Related papers: Numerical evidence for nucleated self-assembly of …
We investigate the power of the Wang tile self-assembly model at temperature 1, a threshold value that permits attachment between any two tiles that share even a single bond. When restricted to deterministic assembly in the plane, no…
Genomes contain rare guanine-rich sequences capable of assembling into four-stranded helical structures, termed G-quadruplexes, with potential roles in gene regulation and chromosome stability. Their mechanical unfolding has only been…
An important goal of self-assembly is to achieve a preprogrammed structure with high fidelity. Here, we control the valence of DNA-functionalized emulsions to make linear and branched model polymers, or `colloidomers'. The distribution of…
We study the self-assembly on a spherical surface of a model for a binary mixture of amphiphilic dimers in the presence of guest particles via Monte Carlo (MC) computer simulation. All particles have a hard core, but one monomer of the…
Inverted repeat (IR) sequences in DNA can form non-canonical cruciform structures to relieve torsional stress. We use Monte Carlo simulations of a recently developed coarse-grained model of DNA to demonstrate that the nucleation of a…
Nanoparticles with "sticky patches" have long been proposed as building blocks for the self-assembly of complex structures. The synthetic realizability of such patchy particles, however, greatly lags behind predictions of patterns they…
We present a lattice Monte Carlo simulation for a multiblock copolymer chain of length N=240 and microarchitecture $(10-10)_{12}$.The simulation was performed using the Monte Carlo method with the Metropolis algorithm. We measured average…
DNA origami consists of a long scaffold strand and short staple strands that self-assemble into a target 2D or 3D shape. It is a widely used construct in nucleic acid nanotechnology, offering a cost-effective way to design and create…
The recently proposed compressed backbone theory suggested that the intrinsic curvature in DNA can result from a geometric mismatch between the specific backbone length and optimal base stacking orientations. It predicted that the curvature…
The evolution of multicellular organisms from monocellular ancestors represents one of the greatest advances of the history of life. The assembly of such multicellular organisms requires signalling and response between cells: over millions…
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…
Understanding the relationship between colloidal building block shape and self-assembled material structure is important for the development of novel materials by self-assembly. In this regard, colloidal superballs are unique building…
We present a numerical analysis of a DNA hydrogel that consists of three-valent Y-shaped DNA molecules. The building blocks self-assemble fully reversibly from complementary single-stranded DNA segments. We compare melting curves from both…
Cellular functions are established through biological evolution, but are constrained by the laws of physics. For instance, the physics of protein folding limits the lengths of cellular polypeptide chains. Consequently, many cellular…
Atomic-accuracy structure prediction of macromolecules is a long-sought goal of computational biophysics. Accurate modeling should be achievable by optimizing a physically realistic energy function but is presently precluded by incomplete…
A series of simulations aimed at elucidating the self-assembly dynamics of spherical virus capsids is described. This little-understood phenomenon is a fascinating example of the complex processes that occur in the simplest of organisms.…
The design of complex materials and the formation of specific patterns often arise from the properties of the individual building blocks. In this respect, colloidal systems offer a unique opportunity because nowadays they can be synthesized…
The sequence-dependent elasticity of double-helical DNA on a nm length scale can be captured by the rigid base-pair model, whose strains are the relative position and orientation of adjacent base-pairs. Corresponding elastic potentials have…
Elastic sheets with macroscopic dimensions are easy to deform by bending and stretching. Yet shaping nanometric sheets by mechanical manipulation is hard. Here we show that nanoparticle self-assembly could be used to this end. We…
Conventional wisdom presumes that low-coordinated crystal ground states require directional interactions. Using our recently introduced optimization procedure to achieve self-assembly of targeted structures (Phys. Rev. Lett. 95, 228301…