Related papers: Dynamical Scaling and Phase Coexistence in Topolog…
We investigate the coalescence of two DNA-bubbles initially located at weak domains and separated by a more stable barrier region in a designed construct of double-stranded DNA. In a continuum Fokker-Planck approach, the characteristic time…
The proper design of DNA sequences allows for the formation of well defined supramolecular units with controlled interactions via a consecution of self-assembling processes. Here, we benefit from the controlled DNA self-assembly to…
In living cells, proteins involved in specialized biochemical functions are often spatially organized within biomolecular condensates. Increasing evidence suggests that some of these condensates, including DNA repair condensates, emerge…
Heterogeneous nucleation is central to many familiar first-order phase transitions such as the freezing of water and the solidification of metals, and it can also play a crucial role in cosmology. We examine nucleation seeded by preexisting…
The role of thermodynamics in the evolution of systems evolving under purely gravitational forces is not completely established. Both the infinite range and singularity in the Newtonian force law preclude the use of standard techniques.…
Recent theoretical predictions on DNA mechanical separation induced by pulling forces are numerically tested within a model in which self-avoidance for DNA strands is fully taken into account. DNA strands are described by interacting pairs…
The twisting deformation of mechanically stretched DNA molecules is studied by a coarse grained Hamiltonian model incorporating the fundamental interactions that stabilize the double helix and accounting for the radial and angular base pair…
The thermally induced denaturation of DNA in the presence of attractive solid surface is studied. The two strands of DNA are modeled via two coupled flexible chains without volume interactions. If the two strands are adsorbed on the…
The phase-field crystal model is by now widely used in order to predict crystal nucleation and growth. For colloidal solidification with completely overdamped individual particle motion, we show that the phase-field crystal dynamics can be…
We predict the existence of a totally new class of phases in weakly coupled, three-dimensional stacks of two-dimensional (2D) XY-models. These ``sliding phases'' behave essentially like decoupled, independent 2D XY-models with precisely…
We devise a field theoretical formalism for a microscopic theory of nucleation processes and phase coexistence in finite dimensional glassy systems. We study disordered $p$-spin models with large but finite range of interaction. We work in…
Advanced Monte Carlo simulations are used to study the effect of nano-slit confinement on metric and topological properties of model DNA chains. We consider both linear and circularised chains with contour lengths in the 1.2--4.8 $\mu$m…
Nonequilibrium states of quantum materials can exhibit exotic properties and enable unprecedented functionality and applications. These transient states are inherently inhomogeneous, characterized by the formation of topologically protected…
We investigate two-dimensional (2d) melting in the presence of a one-dimensional (1d) periodic potential as, for example, realized in recent experiments on 2d colloids subjected to two interfering laser beams. The topology of the phase…
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…
We investigate kinetic pathways of the DNA melting transition using variable-range versions of the Poland-Scheraga (PS) and Peyrard-Dauxois-Bishop (PDB) models of DNA. In the PS model, we construct a phi^4-field theory to calculate the…
We investigate crystal nucleation in supersaturated colloid suspensions using enhanced molecular dynamics simulations augmented with machine learning techniques. The simulations reveal that crystallization in the model colloidal system…
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…
As sections of a strand duplexed DNA denature when exposed to high temperature, the excess linking number is taken up by the undenatured portions of the molecule. The mechanical energy that arises because of the overwinding of the…
DNA supercoils are generated in genome regulation processes such as transcription and replication, and provide mechanical feedback to such processes. Under tension, DNA supercoil can present a coexistence state of plectonemic (P) and…