Related papers: The dimensionality of a coiled helical coil
One-dimensional arrays of nucleosomes (DNA-bound histone octamers separated by stretches of linker DNA) fold into higher-order chromatin structures which ultimately make up eukaryotic chromosomes. Chromatin structure formation leads to…
Mesogenic materials, quinoxaline derivatives with semi-flexible cores, are reported to form new type of 3D columnar structure with large crystallographic unit cell and Fddd symmetry below columnar hexagonal phase. The 3D columnar structure…
The self-assembly of DNA-coated colloids into highly-ordered structures offers great promise for advanced optical materials. However, control of disorder, defects, melting, and crystal growth is hindered by the lack of a microscopic…
For short DNA molecules in crowded environments, we evaluate macroscopic parameters such as the average end-to-end distance and the twist conformation by tuning the strength of the site specific confinement driven by the crowders. The…
In columnar assemblies of helical bio-molecules the azimuthal degrees of freedom, i.e. rotations about the long axes of molecules, may be important in determining the structure of the assemblies especially when the interaction energy…
DNA supercoils are generated in genome regulation processes such as transcription and replication, and provide mechanical feedback to such processes. Under tension, DNA supercoil can present a coexistence state of plectonemic (P) and…
The biggest challenge when using DNA as a storage medium is maintaining its stability. The relative occurrence of Guanine (G) and Cytosine (C) is essential for the longevity of DNA. In addition to that, reverse complementary base pairs…
The primary building block of the body is collagen, which is found in the extracellular matrix and in many stress-bearing tissues such as tendon and cartilage. It provides elasticity and support to cells and tissues while influencing…
The behavior of long DNA molecules in a cell-sized confined space was investigated. We prepared water-in-oil droplets covered by phospholipids, which mimic the inner space of a cell, following the encapsulation of DNA molecules with…
A multiscale approach is used to simulate the translocation of DNA through a nanopore. Within this scheme, the interactions of the molecule with the surrounding fluid (solvent) are explicitly taken into account. By generating polymers of…
Excitons in low-dimensional materials behave mathematically as confined hydrogen atoms. An appealing unified description of confinement in quantum wells or wires, etc., is found by restricting space to a fractional dimension 1 < D <= 3…
The presence of low dimensional chaos in the protein secondary structures, using the binary coded $\alpha$-helices and $\beta$-sheet motifs, has been investigated. In order to analyse symbolic DNA/RNA sequences the assignment, based on the…
The phase behaviour of a single large semiflexible polymer immersed in a suspension of spherical particles is studied. All interactions are simple excluded volume interactions and the diameter of the spherical particles is an order of…
This paper considers cyclic DNA codes of arbitrary length over the ring $R=\F_2[u]/u^4-1$. A mapping is given between the elements of $R$ and the alphabet $\{A,C,G,T\}$ which allows the additive stem distance to be extended to this ring.…
We present a coarse-grained model of DNA-functionalized colloids that is computationally tractable. Importantly, the model parameters are solely based on experimental data. Using this highly simplified model, we can predict the phase…
We study the most general form of a three dimensional classical integrable system with axial symmetry and invariant under the axis reflection. We assume that the three constants of motion are the Hamiltonian, $H$, with the standard form of…
Chirality is a fundamental feature in all domains of nature, ranging from particle physics over electromagnetism to chemistry and biology. Chiral objects lack a mirror plane and inversion symmetry and therefore cannot be spatially aligned…
Chirality in inorganic nanoparticles and nanostructures has gained increasing scientific interest, because of the possibility to tune their ability to interact differently with left- and right-handed circularly polarized light. In some…
While bacterial chromosomes were long thought to be amorphous, recent experiments reveal pronounced organizational features. However, the extent of bacterial chromosome organization remains unclear. Here, we develop a fully data-driven…
We consider domino tilings of $3$-dimensional cubiculated regions. A three-dimensional domino is a 2x2x1 rectangular cuboid. We are particularly interested in regions of the form $R_N = D \times [0,N]$ where $D$ is a fixed quadriculated…