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The three-dimensional organization of chromatin is thought to play an important role in controlling gene expression. Specificity in expression is achieved through the interaction of transcription factors and other nuclear proteins with…
Although a vast amount of experimental information is available on the elongation, compression, and folding of proteins in biochemical processes, very little is known about the real structure and molecular dynamics of DNA at an atomic…
We make use of the previously developed formalism for a monomer ensemble and include angular dependence of the segments of the polymer chains thus described. In particular we show how to deal with stiffness when the polymer chain is…
Equilibration of polymer melts containing highly entangled long polymer chains in confinement or with free surfaces is a challenge for computer simulations. We approach this problem by first studying polymer melts based on the soft-sphere…
We present results from molecular dynamics simulations of a spherically confined neutral polymer in the presence of crowding agents, studying polymer shapes and conformations as a function of the confining potential, solvent quality and the…
Molecular simulations of the self-assembly of cone-shaped particles with specific, attractive interactions are performed. Upon cooling from random initial conditions, we find that the cones self assemble into clusters and that clusters…
Harnessing the topology of ring polymers as a design motif in functional nanomaterials is becoming a promising direction in the field of soft matter. For example, the ring topology of DNA plasmids prevents the relaxation of excess twist…
We develop a model to describe the properties of random assemblies of polydisperse hard spheres. We show that the key features to describe the system are (i) the dependence between the free volume of a sphere and the various coordination…
The ability of virus shells to encapsulate a wide range of functional cargoes, especially multiple cargoes - siRNAs, enzymes, and chromophores - has made them an essential tool in biotechnology for advancing drug delivery applications and…
Assemblies of purely repulsive and frictionless particles, such as emulsions or hard spheres, display very curious properties near their jamming transition, which occurs at the random close packing for mono-disperse spheres. Although such…
A fresh approach to the data from experiments with hard sphere colloids yields seminal insights into the glass transition. The precise determination of the fraction of particles caged by their neighbours is unprecedented and provides…
A framework is presented for understanding the common character of proteins. Proteins are linear chain molecules. However, the simple model of a polymer viewed as spheres tethered together does not account for many of the observed…
The presence of nanoparticles in a diblock copolymer leads to changes in the morphology and properties of the matrix and can produce highly organized hybrid materials. The resulting material properties depend not only on the polymer…
Synthetic copolymers and biopolymers, such as polypeptides and double-stranded DNA, often exhibit strong variations in bending stiffness along their contour, which can significantly impact conformational behavior at larger scales. To…
We study the dynamics of an ideal polymer chain in a crowded, viscoelastic medium and in the presence of active forces. The motion of the centre of mass and of individual monomers is calculated. On time scales that are comparable to the…
Dimerization and subsequent aggregation of polymers and biopolymers often occur under nonequilibrium conditions. When the initial state of the polymer is not collapsed or the final folded native state, the dynamics of dimerization can…
The mechanism and driving forces of chromosome segregation in the bacterial cell cycle of E. coli is one of the least understood events in its life cycle. Using principles of entropic repulsion between polymer loops confined in a cylinder,…
We present micro-rheological measurments of the drag force on colloids pulled through a solution of lambda-DNA (used here as a monodisperse model polymer) with an optical tweezer. The experiments show a violation of the Stokes-Einstein…
Polymer architecture plays critical roles in both bulk rheological properties and microscale macromolecular dynamics in entangled polymer solutions and composites. Ring polymers, in particular, have been the topic of much debate due to the…
When a flexible polymer is sucked into a localized small hole, the chain can initially respond only locally and the sequential nonequilibrium processes follow in line with the propagation of the tensile force along the chain backbone. We…