Related papers: Dynamical Scaling and Phase Coexistence in Topolog…
We present a coarse-grained model of DNA-functionalized colloids that is computationally tractable. Importantly, the model parameters are solely based on experimental data. Using this highly simplified model, we can predict the phase…
We present a self-contained theory for the mechanical response of DNA in single molecule experiments. Our model is based on a 1D continuum description of the DNA molecule and accounts both for its elasticity and for DNA-DNA electrostatic…
The spatial organization of DNA involves DNA loop extrusion and the formation of protein-DNA condensates. While the significance of each process is increasingly recognized, their interplay remains unexplored. Using molecular dynamics…
In colloidal systems, Brownian motion emerges from the massive separation of time and length scales associated to characteristic dynamics of the solute and solvent constituents. This separation of scales produces several temporal regimes in…
The three-dimensional organization of chromatin is thought to play an important role in controlling gene expression. Specificity in expression is achieved through the interaction of transcription factors and other nuclear proteins with…
We propose a new strategy to improve the self-assembly properties of DNA-functionalised colloids. The problem that we address is that DNA-functionalised colloids typically crystallize in a narrow temperature window, if at all. The…
A continuum theory is used to predict scaling laws for the morphological relaxation of crystal surfaces in two independent space dimensions. The goal is to unify previously disconnected experimental observations of decaying surface…
DNA melting and hybridization is a fundamental biological process as well as a crucial step in many modern biotechnology applications. DNA confined on surfaces exhibits different behavior from that in free solutions. The system of…
DNA is an astonishing material that can be used as a molecular building block to construct periodic arrays and devices with nanoscale accuracy and precision. Here, we present simple bead-spring model of DNA nanostars having three, four and…
In a companion paper, we put forth a thermodynamic model for complex formation via a chemical reaction involving multiple macromolecular species, which may subsequently undergo liquid-liquid phase separation and a further transition into a…
The basic physics of nucleation in solid \hl{single-crystal} nanoparticles is revealed by a phase-field theory that includes surface energy, chemical reactions and coherency strain. In contrast to binary fluids, which form arbitrary contact…
We study crystal nucleation under the influence of sedimentation in a model of colloidal hard spheres via Brownian Dynamics simulations. We introduce two external fields acting on the colloidal fluid: a uniform gravitational field (body…
The stability of organic solar cells is strongly affected by the morphology of the photoactive layers, whose separated crystalline and/or amorphous phases are kinetically quenched far from their thermodynamic equilibrium during the…
Computer simulations and scaling theory are used to investigate the damping of oscillations during epitaxial growth on high-symmetry surfaces. The crossover from smooth to rough growth takes place after the deposition of (D/F)^\delta…
The interplay between bending of the molecule axis and appearance of disruptions in circular DNA molecules, with $\sim 100$ base pairs, is addressed. Three minicircles with different radii and almost equal content of AT and GC pairs are…
DNA-spools, structures in which DNA is wrapped and helically coiled onto itself or onto a protein core are ubiquitous in nature. We develop a general theory describing the non-equilibrium behavior of DNA-spools under linear tension. Two…
We investigate the denaturation dynamics of nucleic acids through extensive molecular dynamics simulations of a coarse-grained RNA hairpin model. In apparent contradiction with Arrhenius' law, our findings reveal that the denaturation time…
Bacterial genomes are partitioned into kilobases long domains that are topologically independent from each other, meaning that change of DNA superhelicity in one domain does not propagate to neighbours. This is made possible by proteins…
Non-aligning self-propelled particles with purely repulsive excluded volume interactions undergo athermal motility-induced phase separation into a dilute gas and a dense cluster phase. Here, we use enhanced sampling computational methods…
The phase diagram of a water solution of DNA and oppositely charged spherical macroions is studied. DNA winds around spheres to form beads-on-a-string complexes resembling the chromatin 10 nm fiber. At small enough concentration of spheres…