Related papers: Aggregate geometry in amyloid fibril nucleation
In recent experiments involving PNIPAM copolymers it has been observed that stable spherical nanoparticles are being formed by association of several chains in poor aqueous solution instead of aggregation. This type of mesoscopic structures…
An atomic protein model with a minimalistic potential is developed and then tested on an alpha-helix and a beta-hairpin, using exactly the same parameters for both peptides. We find that melting curves for these sequences to a good…
Polymer-grafted nanoparticles are versatile building blocks that self-assemble into a rich diversity of mesostructures. Coarse-grained molecular simulations have commonly accompanied experiments by resolving structure formation pathways and…
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…
We present a generic model to describe the fractal self-assembly of proteins in terms of electrostatic and hydrophobic interactions. The predictions of the model were correlated with the simulated fractals obtained using patchy…
We discuss the relation between the emergence of new phases with broken symmetry within the framework of simple models of biopolymers. We start with a classic model for a chain molecule of spherical beads tethered together, with the steric…
Filopodia are bundles of actin filaments that extend out ahead of the leading edge of a crawling cell to probe its upcoming environment. {\it In vitro} experiments [D. Vignjevic {\it et al.}, J. Cell Biol. {\bf 160}, 951 (2003)] have…
This paper uses combinatorics and group theory to answer questions about the assembly of icosahedral viral shells. Although the geometric structure of the capsid (shell) is fairly well understood in terms of its constituent subunits, the…
In contrast to extensively studied defects in traditional materials, we report here for the first time a systematic investigation of the formation mechanism of intrinsic defects in self-assembled peptide nanostructures. The Monte Carlo…
The dynamic behavior of bundles of actin filaments growing against a loaded obstacle is investigated through a generalized version of the standard multi filaments Brownian Ratchet model in which the (de)polymerizing filaments are treated…
The formation of bundles composed of actin filaments and cross-linking proteins is an essential process in the maintenance of the cells' cytoskeleton. It has also been recreated by in-vitro experiments, where actin networks are routinely…
Amphiphilic molecules spontaneously form self-assembled structures of various shapes depending on their molecular structures, the temperature, and other physical conditions. The functionalities of these structures are dictated by their…
In the presence of ATP, molecular motors generate active force dipoles that drive suspensions of protein filaments far from thermodynamic equilibrium, leading to exotic dynamics and pattern formation. Microscopic modelling can help to…
Collagen fibrils are the building block of many biological tissues, which viability depend on the fibrils properties. Altered properties of collagen fibrils are central to the appearance of many diseases, while physiological or native…
Prevention of protein aggregation and thus stabilization of proteins has large biological and biotechnological implications. Here, we show that inhibition of amyloid-like aggregates is possible in stoichiometric conjugates of polymer…
Aggregation of like-charged polymers is widely observed in biological and soft matter systems. In many systems, bundles are formed when a short-range attraction of diverse physical origin like charge-bridging, hydrogen-bonding or…
We describe a computational model for studying the complexity of self-assembled structures with active molecular components. Our model captures notions of growth and movement ubiquitous in biological systems. The model is inspired by…
Collagen fibrils are versatile self-assembled structures that provide mechanical integrity within mammalian tissues. The radius of collagen fibrils vary widely depending on experimental conditions \textit{in vitro} or anatomical location…
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…
Remote measurements and in-situ observations confirm the idea that asteroids up to few hundreds of meters in size might be rubble piles. The dynamics of these objects can be studied using N-body simulations of gravitational aggregation. We…