Related papers: Hopping and crawling DNA-coated colloids
The translocation of structured RNA or DNA molecules through narrow pores necessitates the opening of all base pairs. Here, we study the interplay between the dynamics of translocation and base-pairing theoretically, using kinetic Monte…
The motion of a cylindrical crystalline nanoparticle sandwiched between two crystalline planes, one stationary and the other pulled at a constant velocity and pressed down by a normal load, is considered theoretically using a planar model.…
Under appropriate conditions, mixtures of cationic and neutral lipids and DNA in water condense into complexes in which DNA strands form local 2D smectic lattices intercalated between lipid bilayer membranes in a lamellar stack. These…
We study the driving of colloidal molecular crystals over periodic substrates such as those created with optical traps. The n-merization that occurs in the colloidal molecular crystal states produces a remarkably rich variety of distinct…
Recent theoretical studies found that mixtures of active and passive colloidal particles phase separate but only at very high activity ratio. The high value poses serious obstacles for experimental exploration of this phenomenon. Here we…
A model of self-avoiding walk with suitable constraints on self-attraction is developed to describe the conformational behaviour of a single stranded short DNA molecule that form hairpin structure. Using exact enumeration method we…
DNA-coated colloids can self-assemble into an incredible diversity of crystal structures, but applications of this technology are limited by poor understanding and control over the dynamical crystallization pathways. To address this…
In particle systems subject to a nonuniform drive, particle migration is observed from the driven to the non--driven region and vice--versa, depending on details of the hopping dynamics, leading to apparent violations of Fick's law and of…
Activated Random Walks, on $\mathbb{Z}^d$ for any $d\geqslant 1$, is an interacting particle system, where particles can be in either of two states: active or frozen. Each active particle performs a continuous-time simple random walk during…
Active colloids, also known as artificial microswimmers, are self-propelled micro and nanoparticles that convert uniform sources of fuel (e.g. chemical) or uniform external driving fields (e.g. magnetic or electric) into directed motion by…
We study the dynamics of DNA hairpin formation using oxDNA, a nucleotide-level coarse-grained model of DNA. In particular, we explore the effects of the loop stacking interactions and non-native base pairing on the hairpin closing times. We…
We observe, at low temperature, the appearance of propagating events that originate from the inter-conversion between adjacent four and five coordinated water molecules in supercooled liquid water, resulting in the migration of the…
Biological adhesion is a critical mechanical function of complex organisms operating at multiple scales. At the cellular scale, cell-cell adhesion is remarkably tunable to enable both cohesion and malleability during development,…
By taking into account base-base stacking interactions we improve the Generalized Model of Polypeptide Chain (GMPC). Based on a one-dimensional Potts-like model with many-particle interactions, the GMPC describes the helix-coil transition…
We study the behavior of two particles moving in a bistable potential, colliding inelastically with each other and driven by a stochastic heat bath. The system has the tendency to clusterize, placing the particles in the same well at low…
Optical tweezers have become a powerful tool for measuring parameters of microscale and nanoscale local environments. Motion of particles within optical tweezer traps established itself as a probe for local viscosity, temperature as well as…
There is increasing evidence that mammalian cells not only crawl on substrates but can also swim in fluids. To elucidate the mechanisms of the onset of motility of cells in suspension, a model which couples actin and myosin kinetics to…
Many recent studies of liquid-liquid phase separation in biology focus on phase separation as a dynamic control mechanism for cellular function, but it can also result in complex mesoscopic structures. We primarily investigate a model…
We have studied the low-temperature electrical transport properties of Pb$_x$(SiO$_2$)$_{1-x}$ ($x$ being the Pb volume fraction) nanogranular films with thicknesses of $\sim$1000 nm and $x$ spanning the dielectric, transitional, and…
Diverse processes--e.g. bioremediation, biofertilization, and microbial drug delivery--rely on bacterial migration in disordered, three-dimensional (3D) porous media. However, how pore-scale confinement alters bacterial motility is unknown…