Related papers: Designing active colloidal folders
Using an off-lattice model, we fully enumerate folded conformations of polypeptide chains of up to N = 19 monomers. Structures are found to differ markedly in designability, defined as the number of sequences with that structure as a unique…
Colloidal dispersions are prized as model systems to understand basic properties of materials, and are central to a wide range of industries from cosmetics to foods to agrichemicals. Among the key developments in using colloids to address…
Catalytically active colloids maintain non-equilibrium conditions in which they produce and deplete chemicals and hence effectively act as sources and sinks of molecules. While individual colloids that are symmetrically coated do not…
In this paper we show that a dynamical description of the protein folding process provides an effective representation of equilibrium properties and it allows for a direct investigation of the mechanisms ruling the approach towards the…
Biological organisms often have elongated, flexible structures with some degree of chirality in their bodies or movements. In nature, these organisms frequently take advantage of self-encapsulation mechanisms that create folded…
Active matter locally converts chemical energy into mechanical work and, for this reason, it provides new mechanisms of pattern formation. In particular, active gels made of protein motors and filaments are far-from-equilibrium systems that…
Surface-driven flows are ubiquitous in nature, from subcellular cytoplasmic streaming to organ-scale ciliary arrays. Here, we model how confined geometries can be used to engineer complex hydrodynamic patterns driven by activity prescribed…
Exploring and understanding the protein-folding problem has been a long-standing challenge in molecular biology. Here, using molecular dynamics simulation, we reveal how parallel distributed adjacent planar peptide groups of unfolded…
Mechanically induced folding of passive cross-linkers is a fundamental biological phenomenon. A typical example is a conformational change in myosin II responsible for the power-stroke in skeletal muscles. In this paper we present an…
External fields can decidedly alter the free energy landscape of soft materials and can be exploited as a powerful tool for the assembly of targeted nanostructures and colloidal materials. Here, we use computer simulations to demonstrate…
The folding of a polypeptide is an example of the cooperative effects of the amino-acid residues. Of recent interest is how a secondary structure, such as a helix, spontaneously forms during the collapse of a peptide from an initial…
We study the elastic properties of a single A/B copolymer chain with a specific sequence. We predict a rich structure in the force extension relations which can be addressed to the sequence. The variational method is introduced to probe…
The dynamical chaos in Lennard-Jones toy models of heteropolymers is studied by molecular dynamics simulations. It is shown that two nearby trajectories quickly diverge from each other if the heteropolymer corresponds to a random sequence.…
We propose a new and effective means for designing stable and fast-folding polypeptide sequences using a cumulant expansion of the molecular partition function. This method is unique in that $T_{Z}$, the ``cumulant design temperature''…
Inspired by protein folding, we explored the construction of three-dimensional structures and machines from one-dimensional chains of simple building blocks. This approach not only allows us to recreate the self-replication mechanism…
We review recent progress in the theoretical description of anisotropic hard colloidal particles. The shapes considered range from rods and dumbbells to rounded cubes, polyhedra and to biaxial particles with arbitrary shape. Our focus is on…
In spite of decades of research, much remains to be discovered about folding: the detailed structure of the initial (unfolded) state, vestigial folding instructions remaining only in the unfolded state, the interaction of the molecule with…
Functional soft materials, comprising colloidal and molecular building blocks that self-organize into complex structures as a result of their tunable interactions, enable a wide array of technological applications. Inverse methods provide…
The ability to computationally generate novel yet physically foldable protein structures could lead to new biological discoveries and new treatments targeting yet incurable diseases. Despite recent advances in protein structure prediction,…
Folding is emerging as a promising manufacturing process to transform flat materials into functional structures, offering efficiency by reducing the need for welding, gluing, and molding, while minimizing waste and enabling automation.…