Related papers: Assembly Models for Papovaviridae based on Tiling …
The self-assembly of particles into organized structures is a key feature of living organisms and a major engineering challenge. While it may proceed through the binding of perfectly matched, puzzle-pieces-like particles, many other…
This paper considers the problem of invoking auxiliary, unobservable variables to facilitate the structuring of causal tree models for a given set of continuous variables. Paralleling the treatment of bi-valued variables in [Pearl 1986], we…
Contact inhibition plays a crucial role in the motility of cells, the process of wound healing, and the formation of tumors. By mimicking the mechanical motion of calls crawling on a substrate using a pseudopod, we constructed a minimal…
Membrane particles such as proteins and lipids organize into zones that perform unique functions. Here, I introduce a topological and category-theoretic framework to represent particle and zone intra-scale interactions and inter-scale…
We investigate the mechanical origin of polymorphic structures in two-dimensional tubulin assemblies, of which microtubules are the best known example. These structures feature twisted ribbons, flat tubulin sheets, macrotubules, and hoops,…
The tube model is a central concept in polymer physics, and allows to reduce the complex many-filament problem of an entangled polymer solution to a single filament description. We investigate the probability distribution function of…
We examine the budding of a nanoscale particle through a lipid bilayer using molecular dynamics simulations, free energy calculations, and an elastic theory, with the aim of determining the extent to which equilibrium elasticity theory can…
Compliant environments can mediate interactions between mechanically active cells like fibroblasts. Starting with a phenomenological model for the behaviour of single cells, we use extensive Monte Carlo simulations to predict non-trivial…
Entangled states are ubiquitous amongst fibrous materials, whether naturally occurring (keratin, collagen, DNA) or synthetic (nanotube assemblies, elastane). A key mechanical characteristic of these systems is their ability to reorganise in…
If particles interact according to isotropic pair potentials that favor multiple length scales, in principle a large variety of different complex structures can be achieved by self-assembly. We present, motivate, and discuss a conjecture…
Crystallization of biological molecules has high potential to solve some challenges in drug manufacturing. Thus, understanding the process is critical to efficiently adapting crystallization to biopharmaceutical manufacturing. This article…
We propose a general theory to describe the distribution of protein-folding transition paths. We show that transition paths follow a predictable sequence of high-free-energy transient states that are separated by free-energy barriers. Each…
We are surrounded by spatio-temporal patterns resulting from the interaction of the numerous basic units constituting natural or human-made systems. In presence of diffusive-like coupling, Turing theory has been largely applied to explain…
We show that the Tile Assembly Model exhibits a strong notion of universality where the goal is to give a single tile assembly system that simulates the behavior of any other tile assembly system. We give a tile assembly system that is…
Topological constraint theory has become an increasingly popular tool to predict the compositional dependence of glass properties or pinpoint promising compositions with tailored functionalities. This approach reduces complex disordered…
Self-organized complex structures in nature, e.g. viral capsids, hierarchical biopolymers, and bacterial flagella, offer efficiency, adaptability, robustness, and multi-functionality. Can we program the self-assembly of three-dimensional…
Viroporins are small viral proteins that oligomerize in the membrane of host cells and induce the formation of hydrophilic pores in these membranes, thus altering the physiological properties of the host cells. Due to their significance for…
The adhesion approximation is a simple analytical model suggested for explanation of the major geometrical features of the observed structure in the galaxy distribution on scales from 1 to (a few)x100/h Mpc. It is based on Burgers' equation…
When modeling of tumor-driven angiogenesis, a major source of analytical and computational complexity is the strong coupling between the kinetic parameters of the relevant stochastic branching-and-growth of the capillary network, and the…
Cooperation is prevalent in nature, not only in the context of social interactions within the animal kingdom, but also on the cellular level. In cancer for example, tumour cells can cooperate by producing growth factors. The evolution of…