Related papers: The search kinetics of a target inside the cell nu…
A common scenario in a variety of biological systems is that multiple particles are searching in parallel for an immobile target located in a bounded domain, and the fastest among them that arrives to the target first triggers a given…
Transcription factors (TFs) are macromolecules that bind to \textit{cis}-regulatory specific sub-regions of DNA promoters and initiate transcription. Finding the exact location of these binding sites (aka motifs) is important in a variety…
The unzipping transition under the influence of external force of a dsDNA molecule has been studied using the Peyrard-Bishop Hamiltonian. The critical force $F_c(T)$ is found to depend on the potential parameters $k$, represents the…
How long does it take a random searcher to visit all sites of a given domain? This time, known as the cover time, is a key observable to quantify the efficiency of exhaustive searches, which require a complete exploration of an area and not…
Current models for the folding of the human genome see a hierarchy stretching down from chromosome territories, through A/B compartments and TADs (topologically-associating domains), to contact domains stabilized by cohesin and CTCF.…
Understanding transcription factor dynamics is crucial for unraveling the regulatory mechanisms of gene expression that underpin cellular function and development. Measurements of transcription factor subcellular movements are essential for…
The folding of a protein towards its native state is a rather complicated process. However there are empirical evidences that the folding time correlates with the contact order, a simple measure of the spatial organisation of the native…
Searching a database is a central task in computer science and is paradigmatic of transport and optimization problems in physics. For an unstructured search, Grover's algorithm predicts a quadratic speedup, with the search time…
We present a finite blocklength performance bound for a DNA storage channel with insertions, deletions, and substitutions. The considered bound -- the dependency testing (DT) bound, introduced by Polyanskiy et al. in 2010 -- provides an…
The problem of motif detection can be formulated as the construction of a discriminant function to separate sequences of a specific pattern from background. In computational biology, motif detection is used to predict DNA binding sites of a…
We consider diffusion under stochastic resetting to the origin in one dimension and compute the mean time to find both of two targets placed either side of the origin. A surprising result is that increasing the distance between two targets…
It is not known how a cell manages to find a specific DNA sequence sufficiently fast to repair a broken chromosome through homologous recombination. I propose that the solution is based on a parallelized search implemented by freely…
DNA shape readout is an important mechanism of target site recognition by transcription factors, in addition to the sequence readout. Several models of transcription factor-DNA binding which consider DNA shape have been developed in recent…
DNA in sperm cells must undergo an extreme compaction to almost crystalline packing levels. To produce this dense packing, DNA is condensed by protamine, a positively charged protein that loops the DNA into a toroid. Our goal is to…
Collective coordinate and direct numerical integration methods are applied to the analysis of a one-dimensional DNA model. A modification of the coupling constant in an extended region is found to be less selective towards the breather it…
We present a theory of chemokinetic search agents that regulate directional fluctuations according to distance from a target. A dynamic scattering effect reduces the probability to penetrate regions with high fluctuations and thus search…
Finding a target in a complex environment is a fundamental challenge in nature, from chemical reactions to sperm reaching an egg. An effective strategy to reduce the time needed to reach a target is to deploy many searchers, increasing the…
Ranking the binding of small molecules to protein receptors through physics-based computation remains challenging. Though inroads have been made using free energy methods, these fail when the underlying classical mechanical force fields are…
While achieving a compression ratio of 2.0 bits/base, the new algorithm codes non-N bases in fixed length. It dramatically reduces the time of coding and decoding than previous DNA compression algorithms and some universal compression…
In tensor completion, the latent nuclear norm is commonly used to induce low-rank structure, while substantially failing to capture the global information due to the utilization of unbalanced unfolding scheme. To overcome this drawback, a…