Related papers: Modeling capsid self-assembly: Design and analysis
The assembly of virus capsids from free coat proteins proceeds by a complicated cascade of association and dissociation steps, the great majority of which cannot be directly experimentally observed. This has made capsid assembly a rich…
The question of how stiff polymers are able to pack into small containers is particularly relevant to the study of DNA packaging in viruses. A reduced version of the problem based on coarse-grained representations of the main components of…
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…
The recently developed two-stage growth model of synthesis of monodispersed polycrystalline colloidal particles is utilized and improved to explain growth of uniform cadmium sulfide spheres. The model accounts for the coupled processes of…
Many living and non-living complex systems can be modeled and understood as collective systems made of heterogeneous components that self-organize and generate nontrivial morphological structures and behaviors. This chapter presents a brief…
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…
Living cells dynamically modulate the local morphologies of their actin cytoskeletons to perform biological functions, including force transduction, intracellular transport, and cell division. A major challenge is to understand how diverse…
Emergent behaviors occur in a vast array of systems across many scales, and are of fundamental physical importance because of the intrinsic difficulty in linking microscopic system properties to macroscopic behaviors. Here we study the…
Crystallization of proteins, specifically proteins of medical relevance, is performed for various reasons such as to understand the protein structure and to design therapies. Obtaining kinetic constants in rate laws for nucleation and…
Colloidal particles grafted with single-stranded DNA (ssDNA) chains can self-assemble into a number of different crystalline structures, where hybridization of the ssDNA chains creates links between colloids stabilizing their structure.…
We propose a simple model of self-propelled particles to show that coherent structures, such as jets and swirls, can arise from a plausible microscopic mechanisms: (i) the elongated shape of the self-propelled particles with (ii) the…
Dense packing of particles has provided important models to study the structure of matter in various systems such as liquid, glassy and crystalline phase, etc. The simplest sphere packing models are able to represent and capture salient…
The self-assembly of polymer grafted nanoparticles is more and more used in the field of functional materials. However, there is still a lack of analysis on the dynamic transformation paths of different self-assembly morphologies, which…
Organogenesis is a tightly regulated process that has been studied experimentally for decades. Computational models can help to integrate available knowledge and to better understand the underlying regulatory logic. We are currently…
Multifarious assembly models consider multiple structures assembled from a shared set of components, reflecting the efficient usage of components in biological self-assembly. These models are subject to a high-dimensional parameter space,…
Anisotropy at the level of the inter-particle interaction provides the particles with specific instructions for the self-assembly of target structures. The ability to synthesize non-spherical colloids, together with the possibility of…
We propose and investigate an extension of the Caspar-Klug symmetry principles for viral capsid assembly to the programmable assembly of size-controlled triply-periodic polyhedra, discrete variants of the Primitive, Diamond, and Gyroid…
We present a simple kinetic model for the assembly of small single-stranded RNA viruses that can be used to carry out analytical packaging contests between different types of RNA molecules. The RNA selection mechanism is purely kinetic and…
Replication through cell division is one of the most fundamental processes of life and a major driver of dynamics in systems ranging from bacterial colonies to embryogenesis, tissues and tumors. While regulation often plays a role in…
Despite recent developments in management theory, maintaining a manufacturing schedule remains difficult because of production delays and fluctuations in demand and supply of materials. The response of manufacturing systems to such…