Heidelberg Institute For Theoretische Studien

Heidelberg, Germany

Heidelberg Institute For Theoretische Studien

Heidelberg, Germany
Time filter
Source Type

Dugard C.K.,Purdue University | Dugard C.K.,U.S. Food and Drug Administration | Mertz R.A.,Purdue University | Mertz R.A.,University of Missouri | And 11 more authors.
Plant Physiology | Year: 2016

Traditional marker-based mapping and next-generation sequencing was used to determine that the Arabidopsis (Arabidopsis thaliana) low cell wall arabinose mutant murus5 (mur5) encodes a defective allele of REVERSIBLY GLYCOSYLATED POLYPEPTIDE2 (RGP2). Marker analysis of 13 F2 confirmed mutant progeny from a recombinant mapping population gave a rough map position on the upper arm of chromosome 5, and deep sequencing of DNA from these 13 lines gave five candidate genes with G→A (C→T) transitions predicted to result in amino acid changes. Of these five, only insertional mutant alleles of RGP2, a gene that encodes a UDP-arabinose mutase that interconverts UDP-arabinopyranose and UDP-arabinofuranose, exhibited the low cell wall arabinose phenotype. The identities of mur5 and two SALK insertional alleles were confirmed by allelism tests and overexpression of wild-type RGP2 complementary DNA placed under the control of the 35S promoter in the three alleles. The mur5 mutation results in the conversion of cysteine-257 to tyrosine-257 within a conserved hydrophobic cluster predicted to be distal to the active site and essential for protein stability and possible heterodimerization with other isoforms of RGP. © 2016 American Society of Plant Biologists. All rights reserved.

Wise J.H.,Georgia Institute of Technology | Turk M.J.,Columbia University | Norman M.L.,University of California at San Diego | Abel T.,Kavli Institute for Particle Astrophysics and Cosmology | And 2 more authors.
Astrophysical Journal | Year: 2012

By definition, Population III stars are metal-free, and their protostellar collapse is driven by molecular hydrogen cooling in the gas phase, leading to large characteristic masses. Population II stars with lower characteristic masses form when the star-forming gas reaches a critical metallicity of 10 -6-10-3.5 Z⊙. We present an adaptive mesh refinement radiation hydrodynamics simulation that follows the transition from Population III to Population II star formation. The maximum spatial resolution of 1 comoving parsec allows for individual molecular clouds to be well resolved and their stellar associations to be studied in detail. We model stellar radiative feedback with adaptive ray tracing. A top-heavy initial mass function for the Population III stars is considered, resulting in a plausible distribution of pair-instability supernovae and associated metal enrichment. We find that the gas fraction recovers from 5% to nearly the cosmic fraction in halos with merger histories rich in halos above 107 M ⊙. A single pair-instability supernova is sufficient to enrich the host halo to a metallicity floor of 10-3Z⊙ and to transition to Population II star formation. This provides a natural explanation for the observed floor on damped Lyα systems metallicities reported in the literature, which is of this order. We find that stellar metallicities do not necessarily trace stellar ages, as mergers of halos with established stellar populations can create superpositions of t-Z evolutionary tracks. A bimodal metallicity distribution is created after a starburst occurs when the halo can cool efficiently through atomic line cooling. © 2012 The American Astronomical Society. All rights reserved.

Jedamzik K.,Montpellier University | Abel T.,Kavli Institute for Particle Astrophysics and Cosmology | Abel T.,University of Heidelberg | Abel T.,Heidelberg Institute For Theoretische Studien
Journal of Cosmology and Astroparticle Physics | Year: 2013

It is shown that small-scale magnetic fields present before recombination induce baryonic density inhomogeneities of appreciable magnitude. The presence of such inhomogeneities changes the ionization history of the Universe, which in turn decreases the angular scale of the Doppler peaks and increases Silk damping by photon diffusion. This unique signature could be used to (dis)prove the existence of primordial magnetic fields of strength as small as B ≃ 10-11 Gauss by cosmic microwave background observations.

Kim J.-H.,Kavli Institute for Particle Astrophysics and Cosmology | Kim J.-H.,Stanford University | Wise J.H.,Princeton University | Alvarez M.A.,Canadian Institute for Theoretical Astrophysics | And 4 more authors.
Astrophysical Journal | Year: 2011

There is mounting evidence for the coevolution of galaxies and their embedded massive black holes (MBHs) in a hierarchical structure formation paradigm. To tackle the nonlinear processes of galaxy - MBH interaction, we describe a self-consistent numerical framework which incorporates both galaxies and MBHs. The high-resolution adaptive mesh refinement (AMR) code Enzo is modified to model the formation and feedback of molecular clouds at their characteristic scale of 15.2pc and the accretion of gas onto an MBH. Two major channels of MBH feedback, radiative feedback (X-ray photons followed through full three-dimensional adaptive ray tracing) and mechanical feedback (bipolar jets resolved in high-resolution AMR), are employed. We investigate the coevolution of a 9.2 × 1011 M ∞ galactic halo and its 105 M ∞ embedded MBH at redshift 3 in a cosmological ΛCDM simulation. The MBH feedback heats the surrounding interstellar medium (ISM) up to 106 K through photoionization and Compton heating and locally suppresses star formation in the galactic inner core. The feedback considerably changes the stellar distribution there. This new channel of feedback from a slowly growing MBH is particularly interesting because it is only locally dominant and does not require the heating of gas globally on the disk. The MBH also self-regulates its growth by keeping the surrounding ISM hot for an extended period of time. © 2011. The American Astronomical Society. All rights reserved.

Hahn O.,Kavli Institute for Particle Astrophysics and Cosmology | Abel T.,Kavli Institute for Particle Astrophysics and Cosmology | Abel T.,University of Heidelberg | Abel T.,Heidelberg Institute For Theoretische Studien
Monthly Notices of the Royal Astronomical Society | Year: 2011

We discuss a new algorithm to generate multi-scale initial conditions with multiple levels of refinements for cosmological 'zoom-in' simulations. The method uses an adaptive convolution of Gaussian white noise with a real-space transfer function kernel together with an adaptive multi-grid Poisson solver to generate displacements and velocities following first- (1LPT) or second-order Lagrangian perturbation theory (2LPT). The new algorithm achieves rms relative errors of the order of 10-4 for displacements and velocities in the refinement region and thus improves in terms of errors by about two orders of magnitude over previous approaches. In addition, errors are localized at coarse-fine boundaries and do not suffer from Fourier-space-induced interference ringing. An optional hybrid multi-grid and Fast Fourier Transform (FFT) based scheme is introduced which has identical Fourier-space behaviour as traditional approaches. Using a suite of re-simulations of a galaxy cluster halo our real-space-based approach is found to reproduce correlation functions, density profiles, key halo properties and subhalo abundances with per cent level accuracy. Finally, we generalize our approach for two-component baryon and dark-matter simulations and demonstrate that the power spectrum evolution is in excellent agreement with linear perturbation theory. For initial baryon density fields, it is suggested to use the local Lagrangian approximation in order to generate a density field for mesh-based codes that is consistent with the Lagrangian perturbation theory instead of the current practice of using the Eulerian linearly scaled densities. © 2011 The Authors Monthly Notices of the Royal Astronomical Society © 2011 RAS.

Oguchi Y.,University of Heidelberg | Oguchi Y.,German Cancer Research Center | Kummer E.,University of Heidelberg | Kummer E.,German Cancer Research Center | And 13 more authors.
Nature Structural and Molecular Biology | Year: 2012

The ring-forming AAA+ protein ClpB cooperates with the DnaK chaperone system to refold aggregated proteins in Escherichia coli. The M domain, a ClpB-specific coiled-coil structure with two wings, motif 1 and motif 2, is essential to disaggregation, but the positioning and mechanistic role of M domains in ClpB hexamers remain unresolved. We show that M domains nestle at the ClpB ring surface, with both M-domain motifs contacting the first ATPase domain (AAA-1). Both wings contribute to maintaining a repressed ClpB activity state. Motif 2 docks intramolecularly to AAA-1 to regulate ClpB unfolding power, and motif 1 contacts a neighboring AAA-1 domain. Mutations that stabilize motif 2 docking repress ClpB, whereas destabilization leads to derepressed ClpB activity with greater unfolding power that is toxic in vivo. Our results underline the vital nature of tight ClpB activity control and elucidate a regulated M-domain toggle control mechanism. © 2012 Nature America, Inc. All rights reserved.

Loading Heidelberg Institute For Theoretische Studien collaborators
Loading Heidelberg Institute For Theoretische Studien collaborators