Related papers: Modelling DNA Origami Self-Assembly at the Domain …
DNA supercoiling is central to many fundamental processes of living organisms. Its average level along the chromosome and over time reflects the dynamic equilibrium of opposite activities of topoisomerases, which are required to relax…
Simple expressions for the bending and the base-stacking energy of double-stranded semiflexible biopolymers (such as DNA and actin) are derived. The distribution of the folding angle between the two strands is obtained by solving a…
Origami structures have been receiving a lot of attention from engineering and scientific researchers owing to their unique properties such as deployability, multi-stability, negative stiffness, etc. However, dynamic properties of origami…
We explore the surprisingly rich energy landscape of origami-like folding planar structures. We show that the configuration space of rigid-paneled degree-4 vertices, the simplest building blocks of such systems, consists of at least two…
Deployable mechanical systems such as space solar panels rely on the intricate stowage of passive modules, and sophisticated deployment using a network of motorized actuators. As a result, a significant portion of the stowed mass and volume…
In this study, we examine a rapid and reversible origami folding method by exploiting a combination of resonance excitation, asymmetric multi-stability, and active control. The underlying idea is that, by harmonically exciting a…
Polymer filaments form the foundation of biology from cell scaffolding to DNA. Their study and fabrication play an important role in a wide range of processes from tissue engineering to molecular machines. We present a simple method to…
Stiffness degradation and progressive failure of composite laminates are complex processes involving evolution and multi-mode interactions among fiber fractures, intra-ply matrix cracks and inter-ply delaminations. This paper presents a…
The mechanical properties of DNA are typically described by elastic theories with purely local couplings (on-site models). We discuss and analyze coarse-grained (oxDNA) and all-atom simulations, which indicate that in DNA distal sites are…
Phase diagram of the ground states of DNA in a bad solvent is studied for a semi-flexible polymer model with a generalized local elastic bending potential characterized by a nonlinearity parameter $x$ and effective self-attraction promoting…
The mechanical model based on beads and springs, which we recently proposed to study non-specific DNA-protein interactions [J. Chem. Phys. 130, 015103 (2009)], was improved by describing proteins as sets of interconnected beads instead of…
We study the ground-state entanglement of gapped domain walls between topologically ordered systems in two spatial dimensions. We derive a universal correction to the ground-state entanglement entropy, which is equal to the logarithm of the…
We predict the existence of a totally new class of phases in weakly coupled, three-dimensional stacks of two-dimensional (2D) XY-models. These ``sliding phases'' behave essentially like decoupled, independent 2D XY-models with precisely…
Branched junction molecule assembly of DNA nanostructures, pioneered by Seeman's laboratory in the 1980s, has become increasingly sophisticated, as have the assembly targets. A critical design step is finding minimal sets of branched…
Multistep denaturation in a short circular DNA molecule is analyzed by a mesoscopic Hamiltonian model which accounts for the helicoidal geometry. Computation of melting profiles by the path integral method suggests that stacking…
The mechanical properties of molecules are today captured by single molecule manipulation experiments, so that polymer features are tested at a nanometric scale. Yet devising mathematical models to get further insight beyond the commonly…
We present a dynamical model of DNA mechanical unzipping under the action of a force. The model includes the motion of the fork in the sequence-dependent landscape, the trap(s) acting on the bead(s), and the polymeric components of the…
The folding transition of biopolymers from the coil to compact structures has attracted wide research interest in the past and is well studied in polymer physics. Recent seminal works on DNA in confined devices have shown that these long…
DNA bending is biologically important for genome regulation and is relevant to a range of nanotechnological systems. Recent results suggest that sharp bending is much easier than implied by the widely-used worm-like chain model; many of…
We investigate the evolutionary dynamics of an idealised model for the robust self-assembly of two-dimensional structures called polyominoes. The model includes rules that encode interactions between sets of square tiles that drive the…