Related papers: Exploring Programmable Self-Assembly in Non-DNA ba…
We propose that genetic encoding of self-assembling components greatly enhances the evolution of complex systems and provides an efficient platform for inductive generalization, i.e. the inductive derivation of a solution to a problem with…
Surface plasmon resonances generated in metallic nanostructures can be utilized to tailor electromagnetic fields. The precise spatial arrangement of such structures can result in surprising optical properties that are not found in any…
Self-assembly of dilute sequence-defined macromolecules is a complex phenomenon in which the local arrangement of chemical moieties can lead to the formation of long-range structure. The dependence of this structure on the sequence…
Self-assembly, the process by which interacting components form well-defined and often intricate structures, is typically thought of as a spontaneous process arising from equilibrium dynamics. When a system is driven by external…
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…
We propose a computationally lean, two-stage approach that reliably predicts self-assembly behavior of complex charged molecules on a metallic surfaces under electrochemical conditions. Stage one uses ab initio simulations to provide…
Self-assembly processes allow us to design and create complex nanostructures using molecules as building blocks and surfaces as scaffolds. This autonomous driven construction is possible due to a complex thermodynamic balance of…
As computers get faster, researchers -- not hardware or algorithms -- become the bottleneck in scientific discovery. Computational study of colloidal self-assembly is one area that is keenly affected: even after computers generate massive…
The self-assembly of molecules at surfaces can be caused by a range of physical mechanisms. Assembly can be driven by intermolecular forces, or molecule-surface forces, or both; it can result in structures that are in equilibrium or that…
We consider a model of algorithmic self-assembly of geometric shapes out of square Wang tiles studied in SODA 2010, in which there are two types of tiles (e.g., constructed out of DNA and RNA material) and one operation that destroys all…
We report Monte Carlo simulations of a simple off-lattice patchy-particle model for DNA `bricks'. We relate the parameters that characterise this model with the binding free energy of pairs of single-stranded DNA molecules. We verify that…
Branched junction molecule assembly of DNA nanostructures, pioneered by Seeman's laboratory in the 1980s, has become increasingly sophisticated, as have the assembly targets. A critical design step is finding minimal sets of branched…
We use computer simulations to investigate self-assembly in a system of model chaperonin proteins, and in an Ising lattice gas. We discuss the mechanisms responsible for rapid and efficient assembly in these systems, and we use measurements…
The fabrication of nanomaterials involves self-ordering processes of functional molecules on inorganic surfaces. To obtain specific molecular arrangements, a common strategy is to equip molecules with functional groups. However, focusing on…
We apply a recently developed unsupervised machine learning scheme for local atomic environments to characterize large-scale, disordered aggregates formed by sequence-defined macromolecules. This method provides new insight into the…
Molecular-scale computation is crucial for smart materials and nanoscale devices, yet creating single-molecule systems capable of complex computations remains challenging. We present a theoretical framework for a single-molecule computer…
The self-assembly of particles into organized structures is a key feature of living organisms and a major engineering challenge. While it may proceed through the binding of perfectly matched, puzzle-pieces-like particles, many other…
DNA-coated colloids can self-assemble into an incredible diversity of crystal structures, but applications of this technology are limited by poor understanding and control over the dynamical crystallization pathways. To address this…
Geometric frustration offers a pathway to soft matter self-assembly with controllable finite sizes. While the understanding of frustration in soft matter assembly derives almost exclusively from continuum elastic descriptions, a current…
Many living and non-living complex systems can be modeled and understood as collective systems made of heterogeneous components that self-organize and generate nontrivial morphological structures and behaviors. This chapter presents a brief…