Related papers: How do particles with complex interactions self-as…
We explore the use of templated self-assembly to facilitate the formation of complex target structures made from patchy particles. First, we consider the templating of high-symmetry shell structures around a spherical core particle. We find…
We develop coarse-grained models that describe the dynamic encapsidation of functionalized nanoparticles by viral capsid proteins. We find that some forms of cooperative interactions between protein subunits and nanoparticles can…
One emerging approach for the fabrication of complex architectures on the nanoscale is to utilize particles customized to intrinsically self-assemble into a desired structure. Inverse methods of statistical mechanics have proven…
Inside a cell, heterotypic proteins assemble in inhomogeneous, crowded systems where the abundance of these proteins vary with cell types. While some protein complexes form putative structures that can be visualized with imaging, there are…
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…
The native conformation of structured proteins is stabilized by a complex network of interactions. We analyzed the elementary patterns that constitute such network and ranked them according to their importance in shaping protein sequence…
The interaction between a flexible polymer in good solvent and smaller associating solute molecules such as amphiphiles (surfactants) is considered theoretically. Attractive correlations, induced in the polymer because of the interaction,…
We explore the interplay between the protein-protein interactions network and the expression of the interacting proteins. It is shown that interacting proteins are expressed in significantly more similar cellular concentrations. This is…
The observation by Ke et al. [Science 338, 1177 (2012)] that large numbers of short, pre-designed DNA strands can assemble into three-dimensional target structures came as a great surprise, as no colloidal self-assembling system has ever…
Many biological and synthetic materials self-assemble into helical or twisted aggregates. The shape is determined by a complex interplay between elastic forces and the orientation and chirality of the constituent molecules. We study this…
Inspired by biology's most sophisticated computer, the brain, neural networks constitute a profound reformulation of computational principles. Remarkably, analogous high-dimensional, highly-interconnected computational architectures also…
Colloidal particles, amphiphiles, and functionalized nanoparticles are examples of systems that frequently exhibit short-range attractions coupled with long-range repulsions. In this work, we observe striking differences in the dynamics of…
We calculate the configurational entropy of hard particles confined in a cavity using Monte Carlo integration. Multiple combinations of particle and cavity shapes are considered. For small numbers of particles $N$, we show that the entropy…
Particles with directional interactions are promising building blocks for new functional materials and may serve as models for biological structures. Mutually attractive nanoparticles that are deformable due to flexible surface groups, for…
Protein crystallization in vivo provides some fascinating examples of biological self-assembly. Here, we provide a selective survey to show the diversity of functions for which protein crystals are used, and the physical properties of the…
Using Monte Carlo simulations, we study the assembly of colloidal particles interacting via isotropic core-corona potentials in two dimensions and confined in a circular box. We explore the structural variety at low temperatures as function…
At low temperatures, colloidal particles with short-range attractive and long-range repulsive interactions can form various periodic microphases in bulk.In this paper, we investigate the self-assembly behaviour of colloids with competing…
An approach that combines Self-Organizing maps, hierarchical clustering and network components is presented, aimed at comparing protein conformational ensembles obtained from multiple Molecular Dynamic simulations. As a first result the…
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…
Multiple phenotypic protein expressions arising from one genome represent variations in the protein relative abundance and their stoichiometry. A lack of definite compositional parts challenges the modeling of protein megacomplexes and…