相关论文: Model for processive nucleotide and repeat additio…

We enumerate the number of RNA contact structures according to their genus, i.e. the topological character of their pseudoknots. By using a recently proposed matrix model formulation for the RNA folding problem, we obtain exact results for…

Recent single-molecule pulling experiments have shown how it is possible to manipulate RNA molecules using optical tweezers force microscopy. We investigate a minimal model for the experimental setup which includes a RNA molecule connected…

The understanding of mechanisms that control epigenetic changes is an important research area in modern functional biology. Epigenetic modifications such as DNA methylation are in general very stable over many cell divisions. DNA…

Measuring the electrophoretic mobility of molecules is a powerful experimental approach for investigating biomolecular processes. A frequent challenge in the context of single-particle measurements is throughput, limiting the obtainable…

Despite the importance of a thermodynamically stable structure with a conserved fold for protein function, almost all evolutionary models neglect site-site correlations that arise from physical interactions between neighboring amino acid…

DNA Polymerase is an enzyme that participates in the process of DNA replication. In general, forward DNA polymerase moves along the template strand in a 3'-5' direction, and the daughter strand is formed in a 5'-3' direction. This paper…

We study theoretically the denaturation of single RNA molecules by mechanical stretching, focusing on signatures of the (un)folding pathway in molecular fluctuations. Our model describes the interactions between nucleotides by incorporating…

The advent of solid state nanodevices allows for interrogating the physico-chemical properties of a polyelectrolyte chain by electrophoretically driving it through a nanopore. Salient dynamical aspects of the translocation process have been…

Motility initiation in crawling cells requires transformation of a symmetric state into a polarized state. In contrast, motility arrest is associated with re-symmetrization of the internal configuration of a cell. Experiments on keratocytes…

The possibility that the sliding motion of proteins on DNA is influenced by the base sequence through a base pair reading interaction, is considered. Referring to the case of the T7 RNA-polymerase, we show that the protein should follow a…

Due to the potential applications in biomedical engineering, it becomes more and more important to understand the process of engulfment and internalization of nanoparticles (NPs) by cell membranes. Despite the fact that the interaction…

Traditional top-down robotic design often lacks the adaptability needed to handle real-world complexities, prompting the need for more flexible approaches. Therefore, this study introduces a novel cellular plasticity model tailored for…

In the presence of ATP, kinesin proceeds along the protofilament of microtubule by alternated binding of two motor domains on the tubulin binding sites. Since the processivity of kinesin is much higher than other motor proteins, it has been…

It has been recently argued that the depletion attraction may play an important role in different aspects of the cellular organization, ranging from the organization of transcriptional activity in transcription factories to the formation of…

Recent computational efforts have shown that the current potential energy models used in molecular dynamics are not accurate enough to describe the conformational ensemble of RNA oligomers and suggest that molecular dynamics should be…

Molecular motor proteins form the basis of cellular dynamics. Recently, notable efforts have led to the creation of their DNA-based mimics, which can carry out complex nanoscale motion. However, such functional analogues have not yet been…

DNA, RNA and proteins are among the most important macromolecules in a living cell. These molecules are polymerized by molecular machines. These natural nano-machines polymerize such macromolecules, adding one monomer at a time, using…

Cellular decision-making based on information received from the external environment is frequently initiated by transmembrane receptors. These receptors are known to propagate such information by triggering a series of irreversible,…

Phosphorylation, the enzyme-mediated addition of a phosphate group to a molecule, is a ubiquitous chemical mechanism in biology. Multisite phosphorylation, the addition of phosphate groups to multiple sites of a single molecule, may be…

The telegraph model is the standard model of stochastic gene expression, which can be solved exactly to obtain the distribution of mature RNA numbers per cell. A modification of this model also leads to an analytical distribution of the…