Related papers: Kinetics of seeded protein aggregation: theory and…

The adhesion of biomembranes is mediated by the binding of membrane-anchored receptor and ligand proteins. The proteins can only bind if the separation between apposing membranes is sufficiently close to the length of the protein complexes,…

We investigate the kinetics of many-species systems with aggregation of similar species clusters and annihilation of opposite species clusters. We find that the interplay between aggregation and annihilation leads to rich kinetic behaviors…

When trying to maximize the adoption of a behavior in a population connected by a social network, it is common to strategize about where in the network to seed the behavior, often with an element of randomness. Selecting seeds uniformly at…

Protein activity is a significant characteristic for recombinant proteins which can be used as biocatalysts. High activity of proteins reduces the cost of biocatalysts. A model that can predict protein activity from amino acid sequence is…

This study proposes a new full-field approach for modeling grain boundary pinning by second phase particles in two-dimensional polycrystals. These particles are of great importance during thermomechanical treatments, as they produce…

Over the years, advances in experimental and computational methods have helped us to understand the role of thermodynamic, kinetic and active (chaperone-aided) effects in coordinating the folding steps required to achieving a knotted native…

We are now witnessing significant progress of deep learning methods in a variety of tasks (or datasets) of proteins. However, there is a lack of a standard benchmark to evaluate the performance of different methods, which hinders the…

Asymmetric segregation of key proteins at cell division -- be it a beneficial or deleterious protein -- is ubiquitous in unicellular organisms and often considered as an evolved trait to increase fitness in a stressed environment. Here, we…

A theoretical analysis of the unfolding pathway of simple modular proteins in length- controlled pulling experiments is put forward. Within this framework, we predict the first module to unfold in a chain of identical units, emphasizing the…

Function of proteins or a network of interacting proteins often involves communication between residues that are well separated in sequence. The classic example is the participation of distant residues in allosteric regulation.…

A fundamental challenge in protein design is the trade-off between generating structural diversity while preserving motif biological function. Current state-of-the-art methods, such as partial diffusion in RFdiffusion, often fail to resolve…

We present a computational study on the folding and aggregation of proteins in aqueous environment, as function of its concentration. We show how the increase of the concentration of individual protein species can induce a partial unfolding…

Proteins must bind to specific other proteins in vivo in order to function. The proteins must bind only to one or a few other proteins of the of order a thousand proteins typically present in vivo. Using a simple model of a protein,…

Silk is a semi-dilute solution of randomly coiled associating polypeptide chains that crystallise following the stretch-induced disruption, in the strong extensional flow of extrusion, of the solvation shell around their amino acids. We…

Generating novel and functional protein sequences is critical to a wide range of applications in biology. Recent advancements in conditional diffusion models have shown impressive empirical performance in protein generation tasks. However,…

Coarse-graining or model reduction is a term describing a range of approaches used to extend the time-scale of molecular simulations by reducing the number of degrees of freedom. In the context of molecular simulation, standard…

This review is a tutorial for scientists interested in the problem of protein structure prediction, particularly those interested in using coarse-grained molecular dynamics models that are optimized using lessons learned from the energy…

This manuscript proposes a method to enable controlled high-gradient particle acceleration when requiring self-modulation of the drive bunch. While electron bunch seeding of self-modulation (eSSM) has been realised at a plasma electron…

Multilayer networks are the underlying structures of multiple real-world systems where we have more than one type of interaction/relation between nodes: social, biological, computer, or communication, to name only a few. In many cases, they…

We study folding dynamics of protein-like sequences on square lattice using physical move set that exhausts all possible conformational changes. By analytically solving the master equation, we follow the time-dependent probabilities of…