Photoionization and transient Wannier-Stark ladder in silicon: First-principles simulations versus Keldysh theory

Nonlinear photoionization of dielectrics and semiconductors is widely treated in the framework of the Keldysh theory whose validity is limited to photon energies that are small compared to the band gap and relatively low laser intensities. The time-dependent density functional theory (TDDFT) simulations, which are free of these limitations, enable one to gain insight into nonequilibrium dynamics of the electronic structure. Here we apply TDDFT to investigate the photoionization of silicon crystal by ultrashort laser pulses in a wide range of laser wavelengths and intensities and compare the results with predictions of the Keldysh theory. Photoionization rates derived from the simulations considerably exceed the data obtained with the Keldysh theory within the validity range of the latter. Possible reasons for the discrepancy are discussed and we provide fundamental data on the photoionization rates beyond the limits of the Keldysh theory. By investigating the features of the Stark shift as a function of photon energy and laser field strength, a manifestation of the transient Wannier-Stark ladder states is revealed, which become blurred with increasing laser field strength. Finally, it is shown that the TDDFT simulations can potentially provide reliable data on the electron damping time that is of high importance for large-scale modeling

Upper threshold for stability of multipole-mode solitons in nonlocal nonlinear media

We address the stability of multipole-mode solitons in nonlocal Kerr-type nonlinear media. Such solitons comprise several out-of-phase peaks packed together by the forces acting between them. We discover that dipole-, triple-, and quadrupole-mode solitons can be made stable, whereas all higher-order soliton bound states are unstable.Comment: 15 pages, 4 figures, To appear in Optics Letter

The dynamics of the non-heme iron in bacterial reaction centers from Rhodobacter sphaeroides

AbstractWe investigate the dynamical properties of the non-heme iron (NHFe) in His-tagged photosynthetic bacterial reaction centers (RCs) isolated from Rhodobacter (Rb.) sphaeroides. Mössbauer spectroscopy and nuclear inelastic scattering of synchrotron radiation (NIS) were applied to monitor the arrangement and flexibility of the NHFe binding site. In His-tagged RCs, NHFe was stabilized only in a high spin ferrous state. Its hyperfine parameters (IS=1.06±0.01mm/s and QS=2.12±0.01mm/s), and Debye temperature (θD0~167K) are comparable to those detected for the high spin state of NHFe in non-His-tagged RCs. For the first time, pure vibrational modes characteristic of NHFe in a high spin ferrous state are revealed. The vibrational density of states (DOS) shows some maxima between 22 and 33meV, 33 and 42meV, and 53 and 60meV and a very sharp one at 44.5meV. In addition, we observe a large contribution of vibrational modes at low energies. This iron atom is directly connected to the protein matrix via all its ligands, and it is therefore extremely sensitive to the collective motions of the RC protein core. A comparison of the DOS spectra of His-tagged and non-His-tagged RCs from Rb. sphaeroides shows that in the latter case the spectrum was overlapped by the vibrations of the heme iron of residual cytochrome c2, and a low spin state of NHFe in addition to its high spin one. This enabled us to pin-point vibrations characteristic for the low spin state of NHFe

Multipole vector solitons in nonlocal nonlinear media

We show that multipole solitons can be made stable via vectorial coupling in bulk nonlocal nonlinear media. Such vector solitons are composed of mutually incoherent nodeless and multipole components jointly inducing a nonlinear refractive index profile. We found that stabilization of the otherwise highly unstable multipoles occurs below a maximum energy flow. Such threshold is determined by the nonlocality degree.Comment: 13 pages, 3 figures, to appear in Optics Letter

The landscape of Neandertal ancestry in present-day humans

Analyses of Neandertal genomes have revealed that Neandertals have contributed genetic variants to modern humans1–2. The antiquity of Neandertal gene flow into modern humans means that regions that derive from Neandertals in any one human today are usually less than a hundred kilobases in size. However, Neandertal haplotypes are also distinctive enough that several studies have been able to detect Neandertal ancestry at specific loci1,3–8. Here, we have systematically inferred Neandertal haplotypes in the genomes of 1,004 present-day humans12. Regions that harbor a high frequency of Neandertal alleles in modern humans are enriched for genes affecting keratin filaments suggesting that Neandertal alleles may have helped modern humans adapt to non-African environments. Neandertal alleles also continue to shape human biology, as we identify multiple Neandertal-derived alleles that confer risk for disease. We also identify regions of millions of base pairs that are nearly devoid of Neandertal ancestry and enriched in genes, implying selection to remove genetic material derived from Neandertals. Neandertal ancestry is significantly reduced in genes specifically expressed in testis, and there is an approximately 5-fold reduction of Neandertal ancestry on chromosome X, which is known to harbor a disproportionate fraction of male hybrid sterility genes20–22. These results suggest that part of the reduction in Neandertal ancestry near genes is due to Neandertal alleles that reduced fertility in males when moved to a modern human genetic background

Measurements of nitric oxide and ammonia soil fluxes from a wet savanna ecosystem site in West Africa during the DACCIWA field campaign

Biogenic fluxes from soil at a local and regional scale are crucial to study air pollution and climate. Here we present field measurements of soil fluxes of nitric oxide (NO) and ammonia (NH3) observed over four different land cover types, i.e. bare soil, grassland, maize field, and forest, at an inland rural site in Benin, West Africa, during the DACCIWA field campaign in June and July 2016. At the regional scale, urbanization and a massive growth in population in West Africa have been causing a strong increase in anthropogenic emissions. Anthropogenic pollutants are transported inland and northward from the megacities located on the coast, where the reaction with biogenic emissions may lead to enhanced ozone production outside urban areas, as well as secondary organic aerosol formation, with detrimental effects on humans, animals, natural vegetation, and crops. We observe NO fluxes up to 48.05 ngNm 2 s 1. NO fluxes averaged over all land cover types are 4:79 5:59 ngNm 2 s 1, and maximum soil emissions of NO are recorded over bare soil. NH3 is dominated by deposition for all land cover types. NH3 fluxes range between 6:59 and 4.96 ngNm 2 s 1. NH3 fluxes averaged over all land cover types are 0:911:27 ngNm 2 s 1, and maximum NH3 deposition is measured over bare soil. The observations show high spatial variability even for the same soil type, same day, and same meteorological conditions. We compare point daytime average measurements of NO emissions recorded during the field campaign with those simulated by GEOS-Chem (Goddard Earth Observing System Chemistry Model) for the same site and find good agreement. In an attempt to quantify NO emissions at the regional and national scale, we also provide a tentative estimate of total NO emissions for the entire country of Benin for the month of July using two distinct methods: upscaling point measurements and using the GEOS-Chem model. The two methods give similar results: 1:170:6 and 1.44 GgN month 1, respectively. Total NH3 deposition estimated by upscaling point measurements for the month of July is 0.21 GgN month1

Accelerated Profile HMM Searches

Profile hidden Markov models (profile HMMs) and probabilistic inference methods have made important contributions to the theory of sequence database homology search. However, practical use of profile HMM methods has been hindered by the computational expense of existing software implementations. Here I describe an acceleration heuristic for profile HMMs, the “multiple segment Viterbi” (MSV) algorithm. The MSV algorithm computes an optimal sum of multiple ungapped local alignment segments using a striped vector-parallel approach previously described for fast Smith/Waterman alignment. MSV scores follow the same statistical distribution as gapped optimal local alignment scores, allowing rapid evaluation of significance of an MSV score and thus facilitating its use as a heuristic filter. I also describe a 20-fold acceleration of the standard profile HMM Forward/Backward algorithms using a method I call “sparse rescaling”. These methods are assembled in a pipeline in which high-scoring MSV hits are passed on for reanalysis with the full HMM Forward/Backward algorithm. This accelerated pipeline is implemented in the freely available HMMER3 software package. Performance benchmarks show that the use of the heuristic MSV filter sacrifices negligible sensitivity compared to unaccelerated profile HMM searches. HMMER3 is substantially more sensitive and 100- to 1000-fold faster than HMMER2. HMMER3 is now about as fast as BLAST for protein searches

Sources of variation in simulated ecosystem carbon storage capacity from the 5th Climate Model Intercomparison Project (CMIP5)

Ecosystem carbon (C) storage strongly regulates climate-C cycle feedback and is largely determined by both C residence time and C input from net primary productivity (NPP). However, spatial patterns of ecosystem C storage and its variation have not been well quantified in earth system models (ESMs), which is essential to predict future climate change and guide model development. We intended to evaluate spatial patterns of ecosystem C storage capacity simulated by ESMs as part of the 5th Climate Model Intercomparison Project (CMIP5) and explore the sources of multi-model variation from mean residence time (MRT) and/or C inputs. Five ESMs were evaluated, including C inputs (NPP and [gross primary productivity] GPP), outputs (autotrophic/heterotrophic respiration) and pools (vegetation, litter and soil C). ESMs reasonably simulated the NPP and NPP/GPP ratio compared with Moderate Resolution Imaging Spectroradiometer (MODIS) estimates except NorESM. However, all of the models significantly underestimated ecosystem MRT, resulting in underestimation of ecosystem C storage capacity. CCSM predicted the lowest ecosystem C storage capacity (~10 kg C m−2) with the lowest MRT values (14 yr), while MIROC-ESM estimated the highest ecosystem C storage capacity (~36 kg C m−2) with the longest MRT (44 yr). Ecosystem C storage capacity varied considerably among models, with larger variation at high latitudes and in Australia, mainly resulting from the differences in the MRTs across models. Our results indicate that additional research is needed to improve post-photosynthesis C-cycle modelling, especially at high latitudes, so that ecosystem C residence time and storage capacity can be appropriately simulated

The domain architecture of large guanine nucleotide exchange factors for the small GTP-binding protein Arf

BACKGROUND: Small G proteins, which are essential regulators of multiple cellular functions, are activated by guanine nucleotide exchange factors (GEFs) that stimulate the exchange of the tightly bound GDP nucleotide by GTP. The catalytic domain responsible for nucleotide exchange is in general associated with non-catalytic domains that define the spatio-temporal conditions of activation. In the case of small G proteins of the Arf subfamily, which are major regulators of membrane trafficking, GEFs form a heterogeneous family whose only common characteristic is the well-characterized Sec7 catalytic domain. In contrast, the function of non-catalytic domains and how they regulate/cooperate with the catalytic domain is essentially unknown. RESULTS: Based on Sec7-containing sequences from fully-annotated eukaryotic genomes, including our annotation of these sequences from Paramecium, we have investigated the domain architecture of large ArfGEFs of the BIG and GBF subfamilies, which are involved in Golgi traffic. Multiple sequence alignments combined with the analysis of predicted secondary structures, non-structured regions and splicing patterns, identifies five novel non-catalytic structural domains which are common to both subfamilies, revealing that they share a conserved modular organization. We also report a novel ArfGEF subfamily with a domain organization so far unique to alveolates, which we name TBS (TBC-Sec7). CONCLUSION: Our analysis unifies the BIG and GBF subfamilies into a higher order subfamily, which, together with their being the only subfamilies common to all eukaryotes, suggests that they descend from a common ancestor from which species-specific ArfGEFs have subsequently evolved. Our identification of a conserved modular architecture provides a background for future functional investigation of non-catalytic domains