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Many problems in materials science and biology involve particles interacting with strong, short-ranged bonds, that can break and form on experimental timescales. Treating such bonds as constraints can significantly speed up sampling their…
DNA origami is a modular platform for the combination of molecular and colloidal components to create optical, electronic, and biological devices. Integration of such nanoscale devices with microfabricated connectors and circuits is…
A minimal off-lattice model for alpha-helical proteins is presented. It is based on hydrophobicity forces and sequence independent local interactions. The latter are chosen so as to favor the formation of alpha-helical structure. They model…
While the thermodynamics of DNA hybridization is well understood, much less is known about the kinetics of this classic system. Filling this gap in our understanding has new urgency because DNA nanotechnology often depends critically on…
Flat histogram methods, such as Wang--Landau sampling, provide a means for high-throughput calculation of phase diagrams of atomistic/lattice model systems. Many parallelisation schemes with varying degrees of complexity have been proposed…
We use the oxDNA coarse-grained model to provide a detailed characterization of the fundamental structural properties of DNA origamis, focussing on archetypal 2D and 3D origamis. The model reproduces well the characteristic pattern of helix…
Branched molecules of deoxyribonucleic acid (DNA) can self-assemble into nanostructures through complementary cohesive strand base pairing. The production of DNA nanostructures is valuable in targeted drug delivery and biomolecular…
We study some aspects of a Monte Carlo method invented by Maggs and Rossetto for simulating systems of charged particles. It has the feature that the discretized electric field is updated locally when charges move. Results of simulations of…
Flexibility governs the many properties of materials and is crucial for the function of proteins and biopolymers. However, how the self-assembly of flexibly bonded particles can lead to larger structures with global reconfigurability is…
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.…
Origami-based design holds promise for developing materials whose mechanical properties are tuned by crease patterns introduced to thin sheets. Although there has been heuristic developments in constructing patterns with desirable…
We study a one-dimensional two-component Fermi gas in a harmonic trapping potential using finite temperature lattice quantum Monte Carlo methods. We are able to compute observables in the canonical ensemble via an efficient projective…
Recent advances enable the creation of nanoscale building blocks with complex geometries and interaction specificities for self-assembly. This nearly boundless design space necessitates design principles for defining the mutual interactions…
One of the many remarkable properties of graphene is that in the low energy limit the dynamics of its electrons can be effectively described by the massless Dirac equation. This has prompted investigations of graphene based on the lattice…
Self-assembly is traditionally described as the process through which an initially disordered system relaxes towards an equilibrium ordered phase only driven by local interactions between its building blocks. However, This definition is too…
In this paper we consider a physical system in which two DNA molecules braid about each other. The distance between the two molecular ends, on either side of the braid, is held at a distance much larger than supercoiling radius of the…
We report model calculations on DNA single strands which describe the equilibrium dynamics and kinetics of hairpin formation and melting. Modeling is at the level of single bases. Strand rigidity is described in terms of simple polymer…
We investigate the ground state of the Kondo necklace model on geometrically-frustrated lattices by the variational Monte Carlo simulation. To explore the possibility of a partially-ordered phase, we employ an extension of the Yosida-type…
We propose a novel computational framework for modeling and simulating origami structures. In this framework, bilinear solid-shell elements are employed to model the origami panels while crease folding is considered through the angle…
DNA origami is a novel self-assembly technique allowing one to form various 2D shapes and position matter with nanometer accuracy. It has been used to coordinate placement of nanoscale objects, both organic and inorganic; to make molecular…