Related papers: Single-Base DNA Discrimination via Transverse Ioni…
We consider the problem of storing and retrieving information from synthetic DNA media. The mathematical basis of the problem is the construction and design of sequences that may be discriminated based on their collection of substrings…
It is a standard exercise in mechanical engineering to infer the external forces and torques on a body from its static shape and known elastic properties. Here we apply this kind of analysis to distorted double-helical DNA in complexes with…
Single-particle tracking allows to infer the motion of single molecules in living cells. When we observe a long trajectory (more than 100 points), it is possible that the particle switches mode of motion over time. Then, fitting a single…
It has been recently shown that a viscosity gradient could drive electrical current through a negatively charged nanochannel (Wiener and Stein, arXiv: 1807.09106). To understand the physics underlying this phenomenon, we employed the…
Charge diffusion through desoxyribonucleic acid (DNA) is a physico-chemical phenomenon that on the one hand is being explored for technological purposes, on the other hand is applied by nature for various informational processes in life.…
We propose a dynamical model for the secondary structure of DNA, which is based on the finite stacking enthalpies used in thermodynamics calculations. In this model, the two strands can separate and the bases are allowed to rotate…
The sequence-dependent structural variability and conformational dynamics of DNA play pivotal roles in many biological milieus, such as in the site-specific binding of transcription factors to target regulatory elements. To better…
Transfection of an anionic polynucleotide through a negatively charged membrane is an important problem in genetic engineering. The direct association of cationic surfactant to DNA decreases the effective negative charge of the nucleic…
The question of whether DNA is intrinsically conducting or not is still a challenge. The ongoing debate on DNA molecules as an electronic material has so far underestimated a key distinction of the system: the role of base pairing (inter…
We study theoretically the in vitro evolution of a DNA sequence by binding to a transcription factor. Using a simple model of protein-DNA binding and available binding constants for the Mnt protein, we perform large-scale, realistic…
We develop a new approach to electron transport in mesoscopic systems by using a particular single-particle basis. Although this basis generates redundant many-particle amplitudes, it greatly simplifies the treatment. By using our method…
We present a short review of various experiments that measure charge transfer and charge transport in DNA. Some general comments are made on the possible connection between 'chemistry-style' charge transfer experiments that probe…
DNA storage is now being considered as a new archival storage method for its durability and high information density, but still facing some challenges like high costs and low throughput. By reducing sequencing sample size for decoding…
Digital information can be encoded in the building-block sequence of macro-molecules, such as RNA and single-stranded DNA. Methods of "writing" and "reading" macromolecular strands are currently available, but they are slow and expensive.…
Ion channels regulate many essential properties of biological cells, especially the membrane potential. Despite decades of efforts on artificial channels, it remains a great challenge to mimic the dipole potential-an indispensable…
The purpose of this work is to extend the Geant4-DNA Monte Carlo toolkit to include electron interactions with the four DNA bases using a set of cross sections recently implemented in Geant-DNA CPA100 models and available for liquid water.…
Trajectory inference is used to order single-cell omics data along a path that reflects a continuous transition between cells. This approach is useful for studying processes like cell differentiation, where a stem cell matures into a…
Background: Trace quantities of contaminating DNA are widespread in the laboratory environment, but their presence has received little attention in the context of high throughput sequencing. This issue is highlighted by recent works that…
By resorting to a model inspired to the standard Davydov and Holstein-Fr\"ohlich models, in the present paper we study the motion of an electron along a chain of heavy particles modelling a sequence of nucleotides proper to a DNA fragment.…
We introduce a probabilistic model for protein sliding motion along DNA during the search of a target sequence. The model accounts for possible effects due to sequence-dependent interaction between the nonspecific DNA and the protein. As an…