Related papers: Competitive ligand binding kinetics to linear poly…

Comprehensive knowledge of protein-ligand interactions should provide a useful basis for annotating protein functions, studying protein evolution, engineering enzymatic activity, and designing drugs. To investigate the diversity and…

Ring polymers remain a major challenge to our current understanding of polymer dynamics. Experimental results are difficult to interpret because of the uncertainty in the purity and dispersity of the sample. Using both equilibrium and…

We study theoretically situations where competition arises between an interdiffusion process and a cross-linking chemical reaction at interfaces between pieces of the same polymer material. An example of such a situation is observable in…

Protein-ligand modeling underpins computational drug discovery and molecular design. Existing protein-ligand benchmarks typically evaluate whether a protein and ligand interact and how strongly they bind, through tasks such as binary…

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…

We consider the dynamics of a bio-filament under the collective drive of motor proteins. They are attached irreversibly to a substrate and undergo stochastic attachment-detachment with the filament to produce a directed force on it. We…

The translocation of biopolymers, such as DNA and proteins, across cellular or nuclear membranes is essential for numerous biological processes. The translocation dynamics are influenced by the properties of the polymers, such as polymer…

The effect of different Monte Carlo move sets on the the folding kinetics of lattice polymer chains is studied from the geometry of the conformation-network. The networks have the characteristics of small- world. The Monte Carlo move, rigid…

I develop a kinetic mechanism to explain chain folding in polymer crystallization which is based on the competition between the formation of stems, which is due to frequent occupations of trans states along the chains in the supercooled…

The motion involved in barrier crossing for protein folding are investigated in terms of the chain dynamics of the polymer backbone, completing the microscopic description of protein folding presented in the previous paper. Local reaction…

This research paper comprehensively explores the effects of molecular weight and chain architecture on the interfacial and thermodynamic properties of cyclic and linear polymer blends. Utilizing the Kremer-Grest bead-spring model, the study…

We study the effect of physical confinement on the capillary infiltration of polymers into cylindrical nanopores using molecular dynamics simulations. In particular, we probe whether the critical contact angle above which capillary rise…

In this paper we study aggregation kinetics in systems of particles functionalised by complementary linkers. Most of the coarse-grained models currently employed to study large-scale self-assembly of these systems rely on effective…

Rebinding kinetics of molecular ligands plays a critical role in biomachinery, from regulatory networks to protein transcription, and is also a key factor for designing drugs and high-precision biosensors.In this study, we investigate…

Active polymers possess numerous unique properties that are quite different from those observed in the system of small active molecule due to the intricate interplay between their activity and topological constraints. This study focuses on…

Macromolecules can gain special properties by adopting knotted conformations, but engineering knotted macromolecules is a challenging task. Here we surprisingly observed that knotting can be very effectively produced in active polymers.…

Nanoparticles are often covered in ligand monolayers, which can undergo a temperature-dependent order-disorder transition that switches the particle-particle interaction from repulsive to attractive in solution. In this work, we examine how…

Hydrodynamic slippage plays a crucial role in the flow dynamics of thin polymer films, as recently shown by the analysis of the profiles of liquid fronts. For long-chained polymer films it was reported that a deviation from a symmetric…

The extent of coupling between the folding of a protein and its binding to a substrate varies from protein to protein. Some proteins have highly structured native states in solution, while others are natively disordered and only fold fully…

Transient bonds between fast linkers and slower particles are widespread in physical and biological systems. In spite of their diverse structure and function, a commonality is that the linkers diffuse on timescales much faster compared to…