Related papers: Simulations of DNA-origami self-assembly reveal de…
Optical nanoantennas can affect the decay rates of nearby emitters by modifying the local density of photonic states around them. In the weak-coupling limit, and according to the Fermi's Golden Rule, the emission spectrum of a dye is given…
Within biology, it is of interest to construct DNA complexes of a certain shape. These complexes can be represented through graph theory, using edges to model strands of DNA joined at junctions, represented by vertices. Because guided…
The rate of second layer nucleation -- the formation of a stable nucleus on top of a two-dimensional island -- determines both the conditions for layer-by-layer growth, and the size of the top terrace of multilayer mounds in…
Phase transitions ruled by nucleation and growth can occur by nonrandom arrangement of nuclei. This is verified, for instance, in thin film growth at solid surfaces by vapor condensation or by electrodeposition where, around each nucleus, a…
Nanoparticles of plasmonic metals have significantly to the development of spectroscopic techniques, enabling strong confinement of electromagnetic fields at the nanoscale and corresponding signal amplification. However, to date, plasmonic…
The equilibrium statistical properties of DNA denaturation bubbles are examined in detail within the framework of the Peyrard-Bishop-Dauxois model. Bubble formation in homogeneous DNA is found to depend crucially on the presence of…
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…
A theory of the unzipping of double-stranded (ds) DNA is presented, and is compared to recent micromanipulation experiments. It is shown that the interactions which stabilize the double helix and the elastic rigidity of single strands (ss)…
The mechanism and driving forces of chromosome segregation in the bacterial cell cycle of E. coli is one of the least understood events in its life cycle. Using principles of entropic repulsion between polymer loops confined in a cylinder,…
Programmable folding of elastic sheets typically relies on predefined flexible creases or active materials-enabled hinges, which lack intrinsic bistability and limit reprogrammability within a single structure. Here, we present a…
The issue of the nucleation and slow closure mechanisms of non superhelical stress-induced denaturation bubbles in DNA is tackled using coarse-grained MetaDynamics and Brownian simulations. A minimal mesoscopic model is used where the…
We investigate the role of thermal fluctuations and of the finite number of monomers in small clusters of carbon atoms on the nucleation rate of carbonaceous grains. Thermal fluctuations are due to the quantized nature of the energy…
The conventional theory of homogeneous and heterogeneous nucleation in a supersaturated vapor is tested by Monte Carlo simulations of the lattice gas (Ising) model with nearest-neighbor attractive interactions on the simple cubic lattice.…
In this paper we introduce a new method to design interparticle interactions to target arbitrary crystal structures via the process of self-assembly. We show that it is possible to exploit the curvature of the crystal nucleation free-energy…
We investigate the salt-dependent current modulation of bundled DNA nanostructures in a nanopore. To this end, we developed four simulation models for a 2x2 origami structure with increasing level of detail: from the mean-field level to an…
Biopolymer self-assembly pathways are central to biological activity, but are complicated by the ability of the monomeric subunits of biopolymers to adopt different conformational states. As a result, biopolymer nucleation often involves a…
Self assembly is a process by which supramolecular species form spontaneously from their components. This process is ubiquitous throughout the life chemistry and is central to biological information processing. It has been predicted that in…
Background: It is of biological interest to make genome-wide predictions of the locations of DNA melting bubbles using statistical mechanics models. Computationally, this poses the challenge that a generic search through all combinations of…
Experiments [1] have shown that auto-kirigami structures can grow on the surface of graphene because the graphene-graphene adhesion energy is greater than the graphene-substrate interaction. In this work molecular dynamics (MD) simulations…
Associative polymers (APs) with reversible, specific interactions between ``sticker'' sites exhibit a phase behavior that depends on a delicate balance between distinct contributions controlling the binding. For highly-bonded systems, it is…