Related papers: Combinatorial protein-protein interactions on a po…
Clusters of spherical particles with isotropic attraction favour compact structures that maximise the number of energetically optimal nearest-neighbour interactions. In contrast, dipolar interactions lead to the formation of chains with a…
Natural protein sequences that self-assemble to form globular structures are compact with high packing densities in the folded states. It is known that proteins unfold upon addition of denaturants, adopting random coil structures. The…
Building structures with hierarchical order through the self-assembly of smaller blocks is not only a prerogative of nature, but also a strategy to design artificial materials with tailored functions. We explore in simulation the…
Predicting the three-dimensional (3D) functional structures of proteins remains an important computational milestone in molecular biology to be achieved. This feat is hinged on a clear understanding of the mechanism which proteins use to…
This paper proposes a simple model to capture the complexity of multi-layer systems where their constituent layers affect, are affected by, each other. The physical layer is a circuit composed by a power source and resistors in parallel.…
The most important function of proteins may well be to bind to other biomolecules. It has long been felt that kinetic rates of bond formation and dissociation between soluble receptors and ligands might account for most features of the…
We solve a model that takes into account entropic barriers, frustration, and the organization of a protein-like molecule. For a chain of size $M$, there is an effective folding transition to an ordered structure. Without frustration, this…
Current experimental and theoretical studies on the effect of intermolecular interactions on molecular conduction appear to be in conflict with each other. In particular, some experimental results, e.g., the observation of 2-dimensional…
We present the results of analytic calculations and numerical simulations of the behaviour of a new class of chain molecules which we call thick polymers. The concept of the thickness of such a polymer, viewed as a tube, is encapsulated by…
We study theoretically the structure of sliding grafted polymer layers or SGP layers. These interfacial structures are built by attaching each polymer to the substrate with a ring-like molecule such as cyclodextrins. Such a topological…
Despite their considerable practical and biological applications, the link between molecular properties, assembly conditions and self-organized structure in confined polymer solutions remains elusive. Here, we explore the lyotropic nematic…
What can cells gain by using disordered, rather than folded, proteins in the architecture of their skeleton? Disordered proteins take multiple co-existing conformations, and often contain segments which act as random-walk-shaped polymers.…
The formation of chain-folded structures from the melt is observed in molecular dynamics simulations resembling the lamellae of polymer crystals. Crystallization and subsequent melting temperatures are related linearly to the inverse…
Using Brownian dynamics (BD) simulations and an analytical approach we investigate the shear-induced, nonequilibrium dynamics of dense colloidal suspensions confined to a narrow slit-pore. Focusing on situations where the colloids arrange…
Two ring polymers close to each other in space may be either in a segregated phase if there is a strong repulsion between monomers in the polymers, or intermingle in a mixed phase if there is a strong attractive force between the monomers.…
This paper studies a polymer chain in the vicinity of a linear interface separating two immiscible solvents. The polymer consists of random monomer types, while the interface carries random charges. Both the monomer types and the charges…
In this work we showcase the potential of peptides as versatile scaffolds for quantum computing and molecular spintronics. In particular, we focus on lanthanide-binding tags, which were originally developed in the field of biotechnology for…
In this paper, we consider the statistical analysis of a protein interaction network. We propose a Bayesian model that uses a hierarchy of probabilistic assumptions about the way proteins interact with one another in order to: (i) identify…
Although jammed packings of soft spheres exist in potential energy landscapes with a vast number of minima, when subjected to cyclic shear they may revisit the same configurations repeatedly. Simple hysteretic spin models, in which particle…
We demonstrate strong coupling between molecular excited states and surface plasmon modes of a slit array in a thin metal film. The coupling manifests itself as an anti-crossing behavior of the two newly formed polaritons. As the coupling…