Related papers: Combinatorial protein-protein interactions on a po…
The biological functions of proteins often depend on dynamic structural ensembles. In this work, we develop a flow-based generative modeling approach for learning and sampling the conformational landscapes of proteins. We repurpose highly…
Polymer chains decorated with a fraction of monomers capable of forming reversible bonds form transient polymer networks that are important in soft and biological systems. If chains are flexible and the attractive monomers are all of the…
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…
We examine the phase transition of polymer adsorption as well as the underlying kinetics of polymer binding from dilute solutions on a structureless solid surface. The emphasis is put on the properties of regular multiblock copolymers,…
The structure of polymer networks, defined by chain lengths and connectivity patterns, fundamentally influences their bulk properties. While existing polymer network models connect chain properties to emergent network behavior, they are…
The principles underlying protein folding remains one of Nature's puzzles with important practical consequences for Life. An approach that has gathered momentum since the late 1990's, looks at protein hetero-polymers and their folding…
Physical mechanisms underlying the empirical correlation between relative contact order (CO) and folding rate among naturally-occurring small single-domain proteins are investigated by evaluating postulated interaction schemes for a set of…
A theory is presented for the binding of small molecules such as surfactants to semiflexible polymers. The persistence length is assumed to be large compared to the monomer size but much smaller than the total chain length. Such polymers…
Much work has studied effective interactions between micron-sized particles carrying linkers forming reversible, inter-particle linkages. These studies allowed understanding the equilibrium properties of colloids interacting through…
Hybridization between species is an important mechanism for the origin of novel lineages and adaptation to new environments. Increased allelic variation and modification of the transcriptional network are the two recognized forces currently…
The idea that structural disorder might be a novel mechanism of protein interaction is widespread in the Literature, although the number of statistically significant structural studies supporting this is surprisingly low. At variance with…
Via large-scale molecular dynamics simulations, we observe the melting of a topological glass of stiff ring polymers by incorporating flexible ring polymers, along an isobaric path. As more flexible ring polymers are introduced, cluster…
We experimentally investigate the structural behavior of an interacting colloidal monolayer being driven across a decagonal quasiperiodic potential landscape created by an optical interference pattern. When the direction of the driving…
Inspired by the ubiquity of composite filamentous networks in nature we investigate models of biopolymer networks that consist of interconnected floppy and stiff filaments. Numerical simulations carried out in three dimensions allow us to…
During the life cycle of bacterial cells the non-mixing of the two ring-shaped daughter genomes is an important prerequisite for the cell division process. Mimicking the environments inside highly crowded biological cells, we study the…
Geometric and structural constraints greatly restrict the selection of folds adapted by protein backbones, and yet, folded proteins show an astounding diversity in functionality. For structure to have any bearing on function, it is thus…
Multivalent particles bind to targets via many independent ligand-receptor bonding interactions. This microscopic design spans length scales in both synthetic and biological systems. Classic examples include interactions between cells,…
Within self-consistent field theory we study the phase behavior of a symmetrical binary AB polymer blend confined into a thin film. The film surfaces interact with the monomers via short range potentials. One surface attracts the A…
We present several ordering mechanisms in diblock copolymers. For temperatures above the order-disorder temperature and in the weak segregation regime, a linear response theory is presented which gives the polymer density in the vicinity of…
Vitrimers are polymer networks that can undergo bond exchange reactions. They dynamically rearrange their structures while maintaining their overall integrity, thus resulting in unique properties such as self-healing, reprocessability,…