Davide Marenduzzo
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View article: Bridging-Induced Phase Separation and Loop Extrusion Drive Noise in Chromatin Transcription
Bridging-Induced Phase Separation and Loop Extrusion Drive Noise in Chromatin Transcription Open
Cell-to-cell heterogeneity in transcription, or transcriptional noise, is important in cellular development and in disease. The molecular mechanisms driving it are, however, elusive and ill-understood. Here, we use computer simulations to …
View article: Oscillation in the SIRS model
Oscillation in the SIRS model Open
We study the SIRS epidemic model, both analytically and on a square lattice. The analytic model has two stable solutions, post outbreak/epidemic (no infected, I=0) and the endemic state (constant number of infected: I>0). When the model is…
View article: Formation of Topological Bigels in Mixtures of Colloidal Rings and Polymers
Formation of Topological Bigels in Mixtures of Colloidal Rings and Polymers Open
We study a spherically confined mixture of polymers and colloidal rings. Unlike in standard colloid-polymer mixtures, the polymers interact topologically with the rings by threading them. We find that, above a critical value of the ring ra…
View article: Bridging-mediated compaction of mitotic chromosomes
Bridging-mediated compaction of mitotic chromosomes Open
Within living cells, chromosome shapes undergo a striking morphological transition, from loose and uncondensed fibers during interphase to compacted and cylindrical structures during mitosis. ATP driven loop extrusion performed by a specia…
View article: To promote network connectivity in colloidal rod suspensions, end with a tip
To promote network connectivity in colloidal rod suspensions, end with a tip Open
Colloidal gels formed from patchy rods provide a promising platform to design novel functional materials and formulations. Yet, the case for localized interactions at the rod tips remains relatively unexplored. Here we probe the structure …
View article: Clifford algebras and liquid crystalline fermions
Clifford algebras and liquid crystalline fermions Open
We show that Clifford algebras provide a natural language to describe the physics of liquid crystal defects in 3D. This framework shows that most of these defects have fermionic nature, as the director field profile on a 2D cross section c…
View article: Topology controls flow patterns in active double emulsions
Topology controls flow patterns in active double emulsions Open
Active emulsions and liquid crystalline shells are intriguing and experimentally realisable types of topological matter. Here we numerically study the morphology and spatiotemporal dynamics of a double emulsion, where one or two passive sm…
View article: Cluster size determines morphology of transcription factories in human cells
Cluster size determines morphology of transcription factories in human cells Open
Transcription is a fundamental cellular process, and the first step of gene expression. In human cells, it depends on the binding to chromatin of various proteins, including RNA polymerases and numerous transcription factors (TFs). Observa…
View article: Cluster size determines morphology of transcription factories in human cells
Cluster size determines morphology of transcription factories in human cells Open
Transcription is a fundamental cellular process, and the first step of gene expression. In human cells, it depends on the binding to chromatin of various proteins, including RNA polymerases and numerous transcription factors (TFs). Observa…
View article: Equilibrium phases and phase transitions in multicritical magnetic polymers
Equilibrium phases and phase transitions in multicritical magnetic polymers Open
Phase diagram for a magnetic polymer with Blume–Emery–Griffith spins, with snapshots (phases: swollen disordered, SD; compact ordered, CO; compact disordered, CD). These results may be relevant to understand epigenetic memory in chromatin.
View article: Diffusive evaporation dynamics in polymer solutions is ubiquitous
Diffusive evaporation dynamics in polymer solutions is ubiquitous Open
A phase field model predicts the ubiquitous nature of diffusion-limited evaporation (DLE) in polymer solutions, resulting from the formation of high-concentration polymer layer at the solution–air interface, here shown for the two-dimensio…
View article: Modelling transcriptional silencing and its coupling to 3D genome organisation
Modelling transcriptional silencing and its coupling to 3D genome organisation Open
Using 3D simulations, this study uncovers how distinct gene silencing mechanisms reshape chromatin, modulate gene expression noise, and drive unique transcription factor cluster patterns—revealing hidden dynamics of genome regulation.
View article: Majorana quasiparticles and topological phases in 3D active nematics
Majorana quasiparticles and topological phases in 3D active nematics Open
Quasiparticles are low-energy excitations with important roles in condensed matter physics. An intriguing example is provided by Majorana quasiparticles, which are equivalent to their antiparticles. Despite being implicated in neutrino osc…
View article: Topological epigenetics: The biophysics of DNA supercoiling and its relation to transcription and genome instability
Topological epigenetics: The biophysics of DNA supercoiling and its relation to transcription and genome instability Open
Whilst DNA encodes our genetic blueprint as individual nucleobases, as well as epigenetic annotations in the form of biochemical marks, it also carries an extra layer of topological information -, the local over or underwinding of the doub…
View article: Genome-wide chromosome architecture prediction reveals biophysical principles underlying gene structure
Genome-wide chromosome architecture prediction reveals biophysical principles underlying gene structure Open
Classical observations suggest a connection between 3D gene structure and function, but testing this hypothesis has been challenging due to technical limitations. To explore this, we developed epigenetic highly predictive heteromorphic pol…
View article: Multiphase field model of cells on a substrate: From three dimensional to two dimensional
Multiphase field model of cells on a substrate: From three dimensional to two dimensional Open
Multiphase field models have emerged as an important computational tool for understanding biological tissue while resolving single-cell properties. While they have successfully reproduced many experimentally observed behaviors of living ti…
View article: Modeling the 3D Spatiotemporal Organization of Chromatin Replication
Modeling the 3D Spatiotemporal Organization of Chromatin Replication Open
We propose a polymer model to investigate the dynamics of chromatin replication in three dimensions (PolyRep). Our results indicate that replication complexes, the replisomes, may self-assemble during the process and replicate chromatin by…
View article: Intercellular friction and motility drive orientational order in cell monolayers
Intercellular friction and motility drive orientational order in cell monolayers Open
Spatiotemporal patterns in multicellular systems are important to understanding tissue dynamics, for instance, during embryonic development and disease. Here, we use a multiphase field model to study numerically the behavior of a near-conf…
View article: Cyclical MinD membrane affinity differences are not necessary for MinD gradient formation in Bacillus subtilis
Cyclical MinD membrane affinity differences are not necessary for MinD gradient formation in Bacillus subtilis Open
Proteins can diffuse micrometers in seconds, yet bacterial cells are able to maintain stable protein gradients. The best studied bacterial protein gradient is the Min system of Escherichia coli. In rod-shaped bacteria the MinCD proteins pr…
View article: Membrane affinity difference between MinD monomer and dimer is not crucial for MinD gradient formation in Bacillus subtilis
Membrane affinity difference between MinD monomer and dimer is not crucial for MinD gradient formation in Bacillus subtilis Open
Proteins can diffuse micrometers in seconds, yet bacterial cells are able to maintain stable protein gradients. The best studied bacterial protein gradient is the Min system of Escherichia coli. In rod-shaped bacteria the MinCD proteins pr…
View article: Can the AMOEBA forcefield be used for high pressure simulations? The extreme case of methane and water
Can the AMOEBA forcefield be used for high pressure simulations? The extreme case of methane and water Open
We have performed classical molecular dynamics simulations using the fully polarizable Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) forcefield implemented within the Tinker package to determine whether a mor…
View article: Bridging-Induced Phase Separation and Loop Extrusion Drive Noise in Chromatin Transcription
Bridging-Induced Phase Separation and Loop Extrusion Drive Noise in Chromatin Transcription Open
Transcriptional noise, or heterogeneity, is important in cellular development and in disease. The molecular mechanisms driving it are, however, elusive and ill-understood. Here, we use computer simulations to explore the role of 3D chromat…
View article: Nuclear RNA forms an interconnected network of transcription-dependent and tunable microgels
Nuclear RNA forms an interconnected network of transcription-dependent and tunable microgels Open
Summary The human cell nucleus is comprised of proteins, chromatin and RNA, yet how they interact to form supramolecular structures and drive key biological processes remains unknown. Conflicting models have proposed either a fluid-like or…
View article: Combinatorics and topological weights of chromatin loop networks
Combinatorics and topological weights of chromatin loop networks Open
Polymer physics models suggest that chromatin spontaneously folds into loop networks with transcription units (TUs), such as enhancers and promoters, as anchors. Here we use combinatoric arguments to enumerate the emergent chromatin loop n…
View article: Topological Spectra and Entropy of Chromatin Loop Networks
Topological Spectra and Entropy of Chromatin Loop Networks Open
The 3D folding of a mammalian gene can be studied by a polymer model, where the chromatin fiber is represented by a semiflexible polymer which interacts with multivalent proteins, representing complexes of DNA-binding transcription factors…
View article: Membrane affinity difference between MinD monomer and dimer is not crucial for MinD gradient formation in Bacillus subtilis
Membrane affinity difference between MinD monomer and dimer is not crucial for MinD gradient formation in Bacillus subtilis Open
Proteins can diffuse micrometers in seconds, yet bacterial cells are able to maintain stable protein gradients. The best studied bacterial protein gradient is the Min system of Escherichia coli. In rod-shaped bacteria the MinCD proteins pr…
View article: Vertebrate centromeres in mitosis are functionally bipartite structures stabilized by cohesin
Vertebrate centromeres in mitosis are functionally bipartite structures stabilized by cohesin Open
Centromeres are scaffolds for the assembly of kinetochores that ensure chromosome segregation during cell division. How vertebrate centromeres obtain a three-dimensional structure to accomplish their primary function is unclear. Using supe…
View article: Entangled nematic disclinations using multi-particle collision dynamics
Entangled nematic disclinations using multi-particle collision dynamics Open
Colloids dispersed in nematic liquid crystals form topological composites in which colloid-associated defects mediate interactions while adhering to fundamental topological constraints. Better realising the promise of such materials requir…
View article: Multiphase Field Model of Cells on a Substrate: From 3D to 2D
Multiphase Field Model of Cells on a Substrate: From 3D to 2D Open
Multiphase field models have emerged as an important computational tool for understanding biological tissue while resolving single-cell properties. While they have successfully reproduced many experimentally observed behaviors of living ti…