Related papers: Binding branched and linear DNA structures: from i…
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…
The double-helical structure of DNA results from canonical base pairing and stacking interactions. However, variations from steady-state conformations result from mechanical perturbations in cells. These different topologies have…
Gel electrophoresis is a powerful experimental method to probe the topology of DNA and other biopolymers. While there is a large body of experimental work which allows us to accurately separate different topoisomers of a molecule, a full…
Inspired by biology's most sophisticated computer, the brain, neural networks constitute a profound reformulation of computational principles. Remarkably, analogous high-dimensional, highly-interconnected computational architectures also…
A theoretical and numerically study of dynamical properties in the sol-gel transition is presented. In particular, the complex phenomenology observed experimentally and numerically in gelling systems is reproduced in the framework of…
We investigate the linear viscoelasticity of polymer gels produced by the dispersion of gluten proteins in water:ethanol binary mixtures with various ethanol contents, from pure water to 60% v/v ethanol. We show that the complex…
We systematically study the relationship between equilibrium and non-equilibrium phase diagrams of a system of short-ranged attractive colloids. Using Monte Carlo and Brownian dynamics simulations we find a window of enhanced…
Blends of polymers of different topologies, such as ring and supercoiled, naturally occur in biology and often exhibit emergent viscoelastic properties coveted in industry. However, due to their complexity, along with the difficulty of…
Polypeptide-based diblock copolymers forming either well-defined self-assembled micelles or vesicles after direct dissolution in water or in dichloromethane, have been studied combining light and neutron scattering with electron microscopy…
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…
Cells deploy robust mechanisms to repair DNA damage, safeguarding genomic stability and cellular health, but the physical principles underlying these processes remain incompletely understood. Experiments show \emph{in vitro} that upon a DNA…
In this paper we consider a physical system in which two DNA molecules braid about each other. The distance between the two molecular ends, on either side of the braid, is held at a distance much larger than supercoiling radius of the…
Our study aims at a better control and understanding of the transfer of a complex [DNA supercoiled plasmid - dodecyltrimethylammonium surfactant] layer from a liquid-vapour water interface onto a silicon surface without any additional…
The closure dynamics of a pre-equilibrated DNA denaturation bubble is studied using both Brownian dynamics simulations and an analytical approach. The numerical model consists of two semi-flexible interacting single strands (ssDNA) and a…
Nearly thirty years after its inception, the field of DNA-programmed colloidal self-assembly has begun to realize its initial promise. In this review, we summarize recent developments in designing effective interactions and understanding…
Fluorescence microscopy reveals that the contents of many (membrane-free) nuclear "bodies" exchange rapidly with the soluble pool whilst the underlying structure persists; such observations await a satisfactory biophysical explanation. To…
Making use of a simplified model for protein folding, it can be shown that conformations which are particularly stable when their energy is minimized with respect to amino acid sequence (in the sense that they display a large energy gap to…
The dynamical arrest of gels is the consequence of a well defined structural phase transition, leading to the formation of a spanning cluster of bonded particles. The dynamical glass transition, instead, is not accompanied by any clear…
The development of novel strategies for self-assembly in the field of nanotechnology has witnessed remarkable progress in recent years. Here, we present a DNA-driven programmable self-assembly to fabricate the targeted nanophotonic…
We study theoretically a binary system in which an attraction of unlike particles is combined with a type-independent soft core repulsion. The possible experimental implementation of the system is a mixture of DNA-covered colloids, in which…