Related papers: Topological potentials guiding protein self-assemb…
The algorithmic self-assembly of shapes has been considered in several models of self-assembly. For the problem of \emph{shape construction}, we consider an extended version of the Two-Handed Tile Assembly Model (2HAM), which contains…
Experiments have reached a monumental capacity for designing and synthesizing microscopic particles for self-assembly, making it possible to precisely control particle concentrations, shapes, and interactions. However, more physical insight…
Many researches have been working on the protein folding problem from more than half century. Protein folding is indeed one of the major unsolved problems in science. In this work, we discuss a model for the simulation of protein…
Topology optimization is used for the design of high-performance structures but remains fundamentally limited by its iterative nature, requiring repeated finite element analyses that prevent real-time deployment and large-scale design…
This paper provides a method for the simultaneous topology optimization of parts and their corresponding joint locations in an assembly. Therein, the joint locations are not discrete and predefined, but continuously movable. The underlying…
Harnessing the intrinsic dynamics of physical systems for information processing opens new avenues for computation embodied in matter. Using simulations of a model system, we show that assemblies of DNA tiles capable of self-organizing into…
Although machine-learning potentials have recently had substantial impact on molecular simulations, the construction of a robust training set can still become a limiting factor, especially due to the requirement of a reference ab initio…
The efficient and controlled assembly of complex structures from macromolecular building blocks is a critical open question in both biological systems and nanoscience. Using molecular dynamics simulations we study the self-assembly of…
From dumbbells to FCC crystals, we study the self-assembly pathway of amphiphatic, spherical colloidal particles as a function of the size of the hydrophobic region using molecular dynamics simulations. Specifically, we analyze how local…
The self-assembly of polyhedral shells, each constructed from 60 trapezoidal particles, is simulated using molecular dynamics. The spatial organization of the component particles in this shell is similar to the capsomer proteins forming the…
Biology stores information and computes at the molecular scale, yet the ways in which it does so are often distinct from human-engineered computers. Mapping biological computation onto architectures familiar to computer science remains an…
We present a technique for calculating free-energy profiles for the nucleation of multicomponent structures that contain as many species as building blocks. We find that a key factor is the topology of the graph describing the connectivity…
In geometrically frustrated assemblies, equilibrium self-limitation manifests in the form of a minimum in the free energy per subunit at a finite, multi-subunit size which results from the competition between the elastic costs of…
The conformation space of a 20-residue antiparallel $\beta$-sheet peptide, sampled by molecular dynamics simulations, is mapped to a network. Conformations are nodes of the network, and the transitions between them are links. The…
A major goal in nanoscience and nanotechnology is the self-assembly of any desired complex structure with a system of particles interacting through simple potentials. To achieve this objective, intense experimental and theoretical efforts…
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…
We develop a theory of aggregation using statistical mechanical methods. An example of a complicated aggregation system with several levels of structures is peptide/protein self-assembly. The problem of protein aggregation is important for…
Algorithmic self-assembly, a generalization of crystal growth processes, has been proposed as a mechanism for autonomous DNA computation and for bottom-up fabrication of complex nanostructures. A `program' for growing a desired structure…
Topology optimization (TO) is a well-established methodology for structural design under user-defined constraints, e.g. minimum volume and maximum stiffness. However, such methods have traditionally been applied to static, deterministic…
In automated manufacturing, robots must reliably assemble parts of various geometries and low tolerances. Ideally, they plan the required motions autonomously. This poses a substantial challenge due to high-dimensional state spaces and…