To estimate the depth errors in a subsurface model obtained from the inversion of seismic data, the stationary‐phase approximation in a two‐dimensional constant‐velocity model with a dipped reflector ...is applied to migration with a time‐shift extension. This produces two asymptotic solutions: one is a straight line, and the other is a curve. If the velocity differs from the true one, a closed‐form expression of the depth error follows from the depth and apparent dip of the reflector as well as the position of the amplitude peak at a non‐zero time shift, where the two solutions meet and the extended migration image focuses. The results are compared to finite‐frequency results from a finite‐difference code. A two‐dimensional synthetic example with a salt diapir illustrates how depth errors can be estimated in an inhomogeneous model after inverting the seismic data for the velocity model.
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FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
Temporal dispersion correction of second‐order finite‐difference time stepping for numerical wave propagation modelling exploits the fact that the discrete operator is exact but for the wrong ...frequencies. Mapping recorded traces to the correct frequencies removes the numerical error. Most of the implementations employ forward and inverse Fourier transforms. Here, it is noted that these can be replaced by a series expansion involving higher time derivatives of the data. Its implementation by higher‐order finite differencing can be sensitive to numerical noise, but this can be suppressed by enlarging the stencil. Tests with the finite‐element method on a homogeneous acoustic problem with an exact solution show that the method can achieve the same accuracy as higher‐order time stepping, similar to that obtained with Fourier transforms. The same holds for an inhomogeneous problem with topography where the solution on a very fine mesh is used as reference. The series approach costs less than dispersion correction with the Fourier method and can be used on the fly during the time stepping. It does, however, require a wavelet that is sufficiently many times differentiable in time.
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FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
Finite elements with polynomial basis functions on the simplex with a symmetric distribution of nodes should have a unique polynomial representation. Unisolvence not only requires that the number of ...nodes equals the number of independent polynomials spanning a polynomial space of a given degree, but also that the Vandermonde matrix controlling their mapping to the Lagrange interpolating polynomials can be inverted. Here, a necessary condition for unisolvence is presented for polynomial spaces that have non-decreasing degrees when going from the edges and the various faces to the interior of the simplex. It leads to a proof of a conjecture on a necessary condition for unisolvence, requiring the node pattern to be the same as that of the regular simplex.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
This Article describes the electron transfer (ET) kinetics in complexes of CdS nanorods (CdS NRs) and FeFe-hydrogenase I from Clostridium acetobutylicum (CaI). In the presence of an electron donor, ...these complexes produce H2 photochemically with quantum yields of up to 20%. Kinetics of ET from CdS NRs to CaI play a critical role in the overall photochemical reactivity, as the quantum efficiency of ET defines the upper limit on the quantum yield of H2 generation. We investigated the competitiveness of ET with the electron relaxation pathways in CdS NRs by directly measuring the rate and quantum efficiency of ET from photoexcited CdS NRs to CaI using transient absorption spectroscopy. This technique is uniquely suited to decouple CdS→CaI ET from the processes occurring in the enzyme during H2 production. We found that the ET rate constant (k ET) and the electron relaxation rate constant in CdS NRs (k CdS) were comparable, with values of 107 s–1, resulting in a quantum efficiency of ET of 42% for complexes with the average CaI:CdS NR molar ratio of 1:1. Given the direct competition between the two processes that occur with similar rates, we propose that gains in efficiencies of H2 production could be achieved by increasing k ET and/or decreasing k CdS through structural modifications of the nanocrystals. When catalytically inactive forms of CaI were used in CdS–CaI complexes, ET behavior was akin to that observed with active CaI, demonstrating that electron injection occurs at a distal iron–sulfur cluster and is followed by transport through a series of accessory iron–sulfur clusters to the active site of CaI. Using insights from this time-resolved spectroscopic study, we discuss the intricate kinetic pathways involved in photochemical H2 generation in CdS–CaI complexes, and we examine how the relationship between the electron injection rate and the other kinetic processes relates to the overall H2 production efficiency.
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IJS, KILJ, NUK, PNG, UL, UM
Hydrogenases couple electrochemical potential to the reversible chemical transformation of H2 and protons, yet the reaction mechanism and composition of intermediates are not fully understood. In ...this Communication we describe the biophysical properties of a hydride-bound state (Hhyd) of the FeFe-hydrogenase from Chlamydomonas reinhardtii. The catalytic H-cluster of FeFe-hydrogenase consists of a 4Fe-4S subcluster (4Fe-4SH) linked by a cysteine thiol to an azadithiolate-bridged 2Fe subcluster (2FeH) with CO and CN– ligands. Mössbauer analysis and density functional theory (DFT) calculations show that Hhyd consists of a reduced 4Fe-4SH + coupled to a diferrous 2FeH with a terminally bound Fe-hydride. The existence of the Fe-hydride in Hhyd was demonstrated by an unusually low Mössbauer isomer shift of the distal Fe of the 2FeH subcluster. A DFT model of Hhyd shows that the Fe-hydride is part of a H-bonding network with the nearby bridging azadithiolate to facilitate fast proton exchange and catalytic turnover.
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Wave-equation traveltime tomography tries to obtain a subsurface velocity model from seismic data, either passive or active, that explains their traveltimes. A key step is the extraction of ...traveltime differences, or relative phase shifts, between observed and modelled finite-frequency waveforms. A standard approach involves a correlation of the observed and measured waveforms. When the amplitude spectra of the waveforms are identical, the maximum of the correlation is indicative of the relative phase shift. When the amplitude spectra are not identical, however, this argument is no longer valid. We propose an alternative criterion to measure the relative phase shift. This misfit criterion is a weighted norm of the correlation and is less sensitive to differences in the amplitude spectra. For practical application it is important to use a sensitivity kernel that is consistent with the way the misfit is measured. We derive this sensitivity kernel and show how it differs from the standard banana–doughnut sensitivity kernel. We illustrate the approach on a cross-well data set.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
Finite elements with mass lumping allow for explicit time stepping when modelling wave propagation and can be more efficient than finite differences in complex geological settings. In two dimensions ...on quadrilaterals, spectral elements are the obvious choice. Triangles offer more flexibility for meshing, but the construction of polynomial elements is less straightforward. The elements have to be augmented with higher‐degree polynomials in the interior to preserve accuracy after lumping of the mass matrix. With the classic accuracy criterion, triangular elements suitable for mass lumping up to a polynomial degree 9 were found. With a newer, less restrictive criterion, new elements were constructed of degree 5–7. Some of these are more efficient than the older ones. To assess which of all these elements performs best, the acoustic wave equation is solved for a homogeneous model on a square and on a domain with corners, as well as on a heterogeneous example with topography. The accuracy and runtimes are measured using either higher‐order time stepping or second‐order time stepping with dispersion correction. For elements of polynomial degree 2 and higher, the latter is more efficient. Among the various finite elements, the degree‐4 element appears to be a good choice.
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FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
Proton-coupled electron transfer (PCET) is a fundamental process at the core of oxidation–reduction reactions for energy conversion. The FeFe-hydrogenases catalyze the reversible activation of ...molecular H2 through a unique metallocofactor, the H-cluster, which is finely tuned by the surrounding protein environment to undergo fast PCET transitions. The correlation of electronic and structural transitions at the H-cluster with proton-transfer (PT) steps has not been well-resolved experimentally. Here, we explore how modification of the conserved PT network via a Cys → Ser substitution at position 169 proximal to the H-cluster of Chlamydomonas reinhardtii FeFe-hydrogenase (CrHydA1) affects the H-cluster using electron paramagnetic resonance (EPR) and Fourier transform infrared (FTIR) spectroscopy. Despite a substantial decrease in catalytic activity, the EPR and FTIR spectra reveal different H-cluster catalytic states under reducing and oxidizing conditions. Under H2 or sodium dithionite reductive treatments, the EPR spectra show signals that are consistent with a reduced 4Fe-4SH + subcluster. The FTIR spectra showed upshifts of νCO modes to energies that are consistent with an increase in oxidation state of the 2FeH subcluster, which was corroborated by DFT analysis. In contrast to the case for wild-type CrHydA1, spectra associated with Hred and Hsred states are less populated in the Cys → Ser variant, demonstrating that the exchange of −SH with −OH alters how the H-cluster equilibrates among different reduced states of the catalytic cycle under steady-state conditions.
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The epidermis is maintained by multiple stem cell populations whose progeny differentiate along diverse, and spatially distinct, lineages. Here we show that the transcription factor Gata6 controls ...the identity of the previously uncharacterized sebaceous duct (SD) lineage and identify the Gata6 downstream transcription factor network that specifies a lineage switch between sebocytes and SD cells. During wound healing differentiated Gata6
cells migrate from the SD into the interfollicular epidermis and dedifferentiate, acquiring the ability to undergo long-term self-renewal and differentiate into a much wider range of epidermal lineages than in undamaged tissue. Our data not only demonstrate that the structural and functional complexity of the junctional zone is regulated by Gata6, but also reveal that dedifferentiation is a previously unrecognized property of post-mitotic, terminally differentiated cells that have lost contact with the basement membrane. This resolves the long-standing debate about the contribution of terminally differentiated cells to epidermal wound repair.
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IJS, NUK, SBMB, UL, UM, UPUK
Trimethylation of histone H3 at lysine 4 (H3K4me3) is regarded as a hallmark of active human promoters, but it remains unclear how this posttranslational modification links to transcriptional ...activation. Using a
stable
isotope
labeling by
amino acids in
cell culture (SILAC)-based proteomic screening we show that the basal transcription factor TFIID directly binds to the H3K4me3 mark via the plant homeodomain (PHD) finger of TAF3. Selective loss of H3K4me3 reduces transcription from and TFIID binding to a subset of promoters in vivo. Equilibrium binding assays and competition experiments show that the TAF3 PHD finger is highly selective for H3K4me3. In transient assays, TAF3 can act as a transcriptional coactivator in a PHD finger-dependent manner. Interestingly, asymmetric dimethylation of H3R2 selectively inhibits TFIID binding to H3K4me3, whereas acetylation of H3K9 and H3K14 potentiates TFIID interaction. Our experiments reveal crosstalk between histone modifications and the transcription factor TFIID. This has important implications for regulation of RNA polymerase II-mediated transcription in higher eukaryotes.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
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