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

Reconstruction of eye movements during blinks

In eye movement research in reading, the amount of data plays a crucial role for the validation of results. A methodological problem for the analysis of the eye movement in reading are blinks, when readers close their eyes. Blinking rate increases with increasing reading time, resulting in high data losses, especially for older adults or reading impaired subjects. We present a method, based on the symbolic sequence dynamics of the eye movements, that reconstructs the horizontal position of the eyes while the reader blinks. The method makes use of an observed fact that the movements of the eyes before closing or after opening contain information about the eyes movements during blinks. Test results indicate that our reconstruction method is superior to methods that use simpler interpolation approaches. In addition, analyses of the reconstructed data show no significant deviation from the usual behavior observed in readers

Bogoliubov modes of a dipolar condensate in a cylindrical trap

The calculation of properties of Bose-Einstein condensates with dipolar interactions has proven a computationally intensive problem due to the long range nature of the interactions, limiting the scope of applications. In particular, the lowest lying Bogoliubov excitations in three dimensional harmonic trap with cylindrical symmetry were so far computed in an indirect way, by Fourier analysis of time dependent perturbations, or by approximate variational methods. We have developed a very fast and accurate numerical algorithm based on the Hankel transform for calculating properties of dipolar Bose-Einstein condensates in cylindrically symmetric traps. As an application, we are able to compute many excitation modes by directly solving the Bogoliubov-De Gennes equations. We explore the behavior of the excited modes in different trap geometries. We use these results to calculate the quantum depletion of the condensate by a combination of a computation of the exact modes and the use of a local density approximation

V/STOL lift fan commercial short haul transports: Continuing conceptual design study

A design study of commercial V/STOL transport airplanes for a 1985 operational time period has been made. The baseline mission considered was 400 nmi at a cruise speed of M = 0.75 and a 100-passenger payload with VTOL. Variations from the baseline included mission distance, payload, cruise speed, and propulsion system failure philosophy. All designs used propulsion systems consisting of multiple gas generators driving remote tip turbine lift and lift/cruise fans. By considering the fan to be designed for operational reliability, significant simplication of the airplane systems and reduction in airplane size and cost can be achieved

Softening and Broadening of the Zone Boundary Magnons in Pr0.63Sr0.37MnO3

We have studied the spin dynamics in Pr$_{0.63}$Sr$_{0.37}$MnO$_3$ above and below the Curie temperature $T_C=301$ K. Three distinct new features have been observed: a softening of the magnon dispersion at the zone boundary for $T<T_C$, significant broadening of the zone boundary magnons as $T\to T_C$, and no evidence for residual spin-wave like excitations just above $T_C$. The results are inconsistent with double exchange models that have been successfully applied to higher $T_C$ samples, indicating an evolution of the spin system with decreasing $T_C$.Comment: 12 pages, Latex, 3 figure

Conformational properties of compact polymers

Monte Carlo simulations of coarse-grained polymers provide a useful tool to deepen the understanding of conformational and statistical properties of polymers both in physical as well as in biological systems. In this study we sample compact conformations on a cubic LxLxL lattice with different occupancy fractions by modifying a recently proposed algorithm. The system sizes studied extend up to N=256000 monomers, going well beyond the limits of older publications on compact polymers. We analyze several conformational properties of these polymers, including segment correlations and screening of excluded volume. Most importantly we propose a scaling law for the end-to-end distance distribution and analyze the moments of this distribution. It shows universality with respect to different occupancy fractions, i.e. system densities. We further analyze the distance distribution between intrachain segments, which turns out to be of great importance for biological experiments. We apply these new findings to the problem of chromatin folding inside interphase nuclei and show that -- although chromatin is in a compacted state -- the classical theory of compact polymers does not explain recent experimental results

Ferromagnetic Kondo-Lattice Model

We present a many-body approach to the electronic and magnetic properties of the (multiband) Kondo-lattice model with ferromagnetic interband exchange. The coupling between itinerant conduction electrons and localized magnetic moments leads, on the one hand, to a distinct temperature-dependence of the electronic quasiparticle spectrum and, on the other hand, to magnetic properties, as e.~g.the Curie temperature T_C or the magnon dispersion, which are strongly influenced by the band electron selfenergy and therewith in particular by the carrier density. We present results for the single-band Kondo-lattice model in terms of quasiparticle densities of states and quasiparticle band structures and demonstrate the density-dependence of the self-consistently derived Curie temperature. The transition from weak-coupling (RKKY) to strong-coupling (double exchange) behaviour is worked out. The multiband model is combined with a tight-binding-LMTO bandstructure calculation to describe real magnetic materials. As an example we present results for the archetypal ferromagnetic local-moment systems EuO and EuS. The proposed method avoids the double counting of relevant interactions and takes into account the correct symmetry of atomic orbitals.Comment: 15 pages, 10 figure

Loss of molecules in magneto-electrostatic traps due to nonadiabatic transitions

We analyze the dynamics of a paramagnetic, dipolar molecule in a generic "magneto-electrostatic'' trap where both magnetic and electric fields may be present. The potential energy that governs the dynamics of the molecules is found using a reduced molecular model that incorporates the main features of the system. We discuss the shape of the trapping potentials for different field geometries, as well as the possibility of nonadiabatic transitions to untrapped states, i.e., the analog of Majorana transitions in a quadrupole magnetic atomic trap. Maximizing the lifetime of molecules in a trap is of great concern in current experiments, and we assess the effect of nonadiabatic transitions on obtainable trap lifetimes.Comment: 13 pages, 6 figure