The nucleosome: From structure to function through physics

Eukaryotic cells must fit meters of DNA into micron-sized cell nuclei and, at the same time,control and modulate the access to the genetic material. The necessary amount of DNAcompaction is achieved via multiple levels of structural organization, the first being thenucleosome – a unique complex of histone proteins with ~ 150 base pairs of DNA. Herewe use specific examples to demonstrate that many aspects of the structure and functionof nucleosomes can be understood using principles of basic physics, physics-based tools andmodels. For instance, the stability of single nucleosomes and the accessibility to their DNAdepends sensitively on the charges of the histones that in turn can be changed by post-translational modifications. The positions of nucleosomes along DNA molecules depend onthe sequence-dependent shape and elasticity of the DNA double helix that has to be wrappedinto the nucleosome complex. Larger-scale structures composed of multiple nucleosomes, i.e.nucleosome arrays, depend in turn on the interactions between its constituents that resultfrom delicately tuned electrostatics.Theoretical Physic

Dynamical 1/N approach to time-dependent currents through quantum dots

A systematic truncation of the many-body Hilbert space is implemented to study how electrons in a quantum dot attached to conducting leads respond to time-dependent biases. The method, which we call the dynamical 1/N approach, is first tested in the most unfavorable case, the case of spinless fermions (N=1). We recover the expected behavior, including transient ringing of the current in response to an abrupt change of bias. We then apply the approach to the physical case of spinning electrons, N=2, in the Kondo regime for the case of infinite intradot Coulomb repulsion. In agreement with previous calculations based on the non-crossing approximation (NCA), we find current oscillations associated with transitions between Kondo resonances situated at the Fermi levels of each lead. We show that this behavior persists for a more realistic model of semiconducting quantum dots in which the Coulomb repulsion is finite.Comment: 18 pages, 7 eps figures, discussion extended for spinless electrons and typo