Related papers: Irregular model DNA particles self-assemble into a…
We study DNA self-assembly and DNA computation using a coarse-grained DNA model within the directional dynamic bonding framework {[}C. Svaneborg, Comp. Phys. Comm. 183, 1793 (2012){]}. In our model, a single nucleotide or domain is…
Co-assembly of inorganic nanoparticles (NPs) and nanostructured polymer matrix represents an intricate interplay of enthalpic or entropic forces. Particle size largely affects the phase behavior of the nanocomposite. Theoretical studies…
We demonstrate that the self-similarity of some scale-free networks with respect to a simple degree-thresholding renormalization scheme finds a natural interpretation in the assumption that network nodes exist in hidden metric spaces.…
In the frameworks of algebraic topology {\alpha}-helix and different DNA-conformations are determined as the local latticed packing, confined by peculiar minimal surfaces which are similar to helicoids. These structures are defined by…
Natural and man-made transport webs are frequently dominated by dense sets of nested cycles. The architecture of these networks, as defined by the topology and edge weights, determines how efficiently the networks perform their function.…
We simulate the assembly of DNA copolymers from two types of short duplexes (short double strands with a single-stranded overhang at each end), as described by the oxDNA model. We find that the statistics of chain lengths can be well…
The mechanics of complex soft matter often cannot be understood in the classical physical frame of flexible polymers or rigid rods. The underlying constituents are semiflexible polymers, whose finite bending stiffness ($\kappa$) leads to…
Flow-driven rotary motors drive functional processes in human society such as windmills and water wheels. Although examples of such rotary motors also feature prominently in cell biology, their synthetic construction at the nanoscale has…
We use molecular dynamics to study the ordering of a nematic liquid crystal around a spherical particle or droplet. Homeotropic boundary conditions and strong anchoring create a hedgehog director configuration on the particle surface and in…
Colloidal particles grafted with single-stranded DNA (ssDNA) chains can self-assemble into a number of different crystalline structures, where hybridization of the ssDNA chains creates links between colloids stabilizing their structure.…
Short blunt-ended DNA duplexes comprising 6 to 20 base pairs self-assemble into polydisperse semi-flexible chains due to hydrophobic stacking interactions between terminal base pairs. Above a critical concentration, which depends on…
Natural materials often feature a combination of soft and stiff phases, arranged to achieve excellent mechanical properties, such as high strength and toughness. Many natural materials have even independently evolved to have similar…
Ensembles of particles rotating in a two-dimensional fluid can exhibit chaotic dynamics yet develop signatures of hidden order. Such "rotors" are found in the natural world spanning vastly disparate length scales - from the rotor proteins…
Discovery of atomistic systems with desirable properties is a major challenge in chemistry and material science. Here we introduce a novel, autoregressive, convolutional deep neural network architecture that generates molecular equilibrium…
We study two mechanisms for the formation of protein patterns near membranes of living cells by mathematical modelling. Self-assembly of protein domains by electrostatic lipid-protein interactions is contrasted with self-organization due to…
Cooperative self-assembly can result in complex nano-networks with new hyperbolic geometry. However, the relation between the hyperbolicity and spectral and dynamical features of these structures remains unclear. Using the model of…
We explore the use of templated self-assembly to facilitate the formation of complex target structures made from patchy particles. First, we consider the templating of high-symmetry shell structures around a spherical core particle. We find…
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…
We use computer simulations and simple theoretical models to analyze the morphologies that result when rod-like particles end-attach onto a curved surface, creating a finite-thickness monolayer aligned with the surface normal. This geometry…
Proteinaceous shells useful for various biomedical applications exhibit a wide range of anomalous structures that are fundamentally different from icosahedral viral capsids described by the Caspar-Klug paradigmatic model. Exploring the…