Dimensional reduction of dual topological theories

We describe the reduction from four to two dimensions of the SU(2) Donaldson-Witten theory and the dual twisted Seiberg-Witten theory, i.e. the Abelian topological field theory corresponding to the Seiberg--Witten monopole equations.Comment: LateX, 6 page

The geometrical origin of the strain-twist coupling in double helices

The geometrical coupling between strain and twist in double helices is investigated. Overwinding, where strain leads to further winding, is shown to be a universal property for helices, which are stretched along their longitudinal axis when the initial pitch angle is below the zero-twist angle (39.4 deg). Unwinding occurs at larger pitch angles. The zero-twist angle is the unique pitch angle at the point between overwinding and unwinding, and it is independent of the mechanical properties of the double helix. This suggests the existence of zero-twist structures, i.e. structures that display neither overwinding, nor unwinding under strain. Estimates of the overwinding of DNA, chromatin, and RNA are given.Comment: 8 pages, 4 figures; typos fixed; added ref. and acknowledgemen

Domain Wall Junctions in Supersymmetric Field Theories in D=4

We study the possible BPS domain wall junction configurations for general polynomial superpotentials of N=1 supersymmetric Wess-Zumino models in D=4. We scan the parameter space of the superpotential and find different possible BPS states for different values of the deformation parameters and present our results graphically. We comment on the domain walls in F/M/IIA theories obtained from the Calabi-Yau fourfolds with isolated singularities and a background flux.Comment: 26 pages, 4 figure

The ancient art of laying rope

We describe a geometrical property of helical structures and show how it accounts for the early art of ropemaking. Helices have a maximum number of rotations that can be added to them -- and it is shown that this is a geometrical feature, not a material property. This geometrical insight explains why nearly identically appearing ropes can be made from very different materials and it is also the reason behind the unyielding nature of ropes. The maximally rotated strands behave as zero-twist structures. Under strain they neither rotate one or the other way. The necessity for the rope to be stretched while being laid, known from Egyptian tomb scenes, follows straightforwardly, as does the function of the top, an old tool for laying ropes.Comment: 6 pages, 3 figures; v2: discussion of flexibility included; added refs. and acknowledgement, v3: minor modification

Twisting Uneven Ropes

A classical two-stranded rope can be made by twisting two identical strands together under strain. Despite being conceptually simple, the contact-equations for helically twisted identical strands have only been solved within the last 20 years. Our goal here is basic: to understand the twisting of two circular strands, where one is thicker than the other. This is what we call an uneven rope. The geometry of the uneven rope depend on the ratio, $r$, between the diameters of the two strands. In particular, the maximally twisted geometry may be determined as a function of $r$ by solving the contact-equations for the two strands numerically.Comment: 6 pages, 4 figure

The size of the nucleosome

The structural origin of the size of the 11 nm nucleosomal disc is addressed. On the nanometer length-scale the organization of DNA as chromatin in the chromosomes involves a coiling of DNA around the histone core of the nucleosome. We suggest that the size of the nucleosome core particle is dictated by the fulfillment of two criteria: One is optimizing the volume fraction of the DNA double helix; this requirement for close-packing has its root in optimizing atomic and molecular interactions. The other criterion being that of having a zero strain-twist coupling; being a zero-twist structure is a necessity when allowing for transient tensile stresses during the reorganization of DNA, e.g., during the reposition, or sliding, of a nucleosome along the DNA double helix. The mathematical model we apply is based on a tubular description of double helices assuming hard walls. When the base-pairs of the linker-DNA is included the estimate of the size of an ideal nucleosome is in close agreement with the experimental numbers. Interestingly, the size of the nucleosome is shown to be a consequence of intrinsic properties of the DNA double helix.Comment: 11 pages, 5 figures; v2: minor modification

Transcription and the Pitch Angle of DNA

The question of the value of the pitch angle of DNA is visited from the perspective of a geometrical analysis of transcription. It is suggested that for transcription to be possible, the pitch angle of B-DNA must be smaller than the angle of zero-twist. At the zero-twist angle the double helix is maximally rotated and its strain-twist coupling vanishes. A numerical estimate of the pitch angle for B-DNA based on differential geometry is compared with numbers obtained from existing empirical data. The crystallographic studies shows that the pitch angle is approximately 38 deg., less than the corresponding zero-twist angle of 41.8 deg., which is consistent with the suggested principle for transcription.Comment: 7 pages, 3 figures; v2: minor modifications; v3: major modifications compared to v2. Added discussion about transcription, and reference