相关论文: Modelling Biochemical Operations on RNA Secondary …
In higher eukaryotes, alternative splicing is usually regulated by protein factors, which bind to the pre-mRNA and affect the recognition of splicing signals. There is recent evidence that the secondary structure of the pre-mRNA may also…
Detecting chemical modifications on RNA molecules remains a key challenge in epitranscriptomics. Traditional reverse transcription-based sequencing methods introduce enzyme- and sequence-dependent biases and fragment RNA molecules,…
We analyze a microscopic RNA model, which includes two widely used models as limiting cases, namely it contains terms for bond as well as for stacking energies. We numerically investigate possible changes in the qualitative and quantitative…
Nanoscale biosystems are widely used in numerous medical applications. The approaches for structure and function of the nanomachines that are available in the cell (natural nanomachines) are discussed. Molecular simulation studies have been…
Transformers generate valid and diverse chemical structures, but little is known about the mechanisms that enable these models to capture the rules of molecular representation. We present a mechanistic analysis of autoregressive…
Many recursive functions can be defined elegantly as the unique homomorphisms, between two algebras, two coalgebras, or one each, that are induced by some universal property of a distinguished structure. Besides the well-known applications…
The rising demand for high-performing batteries requires new technological concepts. To facilitate fast charge and discharge, hierarchically structured electrodes offer short diffusion paths in the active material. However, there are still…
In this paper we experiment with using neural network structures to predict a protein's secondary structure ({\alpha} helix positions) from only its primary structure (amino acid sequence). We implement a fully connected neural network…
The modelling and analysis of biological systems has deep roots in Mathematics, specifically in the field of ordinary differential equations (ODEs). Alternative approaches based on formal calculi, often derived from process algebras or term…
Many biological functions are executed by molecular machines, which consume energy and convert it into mechanical work. Biological machines have evolved to transport cargo, facilitate folding of proteins and RNA, remodel chromatin and…
Single-nucleotide-resolution chemical mapping for structured RNA is being rapidly advanced by new chemistries, faster readouts, and coupling to computational algorithms. Recent tests have shown that selective 2'-hydroxyl acylation by primer…
Non-coding RNA sequences play a great role in controlling a number of cellular functions, thus raising the need to understand their complex conformational dynamics in quantitative detail. In this perspective, we first show that single…
Our knowledge of how individual cells self-organize to form complex multicellular systems is being revolutionized by a data outburst, coming from high-throughput experimental breakthroughs such as single-cell RNA sequencing and spatially…
Spectral properties od Delsarte transmutation operators are studied, their differential geometrical and topological structure in multidimension is analyzed, the relationships with De Rham-Hodge-Skrypnik theory of generalized differential…
We first discuss two-body and chain regularization methods for direct N-body simulations on HARP-2 and GRAPE-6. The former is used for accurate integration of perturbed binaries and hierarchies, whereas the latter deals with strong…
Structured RNA plays many functionally relevant roles in molecular life. Structural information, while required to understand the functional cycles in detail, is challenging to gather. Computational methods promise to complement…
Biological cells can exchange messages through soluble molecules or membrane-bound receptors. In particular in the latter case, the interaction is usually located in specific regions of the interacting cells and may depend on or induce…
We present a tutorial on setting-up the oxDNA coarse-grained model for simulations of DNA and RNA nanotechnology. The model is a popular tool used both by theorists and experimentalists to simulate nucleic acid systems both in biology and…
RNA/protein interactions play crucial roles in controlling gene expression. They are becoming important targets for pharmaceutical applications. Due to RNA flexibility and to the strength of electrostatic interactions, standard docking…
RNA function is deeply intertwined with its conformational dynamics. In this review, we survey recent advances in the use of atomistic molecular dynamics simulations to characterize RNA dynamics in diverse contexts, including isolated…