CSC - IT Center for Science (Finland)

Electronic structure calculations have become an indispensable tool in many areas of materials science and quantum chemistry. Even though the Kohn-Sham formulation of the density-functional theory (DFT) simplifies the many-body problem significantly, one is still confronted with several numerical challenges. In this article we present the projector augmented-wave (PAW) method as implemented in the GPAW program package (https://wiki.fysik.dtu.dk/gpaw) using a uniform real-space grid representation of the electronic wavefunctions. Compared to more traditional plane wave or localized basis set approaches, real-space grids offer several advantages, most notably good computational scalability and systematic convergence properties. However, as a unique feature GPAW also facilitates a localized atomic-orbital basis set in addition to the grid. The efficient atomic basis set is complementary to the more accurate grid, and the possibility to seamlessly switch between the two representations provides great flexibility. While DFT allows one to study ground state properties, time-dependent density-functional theory (TDDFT) provides access to the excited states. We have implemented the two common formulations of TDDFT, namely the linear-response and the time propagation schemes. Electron transport calculations under finite-bias conditions can be performed with GPAW using non-equilibrium Green functions and the localized basis set. In addition to the basic features of the real-space PAW method, we also describe the implementation of selected exchange-correlation functionals, parallelization schemes, ΔSCF-method, x-ray absorption spectra, and maximally localized Wannier orbitals.

Uterine leiomyomas, or fibroids, are benign tumors that affect millions of women worldwide and that can cause considerable morbidity. To study the genetic basis of this tumor type, we examined 18 uterine leiomyomas derived from 17 different patients by exome sequencing and identified tumor-specific mutations in the mediator complex subunit 12 (MED12) gene in 10. Through analysis of 207 additional tumors, we determined that MED12 is altered in 70% (159 of 225) of tumors from a total of 80 patients. The Mediator complex is a 26-subunit transcriptional regulator that bridges DNA regulatory sequences to the RNA polymerase II initiation complex. All mutations resided in exon 2, suggesting that aberrant function of this region of MED12 contributes to tumorigenesis.

Abstract. Ice flow models of the Antarctic ice sheet are commonly used to simulate its future evolution in response to different climate scenarios and assess the mass loss that would contribute to future sea level rise. However, there is currently no consensus on estimates of the future mass balance of the ice sheet, primarily because of differences in the representation of physical processes, forcings employed and initial states of ice sheet models. This study presents results from ice flow model simulations from 13 international groups focusing on the evolution of the Antarctic ice sheet during the period 2015–2100 as part of the Ice Sheet Model Intercomparison for CMIP6 (ISMIP6). They are forced with outputs from a subset of models from the Coupled Model Intercomparison Project Phase 5 (CMIP5), representative of the spread in climate model results. Simulations of the Antarctic ice sheet contribution to sea level rise in response to increased warming during this period varies between −7.8 and 30.0 cm of sea level equivalent (SLE) under Representative Concentration Pathway (RCP) 8.5 scenario forcing. These numbers are relative to a control experiment with constant climate conditions and should therefore be added to the mass loss contribution under climate conditions similar to present-day conditions over the same period. The simulated evolution of the West Antarctic ice sheet varies widely among models, with an overall mass loss, up to 18.0 cm SLE, in response to changes in oceanic conditions. East Antarctica mass change varies between −6.1 and 8.3 cm SLE in the simulations, with a significant increase in surface mass balance outweighing the increased ice discharge under most RCP 8.5 scenario forcings. The inclusion of ice shelf collapse, here assumed to be caused by large amounts of liquid water ponding at the surface of ice shelves, yields an additional simulated mass loss of 28 mm compared to simulations without ice shelf collapse. The largest sources of uncertainty come from the climate forcing, the ocean-induced melt rates, the calibration of these melt rates based on oceanic conditions taken outside of ice shelf cavities and the ice sheet dynamic response to these oceanic changes. Results under RCP 2.6 scenario based on two CMIP5 climate models show an additional mass loss of 0 and 3 cm of SLE on average compared to simulations done under present-day conditions for the two CMIP5 forcings used and display limited mass gain in East Antarctica.

Abstract. The Fourth IPCC Assessment Report concluded that ice sheet flow models, in their current state, were unable to provide accurate forecast for the increase of polar ice sheet discharge and the associated contribution to sea level rise. Since then, the glaciological community has undertaken a huge effort to develop and improve a new generation of ice flow models, and as a result a significant number of new ice sheet models have emerged. Among them is the parallel finite-element model Elmer/Ice, based on the open-source multi-physics code Elmer. It was one of the first full-Stokes models used to make projections for the evolution of the whole Greenland ice sheet for the coming two centuries. Originally developed to solve local ice flow problems of high mechanical and physical complexity, Elmer/Ice has today reached the maturity to solve larger-scale problems, earning the status of an ice sheet model. Here, we summarise almost 10 yr of development performed by different groups. Elmer/Ice solves the full-Stokes equations, for isotropic but also anisotropic ice rheology, resolves the grounding line dynamics as a contact problem, and contains various basal friction laws. Derived fields, like the age of the ice, the strain rate or stress, can also be computed. Elmer/Ice includes two recently proposed inverse methods to infer badly known parameters. Elmer is a highly parallelised code thanks to recent developments and the implementation of a block preconditioned solver for the Stokes system. In this paper, all these components are presented in detail, as well as the numerical performance of the Stokes solver and developments planned for the future.

BACKGROUND: The growth of high-throughput technologies such as microarrays and next generation sequencing has been accompanied by active research in data analysis methodology, producing new analysis methods at a rapid pace. While most of the newly developed methods are freely available, their use requires substantial computational skills. In order to enable non-programming biologists to benefit from the method development in a timely manner, we have created the Chipster software. RESULTS: Chipster (http://chipster.csc.fi/) brings a powerful collection of data analysis methods within the reach of bioscientists via its intuitive graphical user interface. Users can analyze and integrate different data types such as gene expression, miRNA and aCGH. The analysis functionality is complemented with rich interactive visualizations, allowing users to select datapoints and create new gene lists based on these selections. Importantly, users can save the performed analysis steps as reusable, automatic workflows, which can also be shared with other users. Being a versatile and easily extendable platform, Chipster can be used for microarray, proteomics and sequencing data. In this article we describe its comprehensive collection of analysis and visualization tools for microarray data using three case studies. CONCLUSIONS: Chipster is a user-friendly analysis software for high-throughput data. Its intuitive graphical user interface enables biologists to access a powerful collection of data analysis and integration tools, and to visualize data interactively. Users can collaborate by sharing analysis sessions and workflows. Chipster is open source, and the server installation package is freely available.

Abstract Predictions of marine ice-sheet behaviour require models able to simulate grounding-line migration. We present results of an intercomparison experiment for plan-view marine ice-sheet models. Verification is effected by comparison with approximate analytical solutions for flux across the grounding line using simplified geometrical configurations (no lateral variations, no buttressing effects from lateral drag). Perturbation experiments specifying spatial variation in basal sliding parameters permitted the evolution of curved grounding lines, generating buttressing effects. The experiments showed regions of compression and extensional flow across the grounding line, thereby invalidating the boundary layer theory. Steady-state grounding-line positions were found to be dependent on the level of physical model approximation. Resolving grounding lines requires inclusion of membrane stresses, a sufficiently small grid size (<500 m), or subgrid interpolation of the grounding line. The latter still requires nominal grid sizes of <5 km. For larger grid spacings, appropriate parameterizations for ice flux may be imposed at the grounding line, but the short-time transient behaviour is then incorrect and different from models that do not incorporate grounding-line parameterizations. The numerical error associated with predicting grounding-line motion can be reduced significantly below the errors associated with parameter ignorance and uncertainties in future scenarios.

BACKGROUND: Uterine leiomyomas are benign but affect the health of millions of women. A better understanding of the molecular mechanisms involved may provide clues to the prevention and treatment of these lesions. METHODS: We performed whole-genome sequencing and gene-expression profiling of 38 uterine leiomyomas and the corresponding myometrium from 30 women. RESULTS: Identical variants observed in some separate tumor nodules suggested that these nodules have a common origin. Complex chromosomal rearrangements resembling chromothripsis were a common feature of leiomyomas. These rearrangements are best explained by a single event of multiple chromosomal breaks and random reassembly. The rearrangements created tissue-specific changes consistent with a role in the initiation of leiomyoma, such as translocations of the HMGA2 and RAD51B loci and aberrations at the COL4A5-COL4A6 locus, and occurred in the presence of normal TP53 alleles. In some cases, separate events had occurred more than once in single tumor-cell lineages. CONCLUSIONS: Chromosome shattering and reassembly resembling chromothripsis (a single genomic event that results in focal losses and rearrangements in multiple genomic regions) is a major cause of chromosomal abnormalities in uterine leiomyomas; we propose that tumorigenesis occurs when tissue-specific tumor-promoting changes are formed through these events. Chromothripsis has previously been associated with aggressive cancer; its common occurrence in leiomyomas suggests that it also has a role in the genesis and progression of benign tumors. We observed that multiple separate tumors could be seeded from a single lineage of uterine leiomyoma cells. (Funded by the Academy of Finland Center of Excellence program and others.).

BACKGROUND: A growing amount of scientific evidence suggests that microbes are involved in the aetiology of irritable bowel syndrome (IBS), and the gastrointestinal (GI) microbiota of individuals suffering from diarrhoea-predominant IBS (IBS-D) is distinguishable from other IBS-subtypes. In our study, the GI microbiota of IBS-D patients was evaluated and compared with healthy controls (HC) by using a high-resolution sequencing method. The method allowed microbial community analysis on all levels of microbial genomic guanine plus cytosine (G+C) content, including high G+C bacteria. METHODS: The collective faecal microbiota composition of ten IBS-D patients was analysed by examining sequences obtained using percent G+C (%G+C) -based profiling and fractioning combined with 16S rRNA gene clone library sequencing of 3267 clones. The IBS-D library was compared with an analogous healthy-control library of 23 subjects. Real-time PCR analysis was used to identify phylotypes belonging to the class Gammaproteobacteria and the order Coriobacteriales. RESULTS: Significant differences were found between clone libraries of IBS-D patients and controls. The microbial communities of IBS-D patients were enriched in Proteobacteria and Firmicutes, but reduced in the number of Actinobacteria and Bacteroidetes compared to control. In particular, 16S rDNA sequences belonging to the family Lachnospiraceae within the phylum Firmicutes were in greater abundance in the IBS-D clone library. CONCLUSIONS: In the microbiota of IBS-D sufferers, notable differences were detected among the prominent bacterial phyla (Firmicutes, Actinobacteria, Bacteroidetes, and Proteobacteria) localized within the GI tract.

We model a Kohn-Sham potential with the discontinuity at integer particle numbers starting from the approximation by (GLLB) Gritsenko et al. [Phys. Rev. A 51, 1944 (1995)]. We evaluate the Kohn-Sham gap and the discontinuity to obtain the quasiparticle gap. This allows us to compare the Kohn-Sham gaps to those obtained by accurate many-body perturbation-theory-based optimized potential methods. In addition, the resulting quasiparticle band gap is compared to experimental gaps. In the GLLB model potential, the exchange-correlation hole is modeled using a generalized gradient approximation (GGA) energy density and the response of the hole-to-density variations is evaluated by using the common-denominator approximation and homogeneous electron-gas-based assumptions. In our modification, we have chosen the PBEsol potential as the GGA to model the exchange hole and add a consistent correlation potential. The method is implemented in the GPAW code, which allows efficient parallelization to study large systems. A fair agreement for Kohn-Sham and the quasiparticle band gaps with semiconductors and other band gap materials is obtained with a potential which is as fast as GGA to calculate.

The CODATA Data Science Journal is a peer-reviewed, open access, electronic journal, publishing papers on the management, dissemination, use and reuse of research data and databases across all research domains, including science, technology, the humanities and the arts. The scope of the journal includes descriptions of data systems, their implementations and their publication, applications, infrastructures, software, legal, reproducibility and transparency issues, the availability and usability of complex datasets, and with a particular focus on the principles, policies and practices for open data.All data is in scope, whether born digital or converted from other sources.

The Global Alliance for Genomics and Health (GA4GH) aims to accelerate biomedical advances by enabling the responsible sharing of clinical and genomic data through both harmonized data aggregation and federated approaches. The decreasing cost of genomic sequencing (along with other genome-wide molecular assays) and increasing evidence of its clinical utility will soon drive the generation of sequence data from tens of millions of humans, with increasing levels of diversity. In this perspective, we present the GA4GH strategies for addressing the major challenges of this data revolution. We describe the GA4GH organization, which is fueled by the development efforts of eight Work Streams and informed by the needs of 24 Driver Projects and other key stakeholders. We present the GA4GH suite of secure, interoperable technical standards and policy frameworks and review the current status of standards, their relevance to key domains of research and clinical care, and future plans of GA4GH. Broad international participation in building, adopting, and deploying GA4GH standards and frameworks will catalyze an unprecedented effort in data sharing that will be critical to advancing genomic medicine and ensuring that all populations can access its benefits.

Gold nanoclusters protected by a thiolate monolayer (MPC) are widely studied for their potential applications in site-specific bioconjugate labeling, sensing, drug delivery, and molecular electronics. Several MPCs with 1-2 nm metal cores are currently known to have a well-defined molecular structure, and they serve as an important link between molecularly dispersed gold and colloidal gold to understand the size-dependent electronic and optical properties. Here, we show by using an ab initio method together with atomistic models for experimentally observed thiolate-stabilized gold clusters how collective electronic excitations change when the gold core of the MPC grows from 1.5 to 2.0 nm. A strong localized surface plasmon resonance (LSPR) develops at 540 nm (2.3 eV) in a cluster with a 2.0 nm metal core. The protecting molecular layer enhances the LSPR, while in a smaller cluster with 1.5 nm gold core, the plasmon-like resonance at 540 nm is confined in the metal core by the molecular layer. Our results demonstrate a threshold size for the emergence of LSPR in these systems and help to develop understanding of the effect of the molecular overlayer on plasmonic properties of MPCs enabling engineering of their properties for plasmonic applications.

Sliding velocity and basal drag are strongly influenced by changes in subglacial water pressure or subglacial water storage associated with opening and closing of water cavities in the lee of bedrock obstacles. To better understand this influence, finite‐element simulations of ice flowing past bedrock obstacles with cavity formation are carried out for different synthetic periodic bedrock shapes. In the numerical model, the cavity roof is treated as an unknown free surface and is part of the solution. As an improvement over earlier studies, the cases of nonlinear ice rheology and infinite bedrock slopes are treated. Our results show that the relationship between basal drag and sliding velocity, the friction law, can be easily extended from linear to nonlinear ice rheology and is bounded even for bedrocks with locally infinite slopes. Combining our results with earlier works by others, a phenomenological friction law is proposed that includes three independent parameters that depend only on the bedrock geometry. This formulation yields an upper bound of the basal drag for finite sliding velocity and a decrease in the basal drag at low effective pressure or high velocity. This law should dramatically alter results of models of temperate glaciers and should also have important repercussions on models of glacier surges and fast glacier flows.

Abstract. Over the last two decades, the Greenland ice sheet (GrIS) has been losing mass at an increasing rate, enhancing its contribution to sea-level rise (SLR). The recent increases in ice loss appear to be due to changes in both the surface mass balance of the ice sheet and ice discharge (ice flux to the ocean). Rapid ice flow directly affects the discharge, but also alters ice-sheet geometry and so affects climate and surface mass balance. Present-day ice-sheet models only represent rapid ice flow in an approximate fashion and, as a consequence, have never explicitly addressed the role of ice discharge on the total GrIS mass balance, especially at the scale of individual outlet glaciers. Here, we present a new-generation prognostic ice-sheet model which reproduces the current patterns of rapid ice flow. This requires three essential developments: the complete solution of the full system of equations governing ice deformation; a variable resolution unstructured mesh to resolve outlet glaciers and the use of inverse methods to better constrain poorly known parameters using observations. The modelled ice discharge is in good agreement with observations on the continental scale and for individual outlets. From this initial state, we investigate possible bounds for the next century ice-sheet mass loss. We run sensitivity experiments of the GrIS dynamical response to perturbations in climate and basal lubrication, assuming a fixed position of the marine termini. We find that increasing ablation tends to reduce outflow and thus decreases the ice-sheet imbalance. In our experiments, the GrIS initial mass (im)balance is preserved throughout the whole century in the absence of reinforced forcing, allowing us to estimate a lower bound of 75 mm for the GrIS contribution to SLR by 2100. In one experiment, we show that the current increase in the rate of ice loss can be reproduced and maintained throughout the whole century. However, this requires a very unlikely perturbation of basal lubrication. From this result we are able to estimate an upper bound of 140 mm from dynamics only for the GrIS contribution to SLR by 2100.

Structural biology, homology modelling and rational drug design require accurate three-dimensional macromolecular coordinates. However, the coordinates in the Protein Data Bank (PDB) have not all been obtained using the latest experimental and computational methods. In this study a method is presented for automated re-refinement of existing structure models in the PDB. A large-scale benchmark with 16 807 PDB entries showed that they can be improved in terms of fit to the deposited experimental X-ray data as well as in terms of geometric quality. The re-refinement protocol uses TLS models to describe concerted atom movement. The resulting structure models are made available through the PDB_REDO databank (http://www.cmbi.ru.nl/pdb_redo/). Grid computing techniques were used to overcome the computational requirements of this endeavour.

We review the GPAW open-source Python package for electronic structure calculations. GPAW is based on the projector-augmented wave method and can solve the self-consistent density functional theory (DFT) equations using three different wave-function representations, namely real-space grids, plane waves, and numerical atomic orbitals. The three representations are complementary and mutually independent and can be connected by transformations via the real-space grid. This multi-basis feature renders GPAW highly versatile and unique among similar codes. By virtue of its modular structure, the GPAW code constitutes an ideal platform for the implementation of new features and methodologies. Moreover, it is well integrated with the Atomic Simulation Environment (ASE), providing a flexible and dynamic user interface. In addition to ground-state DFT calculations, GPAW supports many-body GW band structures, optical excitations from the Bethe-Salpeter Equation, variational calculations of excited states in molecules and solids via direct optimization, and real-time propagation of the Kohn-Sham equations within time-dependent DFT. A range of more advanced methods to describe magnetic excitations and non-collinear magnetism in solids are also now available. In addition, GPAW can calculate non-linear optical tensors of solids, charged crystal point defects, and much more. Recently, support for graphics processing unit (GPU) acceleration has been achieved with minor modifications to the GPAW code thanks to the CuPy library. We end the review with an outlook, describing some future plans for GPAW.

Results are presented from direct simulations of turbulent compressible hydromagnetic convection above a stable overshoot layer. Spontaneous dynamo action occurs followed by saturation, with most of the generated magnetic field appearing as coherent flux tubes in the vicinity of strong downdrafts, where both the generation and destruction of magnetic field is most vigorous. Whether or not this field is amplified depends on the sizes of the magnetic Reynolds and magnetic Prandtl numbers. Joule dissipation is balanced mainly by the work done against the magnetic curvature force. It is this curvature force which is also responsible for the saturation of the dynamo.

We present the implementation of the time-dependent density-functional theory both in linear-response and in time-propagation formalisms using the projector augmented-wave method in real-space grids. The two technically very different methods are compared in the linear-response regime where we found perfect agreement in the calculated photoabsorption spectra. We discuss the strengths and weaknesses of the two methods as well as their convergence properties. We demonstrate different applications of the methods by calculating excitation energies and excited state Born-Oppenheimer potential surfaces for a set of atoms and molecules with the linear-response method and by calculating nonlinear emission spectra using the time-propagation method.

The emergence of an global cyberinfrastructure is rapidly increasing the ability of scientists to produce, manage, and use data, leading to new understanding and modes of scientific inquiry that depend on broader data access. As research becomes increasingly global, data intensive, and multifaceted, it is imperative to address national and international data access and sharing issues systematically in a policy arena that transcends national jurisdictions. The authors of this Policy Forum summarize key findings of an international group that studied these issues on behalf of the OECD, and argue that an international framework of principles and guidelines for data access is needed to better realize this potential. They provide a framework for locating and analyzing where improvements can be made in data access regimes, and highlight several topics that require further examination to better inform future policies.

We observe using ab initio methods that localized surface plasmon resonances in icosahedral silver nanoparticles enter the asymptotic region already between diameters of 1 and 2 nm, converging close to the classical quasistatic limit around 3.4 eV. We base the observation on time-dependent density-functional theory simulations of the icosahedral silver clusters ${\mathrm{Ag}}_{55}\phantom{\rule{0.28em}{0ex}}(1.06\phantom{\rule{0.28em}{0ex}}\mathrm{nm})$, ${\mathrm{Ag}}_{147}\phantom{\rule{0.28em}{0ex}}(1.60\phantom{\rule{0.28em}{0ex}}\mathrm{nm})$, ${\mathrm{Ag}}_{309}\phantom{\rule{0.28em}{0ex}}(2.14\phantom{\rule{0.28em}{0ex}}\mathrm{nm})$, and ${\mathrm{Ag}}_{561}\phantom{\rule{0.28em}{0ex}}(2.68 \mathrm{nm})$. The simulation method combines the adiabatic GLLB--SC exchange-correlation functional with real time propagation in an atomic orbital basis set using the projector-augmented wave method. The method has been implemented for the electron structure code GPAW within the scope of this work. We obtain good agreement with experimental data and modeled results, including photoemission and plasmon resonance. Moreover, we can extrapolate the ab initio results to the classical quasistatically modeled icosahedral clusters.