Related papers: Model for processive nucleotide and repeat additio…
Motif finding in DNA, RNA and proteins plays an important role in life science research. Recent patents concerning motif finding in the biomolecular data are recorded in the DNA Patent Database which serves as a resource for policy makers…
During cellular translation, incorporation errors occur. It is the addition of amino acid residues not corresponding to the mRNA code. With an increase in the number of residues in the synthesized molecule, the probability of failure in at…
How to induce differentiated cells into pluripotent cells has elicited researchers' interests for a long time since pluripotent stem cells are able to offer remarkable potential in numerous subfields of biological research. However, the…
The modeling of genomic sequences presents unique challenges due to their length and structural complexity. Traditional sequence models struggle to capture long-range dependencies and biological features inherent in DNA. In this work, we…
The thermodynamic properties of DNA circular molecules are investigated by a new path integral computational method which treats in the real space the fundamental forces stabilizing the molecule. The base pair and stacking contributions to…
Totally asymmetric simple exclusion process (TASEP) was originally introduced as a model for the traffic-like collective movement of ribosomes on a messenger RNA (mRNA) that serves as the track for the motor-like forward stepping of…
A recently experimentally observed biochemical "threshold filtering" mechanism by processes catalyzed by the enzyme malate dehydrogenase is explained in terms of a model that incorporates an unusual mechanism of inhibition of this enzyme…
In the exothermic process of fission decay, an atomic nucleus splits into two or more independent fragments. Several aspects of nuclear fission are not properly understood, in particular the formation of the neck between the nascent…
Genomic foundation models have the potential to decode DNA syntax, yet face a fundamental tradeoff in their input representation. Standard fixed-vocabulary tokenizers fragment biologically meaningful motifs such as codons and regulatory…
The effect of sequence heterogeneity on polynucleotide translocation across a pore and on simple models of molecular motors such as helicases, DNA polymerase/exonuclease and RNA polymerase is studied in detail. Pore translocation of RNA or…
There are many proteins or protein complexes which have multiple DNA binding domains. This allows them to bind to multiple points on a DNA molecule (or chromatin fibre) at the same time. There are also many proteins which have been found to…
We present an analytically solvable model for self-assembly of a molecular complex on a filament. The process is driven by a seed molecule that undergoes facilitated diffusion, which is a search strategy that combines diffusion in…
We present in this paper an original approach to compute the electrophoretic mobility of rigid nucleo-protein complexes like nucleosomes. This model allows to address theoretically the influence of complex position along DNA, as well as…
We extend the live-cell motility Filament Based Lamellipodium Model to incorporate the forces exerted on the lamellipodium of the cells due to cell-cell collision and cadherin induced cell-cell adhesion. We take into account the nature of…
Twisting DNA under a constant applied force reveals a thermally activated transition into a state with a supercoiled structure known as a plectoneme. Using transition state theory, we predict the rate of this plectoneme nucleation to be of…
We present a detailed study of the structure-dynamics relationship of regio-regular and regio-random PEHT using different neutron scattering techniques. Deuteration is employed to modulate the coherent and incoherent cross-sections,…
The efficiency of supported catalysts depends on the porous microstructure of their solid support, which regulates mass transfer, exposure to the active phase, and mechanical strength. Here, we focus on the manufacturing of a specific type…
In the study of life's origins, a key challenge is understanding how RNA could have polymerized and subsequently replicated in early Earth. We present a theoretical and computational framework to model the non-enzymatic polymerization of…
Layered chalcogenides including Bi2Te3, Sb2Te3, Bi-Sb-Te ternary alloys and heterostructures are known as great thermoelectric, topological insulators and recently highlighted as plasmonic building blocks beyond noble metals. Here, we…
The fidelity of DNA replication by DNA polymerase (DNAP) has long been an important issue in biology. While numerous experiments have revealed details of the molecular structure and working mechanism of DNAP which consists of both a…