Related papers: Active flow-driven DNA remodeling generates millim…
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.…
Cytoskeletal active nematics exhibit striking non-equilibrium dynamics that are powered by energy-consuming molecular motors. To gain insight into the structure and mechanics of these materials, we design programmable clusters in which…
We examine the conformations of a model for a short segment of closed DNA. The molecule is represented as a cylindrically symmetric elastic rod with a constraint corresponding to a specification of the linking number. We obtain analytic…
Efficient capture and detection of minute amount of deoxyribonucleic acid (DNA) molecules are pivotal for an array of modern gene technologies which are widely utilized in medical, forensic and defense applications, including DNA…
There is now a certain consensus that Transcription Factors (TFs) reach their target sites, where they regulate gene transcription, via a mechanism dubbed facilitated diffusion (FD). In FD, the TF cycles between events of 3D-diffusion in…
Renaturation of complementary single strands of DNA is one of the important processes that requires better understanding in the view of molecular biology and biological physics. Here we develop a stochastic dynamical model on the DNA…
The response of a short DNA segment to bending is studied, taking into account the anisotropy in the bending rigidities caused by the double-helical structure. It is shown that the anisotropy introduces an effective nonlinear twist-bend…
The tendency for flows in microfluidic systems to behave linearly poses a challenge for designing integrated flow control schemes to carry out complex fluid processing tasks. This hindrance has led to the use of numerous external control…
From a nanoscience perspective, cellular processes and their reduced in vitro imitations provide extraordinary examples for highly robust few or single molecule reaction pathways. A prime example are biochemical reactions involving DNA…
DNA has the potential to realize a controllable liquid-liquid phase separation (LLPS) system, because the design of its base sequences results in programmable interactions. Here, we have developed a novel DNA-based LLPS system which enables…
We investigate the melting transition of non-supercoiled circular DNA of different lengths, employing Brownian dynamics simulation. In the absence of supercoiling, we find that melting of circular DNA is driven by a large bubble, which…
Turbulent shear flows have triggered fundamental research in nonlinear dynamics, like transition scenarios, pattern formation and dynamical modeling. In particular, the control of nonlinear dynamics is subject of research since decades. In…
Genetically encoded regulatory circuits control biological function. A major focus of systems biology is to understand these circuits by establishing the relationship between specific structures and functions. Of special interest are…
Cells operate in part by compartmentalizing chemical reactions. For example, recent work has shown that chromatin, the material that contains the cell's genome, can auto-regulate its structure by utilizing reaction products (proteins, RNA)…
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…
Composites of flexible and rigid polymers are ubiquitous in biology and industry alike, yet the physical principles determining their mechanical properties are far from understood. Here, we couple force spectroscopy with large-scale…
Motor-driven cytoskeletal remodeling in cellular systems can often be accompanied by a diffusive-like effect at local scales, but distinguishing the contributions of the ordering process, such as active contraction of a network, from this…
We study DNA self-assembly and DNA computation using a coarse-grained DNA model within the directional dynamic bonding framework {[}C. Svaneborg, Comp. Phys. Comm. 183, 1793 (2012){]}. In our model, a single nucleotide or domain is…
The macroscopic curvature induced in the double helical B-DNA by regularly repeated adenine tracts (A-tracts) plays an exceptional role in structural studies of DNA because this effect presents the most well-documented example of sequence…
DNA-coated particles are promising as building blocks for functional and finite-sized assemblies because they can be programmed with orthogonal interactions owing to the sequence-specific hybridization of DNA strands. To fully exploit this…