Related papers: Crowding induces entropically-driven changes to DN…
The percentage and sequence of AT and GC base pairs and charges on the DNA backbone contribute significantly to the stiffness of DNA. This elastic property of DNA also changes with small interacting ligands. The single-molecule force…
Molecular combing is a powerful and simple method for aligning DNA molecules onto a surface. Using this technique combined with fluorescence microscopy, we observed that the length of lambda-DNA molecules was extended to about 1.6 times…
Colloidal mixtures represent a versatile model system to study transport in complex environments. They allow for a systematic variation of the control parameters, namely size ratio, total volume fraction and composition. We study the…
We use a nanofluidic system to investigate the emergence of thermally driven collective phenomena along a single polymer chain. In our approach, a single DNA molecule is confined in a nanofluidic slit etched with arrays of embedded…
Many recent studies of liquid-liquid phase separation in biology focus on phase separation as a dynamic control mechanism for cellular function, but it can also result in complex mesoscopic structures. We primarily investigate a model…
According to the experimental evidence damage induced by densely ionizing radiation in mammalian cells is distributed along the DNA molecule in the form of clusters. The most critical constituent of DNA damage are double-strand breaks…
Motivated by the fine compositional control observed in membraneless droplet organelles in cells, we investigate how a sharp binding-unbinding transition can occur between multivalent client molecules and receptors embedded in a porous…
Motivated by recent nanofluidics experiments, we use Brownian dynamics and Monte Carlo simulations to study the conformation, organization and dynamics of two polymer chains confined to a single box-like cavity. The polymers are modeled as…
We examine by extensive computer simulations the self-diffusion of anisotropic star like particles in crowded two-dimensional solutions. We investigate the implications of the area coverage fraction $\phi$ of the crowders and the…
Environmental changes greatly influence the evolution of populations. Here, we study the dynamics of a population of two strains, one growing slightly faster than the other, competing for resources in a time-varying binary environment…
Owing to its longevity and enormous information density, DNA, the molecule encoding biological information, has emerged as a promising archival storage medium. However, due to technological constraints, data can only be written onto many…
As a key molecule of Life, Deoxyribonucleic acid (DNA) is the focus of numbers of investigations with the help of biological, chemical and physical techniques. From a physical point of view, both experimental and theoretical works have…
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…
DNA and other biopolymers differ from classical polymers due to their torsional stiffness. This property changes the statistical character of their conformations under tension from a classical random walk to a problem we call the `torsional…
The diffusion type is determined not only by microscopic dynamics but also by the environment properties. For example, the environment's fractal structure is responsible for the emergence of subdiffusive scaling of the mean square…
We investigate knotting probabilities of long double-stranded DNA strands in a coarse-grained Kratky-Porod model for DNA with Monte Carlo simulations. Various ionic conditions are implemented by adjusting the effective diameter of monomers.…
We present an extensive theoretical investigation of the mechanical unzipping of double-stranded DNA under the influence of an applied force. In the limit of long polymers, there is a thermodynamic unzipping transition at a critical force…
To explore the coupling between a growing population of microorganisms such as E. coli and a nonuniform nutrient distribution, we formulate a minimalistic model. It consists of active Brownian particles that divide and grow at a…
Most living systems rely on double-stranded DNA (dsDNA) to store their genetic information and perpetuate themselves. This biological information has been considered the main target of evolution. However, here we show that symmetries and…
A theory is presented for the binding of small molecules such as surfactants to semiflexible polymers. The persistence length is assumed to be large compared to the monomer size but much smaller than the total chain length. Such polymers…