Related papers: Single Polymer Dynamics for Molecular Rheology
Ring polymers exhibit unique flow properties due to their closed chain topology. Despite recent progress, we have not yet achieved a full understanding of the nonequilibrium flow behavior of rings in nondilute solutions where intermolecular…
This review summarizes recent progress in investigating polymer systems by using Differential dynamic microscopy (DDM), a rapidly emerging approach that transforms a commercial microscope by combining real-space information with the…
Blends of polymers of different topologies, such as ring and supercoiled, naturally occur in biology and often exhibit emergent viscoelastic properties coveted in industry. However, due to their complexity, along with the difficulty of…
In recent years, single molecule force techniques have opened a new avenue to decipher the folding landscapes of biopolymers by allowing us to watch and manipulate the dynamics of individual proteins and nucleic acids. In single molecule…
Single-molecule pulling techniques have emerged as versatile tools for probing the noncovalent forces holding together the secondary and tertiary structure of macromolecules. They also constitute a way to study at the single-molecule level…
Emergent phenomena share the fascinating property of not being obvious consequences of the design of the system in which they appear. This characteristic is no less relevant when attempting to simulate such phenomena, given that the outcome…
This article presents a comprehensive review of the Hydrodynamic Scaling Model for the dynamics of polymers in dilute and nondilute solutions. The Hydrodynamic Scaling Model differs from some other treatments of non-dilute polymer solutions…
In recent years molecular elasticity has emerged as an active area of research: there are experiments that probe mechanical properties of single biomolecules such as DNA and Actin, with a view to understanding the role of elasticity of…
While the dynamics of polymer chains in equilibrium media is well understood by now, the polymer dynamics in active non-equilibrium environments can be very different. Here we study the dynamics of polymers in a viscous medium containing…
We present a multiscale approach to the modeling of polymer dynamics in the presence of a fluid solvent. The approach combines Langevin Molecular Dynamics (MD) techniques with a mesoscopic Lattice-Boltzmann (LB) method for the solvent…
Biological molecules, like all active matter, use free energy to generate force and motion which drive them out of thermal equilibrium, and undergo inherent dynamic interconversion between metastable free energy states separated by levels…
In the past decades, advances in microscopy have made it possible to study the dynamics of individual biomolecules in vitro and resolve intramolecular kinetics that would otherwise be hidden in ensemble averages. More recently,…
Molecular-scale computation is crucial for smart materials and nanoscale devices, yet creating single-molecule systems capable of complex computations remains challenging. We present a theoretical framework for a single-molecule computer…
We present numerical and analytical results describing the effect of hydrodynamic interactions on the dynamics of a short polymer chain in solution. A molecular dynamics algorithm for the polymer is coupled to a direct simulation Monte…
Using molecular dynamics simulations we study the slow dynamics of a hard sphere fluid confined in a disordered porous matrix. The presence of both discontinuous and continuous glass transitions as well as the complex interplay between…
The coupled dynamics of entangled polymers which span a broad time and length scales govern the unique viscoelastic properties of polymers. To follow chain mobility by numerical simulations from the intermediate Rouse and reptation regimes…
Conformations of a single-component bottle-brush polymer with a fully flexible backbone under poor solvent conditions are studied by molecular-dynamics simulations, using a coarse-grained bead-spring model with side chains of up to N=40…
Single molecule manipulation techniques reveal that the mechanical resistance of a protein depends on the direction of the applied force. Using a lattice model of polymers, we show that changing the pulling direction leads to different…
The coarse-grained molecular dynamics (MD) or Brownian dynamics (BD) simulation is a particle-based approach that has been applied to a wide range of biological problems that involve interactions with surrounding fluid molecules or the…
Molecular dynamics simulation methods are used to study the folding of polymer chains into packed cubic states. The polymer model, based on a chain of linked sites moving in the continuum, includes both excluded volume and torsional…