Related papers: RNA-RNA interaction prediction: partition function…
mRNA technology has revolutionized vaccine development, protein replacement therapies, and cancer immunotherapies, offering rapid production and precise control over sequence and efficacy. However, the inherent instability of mRNA poses…
The origin of the $A$-type antiferromagnetic ordering, characterized by ferromagnetic layers coupling antiferromagnetically, in the prototype semiconductor altermagnet $\alpha$-MnTe has been a topic of ongoing debate. Experimentally,…
The folding of RNA and DNA strands plays crucial roles in biological systems and bionanotechnology. However, studying these processes with high-resolution numerical models is beyond current computational capabilities due to the timescales…
We present predictions of inclusive antiproton and antineutron production cross sections in proton-proton collisions relevant to primary and secondary antiproton production in cosmic ray interactions with interstellar matter. Our…
The accurate prediction of protein-RNA binding affinity remains an unsolved problem in structural biology, limiting opportunities in understanding gene regulation and designing RNA-targeting therapeutics. A central obstacle is the…
Partition functions of a canonical ensemble of non-interacting bound electrons are a key ingredient of the super-transition-array approach to the computation of radiative opacity. A few years ago, we published a robust and stable recursion…
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…
In the calculation of the $K^+$-nucleus cross sections, the coupling of the mesons exchanged between the $K^+$ and the target nucleons to the polarization of the Fermi and Dirac seas has been taken into account. This polarization has been…
Phase-separated biomolecular condensates containing proteins and RNAs can assemble into higher-order structures by forming thermodynamically stable interfaces between immiscible phases. Using a minimal model of a protein/RNA interaction…
We introduce a nonparametric algorithm to learn interaction kernels of mean-field equations for 1st-order systems of interacting particles. The data consist of discrete space-time observations of the solution. By least squares with…
Background:Typically, proteins perform key biological functions by interacting with each other. As a consequence, predicting which protein pairs interact is a fundamental problem. Experimental methods are slow, expensive, and may be error…
Molecular dynamics (MD) simulation, which is considered an important tool for studying physical and chemical processes at the atomic scale, requires accurate calculations of energies and forces. Although reliable energies and forces can be…
Faussurier et al. [Phys. Rev. E 65, 016403 (2001)] proposed to use a variational principle relying on Jensen-Feynman (or Gibbs-Bogoliubov) inequality in order to optimize the accounting for two-particle interactions in the calculation of…
The Nucleon-Nucleon interaction is the starting point for ab initio Nuclear Structure and Nuclear reactions calculations. Those are effectively carried out via effective interactions fitting scattering data up to a maximal center of mass…
This article presents two systems that can simulate and predict Particles ratios created in high energy proton-proton (pp) collisions as a function of transverse momentum and the center-of-mass energy. An adaptive neurofuzzy inference…
We consider the problem of determining the maximal $\alpha \in (0,1]$ such that every matching $M$ of size $k$ (or at most $k$) in a bipartite graph $G$ contains an induced matching of size at least $\alpha |M|$. This measure was recently…
We study the structure of two cointeracting bialgebras on noncrossing partitions appearing in the theory of free probability. The first coproduct is given by separation of the blocks of the partitions into two parts, with respect to the…
Motivation: MicroRNAs (miRNAs) play pivotal roles in gene expression regulation by binding to target sites of messenger RNAs (mRNAs). While identifying functional targets of miRNAs is of utmost importance, their prediction remains a great…
The structure of an RNA molecule plays a significant role in its biological function. Predicting structure given a one dimensional sequence of RNA nucleotide bases is a difficult and important problem. Many computer programs (known as in…
We have calculated astrophysical reaction cross-sections for $(\gamma,\alpha)$ reactions of some nuclei important for the calculation of $p$-process reaction-decay network. Reaction rates for $\alpha$-induced reactions are calculated with…