Organisation of transcriptomes : searching for regulatory DNA elements involved in the correlated expression of genomic neighbours

Since the thesis that every gene acts as a single unit which transcription is solely regulated by promoter-binding transcription factors (TF) - irrespective of the surrounding genomic landscape - has been rejected, transcriptional regulation of genes has become a field of ever-growing complexity. Factors like the “state” of chromatin and DNA positioning inside the nucleus have been shown to have a major impact on the activation and repression of the transcription of genes. Furthermore it was discovered that the expression of individual adjacent genes in the genome is not independent, but genomic neighbours are co-expressed more often than what would be expected by chance. These neighbours form clusters of co-expressed genes that can be found all over the genome containing from two to several adjacent entities. In this thesis a possible explanation of this observation was investigated, namely the active alteration of chromatin state by possible interaction of transcription factors or other genomic features. Sequence analysis methods were used to search for possible DNA specific factors that could form “active chromatin hubs (ACH)” in the region of those o-expressed genes and therefore could lead to the revealed correlated expression. The thesis is based on our earlier analysis of the expression of genomic neighbours in mouse/human and proceeds these investigations

Realistic theory of electronic correlations in nanoscopic systems

Nanostructures with open shell transition metal or molecular constituents host often strong electronic correlations and are highly sensitive to atomistic material details. This tutorial review discusses method developments and applications of theoretical approaches for the realistic description of the electronic and magnetic properties of nanostructures with correlated electrons. First, the implementation of a flexible interface between density functional theory and a variant of dynamical mean field theory (DMFT) highly suitable for the simulation of complex correlated structures is explained and illustrated. On the DMFT side, this interface is largely based on recent developments of quantum Monte Carlo and exact diagonalization techniques allowing for efficient descriptions of general four fermion Coulomb interactions, reduced symmetries and spin-orbit coupling, which are explained here. With the examples of the Cr (001) surfaces, magnetic adatoms, and molecular systems it is shown how the interplay of Hubbard U and Hund's J determines charge and spin fluctuations and how these interactions drive different sorts of correlation effects in nanosystems. Non-local interactions and correlations present a particular challenge for the theory of low dimensional systems. We present our method developments addressing these two challenges, i.e., advancements of the dynamical vertex approximation and a combination of the constrained random phase approximation with continuum medium theories. We demonstrate how non-local interaction and correlation phenomena are controlled not only by dimensionality but also by coupling to the environment which is typically important for determining the physics of nanosystems.Comment: tutorial review submitted to EPJ-ST (scientific report of research unit FOR 1346); 14 figures, 26 page

Theory of subcycle time-resolved photoemission: Application to terahertz photodressing in graphene

Motivated by recent experimental progress we revisit the theory of pump–probe time- and angle-resolved photoemission spectroscopy (trARPES), which is one of the most powerful techniques to trace transient pump-driven modifications of the electronic properties. The pump-induced dynamics can be described in different gauges for the light–matter interaction. Standard minimal coupling leads to the velocity gauge, defined by linear coupling to the vector potential. In the context of tight-binding (TB) models, the Peierls substitution is the commonly employed scheme for single-band models. Multi-orbital extensions – including the coupling of the dipole moments to the electric field – have been introduced and tested recently. In this work, we derive the theory of time-resolved photoemission within both gauges from the perspective of nonequilibrium Green’s functions. This approach naturally incorporates the photoelectron continuum, which allows for a direct calculation of the observable photocurrent. Following this route we introduce gauge-invariant expressions for the time-resolved photoemission signal. The theory is applied to graphene pumped with short terahertz pulses, which we treat within a first-principles TB model. We investigate the gauge invariance and discuss typical effects observed in subcycle time-resolved photoemission. Our formalism is an ideal starting point for realistic trARPES simulations including scattering effects

Spatio-temporal dynamics induced by competing instabilities in two asymmetrically coupled nonlinear evolution equations

Pattern formation often occurs in spatially extended physical, biological and chemical systems due to an instability of the homogeneous steady state. The type of the instability usually prescribes the resulting spatio-temporal patterns and their characteristic length scales. However, patterns resulting from the simultaneous occurrence of instabilities cannot be expected to be simple superposition of the patterns associated with the considered instabilities. To address this issue we design two simple models composed by two asymmetrically coupled equations of non-conserved (Swift-Hohenberg equations) or conserved (Cahn-Hilliard equations) order parameters with different characteristic wave lengths. The patterns arising in these systems range from coexisting static patterns of different wavelengths to traveling waves. A linear stability analysis allows to derive a two parameter phase diagram for the studied models, in particular revealing for the Swift-Hohenberg equations a co-dimension two bifurcation point of Turing and wave instability and a region of coexistence of stationary and traveling patterns. The nonlinear dynamics of the coupled evolution equations is investigated by performing accurate numerical simulations. These reveal more complex patterns, ranging from traveling waves with embedded Turing patterns domains to spatio-temporal chaos, and a wide hysteretic region, where waves or Turing patterns coexist. For the coupled Cahn-Hilliard equations the presence of an weak coupling is sufficient to arrest the coarsening process and to lead to the emergence of purely periodic patterns. The final states are characterized by domains with a characteristic length, which diverges logarithmically with the coupling amplitude.Comment: 9 pages, 10 figures, submitted to Chao