相关论文: Modelling Biochemical Operations on RNA Secondary …

Metrics for indirectly predicting the folding rates of RNA sequences are of interest. In this letter, we introduce a simple metric of RNA structural complexity, which accounts for differences in the energetic contributions of RNA base…

We are going to study some conditions on which the Radon transform and its dual are invertible. Two function spaces are introduced that the Radon transform on which is bijective linear operator. In this regards, a reconstruction formula is…

This paper studies a system of Ordinary Differential Equations modeling a chemical reaction network and derives from it a simulation tool mimicking Loss of Function and Gain of Function mutations found in cancer cells. More specifically,…

We investigate theoretically the translocation of structured RNA/DNA molecules through narrow pores which allow single but not double strands to pass. The unzipping of basepaired regions within the molecules presents significant kinetic…

Graph-Rewriting Automata (GRA) are an extension of Cellular Automata to a dynamic structure using local graph-rewriting rules. This work introduces linear algebra based tools that allow for a practical investigation of their behavior in…

The process of RNA base fraying (i.e. the transient opening of the termini of a helix) is involved in many aspects of RNA dynamics. We here use molecular dynamics simulations and Markov state models to characterize the kinetics of RNA…

The Gene Regulatory Network (GRN) of biological cells governs a number of key functionalities that enables them to adapt and survive through different environmental conditions. Close observation of the GRN shows that the structure and…

The folding of biological macromolecules is a fundamental process of which we lack a full comprehension. Mostly studied in proteins and RNA, single-stranded DNA (ssDNA) also folds, at physiological salt conditions, by forming non-specific…

Radiation damage is an unavoidable process when performing structural investigations of biological macromolecules with X-ray sources. In crystallography this process can be limited through damage distribution in a crystal, while for single…

Transformers have become methods of choice in many applications thanks to their ability to represent complex interactions between elements. However, extending the Transformer architecture to non-sequential data such as molecules and…

The dominant paradigm in origin of life research is that of an RNA world. However, despite experimental progress towards the spontaneous formation of RNA, the RNA world hypothesis still has its problems. Here, we introduce a novel…

Although a vast amount of experimental information is available on the elongation, compression, and folding of proteins in biochemical processes, very little is known about the real structure and molecular dynamics of DNA at an atomic…

We address the challenge of identifying all real positive steady states in chemical reaction networks (CRNs) governed by mass-action kinetics. Traditional numerical methods often require specific initial guesses and may fail to find all the…

Processes involving multi-input multi-step reaction cascades are used in developing novel biosensing, biocomputing, and decision making systems. In various applications different changes in responses of the constituent processing steps…

A chemical kinetic model of the elongation dynamics of RNA polymerase along a DNA sequence is introduced. The proposed model governs the discrete movement of the RNA polymerase along a DNA template, with no consideration given to elastic…

We study the force-induced unfolding of random disordered RNA or single-stranded DNA polymers. The system undergoes a second order phase transition from a collapsed globular phase at low forces to an extensive necklace phase with a…

In the frames of Mims transformation matrix method the equation for nuclear magnetization are obtained describing the dynamics of nuclear spin-systems with a strong Larmor and Rabi inhomogeneous broadenings of NMR line in conditions of…

We introduce oxNA, a new model for the simulation of DNA-RNA hybrids which is based on two previously developed coarse-grained models$\unicode{x2014}$oxDNA and oxRNA. The model naturally reproduces the physical properties of hybrid duplexes…

This methods paper presents computational protocols for the identification of non-coding RNA genes or RNA motifs within genomic sequences. An application to bacterial small RNA is proposed.

Biochars have been attracting renewed attention as economical and environmentally friendly carbon sequestration materials with a diverse range of applications. However, experimental developments may be limited by the lack of molecular-level…