The structure and morphology of supernova remnants (SNRs) reflect the properties of the parent supernovae (SNe) and the characteristics of the inhomogeneous environments through which the remnants expand. Linking the morphology of SNRs to…
Aims: The statistics of the photospheric granulation pattern are investigated using continuum images observed by Solar Dynamic Observatory (SDO)/Helioseismic and Magnetic Imager (HMI) taken at 6713~\AA. Methods: The supergranular boundaries…
We present an experimental and theoretical study of the shape of fragments generated by explosive and impact loading of closed shells. Based on high speed imaging, we have determined the fragmentation mechanism of shells. Experiments have…