Related papers: Self-folding Self-replication
We describe a computational model for studying the complexity of self-assembled structures with active molecular components. Our model captures notions of growth and movement ubiquitous in biological systems. The model is inspired by…
AlphaFold 3 represents a transformative advancement in computational biology, enhancing protein structure prediction through novel multi-scale transformer architectures, biologically informed cross-attention mechanisms, and geometry-aware…
Space-filling designs are popular choices for computer experiments. A sliced design is a design that can be partitioned into several subdesigns. We propose a new type of sliced space-filling design called sliced rotated sphere packing…
The coding space of protein sequences is shaped by evolutionary constraints set by requirements of function and stability. We show that the coding space of a given protein family--the total number of sequences in that family--can be…
We present design and implementation of a chain of particles that can be programmed to fold the chain into a given curve. The particles guide an external force to fold, therefore the particles are simple and amenable for miniaturization. A…
With recent advances in both responsive materials and fabrication techniques it is now possible to construct integrated functional structures, composed of both structural and active materials. We investigate the robust design of such…
Synthetic polymeric materials underpin fundamental technologies in the energy, electronics, consumer goods, and medical sectors, yet their development still suffers from prolonged design timelines. Although polymer informatics tools have…
Natural protein sequences contain a record of their history. A common constraint in a given protein family is the ability to fold to specific structures, and it has been shown possible to infer the main native ensemble by analyzing…
A small model polypeptide represented in atomic detail is folded using Monte Carlo dynamics. The polypeptide is designed to have a native conformation similar to the central part of the helix-turn-helix protein ROP. Starting from a…
The process of self-morphing in curved surfaces found in nature, such as with the growth of flowers and leaves, has generated interest in the study of self-morphing bilayers, which has been used in many soft robots or switchers. However,…
Self-organized complex structures in nature, e.g. viral capsids, hierarchical biopolymers, and bacterial flagella, offer efficiency, adaptability, robustness, and multi-functionality. Can we program the self-assembly of three-dimensional…
Natural proteins fold to a unique, thermodynamically dominant state. Modeling of the folding process and prediction of the native fold of proteins are two major unsolved problems in biophysics. Here, we show successful all-atom ab initio…
In the protein sequence space, natural proteins form clusters of families which are characterized by their unique native folds whereas the great majority of random polypeptides are neither clustered nor foldable to unique structures. Since…
DNA self-assembly is an important tool that has a wide range of applications such as building nanostructures, the transport of target virotherapies, and nano-circuitry. Tools from graph theory can be used to encode the biological process of…
We present an efficient algorithm to recover the three dimensional structure of a protein from its contact map representation. First we show that when a physically realizable map is used as target, our method generates a structure whose…
This paper proposes a new mathematical approach to characterize native protein structures based on the discrete differential geometry of tetrahedron tiles. In the approach, local structure of proteins is classified into finite types…
Proteins perform a large variety of functions in living organisms, thus playing a key role in biology. As of now, available learning algorithms to process protein data do not consider several particularities of such data and/or do not scale…
Novel numerical techniques, validated by an analysis of barnase and chymotrypsin inhibitor, are used to elucidate the paramount role played by the geometry of the protein backbone in steering the folding to the correct native state. It is…
Shells, i.e., objects made of a thin layer of material following a surface, are among the most common structures in use. They are highly efficient, in terms of material required to maintain strength, but also prone to deformation and…
We study the problem of deciding whether a crease pattern can be folded by simple folds (folding along one line at a time) under the infinite all-layers model introduced by [Akitaya et al., 2017], in which each simple fold is defined by an…