Workshop on Random Walks in Biological Physics with Focus on DNA and chromosome structure

Contribution List

2. Biological Physics of DNA, Chromosomes and Nuclei (John F. Marko)

Prof. John F. Mark Marko (Northwestern University)

Colloquium

I will present our current understanding of the role of polymer physics and statistical mechanics in illuminating chromosome dynamics in living cells, based on our understanding of DNA organization driven by enzymes studied in single-molecule nanomechanics experiments, as well as experiments done on living cells.

3. Lecture 1: DNA and Protein-DNA Interactions (John F. Marko)

Prof. John F. Marko (Northwestern University)

Lecture 1

DNA structure and biological role; DNA elastic deformation; worm-like-chain stat mech; unzipping of DNA by force; protein-DNA interactions (focus on structural chromosome-organizing proteins HU, Fis, IHF, H-NS, HMG-box proteins; histones and nucleosome).

4. Lecture 2: DNA Twisting and Supercoiling (John F. Marko)

Prof. John F. Marko (Northwestern University)

Lecture 2

DNA Twisting and Supercoiling. Torsional stiffness; biological origin and role of supercoiling; Gauss invariant; Lk = Wr + Tw; TWLC model; plectonemic supercoiling; torsional-stress-driven strand separation; magnetic tweezers experiments; DNA force-torque "phase diagram"; topoisomerases; GapR.

10. Lecture 3: Introduction to Stochastic Theories for Anomalous Diffusion Processes in Living Systems (Jae-Hyung Jeon)

Prof. Jae-Hyung Jeon (POSTECH / APCTP)

Lecture 3

Anomalous diffusion, referring to deviations from classical Brownian motion, is often observed in living cells where macromolecules move in crowded, heterogeneous, and often actively driven environments. This talk offers a pedagogical introduction to the physics of anomalous diffusion in biological systems, starting from the historical foundations of Brownian motion and Einstein–Langevin...

5. Lecture 4: DNA Topology and Its Regulation In Vivo (John F. Marko)

Prof. John F. Marko (Northwestern University)

Lecture 4

DNA Topology and its Regulation in vivo. Polymer entanglement; entanglement and knotting lengths; chromosome dynamics during cell cycle; lengthwise compaction model; active loop extrusion model; SMC complexes (condensin, cohesin, SMC5/6 bacterial SMCs); experiments supporting
loop extrusion model.

6. Lecture 5: Mechanics of Chromosomes and Cell Nuclei (John F. Marko)

Prof. John F. Marko (Northwestern University)

Lecture 5

Mechanics of Chromosomes and Nuclei. Micromanipulation experiments; mechanics of chromosomes; biochemical and genetic modification of chromosomes and what it teaches us; subchromosomal mechanics; epigenetic modifications; mechanics of cell nuclei. of cell nuclei.

7. Lecture 6: Introduction to Stochastic Theories for Anomalous Diffusion Processes in Living Systems (Jae-Hyung Jeon)

Prof. Jae-Hyung Jeon (POSTECH / APCTP)

Lecture 6

Anomalous diffusion, referring to deviations from classical Brownian motion, is often observed in living cells where macromolecules move in crowded, heterogeneous, and often actively driven environments. This talk offers a pedagogical introduction to the physics of anomalous diffusion in biological systems, starting from the historical foundations of Brownian motion and Einstein–Langevin...