Related papers: Controlled DNA compaction within chromatin: the ta…
The chirality-induced spin selectivity (CISS), demonstrated in diverse chiral molecules by numerous experimental and theoretical groups, has been attracting extensive and ongoing interest in recent years. As the secondary structure of DNA,…
Understanding chromatin organization and dynamics is important since they crucially affect DNA functions. In this study, we investigate chromatin dynamics by statistically analyzing single-nucleosome movement in living human cells. Bi-modal…
A solid-state nanopore can electrophoretically capture a DNA molecule and pull it through in a folded configuration. The resulting ionic current signal indicates where along its length the DNA was captured. A statistical study using an 8 nm…
The phase diagram of a water solution of DNA and oppositely charged spherical macroions is studied. DNA winds around spheres to form beads-on-a-string complexes resembling the chromatin 10 nm fiber. At small enough concentration of spheres…
Increasing evidence suggests that chromosome folding and genetic expression are intimately connected. For example, the co-expression of a large number of genes can benefit from their spatial co-localization in the cellular space.…
We study the spontaneous ''sliding'' of histone spools (nucleosomes) along DNA as a result of thermally activated single base pair twist defects. To this end we map the system onto a suitably extended Frenkel-Kontorova model. Combining…
Nucleosomes are the fundamental building blocks of chromatin that not only help in the folding of chromatin but also in carrying epigenetic information. It is known that nucleosome sliding is responsible for dynamically organizing chromatin…
In eukaryote nucleosome, DNA wraps around a histone octamer in a left-handed way. We study the process of chirality formation of nucleosome with Brownian dynamics simulation. We model the histone octamer with a quantitatively adjustable…
DNA in sperm cells must undergo an extreme compaction to almost crystalline packing levels. To produce this dense packing, DNA is condensed by protamine, a positively charged protein that loops the DNA into a toroid. Our goal is to…
This paper focuses on mechanical aspects of chromatin biological functioning. Within a basic geometric modeling of the chromatin assembly, we give for the first time the complete set of elastic constants (twist and bend persistence lengths,…
Our understanding of how chromosomes structurally organize and dynamically interact has been revolutionized through the lens of long-chain polymer physics. Major protein contributors to chromosome structure and dynamics are condensin and…
We use a recently developed coarse-grained model for DNA to study kissing complexes formed by hybridization of complementary hairpin loops. The binding of the loops is topologically constrained because their linking number must remain…
Cells regulate gene expression in part by forming DNA-protein condensates in the nucleus. While existing theories describe the equilibrium size and stability of such condensates, their dynamics remain less understood. Here, we use…
We scrutinize the effect of polyvalent ions on polymer-DNA interactions. We extend a recently developed test charge theory to the case of a stiff polymer interacting with a DNA molecule in an electrolyte mixture. The theory accounts for…
Three-dimensional (3D) chromatin structure is closely related to genome function, in particular transcription. However, the folding path of the chromatin fiber in the interphase nucleus is unknown. Here, we systematically measured the 3D…
A prominent organizational feature of bacterial chromosomes was revealed by Hi-C experiments, indicating anomalously high contacts between the left and right chromosomal arms. These long-range contacts have been attributed to various…
Dynamics of nucleosomes, the building blocks of the chromatin, has crucial effects on expression, replication and repair of genomes in eukaryotes. Beside constant movements of nucleosomes by thermal fluctuations, ATP-dependent chromatin…
The spreading and regulation of epigenetic marks on chromosomes is crucial to establish and maintain cellular identity. Nonetheless, the dynamical mechanism leading to the establishment and maintenance of a given, cell-line specific,…
By means of a minimal physical model, we investigate the interplay of two phase transitions at play in chromatin organization: (1) liquid-liquid phase separation (LLPS) within the fluid solvating chromatin, resulting in the formation of…
Just like atoms combine into molecules, colloids can self-organize into predetermined structures according to a set of design principles. Controlling valence -- the number of inter-particle bonds -- is a prerequisite for the assembly of…