Controlled DNA compaction within chromatin: the tail-bridging effect

We study the mechanism underlying the attraction between nucleosomes, the fundamental packaging units of DNA inside the chromatin complex. We introduce a simple model of the nucleosome, the eight-tail colloid, consisting of a charged sphere with eight oppositely charged, flexible, grafted chains that represent the terminal histone tails. We demonstrate that our complexes are attracted via the formation of chain bridges and that this attraction can be tuned by changing the fraction of charged monomers on the tails. This suggests a physical mechanism of chromatin compaction where the degree of DNA condensation can be controlled via biochemical means, namely the acetylation and deacetylation of lysines in the histone tails.Comment: 4 pages, 5 figures, submitte

Tail bridging vs. patchiness: models for the interaction of nucleosomes

Abstract: The subject of this thesis are the interactions between nucleosome core particles (NCPs). NCPs are the primary storage units of DNA in eucaryotic cells. Each NCP consists of a core of eight histone proteins and a strand of DNA, which is wrapped around about two times. Each histone protein has a terminal tail passing over and between the superhelix of the wrapped DNA. Special emphasis was placed on the role of the histone tails, since experimental findings suggest that the tails have a great influence on the mutual attraction of the NCPs. In those experiments Mangenot et al. observe a dramatic change in the configuration of the tails, which is accompanied by evidence of mutual attraction between NCPs, when a certain salt concentration is reached. Existing models used in the theoretical approaches and in simulations focus on the description of the histone core and the wrapped DNA, but neglect the histone tails. We introduce the multi chain complex as a new simulation model. Here the histone core and the wrapping DNA are modelled via a charged sphere, while the histone tails are represented by oppositely charged chains grafted on the sphere surface. We start by investigating the parameter space describing a single NCP. The Debye-H\"uckel potential is used to model the electrostatic interactions and to determine the effective charge of the NCP core. This value is subsequently used for a study of the pair-interaction of two NCPs via an extensive Molecular Dynamics study. The monomer distribution of the full chain model is investigated. The existence of tail bridges between the cores is demonstrated. Finally, by discriminating between bridging and non-bridging configurations, we can show that the effect of tail bridging between the spheres does indeed account for the observed attraction. The full chain model can serve as a model to study the acetylation of the histone tails of the nucleosome. The reduction of the charge fraction of the tails, that corresponds to the process of acetylation, leads to a reduction or even the disappearance of the attraction. A recent MC study links this effect to the unfolding of the chromatin fiber in the case of acetylated histone tails. In this case the acetylation of the histone tails leads to the formation of heterochromatin, and one could understand how larger regions of the genetic information could be inactivated through this mechanism

Anderson impurity model in nonequilibrium: analytical results versus quantum Monte Carlo data

We analyze the spectral function of the single-impurity two-terminal Anderson model at finite voltage using the recently developed diagrammatic quantum Monte Carlo technique as well as perturbation theory. In the (particle-hole-)symmetric case we find an excellent agreement of the numerical data with the perturbative results of second order up to interaction strengths $U/\Gamma \approx 2$, where $\Gamma$ is the transparency of the impurity-electrode interface. The analytical results are obtained in form of the nonequilibrium self-energy for which we present explicit formulas in the closed form at arbitrary bias voltage. We observe an increase of the spectral density around zero energy brought about by the Kondo effect. Our analysis suggests that a finite applied voltage $V$ acts as an effective temperature of the system. We conclude that at voltages significantly larger than the equilibrium Kondo temperature there is a complete suppression of the Kondo effect and no resonance splitting can be observed. We confirm this scenario by comparison of the numerical data with the perturbative results.Comment: 8 pages, 6 figure

Nonequilibrium many-body dynamics along a dissipative Hubbard chain: Symmetries and Quantum Monte Carlo simulations

The nonequilibrium dynamics of correlated charge transfer along a one-dimensional chain in presence of a phonon environment is investigated within a dissipative Hubbard model. For this generalization of the ubiquitous spin-boson model the crucial role of symmetries is analysed in detail and corresponding invariant subspaces are identified. It is shown that the time evolution typically occurs in each of the disjunct subspaces independently leading e.g. asymptotically to a non-Boltzmann equilibrium state. Based on these findings explicit results are obtained for two interacting electrons by means of a substantially improved real-time quantum Monte Carlo approach. In the incoherent regime an appropriate mapping of the many-body dynamics onto an isomorphic single particle motion allows for an approximate description of the numerical data in terms of rate equations. These results may lead to new control schemes of charge transport in tailored quantum systems as e.g. molecular chains or quantum dot arrays.Comment: 13 pages, 9 figures submitted to Phys. Rev.

Heisenberg's Uncertainty Relation and Bell Inequalities in High Energy Physics

An effective formalism is developed to handle decaying two-state systems. Herewith, observables of such systems can be described by a single operator in the Heisenberg picture. This allows for using the usual framework in quantum information theory and, hence, to enlighten the quantum feature of such systems compared to non-decaying systems. We apply it to systems in high energy physics, i.e. to oscillating meson-antimeson systems. In particular, we discuss the entropic Heisenberg uncertainty relation for observables measured at different times at accelerator facilities including the effect of CP violation, i.e. the imbalance of matter and antimatter. An operator-form of Bell inequalities for systems in high energy physics is presented, i.e. a Bell-witness operator, which allows for simple analysis of unstable systems.Comment: 17 page

Suppressed pi^0 Production at Large Transverse Momentum in Central Au+Au Collisions at sqrt(s_NN) = 200 GeV

Transverse momentum spectra of neutral pions in the range 1 < p_T < 10 GeV/c have been measured at mid-rapidity by the PHENIX experiment at RHIC in Au+Au collisions at sqrt(s_NN) = 200 GeV. The pi^0 multiplicity in central reactions is significantly below the yields measured at the same sqrt(s_NN) in peripheral Au+Au and p+p reactions scaled by the number of nucleon-nucleon collisions. For the most central bin, the suppression factor is ~2.5 at p_T = 2 GeV/c and increases to ~4-5 at p_T ~= 4 GeV/c. At larger p_T, the suppression remains constant within errors. The deficit is already apparent in semi-peripheral reactions and increases smoothly with centrality.Comment: 326 authors, 6 pages text, RevTeX, 3 figures, 2 tables. Submitted to PRL. Plain text data tables for the points plotted in figures for this and previous PHENIX publications are (or will be) publicly available at http://www.phenix.bnl.gov/papers.htm

Flow Measurements via Two-particle Azimuthal Correlations in Au + Au Collisions at sqrt(s_NN) = 130 GeV

Two particle azimuthal correlation functions are presented for charged hadrons produced in Au + Au collisions at RHIC sqrt(s_NN) = 130 GeV. The measurements permit determination of elliptic flow without event-by-event estimation of the reaction plane. The extracted elliptic flow values v_2 show significant sensitivity to both the collision centrality and the transverse momenta of emitted hadrons, suggesting rapid thermalization and relatively strong velocity fields. When scaled by the eccentricity of the collision zone, epsilon, the scaled elliptic flow shows little or no dependence on centrality for charged hadrons with relatively low p_T. A breakdown of this epsilon scaling is observed for charged hadrons with p_T > 1.0 GeV/c for the most central collisions.Comment: 6 pages, RevTeX 3, 4 figures, 307 authors, submitted to Phys. Rev. Lett. on 11 April 2002. Plain text data tables for the points plotted in figures for this and previous PHENIX publications are (will be made) publicly available at http://www.phenix.bnl.gov/phenix/WWW/run/phenix/papers.htm

Deuteron and antideuteron production in Au+Au collisions at sqrt(s_NN)=200 GeV

The production of deuterons and antideuterons in the transverse momentum range 1.1 < p_T < 4.3 GeV/c at mid-rapidity in Au + Au collisions at sqrt(s_NN)=200 GeV has been studied by the PHENIX experiment at RHIC. A coalescence analysis comparing the deuteron and antideuteron spectra with those of protons and antiprotons, has been performed. The coalescence probability is equal for both deuterons and antideuterons and increases as a function of p_T, which is consistent with an expanding collision zone. Comparing (anti)proton yields p_bar/p = 0.73 +/- 0.01, with (anti)deuteron yields: d_bar/d = 0.47 +/- 0.03, we estimate that n_bar/n = 0.64 +/- 0.04.Comment: 326 authors, 6 pages text, 5 figures, 1 Table. Submitted to PRL. Plain text data tables for the points plotted in figures for this and previous PHENIX publications are (or will be) publicly available at http://www.phenix.bnl.gov/papers.htm