Related papers: Single DNA conformations and biological function
We use a coarse-grained model of DNA-functionalized particles to understand the role of DNA chain length on their self-assembly. We find that the increasing chain length for a given particle size decreases the propensity to form ordered…
This dissertation explores the application of machine learning in molecular biology, focusing on gene expression regulation and cellular behavior at the single-cell level. Using modern neural networks, the research addresses key challenges…
Due to its longevity and enormous information density, DNA is an attractive medium for archival data storage. Thanks to rapid technological advances, DNA storage is becoming practically feasible, as demonstrated by a number of experimental…
The computational modelling of DNA is becoming crucial in light of new advances in DNA nanotechnology, single-molecule experiments and in vivo DNA tampering. Here we present a mesoscopic model for double stranded DNA (dsDNA) at the single…
Solid-state nanopore and nanopipette sensors are powerful devices for the detection, quantification and structural analysis of biopolymers such as DNA and proteins, especially in carrier-enhanced resistive-pulse sensing. However, hundreds…
In many cases, transcriptional regulation involves the binding of transcription factors at sites on the DNA that are not immediately adjacent to the promoter of interest. This action at a distance is often mediated by the formation of DNA…
DNA looping has been observed to enhance and suppress transcriptional noise but it is uncertain which of these two opposite effects is to be expected for given conditions. Here, we derive analytical expressions for the main quantifiers of…
Single polymer dynamics offers a powerful approach to study molecular-level interactions and dynamic microstructure in materials. Direct visualization of single chain dynamics has uncovered new ideas regarding the rheology and…
A general theoretical framework is put forth to organize and understand various observed phenomena and mathematical relationships in the field of molecular biology. By modeling each cell in eukaryotic organisms as a processor having a…
We present Brownian dynamics simulations of the facilitated diffusion of a protein, modelled as a sphere with a binding site on its surface, along DNA, modelled as a semi-flexible polymer. We consider both the effect of DNA organisation in…
We study the electric properties of single-stranded DNA molecules with hairpin-like shapes in the presence of a magnetic flux. It is shown that the current amplitude can be modulated by the applied field. The details of the electric…
Just like atoms combine into molecules, colloids can self-organize into predetermined structures according to a set of design principles. Controlling valence -- the number of inter-particle bonds -- is a prerequisite for the assembly of…
Found in all eukaryotic cells, linker histones H1 are known to bind to and rearrange nucleosomal linker DNA. In vitro, the fundamental nature of H1/DNA interactions has attracted wide interest among research communities - for biologists…
We study the elastic behaviour of a supercoiled DNA molecule. The simplest model is that of a rod like chain, involving two elastic constants, the bending and the twist rigidities. We show that this model is singular and needs a small…
The dynamics of particles interacting by key-lock binding of attached biomolecules are studied theoretically. Examples of such systems include DNA-functionalized colloids as well as nanoparticles grafted with antibodies to cell membrane…
Single-molecule biophysics has transformed our understanding of the fundamental molecular processes involved in living biological systems, but also of the fascinating physics of life. Far more exotic than a collection of exemplars of soft…
In living cells, proteins combine 3D bulk diffusion and 1D sliding along the DNA to reach a target faster. This process is known as facilitated diffusion, and we investigate its dynamics in the physiologically relevant case of confined DNA.…
The capture and translocation of biomolecules through nanometer-scale pores are processes with a potential large number of applications, and hence they have been intensively studied in the recent years. The aim of this paper is to review…
DNA is an essential molecule central to the survival and propagation of life, it was imperative to investigate possible electromagnetic properties inherent to it, such as the existence of any non-trivial interactions of this molecule with…
Several processes in the cell, such as gene regulation, start when key proteins recognise and bind to short DNA sequences. However, as these sequences can be hundreds of million times shorter than the genome, they are hard to find by simple…