Related papers: A DNA-encoded recipe to direct multi-stage colloid…
The simulated self-assembly of molecular building blocks into functional complexes is a key area of study in computational biology and materials science. Self-assembly simulations of proteins using physically-motivated potentials for…
We present a modelling framework, and basic model parameterization, for the study of DNA origami folding at the level of DNA domains. Our approach is explicitly kinetic and does not assume a specific folding pathway. The binding of each…
Using large deviation theory and principles of stochastic optimal control, we show that rare molecular dynamics trajectories conditioned on assembling a specific target structure encode a set of interactions and external forces that lead to…
Controlling the size and shape of assembled structures is a fundamental challenge in self-assembly, and is highly relevant in material design and biology. Here, we show that specific, but promiscuous, short-range binding interactions make…
Self-assembly of complex and functional materials remains a grand challenge in soft material science. Efficient assembly depends on a delicate balance between thermodynamic and kinetic effects, requiring fine-tuning affinities and…
Enzymes are nano-scale machines that have evolved to drive chemical reactions out of equilibrium in the right place at the right time. Given the complexity and specificity of enzymatic function, bottom-up design of enzymes presents a…
Cyanobacteria sequester photosynthetic enzymes into microcompartments which facilitate the conversion of carbon dioxide into sugars. Geometric similarities between these structures and self-assembling viral capsids have inspired models that…
Ordered nanoarrays, i.e. regular patterns of quantum structures at the nanometre scale, have recently been synthesized in a wide range of systems. Here I explore a possible route to technological exploitation: assuming a simple form of…
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…
Within simulations of molecules deposited on a surface we show that neuroevolutionary learning can design particles and time-dependent protocols to promote self-assembly, without input from physical concepts such as thermal equilibrium or…
Controlling the topology of structures self-assembled from a set of heterogeneous building blocks is highly desirable for many applications, but is poorly understood theoretically. Here we show that the thermodynamic theory of self-assembly…
Self-assembly in natural and synthetic molecular systems can create complex aggregates or materials whose properties and functionality rises from their internal structure and molecular arrangement. The key microscopic features that control…
Equilibrating proteins and other biomacromolecules is cardinal for molecular dynamics simulation of such biological systems in which they perform free dynamics without any externally-applied mechanical constraint, until thermodynamic…
DNA-coated colloids are a popular model system for self-assembly through tunable interactions. The DNA-encoded linkages between particles theoretically allow for very high specificity, but generally no directionality or long-range…
Short DNA linkers are increasingly being exploited for driving specific self-assembly of Brownian objects. DNA-functionalised colloids can assemble into ordered or amorphous materials with tailored morphology. Recently, the same approach…
Stimulus-responsive DNA-hydrogels with swelling capabilities are a promising class of materials for biomedical applications such as drug delivery and biosensing. However, translation of these systems to microscale applications requires…
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…
Colloidal particles with DNA `legs' that can bind reversibly to receptors on a surface can be made to `walk' if there is a gradient in receptor concentration. We use a combination of theory and Monte Carlo simulations to explore how…
Self-assembly of nanoscale synthetic subunits is a promising bottom-up strategy for fabrication of functional materials. Here, we introduce a design principle for DNA origami nanoparticles of 50-nm size, exploiting modularity, to make a…
Controlled assembly of active-passive colloidal mixtures offers a route to reconfigurable microscale machines, but their self-assembly pathways remain poorly understood. We study the directed assembly of metallo-dielectric Janus particles…