Related papers: Assembly Models for Papovaviridae based on Tiling …
We study the elastic properties and mechanical stability of viral capsids under external force-loading with computer simulations. Our approach allows the implementation of specific geometries corresponding to specific phages such as…
Defective interfering particles arise spontaneously during a viral infection as mutants lacking essential parts of the viral genome. Their ability to replicate in the presence of the wild-type (WT) virus (at the expense of viable viral…
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…
Cell adhesion proteins are transmembrane proteins that bind cells to their environment. These proteins typically cluster into disk-shaped or linear structures. Here we show that such clustering patterns spontaneously emerge when the protein…
Filamentous bacteriophages such as fd-like viruses are monodisperse rod-like colloids that have well defined properties: diameter, length, rigidity, charge and chirality. Engineering those viruses leads to a library of colloidal rods which…
The Tile Assembly Model is a Turing universal model that Winfree introduced in order to study the nanoscale self-assembly of complex (typically aperiodic) DNA crystals. Winfree exhibited a self-assembly that tiles the first quadrant of the…
A pentagonal order formed by 360 proteins in the bovine papilloma viral capsid and structures of some smaller viral capsids are considered from a unified point of view based on the Landau crystallization theory. To simulate the capsid…
Viruses are known to tolerate wide ranges of pH and salt conditions and to withstand internal pressures as high as 100 atmospheres. In this paper we investigate the mechanical properties of viral capsids, calling explicit attention to the…
Capillarity-driven self-assembly at fluidic interfaces offers a scalable route to large, reconfigurable materials. Microscale particles with high horizontal-to-vertical aspect ratios become attractive building blocks for shape-directed…
Multiple dissipative self-assembly protocols designed to create novel structures or to reduce kinetic traps have recently emerged. Specifically, temporal oscillations of particle interactions have been shown effective at both aims, but…
The tubulin-like protein FtsZ is crucial for cytokinesis in bacteria and many archaea, forming a ring-shaped structure called the Z-ring at the site of cell division. Despite extensive research, the self-assembly of Z-rings is not entirely…
We present assembly-theory, a Rust package for computing assembly indices of covalently bonded molecular structures. This is a key complexity measure of assembly theory, a recent theoretical framework quantifying selection across diverse…
In directed assembly, small building clocks are assembled into an organized structures under the influence of guiding fields. Capillary interactions provide a versatile route for structure formation. Colloids adsorbed on fluid interfaces…
Chromatin and associated proteins constitute the highly folded structure of chromosomes. We consider a self-avoiding polymer model of the chromatin, segments of which may get cross-linked via protein binders that repel each other. The…
This paper provides a bridge between the classical tiling theory and the complex neighborhood self-assembling situations that exist in practice. The neighborhood of a position in the plane is the set of coordinates which are considered…
Lipid membranes, the barrier defining living cells and many of their sub-compartments, bind to a wide variety of nano- and micro-meter sized objects. In the presence of strong adhesive forces, membranes can strongly deform and wrap the…
Self-assembly is a process which is ubiquitous in natural, especially biological systems. It occurs when groups of relatively simple components spontaneously combine to form more complex structures. While such systems have inspired a large…
A challenge of molecular self-assembly is to understand how to design particles that self-assemble into a desired structure and not any of a potentially large number of undesired structures. Here we use simulation to show that a strategy of…
To construct models of large, multivariate complex systems, such as those in biology, one needs to constrain which variables are allowed to interact. This can be viewed as detecting "local" structures among the variables. In the context of…
Self-assembly in natural and synthetic molecular systems can create complex aggregates or materials whose properties and functionality rises from their internal structure and molecular arrangement. The key microscopic features that control…