A5054548786- Rheology and Fluid Dynamics Studies
- Cellular Mechanics and Interactions
- Advanced Materials and Mechanics
- Nanopore and Nanochannel Transport Studies
- Material Dynamics and Properties
- Force Microscopy Techniques and Applications
- Micro and Nano Robotics
- Bacteriophages and microbial interactions
- Microfluidic and Bio-sensing Technologies
- Genomics and Chromatin Dynamics
- Diffusion and Search Dynamics
- RNA and protein synthesis mechanisms
- Electrostatics and Colloid Interactions
- Music Technology and Sound Studies
- Theoretical and Computational Physics
- Slime Mold and Myxomycetes Research
- Microtubule and mitosis dynamics
- RNA Research and Splicing
- Computer Graphics and Visualization Techniques
- Protein Structure and Dynamics
- Adhesion, Friction, and Surface Interactions
- 3D Shape Modeling and Analysis
- Pickering emulsions and particle stabilization
- Lipid Membrane Structure and Behavior
- Advanced Thermodynamics and Statistical Mechanics
University of Vienna
2019-2024
University of Southern Denmark
2024
University of Trento
2024
Austrian Economics Center
2021
Max Planck Institute for Polymer Research
2015-2020
New York University
2013-2016
Max Planck Society
2015
University of Fribourg
2008
The last years have witnessed remarkable advances in our understanding of the emergence and consequences topological constraints biological soft matter. Examples are abundant relation to (bio)polymeric systems range from characterization knots single polymers proteins that whole chromosomes polymer melts. At same time, considerable been made description interplay between physical properties complex fluids, with development techniques now allow researchers control formation interaction...
Recent theoretical studies found that mixtures of active and passive colloidal particles phase separate but only at very high activity ratio. The value poses serious obstacles for experimental exploration this phenomenon. Here we show using simulations when the are polymers, critical ratio decreases with polymer length. This not facilitates experiments also has implications on DNA organization in living cell nuclei. Entropy production can be used as an accurate indicator non-equilibrium transition.
The glass transition in soft matter systems is generally triggered by an increase packing fraction or a decrease temperature. It has been conjectured that the internal topology of constituent particles, such as polymers, can cause glassiness too. However, conjecture relies on immobilizing particles and therefore difficult to fulfill experimentally. Here we show dense solutions circular polymers containing (active) segments increased mobility, interplay activity generates unprecedented glassy...
Connecting the viscoelastic behavior of stressed ring melts to various forms entanglement that can emerge in such systems is still an open challenge. Here, we consider active melts, where stress generated internally, and introduce a topology-based method detect track consequential entanglements, namely, deadlocks. We demonstrate that, as accumulates, more rings are co-opted growing web deadlocks entrap many other by threading, bringing system standstill. The ought help study topological...
In order to quantify the effect of mutual threading on conformations and dynamics unconcatenated unknotted rings in melt we computationally examine their minimal surfaces. We found a linear scaling surface area with ring length. Minimal surfaces allow for an unambiguous algorithmic definition between rings. Based it, that, although is frequent, majority cases correspond short loops. These findings explain why approximate theories that neglect are so unexpectedly successful despite having no...
Unconcatenated ring polymers in concentrated solutions and melt are remarkably well described as double-folded conformations on randomly branched primitive trees. This picture though contrasts recent evidence for extensive intermingling between close-by rings the form of long-lived topological constraints or threadings. Here, we employ concept minimal surface to quantify extent threadings polymer vs equilibrated molecular dynamics computer simulations. Our results show that significantly...
Dynamical properties of a long polymer ring in melt unknotted and unconcatenated rings are calculated. We re-examine generalize the well known model confined to lattice topological obstacles light recently developed Flory theory unentangled which maps every on an annealed branched establishes that backbone associated with each follows self-avoiding rather than Gaussian random walk statistics. find scaling relaxation time diffusion coefficient length, as dependence stress modulus, zero shear...
Well-characterized single-chain nanoparticles (SCNPs), synthesized from a linear polystyrene precursor through an intramolecular [4 + 4] thermal cycloaddition cross-linking reaction in dilute conditions, were added to entangled melts at different concentrations. Starting the pure melt, which is much more viscous than melt of SCNPs, zero-shear viscosity increased upon addition and reached maximum before eventually dropping value SCNP melt. Molecular simulations reveal origin this unexpected...
The relationship between polymer topology and bulk rheology remains a key question in soft matter physics. Architecture-specific constraints (or threadings) are thought to control the dynamics of ring polymers ring-linear blends, which thus affects viscosity range that pure rings value larger, but still comparable to, linear melt. Here we consider qualitatively different systems polymers, fused together "chimeric" architectures. simplest example this family is "tadpole"-shaped polymer,...
Ring polymers in dense solutions are among the most intriguing problems polymer physics. Because of its natural occurrence circular form, DNA has been extensively used as a proxy to study fundamental physics ring different topological states. Yet, torsionally constrained-such supercoiled-topologies have largely neglected so far. The applicability existing theoretical models supercoiled is thus unknown. Here, we address this gap by coupling large-scale molecular dynamics simulations with...
Active matter states defy many notions that have been established for systems in thermodynamic equilibrium. Nevertheless, the lack of detailed balance might be utilized to design nonequilibrium materials with unique properties. Recently we shown, employing a model ring polymers containing segments larger mobility than given by equilibrium thermal fluctuations, making intrinsic topology active can result relax extremely slowly, so-called topological glass. In this paper, focus on role phase...
Current theories on the conformation and dynamics of unknotted non-concatenated ring polymers in melt conditions describe each as a tree-like double-folded object. While evidence from simulations supports this picture single level, other works show pairs rings also thread other, feature overlooked tree theories. Here we reconcile dichotomy using Monte Carlo melts with different bending rigidities. We find that are (more strongly for stiffer rings)
We use computer simulations to study a system of two unlinked ring polymers, whose length and bending stiffness are systematically varied. derive the effective potentials between rings, calculate areas minimal surfaces same, characterize threading them. When rings same kind, one through surface other is immanent for small ring-ring separations. Flexible pierce several times but only shallowly, as compared stiff which less frequently deeply. Typically, that being threaded swells flattens up...
We study active topological glass under spherical confinement, allowing us to exceed the chain lengths simulated previously and determine critical exponents of arrested conformations. find a unresolved "tank-treading" dynamic mode segments along ring contour. This can enhance active-passive phase separation in state when both diffusional conformational relaxation rings are significantly suppressed. Within observational time, we see no systematic trends positioning separated domains within...
We apply monomer-resolved computer simulations of supercoiled ring polymers under shear, taking full account the hydrodynamic interactions, accompanied, in parallel, by which these are switched off.
Active matter consists of particles that dissipate energy, from their own sources, in the form mechanical work on surroundings. Recent interest active-passive polymer mixtures has been driven by relevance phase separation (e.g., transcriptionally) active and inactive (transcriptionally silent) DNA strands nuclei living cells. In this paper, we study interfacial properties separated steady states compare them with equilibrium separation. We model constituents assigning stronger-than-thermal...
We use molecular dynamics simulations to explore concentrated solutions of semiflexible polyelectrolyte ring polymers, akin the DNA mini-circles, with counterions different valences. find that assembly rings into nanoscopic cylindrical stacks is a generic feature systems, but morphology and such cluster can be steered by counterion conditions. In general, small addition trivalent ions stabilize emergence clusters due condensation, which mitigates repulsion between like-charged rings....
Motivated by the chromosomes enclosed in a cell nucleus, we study spherically confined system of small number long unknotted and nonconcatenated polymer rings melt systematically compare it with bulk results. We find that universal scaling exponents also apply case; however, certain important differences arise. First, due to confinement effects, static threading properties depend on their radial position within confining sphere. Second, rings' dynamics is overall subdiffusive, but...
We explore effective interactions in dilute polydisperse ring polymer solutions. Based on a topological and threading analysis, we deduce the steric, contributions to potentials for differently sized rings. Additionally, quantify contribution of constraints different asymmetries length. Further, compare how change when mutual is restricted characterise depth distributions at center-of-mass separations.
The authors study how conformation properties of globular DNA affect facilitated diffusion proteins targeting DNA. They find that crumpled globules promote faster than conformations with smooth surfaces.
Polymers with active segments constitute prospective future materials and are used as a model for some biological systems such chromatin. The directions of the forces typically introduced temporal or spatial correlations to establish directional motion chain corresponding dynamics. Instead, here we consider an active-passive copolymer, where two differ only by magnitude their fluctuations feature no artificial correlations. Here show that although itself does not possess dynamics, if chains...
Understanding the behaviour of ring polymers in dense solutions is one most intriguing problems polymer physics with far-reaching implications from material science to genome biology. Thanks its natural occurrence circular form, DNA has been intensively employed as a proxy study fundamental different topological states. Yet, torsionally constrained – such supercoiled topologies have largely neglected so far. Extreme entanglement and high supercoiling levels are commonly found genetic both...