Related papers: Modelling the Self-Assembly of Virus Capsids
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…
We show that geometric frustration in a broad class of deformable and naturally curved, shell-like colloidal particles gives rise to self-limiting assembly of finite-sized stacks that far exceed particle dimensions. When inter-particle…
Entropy alone can self-assemble hard particles into colloidal crystals of remarkable complexity whose structures are the same as atomic and molecular crystals, but with larger lattice spacings. Although particle-based molecular simulation…
In this paper we revisit the notion of grouped dispersal that have been introduced by Soubeyrand and co-authors \cite{soubeyrand2011patchy} to model the simultaneous (and hence dependent) dispersal of several propagules from a single source…
Colloidal particles can spontaneously self-assemble into ordered structures, which not only can manipulate the propagation of light, but also vibration or phonons. Using Monte Carlo simulation, we study the self-assembly of perfectly…
Self-assembly due to capillary forces is a common method for generating 2D mesoscale structures from identical floating particles at the liquid-air interface. Designing building blocks to obtain a desired mesoscopic structure is a…
Patchy particles have proven to be a prominent model for studying the self-assembly behavior of various systems, ranging from finite clusters to bulk crystal assemblies, and from synthetic colloidal particles to viruses. The patchy particle…
We introduce a simple "patchy particle" model to study the thermodynamics and dynamics of self-assembly of homomeric protein complexes. Our calculations allow us to rationalize recent results for dihedral complexes. Namely, why evolution of…
We use statistical mechanics to study model-based Bayesian data clustering. In this approach, each partition of the data into clusters is regarded as a microscopic system state, the negative data log-likelihood gives the energy of each…
Colloidal self-assembly -- the spontaneous organization of colloids into ordered structures -- has been considered key to produce next-generation materials. However, the present-day staggering variety of colloidal building blocks and the…
Emergent phenomena share the fascinating property of not being obvious consequences of the design of the system in which they appear. This characteristic is no less relevant when attempting to simulate such phenomena, given that the outcome…
Polymorphism has been observed in viral capsid assembly, demonstrating the ability of identical protein dimers to adopt multiple geometries under the same solution conditions. A well-studied example is the hepatitis B virus (HBV), which…
Formation and rupture of vesicles is a fundamental process underlying diverse phenomena in biology, materials science, and biomedical applications. Vesicles form when the area of a growing disk-like membrane exceeds a critical value at…
While colloids are promising building blocks for the self-assembly of materials with novel microstructures, their numerous tunable parameters inhibit brute force searching for appropriate parameter combinations that yield self-assembly of a…
In collective robotic systems, the automatic generation of controllers for complex tasks is still a challenging problem. Open-ended evolution of complex robot behaviors can be a possible solution whereby an intrinsic driver for pattern…
Understanding interactions between microparticles and lipid membranes is of increasing importance, especially for unraveling the influence of microplastics on our health and environment. Here, we study how a short-ranged adhesive force…
We study theoretically in the present work the self-assembly of molecules in an open system, which is fed by monomers and depleted in partial or complete clusters. Such a scenario is likely to occur for example in the context of viral…
Motile organisms can form stable agglomerates such as cities or colonies. In the outbreak of a highly contagious disease, the control of large-scale epidemic spread depends on factors like the number and size of agglomerates, travel rate…
The design of complex materials and the formation of specific patterns often arise from the properties of the individual building blocks. In this respect, colloidal systems offer a unique opportunity because nowadays they can be synthesized…
Self-assembly is a vital part of the life cycle of certain icosahedral RNA viruses. Furthermore, the assembly process can be harnessed to make icosahedral virus-like particles (VLPs) from coat protein and RNA in vitro. Although much…