Related papers: Entropic contributions to the splicing process
Sensitive detection of low-abundance molecular targets is widely assumed to require enzymatic amplification, such as PCR, to achieve low detection limits. In amplification-free platforms, sensitivity is traditionally constrained by…
A lattice model of RNA denaturation which fully accounts for the excluded volume effects among nucleotides is proposed. A numerical study shows that interactions forming pseudoknots must be included in order to get a sharp continuous…
Understanding the thermodynamics of the duplication process is a fundamental step towards a comprehensive physical theory of biological systems. However, the immense complexity of real cells obscures the fundamental tensions between energy…
We deploy Shannon's information entropy to the distribution of branching fractions in a particle decay. This serves to quantify how important a given new reported decay channel is, from the point of view of the information that it adds to…
This work examines the impact of energy over-minimization on an ensemble of biological molecules subjected to the potential energy minimization procedure in vacuum. In the studied structures, long potential energy minimization stage leads…
Alternative splicing is crucial in gene regulation, with significant implications in clinical settings and biotechnology. This review article compiles bioinformatics RNA-seq tools for investigating differential splicing; offering a detailed…
RNA folding is a kinetic process governed by the competition of a large number of structures stabilized by the transient formation of base pairs that may induce complex folding pathways and the formation of misfolded structures. Despite of…
One of the key characteristics of cancer cells is an increased phenotypic plasticity, driven by underlying genetic and epigenetic perturbations. However, at a systems-level it is unclear how these perturbations give rise to the observed…
Constancy of life vitally depends on the internalization of particles through biomembranes. Of particular interest, cellular uptake, including phagocytosis, receptor-mediated endocytosis, and membrane fusion, critically depends on the…
In the framework of a phase field model of a single cell crawling on a substrate, we investigate how the properties of the cell membrane affect the shape and motility of the cell. Since the membrane influences the cell dynamics on multiple…
Background: We study the sparsification of dynamic programming folding algorithms of RNA structures. Sparsification applies to the mfe-folding of RNA structures and can lead to a significant reduction of time complexity. Results: We analyze…
Understanding and manipulating the interactions between foreign bodies and cell membranes during endo- and phagocytosis is of paramount importance, not only for the fate of living cells but also for numerous biomedical applications. This…
The essential role of long range elastic interactions in recrystallization is demonstrated using a simple analytical model: pileup rearrangements following absorption of leading dislocations by a dislocation-free embryo provides an…
Langevin dynamics is employed to study the looping kinetics of self-avoiding polymers both in ideal and crowded solutions. A rich kinetics results from the competition of two crowding-induced effects: the depletion attraction and the…
Open-world link prediction supports the knowledge representation and link prediction of new entities, enhancing the practical value of knowledge graphs in real-world applications. However, as research deepens, the performance improvements…
Dynamics of a single stranded DNA, which can form a hairpin have been studied in the constant force ensemble. Using Langevin dynamics simulations, we obtained the force-temperature diagram, which differs from the theoretical prediction…
The translation of messenger RNA transcripts to proteins is commonly modeled as a one-dimensional totally asymmetric exclusion process with extended particles. Here we focus on the effects of premature termination of translation through the…
A theory is presented of DNA hairpins enclosed in a nanochannel. A hairpin becomes constrained as it approaches the wall of a channel which leads to an entropic force causing the hairpin to tighten. The free energy of the hairpin computed…
Neural networks have dramatically increased our capacity to learn from large, high-dimensional datasets across innumerable disciplines. However, their decisions are not easily interpretable, their computational costs are high, and building…
In eukaryotic genomes, nucleosomes function to compact DNA and to regulate access to it both by simple physical occlusion and by providing the substrate for numerous covalent epigenetic tags. While nucleosome positions in vitro are…