Related papers: Modelling DNA Origami Self-Assembly at the Domain …
Origami inspired architectures offer a powerful route toward lightweight, reconfigurable, and programmable robotic systems. Yet, a unified mechanics framework capable of seamlessly bridging rigid folding, elastic deformation, and stability…
All observations of photodegradation and self healing follow the predictions of the correlated chromophore domain model. [Ramini et.al. Polym. Chem., 2013, 4, 4948.] In the present work, we generalize the domain model to describe the…
We characterize the equilibrium thermodynamics of a thick polymer confined in a spherical region of space. This is used to gain insight into the DNA packaging process. The experimental reference system for the present study is the recent…
The observation by Ke et al. [Science 338, 1177 (2012)] that large numbers of short, pre-designed DNA strands can assemble into three-dimensional target structures came as a great surprise, as no colloidal self-assembling system has ever…
The dynamics of loops at the DNA denaturation transition is studied. A scaling argument is used to evaluate the asymptotic behavior of the autocorrelation function of the state of complementary bases (either open or closed). The long-time…
There is a long-standing experimental observation that the melting of topologically constrained DNA, such as circular-closed plasmids, is less abrupt than that of linear molecules. This finding points to an intriguing role of topology in…
We present an analytically solvable model for self-assembly of a molecular complex on a filament. The process is driven by a seed molecule that undergoes facilitated diffusion, which is a search strategy that combines diffusion in…
The binding of proteins onto DNA contributes to the shaping and packaging of genome as well as to the expression of specific genetic messages. With a view to understanding the interplay between the presence of proteins and the deformation…
Tile assembly systems in the abstract Tile Assembly Model (aTAM) are computationally universal and capable of building complex shapes, but DNA-based implementations encounter formidable error rates that stifle this theoretical potential.…
In this paper we show that a dynamical description of the protein folding process provides an effective representation of equilibrium properties and it allows for a direct investigation of the mechanisms ruling the approach towards the…
Propagating transition fronts, in which local interactions sequentially trigger state changes, are widely observed across natural, biological, and engineered systems. While such propagation has been engineered using energy-driven…
Using theory and simulations, we carried out a first systematic characterization of DNA unzipping via nanopore translocation. Starting from partially unzipped states, we found three dynamical regimes depending on the applied force, f: (i)…
Recent advancements in microbiology have motivated the study of the production of nanostructures with applications such as biomedical computing and molecular robotics. One way to construct these structures is to construct branched DNA…
We develop a continuum elastic approach to examining the bending mechanics of semiflexible filaments with a local internal degree of freedom that couples to the bending modulus. We apply this model to study the nonlinear mechanics of a…
We study sequence dependent complexation between oligonucleotides (single strand DNA) and various generation ethylene diamine (EDA) cored poly amido amide (PAMAM) dendrimers through atomistic molecular dynamics simulations accompanied by…
In many biopolymer solutions, attractive interactions that stabilize finite-sized clusters at low concentrations also promote phase separation at high concentrations. Here we study a model biopolymer system that exhibits the opposite…
The mechanical properties of thermally excited two-dimensional crystalline membranes can depend dramatically on their geometry and topology. A particularly relevant example is the effect on the crumpling transition of holes in the membrane.…
The use of origami in engineering has significantly expanded in recent years, spanning deployable structures across scales, folding robotics, and mechanical metamaterials. However, finding foldable paths can be a formidable task as the…
Self-positioned nanomembranes such as rolled-up tubes and wrinkled thin films have been potential systems for a variety of applications and basic studies on elastic properties of nanometer-thick systems. Although there is a clear driving…
Several controversial issues concerning the packing of linear DNA in bacteriophages and globules are discussed. Exact relations for the osmotic pressure, capsid pressure and loading force are derived in terms of the hole size inside phages…