Efficient all-electron hybrid density functionals for atomistic simulations beyond 10 000 atoms.

Hybrid density functional approximations (DFAs) offer compelling accuracy for ab initio electronic-structure simulations of molecules, nanosystems, and bulk materials, addressing some deficiencies of computationally cheaper, frequently used semilocal DFAs. However, the computational bottleneck of hybrid DFAs is the evaluation of the non-local exact exchange contribution, which is the limiting factor for the application of the method for large-scale simulations. In this work, we present a drastically optimized resolution-of-identity-based real-space implementation of the exact exchange evaluation for both non-periodic and periodic boundary conditions in the all-electron code FHI-aims, targeting high-performance central processing unit (CPU) compute clusters.

Quantitative three-dimensional imaging of chemical short-range order via machine learning enhanced atom probe tomography.

Chemical short-range order (CSRO) refers to atoms of specific elements self-organising within a disordered crystalline matrix to form particular atomic neighbourhoods. CSRO is typically characterized indirectly, using volume-averaged or through projection microscopy techniques that fail to capture the three-dimensional atomistic architectures. Here, we present a machine-learning enhanced approach to break the inherent resolution limits of atom probe tomography enabling three-dimensional imaging of multiple CSROs.

Nonlinear pulse compression of a 200 mJ and 1 kW ultrafast thin-disk amplifier.

We present a high-energy laser source consisting of an ultrafast thin-disk amplifier followed by a nonlinear compression stage. At a repetition rate of 5 kHz, the drive laser provides a pulse energy of up to 200 mJ with a pulse duration below 500 fs. Nonlinear broadening is implemented inside a Herriott-type multipass cell purged with noble gas, allowing us to operate under different seeding conditions.

From Dual Unitarity to Generic Quantum Operator Spreading.

Dual-unitary circuits are paradigmatic examples of exactly solvable yet chaotic quantum many-body systems, but solvability naturally goes along with a degree of nongeneric behavior. By investigating the effect of weakly broken dual unitarity on the spreading of local operators, we study whether, and how, small deviations from dual unitarity recover fully generic many-body dynamics. We present a discrete path-integral formula for the out-of-time-order correlator and recover a butterfly velocity smaller than the light-cone velocity, v_{B} View Article and Find Full Text PDF

Topologically Enabled Superconductivity.

Majorana zero modes are a much sought-after consequence of one-dimensional topological superconductivity. Here, we show that, in turn, zero modes accompanying dynamical instanton events strongly enhance-in some cases even enable-superconductivity. We find that the dynamics of a one-dimensional topological triplet superconductor is governed by a θ term in the action.

Nonlinear pulse compression of a thin-disk amplifier and contrast enhancement via nonlinear ellipse rotation.

We demonstrate pulse compressibility from 840 fs to 38 fs of 10 mJ pulses from a thin-disk amplifier at a repetition rate of 3 kHz after nonlinear broadening in a multipass cell. In addition, the temporal-intensity contrast is enhanced via nonlinear ellipse rotation of more than a factor 50 with an optical efficiency of 56%. We believe this is the first published experimental combination of multipass cell-based nonlinear compression and nonlinear ellipse rotation-based contrast enhancement preserving both pulse compressibility and beam quality.

Pre-Exascale Computing of Protein-Ligand Binding Free Energies with Open Source Software for Drug Design.

Nowadays, drug design projects benefit from highly accurate protein-ligand binding free energy predictions based on molecular dynamics simulations. While such calculations have been computationally expensive in the past, we now demonstrate that workflows built on open source software packages can efficiently leverage pre-exascale computing resources to screen hundreds of compounds in a matter of days. We report our results of free energy calculations on a large set of pharmaceutically relevant targets assembled to reflect industrial drug discovery projects.

Validation tests for cryo-EM maps using an independent particle set.

Cryo-electron microscopy (cryo-EM) has revolutionized structural biology by providing 3D density maps of biomolecules at near-atomic resolution. However, map validation is still an open issue. Despite several efforts from the community, it is possible to overfit 3D maps to noisy data.

NECI: N-Electron Configuration Interaction with an emphasis on state-of-the-art stochastic methods.

We present NECI, a state-of-the-art implementation of the Full Configuration Interaction Quantum Monte Carlo (FCIQMC) algorithm, a method based on a stochastic application of the Hamiltonian matrix on a sparse sampling of the wave function. The program utilizes a very powerful parallelization and scales efficiently to more than 24 000 central processing unit cores. In this paper, we describe the core functionalities of NECI and its recent developments.

Octopus, a computational framework for exploring light-driven phenomena and quantum dynamics in extended and finite systems.

Over the last few years, extraordinary advances in experimental and theoretical tools have allowed us to monitor and control matter at short time and atomic scales with a high degree of precision. An appealing and challenging route toward engineering materials with tailored properties is to find ways to design or selectively manipulate materials, especially at the quantum level. To this end, having a state-of-the-art ab initio computer simulation tool that enables a reliable and accurate simulation of light-induced changes in the physical and chemical properties of complex systems is of utmost importance.

Transferring the entatic-state principle to copper photochemistry.

The entatic state denotes a distorted coordination geometry of a complex from its typical arrangement that generates an improvement to its function. The entatic-state principle has been observed to apply to copper electron-transfer proteins and it results in a lowering of the reorganization energy of the electron-transfer process. It is thus crucial for a multitude of biochemical processes, but its importance to photoactive complexes is unexplored.

Myocardial ischemia detection with single-phase CT perfusion in symptomatic patients using high-pitch helical image acquisition technique.

Coronary CT angiography (CCTA) suffers from a reduced diagnostic accuracy in patients with heavily calcified coronary arteries or prior myocardial revascularisation due to artefacts caused by calcifications and stent material. CT myocardial perfusion imaging (CTMPI) yields high potential for the detection of myocardial ischemia and might help to overcome the above mentioned limitations. We analysed CT single-phase perfusion using high-pitch helical image acquisition technique in patients with prior myocardial revascularisation.

Photocontrolled chignolin-derived β-hairpin peptidomimetics.

The synthesis of novel, chignolin-derived peptides comprising the azobenzene photoswitch [3-(3-aminomethyl)phenylazo]phenylacetic acid (AMPP) is reported. Reversible photoswitching behavior led to folding into β-hairpin-like structures, as unequivocally demonstrated by CD, FT-IR and NMR spectroscopy.

Isomerization- and temperature-jump-induced dynamics of a photoswitchable β-hairpin.

Conformational changes in proteins and peptides can be initiated by diverse processes. This raises the question how the variation of initiation mechanisms is connected to differences in folding or unfolding processes. In this work structural dynamics of a photoswitchable β-hairpin model peptide were initiated by two different mechanisms: temperature jump (T-jump) and isomerization of a backbone element.

Dnmt2-dependent methylomes lack defined DNA methylation patterns.

Several organisms have retained methyltransferase 2 (Dnmt2) as their only candidate DNA methyltransferase gene. However, information about Dnmt2-dependent methylation patterns has been limited to a few isolated loci and the results have been discussed controversially. In addition, recent studies have shown that Dnmt2 functions as a tRNA methyltransferase, which raised the possibility that Dnmt2-only genomes might be unmethylated.

Genome of the haloarchaeon Natronomonas moolapensis, a neutrophilic member of a previously haloalkaliphilic genus.

The genus Natronomonas contains two species, one haloalkaliphile (N. pharaonis) and one neutrophile (N. moolapensis).

Chloride and organic osmolytes: a hybrid strategy to cope with elevated salinities by the moderately halophilic, chloride-dependent bacterium Halobacillus halophilus.

Salt acclimation in moderately halophilic bacteria is the result of action of a grand interplay orchestrated by signals perceived from the environment. To elucidate the cellular players involved in sensing and responding to changing salinities we have determined the genome sequence of Halobacillus halophilus, a Gram-positive moderate halophilic bacterium that has a strict requirement for the anion chloride. Halobacillus halophilus synthesizes a multitude of different compatible solutes and switches its osmolyte strategy with the external salinity and growth phase.

Haloquadratum walsbyi: limited diversity in a global pond.

Background: Haloquadratum walsbyi commonly dominates the microbial flora of hypersaline waters. Its cells are extremely fragile squares requiring >14%(w/v) salt for growth, properties that should limit its dispersal and promote geographical isolation and divergence. To assess this, the genome sequences of two isolates recovered from sites at near maximum distance on Earth, were compared.

A blueprint of ectoine metabolism from the genome of the industrial producer Halomonas elongata DSM 2581 T.

The halophilic γ-proteobacterium Halomonas elongata DSM 2581(T) thrives at high salinity by synthesizing and accumulating the compatible solute ectoine. Ectoine levels are highly regulated according to external salt levels but the overall picture of its metabolism and control is not well understood. Apart from its critical role in cell adaptation to halophilic environments, ectoine can be used as a stabilizer for enzymes and as a cell protectant in skin and health care applications and is thus produced annually on a scale of tons in an industrial process using H.

Genome information management and integrated data analysis with HaloLex.

HaloLex is a software system for the central management, integration, curation, and web-based visualization of genomic and other -omics data for any given microorganism. The system has been employed for the manual curation of three haloarchaeal genomes, namely Halobacterium salinarum (strain R1), Natronomonas pharaonis, and Haloquadratum walsbyi. HaloLex, in particular, enables the integrated analysis of genome-wide proteomic results with the underlying genomic data.

The MIGenAS integrated bioinformatics toolkit for web-based sequence analysis.

We describe a versatile and extensible integrated bioinformatics toolkit for the analysis of biological sequences over the Internet. The web portal offers convenient interactive access to a growing pool of chainable bioinformatics software tools and databases that are centrally installed and maintained by the RZG. Currently, supported tasks comprise sequence similarity searches in public or user-supplied databases, computation and validation of multiple sequence alignments, phylogenetic analysis and protein-structure prediction.

The genome of the square archaeon Haloquadratum walsbyi : life at the limits of water activity.

Background: The square halophilic archaeon Haloquadratum walsbyi dominates NaCl-saturated and MgCl2 enriched aquatic ecosystems, which imposes a serious desiccation stress, caused by the extremely low water activity. The genome sequence was analyzed and physiological and physical experiments were carried out in order to reveal how H. walsbyi has specialized into its narrow and hostile ecological niche and found ways to cope with the desiccation stress.

Metagenomics to paleogenomics: large-scale sequencing of mammoth DNA.

We sequenced 28 million base pairs of DNA in a metagenomics approach, using a woolly mammoth (Mammuthus primigenius) sample from Siberia. As a result of exceptional sample preservation and the use of a recently developed emulsion polymerase chain reaction and pyrosequencing technique, 13 million base pairs (45.4%) of the sequencing reads were identified as mammoth DNA.