J. F. Marko

Cell-cycle and Age-Related Modulations in Mouse Chromosome Stiffness

This study measures chromosome stiffness in mouse oocytes across cell cycle stages and age, finding increased stiffness in metaphase I oocytes and age-related stiffness changes.

DNA tension-modulated translocation and loop extrusion by SMC complexes revealed by molecular dynamics simulations

This study uses molecular dynamics simulations to show how DNA tension modulates SMC complex translocation and loop extrusion, revealing distinct behaviors under different tension conditions.

Heterochromatin flexibility contributes to chromosome segregation in the cell nucleus

This study uses molecular dynamics simulations to show that heterochromatin flexibility influences its distribution in the nucleus, with less flexible heterochromatin segregating toward the interior in the absence of shell interactions.

Micromanipulation of prophase I chromosomes from mouse spermatocytes reveals high stiffness and gel-like chromatin organization

The paper measures physical properties of mouse meiotic prophase I chromosomes, finding they are stiffer than mitotic chromosomes and have a gel-like chromatin organization.

Chromosome organization by one-sided and two-sided loop extrusion

This study investigates one-sided and two-sided loop extrusion by SMC complexes, showing that one-sided extrusion cannot recapitulate in vivo observations but variants can, suggesting SMC complexes may function as two-sided motors or have biased loading.

Measurement of the torque in braided DNAs using a thermodynamic Maxwell relation

The paper measures torque in braided DNAs using magnetic tweezers and a thermodynamic Maxwell relation, finding torques up to 76 pN·nm and a twist modulus comparable to single DNA.

Coarse-Grained Modelling of DNA Plectoneme Pinning in the Presence of Base-Pair Mismatches

This study uses coarse-grained MD simulations to show that DNA plectoneme pinning at mismatches is deterministic under high force and salt, but probabilistic under physiological conditions, with pinning probability increasing with mismatch size.

Chromosome disentanglement driven via optimal compaction of loop-extruded brush structures

The paper models chromosome disentanglement during cell division using loop-extruded brush structures, showing optimal loop organization minimizes entanglements and supports genome stability.

DNA-segment-capture model for loop extrusion by structural maintenance of chromosome (SMC) protein complexes

The paper introduces a DNA-segment-capture model for SMC protein loop extrusion, predicting tension-dependent translocation velocity and step size.

Effects of altering histone post-translational modifications on mitotic chromosome structure and mechanics

This study investigates how histone post-translational modifications affect mitotic chromosome stiffness using force measurements and epigenetic drugs, finding that methylation, not acetylation, contributes to mitotic structure.

Multimodal interferometric imaging of nanoscale structure and macromolecular motion uncovers UV induced cellular paroxysm

This paper introduces a multimodal interferometric imaging platform to study nanoscale structure and macromolecular dynamics in live cells, revealing a new phenomenon called cellular paroxysm induced by UV light.

Physicochemical mechanotransduction alters nuclear shape and mechanics via heterochromatin formation

This study shows that extracellular cations alter nuclear shape and mechanics through heterochromatin formation, rescuing nuclear morphology in disease models.

Twist-bend coupling and the statistical mechanics of DNA: perturbation theory and beyond

This paper investigates the effect of twist-bend coupling on DNA mechanics using perturbation theory and validates results with numerical models.

Defect-Facilitated Buckling in Supercoiled Double-Helix DNA

The paper develops a statistical-mechanical model to study DNA buckling and plectoneme domain behavior under stretching forces and ionic conditions, showing defect-facilitated kink formation and energy reduction.

Bend-Induced Twist Waves and the Structure of Nucleosomal DNA

The paper shows that twist-bend coupling in bent DNA creates standing twist waves, with analytical solutions matching simulations and experimental data on nucleosomal DNA.

Mechanics and buckling of biopolymeric shells and cell nuclei

This study uses simulations and experiments to show how biopolymeric shells and cell nuclei deform under tension, exhibiting different mechanical behaviors depending on force magnitude and temperature.

Nucleation of multiple buckled structures in intertwined DNA double helices

The paper investigates the statistical-mechanical behavior of intertwined DNA double helices, finding that torsionally stressed braids undergo an abrupt buckling transition with nucleation of end loops and multiple domains.

Facilitated Dissociation Of Transcription Factors From Single DNA Binding Sites

This study investigates facilitated dissociation (FD) of transcription factors from DNA binding sites using single-molecule imaging and molecular dynamics simulations, showing FD occurs at the single-binding-site level and is independent of salt concentration.