Topological interactions between ring polymers: Implications for chromatin loops

Chromatin looping is a major epigenetic regulatory mechanism in higher eukaryotes. Besides its role in transcriptional regulation, chromatin loops have been proposed to play a pivotal role in the segregation of entire chromosomes. The detailed topological and entropic forces between loops still remain elusive. Here, we quantitatively determine the potential of mean force between the centers of mass of two ring polymers, i.e. loops. We find that the transition from a linear to a ring polymer induces a strong increase in the entropic repulsion between these two polymers. On top, topological interactions such as the non-catenation constraint further reduce the number of accessible conformations of close-by ring polymers by about 50%, resulting in an additional effective repulsion. Furthermore, the transition from linear to ring polymers displays changes in the conformational and structural properties of the system. In fact, ring polymers adopt a markedly more ordered and aligned state than linear ones. The forces and accompanying changes in shape and alignment between ring polymers suggest an important regulatory function of such a topology in biopolymers. We conjecture that dynamic loop formation in chromatin might act as a versatile control mechanism regulating and maintaining different local states of compaction and order.Comment: 12 pages, 11 figures. The article has been accepted by The Journal Of Chemical Physics. After it is published, it will be found at http://jcp.aip.or

Chaotic Orbits in Thermal-Equilibrium Beams: Existence and Dynamical Implications

Phase mixing of chaotic orbits exponentially distributes these orbits through their accessible phase space. This phenomenon, commonly called ``chaotic mixing'', stands in marked contrast to phase mixing of regular orbits which proceeds as a power law in time. It is operationally irreversible; hence, its associated e-folding time scale sets a condition on any process envisioned for emittance compensation. A key question is whether beams can support chaotic orbits, and if so, under what conditions? We numerically investigate the parameter space of three-dimensional thermal-equilibrium beams with space charge, confined by linear external focusing forces, to determine whether the associated potentials support chaotic orbits. We find that a large subset of the parameter space does support chaos and, in turn, chaotic mixing. Details and implications are enumerated.Comment: 39 pages, including 14 figure

Investigation of the aerodynamic characteristics and wing-deployment transients of the NASA DL-4 body with a sailwing landing aid Final report

Aerodynamic characteristics and wing deployment transients of NASA DL-4 lifting body fitted with sailwing landing ai

Mol. Cell. Proteomics

Chemical cross-linking in combination with mass spectrometric analysis offers the potential to obtain low-resolution structural information from proteins and protein complexes. Identification of peptides connected by a cross-link provides direct evidence for the physical interaction of amino acid side chains, information that can be used for computational modeling purposes. Despite impressive advances that were made in recent years, the number of experimentally observed cross-links still falls below the number of possible contacts of cross-linkable side chains within the span of the cross-linker. Here, we propose two complementary experimental strategies to expand cross-linking data sets. First, enrichment of cross-linked peptides by size exclusion chromatography selects cross-linked peptides based on their higher molecular mass, thereby depleting the majority of unmodified peptides present in proteolytic digests of cross-linked samples. Second, we demonstrate that the use of proteases in addition to trypsin, such as Asp-N, can additionally boost the number of observable cross-linking sites. The benefits of both SEC enrichment and multiprotease digests are demonstrated on a set of model proteins and the improved workflow is applied to the characterization of the 20S proteasome from rabbit and Schizosaccharomyces pombe

Could Stannern-trend eucrites be crustal-contaminated melts?

In this paper, we show that the composition of Stannern trend eucrites can be satisfactorily explained by contamination of normal main group eucrites by a crustal partial melt

Pair Wave Functions in Atomic Fermi Condensates

Recent experiments have observed condensation behavior in a strongly interacting system of fermionic atoms. We interpret these observations in terms of a mean-field version of resonance superfluidity theory. We find that the objects condensed are not bosonic molecules composed of bound fermion pairs, but are rather spatially correlated Cooper pairs whose coherence length is comparable to the mean spacing between atoms. We propose experiments that will help to further probe these novel pairs

What does a binary black hole merger look like?

We present a method of calculating the strong-field gravitational lensing caused by many analytic and numerical spacetimes. We use this procedure to calculate the distortion caused by isolated black holes and by numerically evolved black hole binaries. We produce both demonstrative images illustrating details of the spatial distortion and realistic images of collections of stars taking both lensing amplification and redshift into account. On large scales the lensing from inspiraling binaries resembles that of single black holes, but on small scales the resulting images show complex and in some cases self-similar structure across different angular scales.Comment: 10 pages, 12 figures. Supplementary images and movies can be found at http://www.black-holes.org/the-science-numerical-relativity/numerical-relativity/gravitational-lensin

Parameter Optimisation of a Virtual Synchronous Machine in a Microgrid

Parameters of a virtual synchronous machine in a small microgrid are optimised. The dynamical behaviour of the system is simulated after a perturbation, where the system needs to return to its steady state. The cost functional evaluates the system behaviour for different parameters. This functional is minimised by Parallel Tempering. Two perturbation scenarios are investigated and the resulting optimal parameters agree with analytical predictions. Dependent on the focus of the optimisation different optima are obtained for each perturbation scenario. During the transient the system leaves the allowed voltage and frequency bands only for a short time if the perturbation is within a certain range.Comment: 17 pages, 5 figure