Related papers: A Minimal Model of B-DNA
Graphynes offer a chemically heterogeneous $sp/sp^{2}$ carbon framework with distinct electronic regimes and site-selective reactivity. Here, Density Functional Theory and Reactive Molecular Dynamics Simulations are combined to evaluate…
The collective behavior of the shortest DNA oligomers in high concentration aqueous solutions is an unexplored frontier of DNA science and technology. Here we broaden the realm of DNA nanoscience by demonstrating that single-component…
The spectroscopy and structural dynamics of a deep eutectic mixture (KSCN/acetamide) with varying water content is investigated from 2D IR (with the C-N stretch vibration of the SCN$^-$ anions as the reporter) and THz spectroscopy.…
Nanoscale molecular systems such as DNA require an atomistic quantum treatment to accurately capture their electrical properties, owing to their small dimensions. A central challenge in modeling transport through these systems is the…
The volume occupied by unconstrained bacterial DNA in physiological solutions exceeds 1000 times the volume of the cell. Still, it is confined to a well defined region of the cell called the nucleoid, which occupies only a fraction of the…
To study the elastic properties of rod-like DNA nanostructures, we perform long simulations of these structure using the oxDNA coarse-grained model. By analysing the fluctuations in these trajectories we obtain estimates of the bend and…
Biomolecular condensates are formed via liquid-liquid phase separation of proteins, often together with nucleic acids, typically driven by interactions between low-affinity binding sites. The computational study of such condensates that…
A new methodology is developed to integrate numerically the equations of motion for classical many-body systems in molecular dynamics simulations. Its distinguishable feature is the possibility to preserve, independently on the size of the…
The underlying mechanisms and physics of catalytic Janus microswimmers is highly complex, requiring details of the associated phoretic fields and the physiochemical properties of catalyst, particle, boundaries, and the fuel used. Therefore,…
DNA supercoiling, the under or overwinding of DNA, is a key physical mechanism both participating to compaction of bacterial genomes and making genomic sequences adopt various structural forms. DNA supercoiling may lead to the formation of…
Understanding how soft matter systems, including biological ones, can develop collective electromagnetic phenomena under external fields at ambient conditions remains a central challenge, as thermal fluctuations are generally expected to…
Motivated by explosive releases of energy in fusion, space and astrophysical plasmas, we consider the nonlinear stability of stratified magnetohydrodynamic (MHD) equilibria against two-dimensional interchanges of straight magnetic-flux…
Osmosis plays a central role in the function of living and soft matter systems. While the thermodynamics of osmosis is well understood, the underlying microscopic dynamical mechanisms remain the subject of discussion. Unraveling these…
The effective interaction between two parallel strands of helical bio-molecules, such as deoxyribose nucleic acids (DNA), is calculated using computer simulations of the "primitive" model of electrolytes. In particular we study a simple…
In this work, we show that by varying the experimental conditions, the driving amplitude, a dynamic force microscope allows DNA properties to be selectively imaged. The substrate on which the DNA is fixed is a silica surface grafted with…
The first paper of this series presents a discretely entropy stable discontinuous Galerkin (DG) method for the resistive magnetohydrodynamics (MHD) equations on three-dimensional curvilinear unstructured hexahedral meshes. Compared to other…
Driven dissipative systems at ambient conditions typically exhibit continuous responses shaped by fluctuations and relaxation, with discrete macroscopic states arising only under specific dynamical constraints. Here, we report the emergence…
To survive in ever-changing environments, living organisms need to continuously combine the ongoing external inputs they receive, representing present conditions, with their dynamical internal state, which includes influences of past…
At low densities, electrons confined to two dimensions in a delta-doped heterostructure can arrange themselves into self-consistent droplets due to disorder and screening effects. We use this observation to show that at low temperatures,…
The control over DNA elongation in nanofluidic devices holds great potential for large-scale genomic analysis. So far, the manipulation of DNA in nanochannels has been mostly carried out with electrophoresis and seldom with hydrodynamics,…