相关论文: Modelling Biochemical Operations on RNA Secondary …

As a consequence of the rugged landscape of RNA molecules their folding is described by the kinetic partitioning mechanism according to which only a small fraction ($\phi_F$) reaches the folded state while the remaining fraction of…

It is a standard exercise in mechanical engineering to infer the external forces and torques on a body from its static shape and known elastic properties. Here we apply this kind of analysis to distorted double-helical DNA in complexes with…

Chemical probing experiments such as SHAPE are routinely used to probe RNA molecules. In this work, we use atomistic molecular dynamics simulations to test the hypothesis that binding of RNA with SHAPE reagents is affected by cooperative…

The increasing importance of RNA as a prime player in biology can hardly be overstated. Problems in RNA, such as folding and RNA-RNA interactions that drive phase separation, require cations. Because experiments alone cannot reveal the…

Encoding the electronic structure of molecules using 2-electron reduced density matrices (2RDMs) as opposed to many-body wave functions has been a decades-long quest as the 2RDM contains sufficient information to compute the exact molecular…

We study the folding of RNA secondary structures with quenched sequence randomness by means of the constrained annealing method. A thermodynamic phase transition is induced by including the conformational weight of loop structures. In…

We analyze the dynamics of structural transitions between normal right-handed B form and unusual left-handed Z form for a linear DNA molecule. The dynamics under the external torque in physiological buffer is modeled by a Langevin equation,…

The newly developed deep-sequencing technologies make it possible to acquire both quantitative and qualitative information regarding transcript biology. By measuring messenger RNA levels for all genes in a sample, RNA-seq provides an…

This paper is mainly devoted to a structure study of Hom-alternative algebras . Equivalent conditions for Hom-alternative algebras being solvable, simple and semi-simple are displayed. Moreover some results about Hom-alternative bimodule…

We study plane trees as a model for RNA secondary structure, assigning energy to each tree based on the Nearest Neighbor Thermodynamic Model, and defining a corresponding Gibbs distribution on the trees. Through a bijection between plane…

The Turing completeness of continuous chemical reaction networks (CRNs) states that any computable real function can be computed by a continuous CRN on a finite set of molecular species, possibly restricted to elementary reactions, i.e.…

We develop the spectral radius technique and the theory of tensor radicals. As applications we obtain numerous results on mutiplication operators in Banach algebras and Operator bimodules.

Modelling gene regulatory networks not only requires a thorough understanding of the biological system depicted but also the ability to accurately represent this system from a mathematical perspective. Throughout this chapter, we aim to…

Reactive oxygen and nitrogen species (ROS and RNS) play important roles in various physiological processes (e.g., phagocytosis) and pathological conditions (e.g., cancer). The primary ROS/RNS, viz., hydrogen peroxide, peroxynitrite ion,…

RNA molecules follow a succession of enzyme-mediated processing steps from transcription until maturation. The participating enzymes, for example the spliceosome for mRNAs and Drosha and Dicer for microRNAs, are also produced in the cell…

Arc-annotated sequences are useful for representing structural information of RNAs and have been extensively used for comparing RNA structures in both terms of sequence and structural similarities. Among the many paradigms referring to…

RNA's diversity of structures and functions impacts all life forms since primordia. We use calorimetric force spectroscopy to investigate RNA folding landscapes in previously unexplored low-temperature conditions. We find that Watson-Crick…

The recent success of large foundation models in artificial intelligence has prompted the emergence of chemical pre-trained models. Despite the growing interest in large molecular pre-trained models that provide informative representations…

The Radon transform and its dual are central objects in geometric analysis on Riemannian symmetric spaces of the noncompact type. In this article we study algebraic versions of those transforms on inductive limits of symmetric spaces. In…

Benchmarks of molecular machine learning models often treat the molecular representation as a neutral input format, yet the representation defines the syntax of validity, edit operations, and invariances that models implicitly learn. We…