Related papers: Programmable Control of Nucleation for Algorithmic…
We show the first non-trivial positive algorithmic results (i.e. programs whose output is larger than their size), in a model of self-assembly that has so far resisted many attempts of formal analysis or programming: the planar…
In the self-assembly process which drives the formation of cellular membranes, micelles, and capsids, a collection of separated subunits spontaneously binds together to form functional and more ordered structures. In this work, we study the…
Winfree (1998) showed that discrete Sierpinski triangles can self-assemble in the Tile Assembly Model. A striking molecular realization of this self-assembly, using DNA tiles a few nanometers long and verifying the results by atomic-force…
One of the challenges of self-assembling finite-sized colloidal aggregates with a sought morphology is the necessity of precisely sorting the position of the colloids at the microscopic scale to avoid the formation of off-target structures.…
We use a coarse-grained model of DNA-functionalized particles to understand the role of DNA chain length on their self-assembly. We find that the increasing chain length for a given particle size decreases the propensity to form ordered…
By exploiting the exquisite selectivity of DNA hybridization, DNA-Coated Colloids (DNACCs) can be made to self-assemble in a wide variety of structures. The beauty of this system stems largely from its exceptional versatility and from the…
Large protein complexes are assembled from protein subunits to form a specific structure. In our theoretic work, we propose that assembly into the correct structure could be reliably achieved through an assembly line with a specific…
Atomistic simulations have now established themselves as an indispensable tool in understanding deformation mechanisms of materials at the atomic scale. Large scale simulations are regularly used to study the behavior of polycrystalline…
Curved structures in soft matter and biological systems commonly emerge as a result of self-assembly processes where building blocks aggregate in a controlled manner, giving rise to specific system structure and properties. Learning how to…
A physically-motivated genetic algorithm (GA) and full enumeration for a tile-based model of self-assembly (JaTAM) is implemented using a graphics processing unit (GPU). We observe performance gains with respect to state-of-the-art…
The molecular self-assembly of various structures such as micelles and vesicles has been the subject of comprehensive studies. Recently, a new approach to design these structures, the frame-guided assembly, has been developed to progress…
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…
The design space for a self-assembled multicomponent objects ranges from a solution in which every building block is unique to one with the minimum number of distinct building blocks that unambiguously define the target structure. Using a…
Rational design strategies for self-assembly require a detailed understanding of both the equilibrium state and the assembly kinetics. While the former is starting to be well understood, the latter remains a major theoretical challenge,…
Colloidal molecules are designed to mimic their molecular analogues through their anisotropic shape and interactions. However, current experimental realizations are missing the structural flexibility present in real molecules thereby…
We introduce allostery-mimetic building blocks model for self-assembly of 3D structures. We represent the building blocks as patchy particles, where each binding site (patch) can be irreversibly activated or deactivated by binding of the…
Crystallization, a prototypical self-organization process during which a disordered state spontaneously transforms into a crystal characterized by a regular arrangement of its building blocks, usually proceeds by nucleation and growth. In…
We introduce a new DNA tile self-assembly model: the Surface Flexible Tile Assembly Model (SFTAM), where 2D tiles are placed on host 3D surfaces made of axis-parallel unit cubes glued together by their faces, called polycubes. The bonds are…
Living neural networks emerge through a process of growth and self-organization that begins with a single cell and results in a brain, an organized and functional computational device. Artificial neural networks, however, rely on…
The Self-Assembly of Nano-Objects (SANO) code we implemented demonstrates the ability to predict the molecular self-assembly of different structural motifs by tuning the molecular building blocks as well as the metallic substrate. It…