D. Marenduzzo

Membrane affinity difference between MinD monomer and dimer is not crucial for MinD gradient formation in Bacillus subtilis

The paper shows that membrane affinity differences between MinD monomer and dimer are not crucial for MinD gradient formation in Bacillus subtilis, instead diffusion rate differences are important.

The role of cellular filamentation in bacterialaggregation and cluster-cluster assembly

This study investigates how bacterial filamentation affects aggregate formation, network connectivity, and mechanical properties through experimental and computational analysis.

Cluster size determines internal structure of transcription factories in human cells

This study develops a chromatin polymer model to show that cluster size determines whether transcription factories are specialised or mixed, reconciling conflicting experimental results.

Bridging-mediated compaction of mitotic chromosomes

This paper uses simulations to show bridging factors create mitotic-like chromosome structures without energy input, matching experimental observations.

Topological Gelation of Reconnecting Polymers

This study investigates topological gelation in semiflexible polymer rings under confinement, showing that stiffness or concentration can trigger a transition from segregated to linked polymer networks.

Condensin reorganizes centromeric chromatin during mitotic entry into a bipartite structure stabilized by cohesin

This study shows vertebrate centromeres form a bipartite structure during mitosis, stabilized by condensin and linked by cohesin, which prevents merotelic attachments and chromosomal instability.

Transcription modulates chromatin dynamics and locus configuration sampling

The paper uses simulations and experiments to show transcription affects chromatin dynamics and locus configurations in mouse cells.

Complex small-world regulatory networks emerge from the 3D organisation of the human genome

This study shows that 3D genome organization leads to complex small-world regulatory networks and stochastic transcription, explaining how GWAS results align with overexpression experiments.

Phase separation induced by cohesin SMC protein complexes

Yeast cohesin phase separates with DNA into liquid droplets via ATP-independent DNA bridging.

A nonequilibrium strategy for fast target search on the genome

The paper introduces a nonequilibrium mechanism for efficient DNA target search using chromophoresis, showing it can enhance search efficiency on inaccessible genomic regions.

Magnetic Polymer Models for Epigenetics-Driven Chromosome Folding

This paper uses magnetic polymer models to study how epigenetic modifications affect chromosome folding and gene expression, showing phase transitions and validating results with simulations.

Nonequilibrium Theory of Epigenomic Microphase Separation in the Cell Nucleus

The paper develops a non-equilibrium theory to explain epigenomic microphase separation in the nucleus, showing that non-equilibrium processes stabilize epigenomic domains.

Synergy of Topoisomerase and Structural-Maintenance-of Chromosomes Proteins Creates a Universal Pathway to Simplify Genome Topology

The paper identifies a synergistic mechanism between Topoisomerase and SMC proteins that simplifies genome topology by localizing entanglements, enabling efficient resolution in various cellular conditions.

Physical Principles of Retroviral Integration in the Human Genome

This study develops a biophysical model to explain retroviral integration site selection in the human genome, showing that physical factors like DNA accessibility and elasticity influence integration preferences.

Lamina and Heterochromatin Direct Chromosome Organisation in Senescence and Progeria

This study uses polymer physics simulations to show that lamina and heterochromatin interactions drive nuclear organization in senescence and progeria through phase transitions.

Nucleosome positions alone determine micro-domains in yeast chromosomes.

The paper uses nucleosome positioning data to predict chromatin 3-D structure in yeast, showing that nucleosome positions alone can accurately determine micro-domain patterns observed experimentally.

Magnetic Polymer Models for Epigenomic Organisation and Phase Separation

This paper uses magnetic polymer models to study how epigenetic marks and 3D genome organization interact, showing that epigenetic switches stabilize micro-phase separated compartments in the nucleus.

Complementary chromosome folding by transcription factors and cohesin

This study combines transcription factor and loop extrusion models to show cohesin acts as a molecular slip-link, not an active motor, in chromosome folding.

Effect of chromatin flexibility on diffusive loop extrusion via molecular slip-links

This study shows that chromatin stiffness and proximity of cohesin and CTCF sites enhance diffusive loop extrusion efficiency.

Shaping Epigenetic Memory via Genomic Bookmarking

This paper introduces a biophysical model of genomic bookmarking to explain how epigenetic domains are maintained and modified through histone marks and protein interactions in Drosophila.

Epigenetic Transitions And Knotted Solitons In Stretched Chromatin

This study investigates how stretching and knotting of chromatin fibers influence epigenetic order through in silico simulations.

Dynamical Scaling And Phase Coexistence In Topologically-Constrained DNA Melting

The paper investigates DNA melting in topologically constrained systems using simulations and theory, finding phase coexistence and topology-dependent scaling laws.

Non-equilibrium chromosome looping via molecular slip-links

This paper introduces a model for chromatin loop formation through diffusive sliding of molecular slip-links, showing it can explain experimental biases without requiring motor activity.

A Polymer Model with Epigenetic Recolouring Reveals a Pathway for the de novo Establishment and 3D Organisation of Chromatin Domains

The paper introduces a polymer model with epigenetic recolouring to simulate chromatin domain establishment and 3D organization, showing phase transitions and glassy behavior under certain conditions.