This work investigates whether mRNA has a lower estimated folding free energy than random sequences. The free energy estimates are calculated by the mfold program for prediction of RNA secondary structures. For a set of 46 mRNAs it is shown that the predicted free energy is not significantly different from random sequences with the same dinucleotide distribution. For random sequences with the s...

Three-way junctions (3H) are the simplest and most commonly occurring branched nucleic acids. They consist of three double helical arms (A to C), connected at the junction point, with or without a number of unpaired bases in one or more of the three different strands. Three-way junctions with two unpaired bases in one strand (3HS2) have a high tendency to adopt either of two alternative stacked...

The present study adds to the knowledge of free vibration antisymmetric angle-ply annular circular plates with variable thickness for simply supported boundary conditions. differential equations in terms displacement and rotational functions are approximated using cubic spline approximation. A generalized eigenvalue problem is obtained solved numerically an eigenfrequency parameter associated e...

As the most abundant RNA methylation modification, N6-methyladenosine (m6A) could regulate asymmetric and symmetric division of hematopoietic stem cells play an important role in various diseases. Therefore, precise identification m6A sites around genomes different species is a critical step to further revealing their biological functions influence on these However, traditional wet-lab experime...

We study the parameter sensitivity of hetero-polymeric DNA within the purview of DNA breathing dynamics. The degree of correlation between the mean bubble size and the model parameters is estimated for this purpose for three different DNA sequences. The analysis leads us to a better understanding of the sequence dependent nature of the breathing dynamics of hetero-polymeric DNA. Out of the 14 m...

Force-induced structural transitions both in relatively random and in designed single-stranded DNA (ssDNA) chains are studied theoretically. At high salt conditions, ssDNA forms compacted hairpin patterns stabilized by base-pairing and base-pair stacking interactions, and a threshold external force is needed to pull the hairpinned structure into a random coiled one. The base-pair stacking inter...

2D layered materials have recently attracted tremendous interest due to their fascinating properties and potential applications. The interlayer interactions are much weaker than the intralayer bonds, allowing the as-synthesized materials to exhibit different stacking sequences, leading to different physical properties. Here, we show that regardless of the space group of the 2D materials, the Ra...

Lab-on-a-chip provides an ideal platform for short tandem repeat (STR) genotyping due to its intrinsic low sample consumption, rapid analysis, and high-throughput capability. One of the challenges, however, in the forensic human identification on the microdevice is the detection sensitivity derived from the nanoliter volume sample handling. To overcome such a sensitivity issue, here we develope...

Classical hard spheres crystallize at equilibrium at high enough density. Crystals made up of stackings of 2-dimensional hexagonal close-packed layers (e.g. fcc , hcp , etc.) differ in entropy by only about 10−3kB per sphere (all configurations are degenerate in energy). To readily resolve and study these small entropy differences, we have implemented two different multicanonical Monte Carlo al...

Recent single-macromolecule observations revealed that the force/extension characteristics of single-stranded DNA (ssDNA) are closely related to solution ionic concentration and DNA sequence composition. To understand this, we studied the elastic property of ssDNA through the Monte Carlo implementation of a modified freely jointed chain (FJC), with electrostatic, base-pairing, and base-pair sta...