The objective of the Earth Cloud, Aerosol, and Radiation Explorer (EarthCARE) mission is to infer attributes of cloud, aerosol, precipitation, and radiation from observations made by four complementary instruments. This requires the development of single-instrument and multiple-instrument (i.e. synergistic) retrieval algorithms that employ measurements made by one, or more, of EarthCARE's cloud-profiling radar (CPR), atmospheric lidar (ATLID), and multi-spectral imager (MSI); its broadband radiometer (BBR) places the retrieved quantities in the context of the surface–atmosphere radiation budget. To facilitate the development and evaluation of ESA's EarthCARE production model prior to launch, sophisticated instrument simulators were developed to produce realistic synthetic EarthCARE measurements for simulated conditions provided by cloud-resolving models. While acknowledging that the physical and radiative representations of cloud, aerosol, and precipitation in the test scenes are based on numerical models, the opportunity to perform detailed evaluations wherein the “truth” is known provides insights into the performance of EarthCARE's instruments and retrieval algorithms. This level of omniscience will not be available for the evaluation of in-flight EarthCARE retrieval products, even during validation activities coordinated with ground-based and airborne measurements. In this study, we compare EarthCARE retrieval products both statistically across all simulated scenes and from a specific time series from a single scene.
For ice clouds, it is shown that retrieved profiles of ice water content and effective particle size made by the ATLID-CPR-MSI cloud, aerosols, and precipitation (ACM-CAP) synergistic algorithm are consistently more accurate than those from its single-instrument counterparts. While liquid clouds are often difficult to detect from satellite-borne sensors, especially for multi-layered clouds, ACM-CAP benefits from combined constraints from lidar backscatter, solar radiances, and radar-path-integrated attenuation but still exhibits non-trivial random error. For precipitation retrievals, the CPR cloud and precipitation product (C-CLD) and ACM-CAP have a similar performance when well-constrained by CPR measurements. The greatest differences are in coverage, with ACM-CAP reporting retrievals in the melting layer, and in heavy precipitation, where CPR signals are dominated by multiple scattering and attenuation. Aerosol retrievals from ATLID compensate for a high degree of measurement noise in a number of ways, with the ATLID extinction, backscatter, and depolarisation (A-EBD) product and ACM-CAP demonstrating similar performance. The multi-spectral imager (MSI) cloud optical properties (M-COP) product performs very well for unambiguous cloud layers. Similarly, the MSI aerosol optical thickness (M-AOT) product performs well when radiances are unaffected by cloud, but both products provide little information about vertical profiles of properties. Finally, a summary of the performance of all retrieval products and their random errors is provided.
Weniger anzeigenThe Earth Cloud, Aerosol and Radiation Explorer (EarthCARE) is a combination of multiple active and passive instruments on a single platform. The Atmospheric Lidar (ATLID) provides vertical information of clouds and aerosol particles along the satellite track. In addition, the Multi-Spectral Imager (MSI) collects multi-spectral information from the visible to the infrared wavelengths over a swath width of 150 km across the track. The ATLID–MSI Column Products processor (AM-COL) described in this paper combines the high vertical resolution of the lidar along track and the horizontal resolution of the imager across track to better characterize a three-dimensional scene. ATLID Level 2a (L2a) data from the ATLID Layer Products processor (A-LAY), MSI L2a data from the MSI Cloud Products processor (M-CLD) and the MSI Aerosol Optical Thickness processor (M-AOT), and MSI Level 1c (L1c) data are used as input to produce the synergistic columnar products: the ATLID–MSI Cloud Top Height (AM-CTH) and the ATLID–MSI Aerosol Column Descriptor (AM-ACD). The coupling of ATLID (measuring at 355 nm) and MSI (at ≥670 nm) provides multi-spectral observations of the aerosol properties. In particular, the Ångström exponent from the spectral aerosol optical thickness (AOT 355/670 nm) adds valuable information for aerosol typing. The AOT across track, the Ångström exponent and the dominant aerosol type are stored in the AM-ACD product. The accurate detection of the cloud top height (CTH) with lidar is limited to the ATLID track. The difference in the CTH detected by ATLID and retrieved by MSI is calculated along track. The similarity of MSI pixels across track with those along track is used to transfer the calculated CTH difference to the entire MSI swath. In this way, the accuracy of the CTH is increased to achieve the EarthCARE mission's goal of deriving the radiative flux at the top of the atmosphere with an accuracy of 10 W m−2 for a 100 km2 snapshot view of the atmosphere. The synergistic CTH difference is stored in the AM-CTH product. The quality status is provided with the products. It depends, e.g., on day/night conditions and the presence of multiple cloud layers. The algorithm was successfully tested using the common EarthCARE test scenes. Two definitions of the CTH from the model truth cloud extinction fields are compared: an extinction-based threshold of 20 Mm−1 provides the geometric CTH, and a cloud optical thickness threshold of 0.25 describes the radiative CTH. The first CTH definition was detected with ATLID and the second one with MSI. The geometric CTH is always higher than or equal to the radiative CTH.
Weniger anzeigenMonolayers of transition metal dichalcogenides (TMDCs) are direct-gap semiconductors with strong light–matter interactions featuring tightly bound excitons, while plasmonic crystals (PCs), consisting of metal nanoparticles that act as meta-atoms, exhibit collective plasmon modes and allow one to tailor electric fields on the nanoscale. Recent experiments show that TMDC-PC hybrids can reach the strong-coupling limit between excitons and plasmons, forming new quasiparticles, so-called plexcitons. To describe this coupling theoretically, we develop a self-consistent Maxwell-Bloch theory for TMDC-PC hybrid structures, which allows us to compute the scattered light in the near- and far-fields explicitly and provide guidance for experimental studies. One of the key findings of the developed theory is the necessity to differentiate between bright and originally momentum-dark excitons. Our calculations reveal a spectral splitting signature of strong coupling of more than 100 meV in gold-MoSe2 structures with 30 nm nanoparticles, manifesting in a hybridization of the plasmon mode with momentum-dark excitons into two effective plexcitonic bands. The semianalytical theory allows us to directly infer the characteristic asymmetric line shape of the hybrid spectra in the strong coupling regime from the energy distribution of the momentum-dark excitons. In addition to the hybridized states, we find a remaining excitonic mode with significantly smaller coupling to the plasmonic near-field, emitting directly into the far-field. Thus, hybrid spectra in the strong coupling regime can contain three emission peaks.
Weniger anzeigenIn this study, we examine the surface-derived electronic and chemical structures of nanostructured GaRh alloys as a model system for supported catalytically active liquid metal solutions (SCALMS), a novel catalyst candidate for dehydrogenation reactions that are important for the petrochemical and hydrogen energy industry. It is reported that under ambient conditions, SCALMS tends to form a gallium oxide shell, which can be removed by an activation treatment at elevated temperatures and hydrogen flow to enhance the catalytic reactivity. We prepared a 7 at. % Rh containing the GaRh sample and interrogated the evolution of the surface chemical and electronic structure by photoelectron spectroscopy (complemented by scanning electron microscopy) upon performing surface oxidation and (activation treatment mimicking) annealing treatments in ultrahigh vacuum conditions. The initially pronounced Rh 4d and Fermi level-derived states in the valence band spectra disappear upon oxidation (due to formation of a GaOx shell) but reemerge upon annealing, especially for temperatures of 600 °C and above, i.e., when the GaOx shell is efficiently being removed and the Ga matrix is expected to be liquid. At the same temperature, new spectroscopic features at both the high and low binding energy sides of the Rh 3d5/2 spectra are observed, which we attribute to new GaRh species with depleted and enriched Rh contents, respectively. A liquefied and GaOx-free surface is also expected for GaRh SCALMS at reaction conditions, and thus the revealed high-temperature properties of the GaRh alloy provide insights about respective catalysts at work.
Weniger anzeigenChromium (Cr) leached from iron (Fe) (oxyhydr)oxide-rich tropical laterites can substantially impact downstream groundwater, ecosystems, and human health. However, its partitioning into mineral hosts, its binding, oxidation state, and potential release are poorly defined. This is in part due to the current lack of well-designed and validated Cr-specific sequential extraction procedures (SEPs) for laterites. To fill this gap, we have (i) first optimized a Cr SEP for Fe (oxyhydr)oxide-rich laterites using synthetic and natural Cr-bearing minerals and laterite references, (ii) used a complementary suite of techniques and critically evaluated existing non-laterite and non-Cr-optimized SEPs, compared to our optimized SEP, and (iii) confirmed the efficiency of our new SEP through analyses of laterites from the Philippines. Our results show that other SEPs inadequately leach Cr host phases and underestimate the Cr fractions. Our SEP recovered up to seven times higher Cr contents because it (a) more efficiently dissolves metal-substituted Fe phases, (b) quantitatively extracts adsorbed Cr, and (c) prevents overestimation of organic Cr in laterites. With this new SEP, we can estimate the mineral-specific Cr fractionation in Fe-rich tropical soils more quantitatively and thus improve our knowledge of the potential environmental impacts of Cr from lateritic areas.
Weniger anzeigenNaturally available, stable, and heavy water molecules such as HDO and HO have a lower saturation vapour pressure than the most abundant light water molecule HO; therefore, these heavy water molecules preferentially condense and rain out during cloud formation. Stable water isotope observations thus have the potential to provide information on cloud processes in the trade-wind region, in particular when combined with high-resolution model simulations. In order to evaluate this potential, nested COSMOiso (isotope-enabled Consortium for Small Scale Modelling; Steppeler et al., 2003; Pfahl et al., 2012) simulations with explicit convection and horizontal grid spacings of 10, 5, and 1 km were carried out in this study over the tropical Atlantic for the time period of the EUREC4A (Elucidating the role of clouds-circulation coupling in climate; Stevens et al., 2021) field experiment. The comparison to airborne in situ and remote sensing observations shows that the three simulations are able to distinguish between different mesoscale cloud organisation patterns as well as between periods with comparatively high and low rain rates. Cloud fraction and liquid water content show a better agreement with aircraft observations with higher spatial resolution, because they show strong spatial variations on the scale of a few kilometres. A low-level cold-dry bias, including too depleted vapour in the subcloud and cloud layer and too enriched vapour in the free troposphere, is found in all three simulations. Furthermore, the simulated secondary isotope variable d-excess in vapour is overestimated compared to observations. Special attention is given to the cloud base level, which is the formation altitude of shallow cumulus clouds. The temporal variability of the simulated isotope variables at cloud base agrees reasonably well with observations, with correlations of the flight-to-flight data as high as 0.7 for δ2H and d-excess. A close examination of isotopic characteristics under precipitating clouds, non-precipitating clouds, clear-sky and dry-warm patches at the altitude of cloud base shows that these different environments are represented faithfully in the model with similar frequencies of occurrence, isotope signals, and specific-humidity anomalies as found in the observations. Furthermore, it is shown that the δ2H of cloud base vapour at the hourly timescale is mainly controlled by mesoscale transport and not by local microphysical processes, while the d-excess is mainly controlled by large-scale drivers. Overall, this evaluation of COSMOiso, including the isotopic characterisation of different cloud base environments, suggests that the simulations can be used for investigating the role of atmospheric circulations on different scales for controlling the formation of shallow cumulus clouds in the trade-wind region, as will be done in part 2 of this study.
Weniger anzeigenSystematic structural studies of model oligopeptides revealed important aspects of protein folding and offered design principles to access non-natural materials. In the same way, the rules that regulate glycan folding could be established by studying synthetic oligosaccharide models. However, their analysis is often limited due to the synthetic and analytical complexity. By utilizing a glycan capable of spontaneously folding into a hairpin conformation as a model system, we investigated the factors that contribute to its conformational stability in aqueous solution. The modular design of the hairpin model featured a trisaccharide turn unit and two β-1,4-oligoglucoside stacking strands that allowed for systematic chemical modifications of the glycan sequence, including the introduction of NMR labels and staples. Nuclear magnetic resonance assisted by molecular dynamics simulations revealed that stereoelectronic effects and multiple glycan–glycan interactions are the major determinants of folding stabilization. Chemical modifications in the glycan primary sequence (e.g., strand elongation) can be employed to fine-tune the rigidity of structural motifs distant from the modification sites. These results could inspire the design of other glycan architectures, with implications in glycobiology and material sciences.
Weniger anzeigenThis study presents the simulated response of regional climate and the oxygen isotopic composition of precipitation (δ18Op) to different along-strike topographic evolution scenarios. These simulations are conducted to determine if the previously hypothesized diachronous surface uplift in the Western and Eastern Alps would produce δ18Op signals in the geologic record that are sufficiently large and distinct to be detected using stable isotope paleoaltimetry. We present a series of topographic sensitivity experiments conducted with the water-isotope-tracking atmospheric general circulation model (GCM) ECHAM5-wiso. The topographic scenarios are created from the variation of two free parameters, (1) the elevation of the Western–Central Alps and (2) the elevation of the Eastern Alps. The results indicate Δδ18Op values (i.e., the difference between δ18Op values at the low- and high-elevation sites) of up to −8 ‰ along the strike of the Alps for the diachronous uplift scenarios, primarily due to changes in orographic precipitation and adiabatic lapse rate driven localized changes in near-surface variables. These simulated magnitudes of Δδ18Op values suggest that the expected isotopic signal would be significant enough to be preserved and measured in geologic archives. Moreover, the simulated slight δ18Op differences of 1 ‰–2 ‰ across the low-elevation sites support the use of the δ–δ paleoaltimetry approach and highlight the importance of sampling far-field low-elevation sites to differentiate between the different surface uplift scenarios. The elevation-dependent rate of change in δ18Op (“isotopic lapse rate”) varies depending on the topographic configuration and the extent of the surface uplift. Most of the changes are significant (e.g., −1.04 ‰ km−1 change with slope error of ±0.09 ‰ km−1), while others were within the range of the statistical uncertainties (e.g., −0.15 ‰ km−1 change with slope error of ±0.13 ‰ km−1). The results also highlight the plausible changes in atmospheric circulation patterns and associated changes in moisture transport pathways in response to changes in the topography of the Alps. These large-scale atmospheric dynamics changes can complicate the underlying assumption of stable isotope paleoaltimetry and therefore require integration with paleoclimate modeling to ensure accurate reconstruction of the paleoelevation of the Alps.
Weniger anzeigenAt the interface of Chinese diaspora studies, migration studies, and urban studies, this introduction argues for a shift towards city-based migration studies. The city is understood here not as a self-contained social cosmos, but as a globally and socially embedded urban level that opens up a more flexible perspective on the unfolding of migration processes at the micro, meso, and macro levels. It begins with a brief overview of recent trends in Chinese diaspora studies, global migration and urbanisation trends, and debates in critical geography on multi-scale urban theories. Then, it raises the question of the empirical feasibility of such an approach and argues for conceptualising migrants’ agency as a starting point for migration research, rather than pursuing a policy-driven, normative approach. Finally, it presents the five empirical contributions to this Special Issue. They are based on fieldwork in Paris, Berlin, Manchester (UK), Mexico City, Lagos, Gaborone, and Windhoek.
Weniger anzeigenIntroduction/objective: Suppression of the SOS response in combination with drugs damaging DNA has been proposed as a potential target to tackle antimicrobial resistance. The SOS response is the pathway used to repair bacterial DNA damage induced by antimicrobials such as quinolones. The extent of lexA-regulated protein expression and other associated systems under pressure of agents that damage bacterial DNA in clinical isolates remains unclear. The aim of this study was to assess the impact of this strategy consisting on suppression of the SOS response in combination with quinolones on the proteome profile of Escherichia coli clinical strains.
Materials and methods: Five clinical isolates of E. coli carrying different chromosomally- and/or plasmid-mediated quinolone resistance mechanisms with different phenotypes were selected, with E. coli ATCC 25922 as control strain. In addition, from each clinical isolate and control, a second strain was created, in which the SOS response was suppressed by deletion of the recA gene. Bacterial inocula from all 12 strains were then exposed to 1xMIC ciprofloxacin treatment (relative to the wild-type phenotype for each isogenic pair) for 1 h. Cell pellets were collected, and proteins were digested into peptides using trypsin. Protein identification and label-free quantification were done by liquid chromatography-mass spectrometry (LC–MS) in order to identify proteins that were differentially expressed upon deletion of recA in each strain. Data analysis and statistical analysis were performed using the MaxQuant and Perseus software.
Results: The proteins with the lowest expression levels were: RecA (as control), AphA, CysP, DinG, DinI, GarL, PriS, PsuG, PsuK, RpsQ, UgpB and YebG; those with the highest expression levels were: Hpf, IbpB, TufB and RpmH. Most of these expression alterations were strain-dependent and involved DNA repair processes and nucleotide, protein and carbohydrate metabolism, and transport. In isolates with suppressed SOS response, the number of underexpressed proteins was higher than overexpressed proteins.
Conclusion: High genomic and proteomic variability was observed among clinical isolates and was not associated with a specific resistant phenotype. This study provides an interesting approach to identify new potential targets to combat antimicrobial resistance.
Weniger anzeigenFuture dynamics of biological invasions are highly uncertain because they depend on multiple social–ecological drivers. We used a scenario-based approach to explore potential management options for invasive species in Europe. During two workshops involving a multidisciplinary team of experts, we developed a management strategy arranged into 19 goals relating to policy, research, public awareness, and biosecurity. We conceived solutions for achieving these goals under different plausible future scenarios, and identified four interrelated recommendations around which any long-term strategy for managing invasive species can be structured: (1) a European biosecurity regime, (2) a dedicated communication strategy, (3) data standardization and management tools, and (4) a monitoring and assessment system. Finally, we assessed the feasibility of the management strategy and found substantial differences among scenarios. Collectively, our results indicate that it is time for a new strategy for managing biological invasions in Europe, one that is based on a more integrative approach across socioeconomic sectors and countries.
Weniger anzeigenMemory effects emerge as a fundamental consequence of dimensionality reduction when low-dimensional observables are used to describe the dynamics of complex many-body systems. In the context of molecular dynamics (MD) data analysis, accounting for memory effects using the framework of the generalized Langevin equation (GLE) has proven efficient, accurate, and insightful, particularly when working with high-resolution time series data. However, in experimental systems, high-resolution data are often unavailable, raising questions about the impact of the data resolution on the estimated GLE parameters. This study demonstrates that direct memory extraction from time series data remains accurate when the discretization time is below the memory time. To obtain memory functions reliably, even when the discretization time exceeds the memory time, we introduce a Gaussian Process Optimization (GPO) scheme. This scheme minimizes the deviation of discretized two-point correlation functions between time series data and GLE simulations and is able to estimate accurate memory kernels as long as the discretization time stays below the longest time scale in the data, typically the barrier crossing time.
Weniger anzeigenBimetallic Al(III) catalysis mediates thioanhydride/epoxide copolymerisation at greatly improved rates and monomer tolerance than analogous Cr(III) catalysis. Moving to sulfurated monomers furthermore generally improves rates and selectivites.
Background
We investigated the effect of a 5-day low-dose ritonavir therapy, as it is used in the treatment of COVID-19 with nirmatrelvir/ritonavir, on the pharmacokinetics of three factor Xa inhibitors (FXaI). Concurrently, the time course of the activities of the cytochromes P450 (CYP) 3A4, 2C19, and 2D6 was assessed.
Methods
In an open-label, fixed sequence clinical trial, the effect and duration of a 5-day oral ritonavir (100 mg twice daily) treatment on the pharmacokinetics of three oral microdosed FXaI (rivaroxaban 25 µg, apixaban 25 µg, and edoxaban 50 µg) and microdosed probe drugs (midazolam 25 µg, yohimbine 50 µg, and omeprazole 100 µg) was evaluated in eight healthy volunteers. The plasma concentrations of all drugs were quantified using validated liquid chromatography–tandem mass spectrometry (LC-MS/MS) methods and pharmacokinetics were analysed using non-compartmental analyses.
Results
Ritonavir increased the exposure of apixaban, edoxaban, and rivaroxaban, but to a different extent the observed area under the plasma concentration–time curve (geometric mean ratio 1.29, 1.46, and 1.87, respectively). A strong CYP3A4 inhibition (geometric mean ratio > 10), a moderate CYP2C19 induction 2 days after ritonavir (0.64), and no alteration of CYP2D6 were observed. A CYP3A4 recovery half-life of 2.3 days was determined.
Conclusion
This trial with three microdosed FXaI suggests that at most the rivaroxaban dose should be reduced during short-term ritonavir, and only in patients receiving high maintenance doses. Thorough time series analyses demonstrated differential effects on three different drug-metabolising enzymes over time with immediate profound inhibition of CYP3A4 and only slow recovery after discontinuation.
Clinical Trial Registration
EudraCT number: 2021-006643-39.
Weniger anzeigenDeviations between macrorheological and particle-based microrheological measurements are often considered to be a nuisance and neglected. We study aqueous poly(ethylene oxide) (PEO) hydrogels for varying PEO concentrations and chain lengths that contain microscopic tracer particles and show that these deviations reveal the nanoscopic viscoelastic properties of the particle–hydrogel interface. Based on the transient Stokes equation, we first demonstrate that the deviations are not due to finite particle radius, compressibility, or surface-slip effects. Small-angle neutron scattering rules out hydrogel heterogeneities. Instead, we show that a generalized Stokes–Einstein relation, accounting for an interfacial shell around tracers with viscoelastic properties that deviate from bulk, consistently explains our macrorheological and microrheological measurements. The extracted shell diameter is comparable to the PEO end-to-end distance, indicating the importance of dangling chain ends. Our methodology reveals the nanoscopic interfacial rheology of hydrogels and is applicable to different kinds of viscoelastic fluids and particles.
Weniger anzeigenIn this paper I argue that the pervasive reality of unjust heterosex necessitates greater attention to the concept of “sexual fluency” (Cahill 2014). This paper elaborates on what it means to be a sexually fluent and disfluent subject, and its broader ethical and political significance. As part of this discussion, I explore the relationship between sexual (dis)fluency and embedded imaginaries, and critically reflect on the promise and limitations of particular interventions to disrupt patterns of sexual disfluency among sexual actors.
Weniger anzeigenThis study examined the effects of a 3-strain Bacillus-based probiotic (BP; Bacillus amyloliquefaciens and two Bacillus subtilis) in broiler diets with different rye levels on performance, mucus, viscosity, and nutrient digestibility. We distributed 720 one-d-old female broilers into 72 pens and designed nine diets using a 3 × 3 factorial approach, varying BP levels (0, 1.2 × 106, and 1.2 × 107 CFU/g) and rye concentrations (0, 200, 400 g/kg). On d 35, diets with 200 or 400 g/kg rye reduced broiler weight gain (BWG). Diets with 400 g/kg rye had the highest FCR, while rye-free diets had the lowest (p ≤0.05). Adding BP increased feed intake and BWG in weeks two and three (p ≤0.05). It should be noted that the overall performance fell below the goals of the breed. Including rye in diets reduced the coefficient of apparent ileal digestibility (CAID) for protein, ether extract (EE), calcium, phosphorus, and all amino acids (p ≤0.05). Rye-free diets exhibited the highest CAID for all nutrients, except for methionine, EE, and calcium, while diets with 400 g/kg of rye demonstrated the lowest CAID (p ≤0.05). BP in diets decreased phosphorus CAID (p ≤0.05). Diets containing 1.2 × 107 CFU/g (10X) of BP exhibited higher CAID of methionine than the other two diets (p ≤0.05). Diets containing 10X of BP showed higher CAID of cysteine than diets with no BP (p ≤0.05). Ileal viscosity increased as the inclusion level of rye in the diets increased (p ≤0.05). The ileal concentration of glucosamine in chickens fed diets with 400 g/kg of rye was higher than in those fed diets with no rye (p ≤0.05). Furthermore, ileal galactosamine concentrations were elevated in diets with 200 and 400 g/kg of rye when compared to rye-free diets (p ≤0.05). However, BP in diets had no impact on ileal viscosity, galactosamine, or glucosamine (p > 0.05). In conclusion, the applied Bacillus strains appeared to have a limited capacity to produce arabinoxylan-degrading enzymes and were only partially effective in mitigating the negative impacts of rye arabinoxylans on broilers.
Weniger anzeigenTriphenylpnictogens EPh3 (E = N, P, As, Sb, Bi) are able to displace the perfluorinated Cp* ligand in [Rh(COD)(C5(CF3)5)] (COD = 1,5-cyclooctadiene) in up to quantitative yield. The resulting ionic products contain [C5(CF3)5]− as uncoordinated counter anion. The cations feature [Rh(COD)]+ fragments, coordinated by one (N, Bi), two (P, As) or three (Sb) triphenylpnictogen moieties. Whereas coordination via the pnictogen is observed for P, As and Sb, π-coordination of the aryl rings is observed for N and Bi.
Weniger anzeigenFor a detailed understanding of chemical processes in nature and industry, we need accurate models of chemical reactions in complex environments. While Eyring transition state theory is commonly used for modeling chemical reactions, it is most accurate for small molecules in the gas phase. A wide range of alternative rate theories exist that can better capture reactions involving complex molecules and environmental effects. However, they require that the chemical reaction is sampled by molecular dynamics simulations. This is a formidable challenge since the accessible simulation timescales are many orders of magnitude smaller than typical timescales of chemical reactions. To overcome these limitations, rare event methods involving enhanced molecular dynamics sampling are employed. In this work, thermal isomerization of retinal is studied using tight-binding density functional theory. Results from transition state theory are compared to those obtained from enhanced sampling. Rates obtained from dynamical reweighting using infrequent metadynamics simulations were in close agreement with those from transition state theory. Meanwhile, rates obtained from application of Kramers' rate equation to a sampled free energy profile along a torsional dihedral reaction coordinate were found to be up to three orders of magnitude higher. This discrepancy raises concerns about applying rate methods to one-dimensional reaction coordinates in chemical reactions.
Weniger anzeigen