Related papers: Parametric analysis of RNA folding
(abbreviated version of the abstract) We study the physics of cyclotron line formation in the high-energy spectra of accreting X-ray pulsars using Monte Carlo methods, assuming that the line-forming region is a low-density electron plasma…
In this paper, we will show that the recently introduced graphical model: Conditional Random Fields (CRF) provides a template to integrate micro-level information about biological entities into a mathematical model to understand their…
We study the asymptotic rank of adjacency matrices of a large class of edge-weighted configuration models. Here, the weight of a (multi-)edge can be any fixed non-zero element from an arbitrary field, as long as it is independent of the…
This work examines a field theory for RNA-like molecules in a good solvent. The field theory is based on a lattice model for single- and double-strand RNA with a periodic base sequence, and otherwise contains all known relevant details…
Understanding the differences between the distribution of quarks bound in protons and neutrons is key for constraining the mechanisms of SU(6) spin-flavor symmetry breaking in Quantum Chromodynamics (QCD). While vast amounts of proton…
Secondary structure plays an important role in determining the function of non-coding RNAs. Hence, identifying RNA secondary structures is of great value to research. Computational prediction is a mainstream approach for predicting RNA…
The alignment of biological sequences such as DNA, RNA, and proteins, is one of the basic tools that allow to detect evolutionary patterns, as well as functional/structural characterizations between homologous sequences in different…
We stress the importance of the circa 20 parameters in the Standard Model, which are not fixed by the model but only determined experimentally, as a window to the physics beyond the Standard Model. However, it is a tiny window in as far as…
We present a survey of the phenomenological adjustment of the parameters of the Skyrme-Hartree-Fock (SHF) model for a self-consistent description of nuclear structure and low-energy excitations. A large sample of reliable input data from…
Predicting protein secondary structure using lattice model is one of the most studied computational problem in bioinformatics. Here secondary structure or three dimensional structure of protein is predicted from its amino acid sequence.…
The relativistic mean-field models tested in previous works against nuclear matter experimental values, critical parameters and macroscopic stellar properties are revisited and used in the evaluation of the symmetry energy $\gamma$…
This paper deepens into the analysis of the protein secondary structure using Frenet frame to describe the curvature and torsion of the discrete curve formed by the protein $\alpha$-carbons. We show how a simple criterion based on the…
We analyze the low-energy spin structure of the nucleon in a covariant effective field theory with explicit spin-3/2 degrees of freedom to third order in the small scale expansion. Using the available data on the strong and electromagnetic…
How accurate is pair additivity in describing interactions between soft polymer-based nanoparticles? Using numerical simulations we compute the free energy cost required to overlap multiple chains in the same region of space, and provide a…
RNAs self-interact through hydrogen-bond base-pairing between nucleotides and fold into specific, stable structures that substantially govern their biochemical behaviour. Experimental characterization of these structures remains difficult,…
We investigate the linear regime of f(R) = R + alpha R^2 gravity for static, spherically symmetric and asymptotically flat configurations of matter. We show that, in vacuum and deep inside the range of the extra scalar degree of freedom,…
Structural prediction has long been considered critical in RNA research, especially following the success of AlphaFold2 in protein studies, which has drawn significant attention to the field. While recent advances in machine learning and…
Recently, a framework considering RNA sequences and their RNA secondary structures as pairs, led to some information-theoretic perspectives on how the semantics encoded in RNA sequences can be inferred. In this context, the pairing arises…
In this Letter we report new effects of resonance detuning on various dynamical parameters of a generic 3-wave system. Namely, for suitably chosen values of detuning the variation range of amplitudes can be significantly wider than for…
We study pairing of an interacting three component Fermi gas in two dimensions. By using a mean field theory to decouple the interactions between different pairs of Fermi components, we study the free energy landscapes as a function of…