A5089038178- Theoretical and Computational Physics
- Force Microscopy Techniques and Applications
- Material Dynamics and Properties
- Geometric and Algebraic Topology
- Protein Structure and Dynamics
- Nanopore and Nanochannel Transport Studies
- Liquid Crystal Research Advancements
- Lattice Boltzmann Simulation Studies
- DNA and Nucleic Acid Chemistry
- Genomics and Chromatin Dynamics
- Advanced Thermodynamics and Statistical Mechanics
- Stochastic processes and statistical mechanics
- Advanced Materials and Mechanics
- Micro and Nano Robotics
- Diffusion and Search Dynamics
- Lipid Membrane Structure and Behavior
- Adhesion, Friction, and Surface Interactions
- Pickering emulsions and particle stabilization
- Fluid Dynamics and Turbulent Flows
- Nonlinear Dynamics and Pattern Formation
- Bacteriophages and microbial interactions
- Rheology and Fluid Dynamics Studies
- Statistical Mechanics and Entropy
- Microtubule and mitosis dynamics
- Block Copolymer Self-Assembly
University of Padua
2016-2025
Istituto Nazionale di Fisica Nucleare, Sezione di Padova
2016-2025
Istituto Nazionale di Fisica Nucleare, Sezione di Bari
2024
University of Trento
2022-2024
University of Southern Denmark
2024
University of Vienna
2022
Istituto Nazionale di Fisica Nucleare, Trento Institute for Fundamental Physics And Applications
2022
Istituto Nazionale di Fisica Nucleare
1992-2021
Institute of Ionized Gas
2020
National Interuniversity Consortium for the Physical Sciences of Matter
2008-2020
We present the details of a lattice Boltzmann approach to phase separation in nonideal one- and two-component fluids. The collision rules are chosen such that equilibrium state corresponds an input free energy bulk flow is governed by continuity, Navier-Stokes, and, for binary fluid, convection-diffusion equation. Numerical results compared simple analytic predictions confirm indeed thermodynamically consistent kinetics lie within expected universality classes. other simulations systems....
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...
We report hybrid lattice Boltzmann (HLB) simulations of the hydrodynamics an active nematic liquid crystal sandwiched between confining walls with various anchoring conditions. confirm existence a transition passive phase and phase, in which there is spontaneous flow steady state. This attained for sufficiently "extensile" rods, case flow-aligning crystals, "contractile" ones flow-tumbling materials. In quasi-one-dimensional geometry, deep materials, our give evidence hysteresis...
We describe a lattice Boltzmann algorithm to simulate liquid crystal hydrodynamics. The equations of motion are written in terms tensor order parameter. This allows both the isotropic and nematic phases be considered. Backflow effects hydrodynamics topological defects naturally included simulations, as viscoelastic properties such shear-thinning shear-banding.
Topological entanglement in polymers and biopolymers is a topic that involves different fields of science such as chemistry, biology, physics, mathematics. One the main issues this to understand how complexity can depend on factors degree polymerization, quality solvent, temperature or confinement macromolecule. In respect statistical approach problem natural last few years there has been lot work study within mechanics framework. A review given here stressing results obtained describing...
We introduce a lattice Boltzmann model for simulating an immiscible-binary-fluid mixture. Our collision rules are derived from macroscopic thermodynamic description of the fluid in way motivated by Cahn-Hilliard approach to non-equilibrium dynamics and ensure that thermodynamically consistent state is reached equilibrium. The investigated numerically found agree with simple analytic predictions both one-phase two-phase region phase diagram.
Recent experiments showed that the linear double-stranded DNA in bacteriophage capsids is both highly knotted and neatly structured. What physical basis of this organization? Here we show evidence from stochastic simulation techniques suggests a key element tendency contacting strands to order, as cholesteric liquid crystals. This interaction favors their preferential juxtaposition at small twist angle, thus promoting an approximately nematic (and apolar) local order. The ordering effect...
We study numerically the rheological properties of a slab active gel close o isotropic-nematic transition. The flow behavior shows strong dependence on sample size, boundary conditions, and bulk constitutive curve, which, entering nematic phase, acquires an activity-induced discontinuity at origin. precursor this within metastable isotropic phase for contractile systems ({\em e.g.,} actomyosin gels) gives viscosity divergence; its counterpart extensile {\em B. subtilis}) suspensions admits...
The interplay between the topological and geometrical properties of a polymer ring can be clarified by establishing entanglement trapped in any portion (arc) ring. task requires to close open arcs into ring, resulting state may depend on specific closure scheme that is followed. To understand impact this ambiguity contexts practical interest, such as knot localization with non trivial topology, we apply various schemes model polymers. rings have same length (a trefoil knot) but different...
Significance Bacteriophages are viruses which infect bacteria. Many of these contain double-stranded DNA packed to almost crystalline density and exploit the resulting pressure trigger ejection into infected bacterial cell. We show that kinetics is highly sensitive ordering knotting packaged which, in turn, controlled by self-interactions. The latter favor ordered spools have a lower effective or topological friction than disordered entangled structures. also find torus knots (which can be...
One of the most important problems in development is how epigenetic domains can first be established, and then maintained, within cells. To address this question, we propose a framework that couples three-dimensional chromatin folding dynamics to "recoloring" process modeling writing marks. Because many intrachromatin interactions are mediated by bridging proteins, consider "two-state" model with self-attractive between two marks alike (either active or inactive). This displays...
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...
We study both the dynamics of dissolution an equilibrium interface and phase separation in two-dimensional fluids using lattice Boltzmann simulations. Results for a liquid-gas system binary fluid are compared. For symmetric quenches system, single-phase domains grow like ${t}^{\ensuremath{\alpha}}$, where $\ensuremath{\alpha}=\frac{1}{2}$ high viscosities (corresponding to early times), crossing over $\ensuremath{\alpha}=\frac{2}{3}$ low (later times). crossover is between...
We give statistical definitions of the length, l, a loose prime knot tied into long, fluctuating ring macromolecule. Monte Carlo results for equilibrium, good solvent regime show that ⟨l⟩ ∼ Nt, where N is length and t ≃ 0.75 independent type. In collapsed below theta temperature, determinations based on entropic competition different knots within same delocalization (t 1).
We report numerical studies of the hydrodynamics and rheology an active liquid crystal. confirm existence a transition between passive phase, with spontaneous flow in steady state. explore how velocity profile changes activity, we point out difference behavior for flow-aligning tumbling materials. find that material can thicken or thin under flow, even exhibit both behaviors as forcing changes.
We study a suspension of active dumbbells variable density, as minimal example an polar fluid. As in fluid spherical swimmers, we find that motility triggers nonequilibrium phase separation if the density exceeds critical threshold. also show is lost when force becomes too large, ultimately due to inertial effects. Remarkably, aggregates which assemble spontaneously break chiral symmetry and rotate; they display nematic ordering with spiral patterns.
Reconciling the stability of epigenetic patterns with rapid turnover histone modifications and their adaptability to external stimuli is an outstanding challenge. Here, we propose a new biophysical mechanism that can establish maintain robust yet plastic domains via genomic bookmarking (GBM). We model chromatin as recolourable polymer whose segments bear non-permanent marks (or colours) which be modified by "writer" proteins. The three-dimensional organisation mediated protein bridges, or...
Significance Vital biological processes such as gene transcription and cell division may be severely impaired by inevitable entanglements ensuing from the extreme length confinement of genome. The family topoisomerase proteins has independently evolved in different organisms to resolve these topological problems, yet no existing model can explain how alone reduce complexity DNA vivo. We propose that a synergistic mechanism between slip-link–like called structural maintenance chromosomes...
We report studies of the equilibrium and dynamics a general set lattice models which capture essence force-induced or mechanical DNA unzipping transition. Besides yielding whole phase diagram in force vs temperature plane, reveals presence an interesting re-entrant transition for low T, these enable us to characterize process starting from non-equilibrium initial condition. The thermal melting strands displays model dependent time evolution. On contrary, our results suggest that dynamical...
We use Monte Carlo methods to investigate the asymptotic behaviour of number and mean-square radius gyration polygons in simple cubic lattice with fixed knot type. Let be n-edge a type lattice, let mean square all counted by . If we assume that , where is growth constant entropic exponent then our numerical data are consistent relation unknot prime factors both being independent These results support claims made Janse van Rensburg Whittington (1991a 24 3935) Orlandini et al (1996 29 L299,...
The nature and the universal properties of DNA thermal denaturation are investigated by Monte Carlo simulations. For suitable lattice models we determine exponent $c$ describing decay probability distribution denaturated loops length $l$, $P\ensuremath{\sim}{l}^{\ensuremath{-}c}$. If excluded volume effects fully taken into account, $c\phantom{\rule{0ex}{0ex}}=\phantom{\rule{0ex}{0ex}}2.10(4)$ is consistent with a first order transition. stiffness double stranded chain has effect sharpening...