Related papers: Self-assembly of polyhedral shells: A molecular dy…
In living cells, proteins self-assemble into large functional structures based on specific interactions between molecularly complex patches. Due to this complexity, protein self-assembly results from a competition between a large number of…
The surface curvature of membranes, interfaces, and substrates plays a crucial role in shaping the self-assembly of particles adsorbed on these surfaces. However, little is known about the interplay between particle anisotropy and surface…
Highly symmetric nano-shells are found in many biological systems, such as clathrin cages and viral shells. Several studies have shown that symmetric shells appear in nature as a result of the free energy minimization of a generic…
From dumbbells to FCC crystals, we study the self-assembly pathway of amphiphatic, spherical colloidal particles as a function of the size of the hydrophobic region using molecular dynamics simulations. Specifically, we analyze how local…
We use numerical simulations to show how noninteracting hard particles binding to a deformable elastic shell may self-assemble into a variety of linear patterns. This is a result of the nontrivial elastic response to deformations of shells.…
The regular polyhedra have the highest order of 3D symmetries and are exceptionally at- tractive templates for (self)-assembly using minimal types of building blocks, from nano-cages and virus capsids to large scale constructions like glass…
The self-assembly of molecules at surfaces can be caused by a range of physical mechanisms. Assembly can be driven by intermolecular forces, or molecule-surface forces, or both; it can result in structures that are in equilibrium or that…
This review article discusses some common enhanced sampling methods in relation to the process of self-assembly of biomolecules. An introduction to self-assembly and its challenges is covered followed by a brief overview of the methods and…
Understanding how highly symmetric, robust, monodisperse protein cages self-assemble can have major applications in various areas of bio-nanotechnology, such as drug delivery, biomedical imaging and gene therapy. We develop a model to…
Cellular functions are established through biological evolution, but are constrained by the laws of physics. For instance, the physics of protein folding limits the lengths of cellular polypeptide chains. Consequently, many cellular…
In many virus families, tens to thousands of proteins assemble spontaneously into a capsid (protein shell) while packaging the genomic nucleic acid. This review summarizes recent advances in computational modeling of these dynamical…
We study DNA self-assembly and DNA computation using a coarse-grained DNA model within the directional dynamic bonding framework {[}C. Svaneborg, Comp. Phys. Comm. 183, 1793 (2012){]}. In our model, a single nucleotide or domain is…
The cytoplasm is a heterogeneous mixture containing many types of proteins that self-assemble into a wide variety of complexes. The accuracy and speed of cytoplasmic self-assembly is astonishing because it involves the correct…
We study two mechanisms for the formation of protein patterns near membranes of living cells by mathematical modelling. Self-assembly of protein domains by electrostatic lipid-protein interactions is contrasted with self-organization due to…
Controlling the self-assembly of supramolecular structures is vital for living cells, and a central challenge for engineering at the nano- and microscales. Nevertheless, even particles without optimized shapes can robustly form well-defined…
A modulated icosahedral shell with an inclusion is a concise description of many viruses, including recently-discovered large double-stranded DNA ones. Many X-ray scattering patterns of such viruses show major polygonal fringes, which can…
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…
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…
We present a quantitative measure of physical complexity, based on the amount of information required to build a given physical structure through self-assembly. Our procedure can be adapted to any given geometry, and thus to any given type…
In contrast to most self-assembling synthetic materials, which undergo unbounded growth, many biological self-assembly processes are self-limited. That is, the assembled structures have one or more finite dimensions that are much larger…