Related papers: Nanosecond chain dynamics of single-stranded nucle…
Nucleic acids have been regarded as stiff polymers with long-range flexibility and generally modeled using elastic rod models of polymer physics. Notwithstanding, investigations carried out over the past few years on single fragments of…
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…
We explore the dynamics of a tracer in an active particle harmonic chain, investigating the influence of interactions. Our analysis involves calculating mean-squared displacements (MSD) and space-time correlations through Green's function…
The proper design of DNA sequences allows for the formation of well defined supramolecular units with controlled interactions via a consecution of self-assembling processes. Here, we benefit from the controlled DNA self-assembly to…
Numerical modeling of electrodynamic aggregation is carried out for a random ensemble of magnetized nanodust taken as a many body system of strongly magnetized thin rods (i.e., one-dimensional static magnetic dipoles), which possess…
Nucleic acids are highly deformable helical molecules constantly stretched, twisted and bent in their biological functioning. Single molecule experiments have shown that double stranded (ds)-RNA and standard ds-DNA have opposite…
Single-chain nanoparticles (SCNPs) are ultrasoft objects obtained through purely intramolecular cross-linking of single polymer chains. By means of computer simulations with implemented hydrodynamic interactions, we investigate for the…
Shear banding, or localization of intense strains along narrow bands, is a plastic instability in solids with important implications for material failure in a wide range of materials and across length-scales. In this paper, we report on a…
The structural flexibility of nucleic acids plays a key role in many fundamental life processes, such as gene replication and expression, DNA-protein recognition, and gene regulation. To obtain a thorough understanding of nucleic acid…
Crystallization of supersaturated liquids usually starts by heterogeneous nucleation. Mounting evidence shows that even homogeneous nucleation in simple liquids takes place in two steps; first a dense amorphous precursor forms, and the…
Simple elastic network models of DNA were developed to reveal the structure-dynamics relationships for several nucleotide sequences. First, we propose a simple all-atom elastic network model of DNA that can explain the profiles of…
Using nonequilibrium computer simulations, we study the response of ferromagnetic nanofilaments, consisting of stabilized onedimensional chains of ferromagnetic nanoparticles, under external rotating magnetic fields. In difference with…
Polylactic acid (PLA) nanofibrous networks have gained substantial interest across various engineering and scientific disciplines, such as tissue engineering, drug delivery, and filtration, due to their unique and multifunctional…
We uncover a chain of nonlinear modal interactions in softly clamped nanostring resonators. The process involves the sequential coupling of five mechanical modes, during frequency sweeps, yielding a broad nonlinear response with nearly…
Charged colloidal particles can self-assemble into gel networks upon screening of electrostatic repulsion by added salt. While gelation of spherical colloids has been extensively studied, much less is known about the gelation dynamics of…
By means of extensive simulations, we investigate concentrated solutions of globular single-chain nanoparticles (SCNPs), an emergent class of synthetic soft nano-objects. By increasing the concentration, the SCNPs show a reentrant behaviour…
The two strands of a DNA molecule with a repetitive sequence can pair into many different basepairing patterns. For perfectly periodic sequences, early bulk experiments of Poerschke indicate the existence of a sliding process, permitting…
Biomolecular condensates form by phase separation of biological polymers and have important functions in the cell $-$ functions that are inherently connected to their physical properties. A remarkable aspect of such condensates is that…
Atomically detailed simulations of RNA folding have proven very challenging in view of the difficulties of developing realistic force fields and the intrinsic computational complexity of sampling rare conformational transitions. To tackle…
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…