Related papers: Assembly Models for Papovaviridae based on Tiling …
We report on the construction of multiarm colloidal molecules by tip-linking filamentous bacteriophages, functionalized either by biological engineering or chemical conjugation. The affinity for streptavidin of a genetically modified vector…
Self-assembly of proteins into amyloid aggregates is an important biological phenomenon associated with human diseases such as Alzheimer's disease. Amyloid fibrils also have potential applications in nano-engineering of biomaterials. The…
Biomolecular condensates self-assemble when proteins and nucleic acids spontaneously demix to form droplets within the crowded intracellular milieu. This simple mechanism underlies the formation of a wide variety of membraneless…
Proteins can combine into functional elements in living cells or self-assemble into unwanted structures in a number of diseases. The resulting aggregates often display filamentous morphologies across a large range of protein shapes and…
Cells in tissues can organize into a broad spectrum of structures according to their function. Drastic changes of organization, such as epithelial-mesenchymal transitions or the formation of spheroidal aggregates, are often associated…
In the abstract Tile Assembly Model, self-assembling systems consisting of tiles of different colors can form structures on which colored patterns are ``painted.'' We explore the complexity, in terms of the numbers of unique tile types…
A molecular-level model is used to study the mechanical response of empty cowpea chlorotic mottle virus (CCMV) and cowpea mosaic virus (CPMV) capsids. The model is based on the native structure of the proteins that consitute the capsids and…
The relation between a structure and the function running on that structure is of central interest in many fields, including computer science, biology (organ vs. function), psychology (body vs. mind), architecture (designs vs.…
A scaling theory is developed for diffusion-limited cluster aggregation in a porous medium, where the primary particles and clusters stick irreversibly to the walls of the pore space as well as to each other. Three scaling regimes are…
Since the time of Darwin, scientists have struggled to reconcile the evolution of biological forms in a universe determined by fixed laws. These laws underpin the origin of life, evolution, human culture and technology, as set by the…
Within biology, it is of interest to construct DNA complexes of a certain shape. These complexes can be represented through graph theory, using edges to model strands of DNA joined at junctions, represented by vertices. Because guided…
Multipartite viruses replicate through a puzzling evolutionary strategy. Their genome is segmented into two or more parts, and encapsidated in separate particles that appear to propagate independently. Completing the replication cycle,…
Multilevel self-assembly involving small structured groups of nano-particles provides new routes to development of functional materials with a sophisticated architecture. Apart from the inter-particle forces, the geometrical shapes and…
We present a macroscopic theory of capillary condensation in slits formed by parallel walls of unequal length. Using the concept of an edge contact angle, we identify four distinct condensation states and derive Kelvin-like relations for…
We present a braided circuit topology framework for investigating topology and structural phase transitions in aggregates of semiflexible polymers. In the conventional approach to circuit topology, which specifically applies to single…
We investigate the power of the Wang tile self-assembly model at temperature 1, a threshold value that permits attachment between any two tiles that share even a single bond. When restricted to deterministic assembly in the plane, no…
The statistical mechanics of a treelike polymer in a confining volume is relevant to the packaging of the genome in RNA viruses. Making use of the mapping of the grand partition function of this system onto the statistical mechanics of a…
Soft matter systems are common in nature and make up nearly all the essential components necessary for life, from cells to the organelles within those cells. The ability of these soft materials to deform is crucial for the proper…
HIV-1 virions assemble as immature particles containing Gag polyproteins that are processed by the viral protease into individual components, resulting in the formation of mature infectious particles. There are two competing models for the…
The protein folding problem is stated and a list of properties that do not depend upon specific molecules is compiled and analyzed. The relationship of this analysis to future simulations is emphasized. The choice of power and time as…