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Kasper Olsen

Publications and source records attributed to Kasper Olsen.

At least 19 recordsLinked to original sources
arXiv2012

First principles structures and circular dichroism spectra for the close-packed and the 7/2 motif of collagen

The recently proposed close-packed motif for collagen is investigated using first principles semi-empirical wave function theory and Kohn-Sham density functional theory. Under these refinements the close-packed motif is shown to be stable. For the case of the 7/2 motif a similar stability exists. The electronic circular dichroism of the close-packed model has a significant negative bias and a large signal. An interesting feature of the close-packed structure is the existence of a central channel. Simulations show that, if hydrogen atoms are placed in the cavity, a chain of molecular hydrogens is formed suggesting a possible biological function for molecular hydrogen.

physics.bio-ph↗
arXiv2011

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.

physics.bio-ph↗
arXiv2010

Hidden Beauty in Twisted Viking Neck Rings

Many hoards found in Ireland, Scotland, Orkney Islands, and Scandinavia demonstrate the vikings ability to fabricate beautiful arm and neck rings of twisted silver and gold rods. Characteristic for such rings is the uniform appearance of the twisted pattern along the length of the arm ring, as well as from one arm ring to another, also when found at distant geographical locations. How can the appearance of the twisted wires be so perfectly repetitive? We demonstrate that the answer is that the vikings utilized a self-forming motif: The pattern arises from a twisting of the wires to a maximally rotated configuration. That is why the twist patterns in these arm and neck rings are beautiful, repetitive, and universal.

physics.pop-ph↗
arXiv2010

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.

physics.pop-ph↗
arXiv2010

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.

physics.bio-ph↗
arXiv2010

The close-packed triple helix as a possible new structural motif for collagen

The one-dimensional problem of selecting the triple helix with the highest volume fraction is solved and hence the condition for a helix to be close-packed is obtained. The close-packed triple helix is shown to have a pitch angle of $v_{CP} =43.3 ^\circ$. Contrary to the conventional notion, we suggest that close packing form the underlying principle behind the structure of collagen, and the implications of this suggestion are considered. Further, it is shown that the unique zero-twist structure with no strain-twist coupling is practically identical to the close-packed triple helix. Some of the difficulties for the current understanding of the structure of collagen are reviewed: The ambiguity in assigning crystal structures for collagen-like peptides, and the failure to satisfactorily calculate circular dichroism spectra. Further, the proposed new geometrical structure for collagen is better packed than both the 10/3 and the 7/2 structure. A feature of the suggested collagen structure is the existence of a central channel with negatively charged walls. We find support for this structural feature in some of the early x-ray diffraction data of collagen. The central channel of the structure suggests the possibility of a one-dimensional proton lattice. This geometry can explain the observed magic angle effect seen in NMR studies of collagen. The central channel also offers the possibility of ion transport and may cast new light on various biological and physical phenomena, including biomineralization.

physics.bio-ph↗
arXiv2009

Critical behavior of collapsing surfaces

We consider the mean curvature evolution of rotationally symmetric surfaces. Using numerical methods, we detect critical behavior at the threshold of singularity formation resembling the one of gravitational collapse. In particular, the mean curvature simulation of a one-parameter family of initial data reveals the existence of a critical initial surface that develops a degenerate neckpinch. The limiting flow of the Type II singularity is accurately modeled by the rotationally symmetric translating soliton.

math-ph↗
arXiv2001

Comments on Brane World Cosmology

In this paper we consider some constraints on brane-world cosmologies. In the first part we analyze different behaviors for the expansion of our universe by imposing constraints on the speed of sound. In the second part, we study the nature of matter on the brane world by means of the well-known energy conditions. We find that the strong energy condition must be completely violated at late stages of the universe.

hep-th↗
arXiv2000

Quantum Cosmology and AdS/CFT

In this paper we study the creation of brane-worlds in $AdS$ bulk. We first consider the simplest case of onebranes in $AdS_3$. In this case we are able to properly describe the creation of a spherically symmetric brane-world deriving a general expression for its wavefunction. Then, we sketch the $AdS_{d+1}$ set-up within the context of the WKB approximation. Finally, we comment on these scenarios in light of the $AdS/CFT$ correspondence.

hep-th↗
arXiv2000

From Noncommutative Bosonization to S-Duality

We extend standard path-integral techniques of bosonization and duality to the setting of noncommutative geometry. We start by constructing the bosonization prescription for a free Dirac fermion living in the noncommutative plane R_θ^2. We show that in this abelian situation the fermion theory is dual to a noncommutative Wess-Zumino-Witten model. The non-abelian situation is also constructed along very similar lines. We apply the techniques derived to the massive Thirring model on noncommutative R_θ^2 and show that it is dualized to a noncommutative WZW model plus a noncommutative cosine potential (like in the noncommutative Sine-Gordon model). The coupling constants in the fermionic and bosonic models are related via strong-weak coupling duality. This is thus an explicit construction of S-duality in a noncommutative field theory.

hep-th↗
arXiv2000

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.

hep-th↗
arXiv1999

Aspects of duality

This thesis discusses various aspects of duality in quantum field theory and string theory. In the first part we consider duality in topological quantum field theories, concentrating on the Donaldson and Seiberg-Witten theories as (dual) approaches to the study of four-manifolds. Lower-dimensional variants of these theories are also discussed. In the second part of the thesis we discuss duality in 2D sigma models by studying the interplay between renormalization group flows - as generated by the beta functions - and T-duality. The hypothesis put forward in the thesis is that for these to be mutually consistent, they should commute as operators in parameter space. The last part of the thesis bring these subjects into perspective by reviewing some nonperturbative dualities in string theory.

hep-th↗
arXiv1999

Constructing D-Branes from K-Theory

A detailed review of recent developments in the topological classification of D-branes in superstring theory is presented. Beginning with a thorough, self-contained introduction to the techniques and applications of topological K-theory, the relationships between the classic constructions of K-theory and the recent realizations of D-branes as tachyonic solitons, coming from bound states of higher dimensional systems of unstable branes, are described. It is shown how the K-theory formalism naturally reproduces the known spectra of BPS and non-BPS D-branes, and how it can be systematically used to predict the existence of new states. The emphasis is placed on the new interpretations of D-branes as conventional topological solitons in other brane worldvolumes, how the mathematical formalism can be used to deduce the gauge field content on both supersymmetric and non-BPS branes, and also how K-theory predicts new relationships between the various superstring theories and their D-brane spectra. The implementations of duality symmetries as natural isomorphisms of K-groups are discussed. The relationship with the standard cohomological classification is presented and used to derive an explicit formula for D-brane charges. Some string theoretical constructions of the K-theory predictions are also briefly described.

hep-th↗
arXiv1999

Brane Descent Relations in K-theory

The various descent and duality relations among BPS and non-BPS D-branes are classified using topological K-theory. It is shown how the descent procedures for producing type-II D-branes from brane-antibrane bound states by tachyon condensation and $\klein$ projections arise as natural homomorphisms of K-groups generating the brane charges. The transformations are generalized to type-I theories and type-II orientifolds, from which the complete set of vacuum manifolds and field contents for tachyon condensation is deduced. A new set of internal descent relations is found which describes branes over orientifold planes as topological defects in the worldvolumes of brane-antibrane pairs on top of planes of higher dimension. The periodicity properties of these relations are shown to be a consequence of the fact that all fundamental bound state constructions and hence the complete spectrum of brane charges are associated with the topological solitons which classify the four Hopf fibrations.

hep-th↗
arXiv1998

Heterotic T-Duality and the Renormalization Group

We consider target space duality transformations for heterotic sigma models and strings away from renormalization group fixed points. By imposing certain consistency requirements between the T-duality symmetry and renormalization group flows, the one loop gauge beta function is uniquely determined, without any diagram calculations. Classical T-duality symmetry is a valid quantum symmetry of the heterotic sigma model, severely constraining its renormalization flows at this one loop order. The issue of heterotic anomalies and their cancelation is addressed from this duality constraining viewpoint.

hep-th↗
arXiv1997

Two-Loop Beta Functions Without Feynman Diagrams

Starting from a consistency requirement between T-duality symmetry and renormalization group flows, the two-loop metric beta function is found for a d=2 bosonic sigma model on a generic, torsionless background. The result is obtained without Feynman diagram calculations, and represents further evidence that duality symmetry severely constrains renormalization flows.

hep-th↗
arXiv1997

T-Duality and Two-Loop Renormalization Flows

Manifest T-duality covariance of the one-loop renormalization group flows is shown for a generic bosonic sigma model with an abelian isometry, by referring a set of previously derived consistency conditions to the tangent space of the target. For a restricted background, T-duality transformations are then studied at the next order, and the ensuing consistency conditions are found to be satisfied by the two-loop Weyl anomaly coefficients of the model. This represents an extremely non-trivial test of the covariance of renormalization group flows under T-duality, and a stronger condition than T-duality invariance of the string background effective action.

hep-th↗