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The composition of protoplanetary disks, and hence the initial conditions of planet formation, may be strongly influenced by the infall and thermal processing of material during the protostellar phase. Composition of dust and ice in protostellar envelopes, shaped by energetic processes driven by the protostar, serves as the fundamental building material for planets and complex organic molecules. As part of the JWST GO program, "Investigating Protostellar Accretion" (IPA), we observed an intermediate-mass protostar HOPS 370 (OMC2-FIR3) using NIRSpec/IFU and MIRI/MRS. This study presents the gas and ice phase chemical inventory revealed with the JWST in the spectral range of $\sim$2.9 to 28 $\mu$m and explores the spatial variation of volatile ice species in the protostellar envelope. We find evidence for thermal processing of ice species throughout the inner envelope. We present the first high-spatial resolution ($\sim 80$ au) maps of key volatile ice species H$_{2}$O, CO$_{2}$, $^{13}$CO$_2$, CO, and OCN$^-$, which reveal a highly structured and inhomogeneous density distribution of the protostellar envelope, with a deficiency of ice column density that coincides with the jet/outflow shocked knots. Further, we observe high relative crystallinity of H$_{2}$O ice around the shocked knot seen in the H$_2$ and OH wind/outflow, which can be explained by a lack of outer colder material in the envelope along the line of sight due to the irregular structure of the envelope. These observations show clear evidence of thermal processing of the ices in the inner envelope, close to the outflow cavity walls, heated by the luminous protostar., Comment: Submitted to ApJ. Main text:16 pages with 11 figures

The carbon isotope ratio is a powerful tool for studying the evolution of stellar systems. Recent detections of CO isotopologues in disks and exoplanet atmospheres pointed towards significant fractionation in these systems. In order to understand the evolution of this quantity, it is crucial to trace the isotope abundance from stellar nurseries to planetary systems. During the protostellar stage the multiple vibrational modes of CO$_2$ and CO ice provide a unique opportunity to examine the carbon isotope ratio in the solid state. Now with the sensitivity of the \textit{James Webb Space Telescope}, these absorption features have become accessible at high S/N in Solar-mass systems. We quantify the $^{12}$CO$_2$/$^{13}$CO$_2$ and the $^{12}$CO/$^{13}$CO isotope ratios in 17 class 0/I low mass protostars from the $^{12}$CO$_2$ combination modes (2.70 ${\mu}$m and 2.77 ${\mu}$m), the $^{12}$CO$_2$ stretching mode (4.27 ${\mu}$m), the $^{13}$CO$_2$ stretching mode (4.39 ${\mu}$m), the $^{12}$CO$_2$ bending mode (15.2 ${\mu}$m), the $^{12}$CO stretching mode (4.67 ${\mu}$m) and the $^{13}$CO stretching mode (4.78 ${\mu}$m) using JWST observations. We also report a detection of the $^{12}$CO overtone mode at 2.35 ${\mu}$m. The $^{12}$CO$_2$/$^{13}$CO$_2$ ratios are in agreement and we find mean ratios of 85 $\pm$ 23, 76 $\pm$ 12 and 97 $\pm$ 17 for the 2.70 ${\mu}$m, 4.27 ${\mu}$m and the 15.2 ${\mu}$m bands, respectively. The main source of uncertainty stem from the error on the band strengths. The $^{12}$CO/$^{13}$CO ratios derived from the 4.67 ${\mu}$m bands are consistent, albeit elevated with respect to the $^{12}$CO$_2$/$^{13}$CO$_2$ ratios and we find a mean ratio of 165 $\pm$ 52. These findings indicate that ices leave the pre-stellar stage with elevated carbon isotope ratios relative to the interstellar medium and that fractionation becomes significant during the later stages.

Protein-protein interactions (PPIs) play a crucial role in numerous biological processes. Developing methods that predict binding affinity changes under substitution mutations is fundamental for modelling and re-engineering biological systems. Deep learning is increasingly recognized as a powerful tool capable of bridging the gap between in-silico predictions and in-vitro observations. With this contribution, we propose eGRAL, a novel SE(3) equivariant graph neural network (eGNN) architecture designed for predicting binding affinity changes from multiple amino acid substitutions in protein complexes. eGRAL leverages residue, atomic and evolutionary scales, thanks to features extracted from protein large language models. To address the limited availability of large-scale affinity assays with structural information, we generate a simulated dataset comprising approximately 500,000 data points. Our model is pre-trained on this dataset, then fine-tuned and tested on experimental data.

This work aims to utilize the increased sensitivity and resolution of the JWST to quantify the HDO/H$_{2}$O ratio in ices toward young stellar objects (YSOs) and to determine if the HDO/H$_{2}$O ratios measured in the gas phase toward massive YSOs (MYSOs) are representative of the ratios in their ice envelopes. Two protostars observed in the Investigating Protostellar Accretion (IPA) program using JWST NIRSpec were analyzed: HOPS 370, an intermediate-mass YSO (IMYSO), and IRAS 20126+4104, a MYSO. The HDO ice toward these sources was detected above the 3$\sigma$ level and quantified via its 4.1 $\mu$m band. The contributions from the CH$_{3}$OH combination modes to the observed optical depth in this spectral region were constrained via the CH$_{3}$OH 3.53 $\mu$m band to ensure that the integrated optical depth of the HDO feature was not overestimated. H$_{2}$O ice was quantified via its 3 $\mu$m band. From these fits, ice HDO/H$_{2}$O abundance ratios of 4.6$\pm$1.8$\times$10$^{-3}$ and 2.6$\pm$1.2$\times$10$^{-3}$ are obtained for HOPS 370 and IRAS 20126+4104, respectively. The simultaneous detections of both crystalline HDO and crystalline H$_{2}$O corroborate the assignment of the observed feature at 4.1 $\mu$m to HDO ice. The ice HDO/H$_{2}$O ratios are similar to the highest reported gas HDO/H$_{2}$O ratios measured toward MYSOs as well as the hot inner regions of isolated low-mass protostars, suggesting that at least some of the gas HDO/H$_{2}$O ratios measured toward massive hot cores are representative of the HDO/H$_{2}$O ratios in ices. The need for an H$_{2}$O-rich CH$_{3}$OH component in the CH$_{3}$OH ice analysis supports recent experimental and observational results that indicate that some CH$_{3}$OH ice may form prior to the CO freeze-out stage in H$_{2}$O-rich ice layers., Comment: Accepted for publication in A&A. 23 pages, 17 figures, 10 tables

Accretion and ejection sets the outcome of the star and planet formation process. The mid-infrared wavelength range offers key tracers of those processes that were difficult to detect and spatially resolve in protostars until now. We aim to characterize the interplay between accretion and ejection in the low-mass Class I protobinary system TMC1, comprising two young stellar objects: TMC1-W and TMC1-E with 85 au separation. With the {\it James Webb} Space Telescope (JWST) - Mid-Infrared Instrument (MIRI) observations in 5 - 28 $\mu$m range, we measure intensities of emission lines of H$_2$, atoms and ions, e.g., [Fe II] and [Ne II], and HI recombination lines. We detect H$_2$ outflow coming from TMC1-E, with no significant H$_2$ emission from TMC1-W. The H$_2$ emission from TMC1-E outflow appears narrow and extends to wider opening angles with decreasing E$_{up}$ from S(8) to S(1) rotational transitions, indicating a disk wind origin. The outflow from TMC1-E protostar shows spatially extended emission lines of [Ne II], [Ne III], [Ar II], and [Ar III], with their line ratios consistent with UV radiation as a source of ionization. With ALMA, we detect accretion streamer infalling from $>$ 1000 au scales onto the TMC1-E component. TMC1-W protostar powers a collimated jet, detected with [Fe II] and [Ni II] consistent with energetic flow. A much weaker ionized jet is observed from TMC1-E. TMC1-W is associated with strong emission from hydrogen recombination lines, tracing the accretion onto the young star. Observations of a binary Class I protostellar system show that the two processes are clearly intertwined, with accretion from the envelope onto the disk influencing a wide-angle wind ejected on disk scales, while accretion from the protostellar disk onto the protostar is associated with the source launching a collimated high-velocity jet within the innermost regions of the disk., Comment: 18 pages, 13 figures, accepted for publication in Astronomy and Astrophysics

The structure and composition of simple ices can be modified during stellar evolution by protostellar heating. Key to understanding the involved processes are thermal and chemical tracers that can diagnose the history and environment of the ice. The 15.2 $\mu$m bending mode of $^{12}$CO$_2$ has proven to be a valuable tracer of ice heating events but suffers from grain shape and size effects. A viable alternative tracer is the weaker $^{13}$CO$_2$ isotopologue band at 4.39 $\mu$m which has now become accessible at high S/N with the $\textit{James Webb}$ Space Telescope (JWST). We present JWST NIRSpec observations of $^{13}$CO$_2$ ice in five deeply embedded Class 0 sources spanning a wide range in luminosities (0.2 - 10$^4$ L$_{\odot}$ ) taken as part of the Investigating Protostellar Accretion Across the Mass Spectrum (IPA) program. The band profiles vary significantly, with the most luminous sources showing a distinct narrow peak at 4.38 $\mu$m. We first apply a phenomenological approach and show that a minimum of 3-4 Gaussian profiles are needed to fit the $^{13}$CO$_2$ absorption feature. We then combine these findings with laboratory data and show that a 15.2 $\mu$m $^{12}$CO$_2$ band inspired five-component decomposition can be applied for the isotopologue band where each component is representative of CO$_2$ ice in a specific molecular environment. The final solution consists of cold mixtures of CO$_2$ with CH$_3$OH, H$_2$O and CO as well as segregated heated pure CO$_2$ ice. Our results are in agreement with previous studies of the $^{12}$CO$_2$ ice band, further confirming that $^{13}$CO$_{2}$ is a useful alternative tracer of protostellar heating events. We also propose an alternative solution consisting only of heated CO$_2$:CH$_3$OH and CO$_2$:H$_2$O ices and warm pure CO$_2$ ice for decomposing the ice profiles of the two most luminous sources in our sample.

Nitrogen-bearing complex organic molecules have been commonly detected in the gas phase but not yet in interstellar ices. This has led to the long-standing question of whether these molecules form in the gas phase or in ices. $\textit{James Webb}$ Space Telescope ($\textit{JWST}$) offers the sensitivity, spectral resolution, and wavelength coverage needed to detect them in ices and investigate whether their abundance ratios are similar in gas and ice. We report the first tentative detection of CH$_3$CN, C$_2$H$_5$CN, and the simple molecule, N$_2$O, based on the CN-stretch band in interstellar ices toward three (HOPS 153, HOPS 370, and IRAS 20126+4104) out of the five protostellar systems observed as part of the Investigating Protostellar Accretion (IPA) GO program with $\textit{JWST}$-NIRSpec. We also provide upper limits for the two other sources with smaller luminosities in the sample. We detect OCN$^-$ in the ices of all sources with typical CH$_3$CN/OCN$^-$ ratios of around 1. Ice and gas column density ratios of the nitrogen-bearing species with respect to each other are better matched than those with respect to methanol, which are a factor of ${\sim}5$ larger in the ices than the gas. We attribute the elevated ice column densities with respect to methanol to the difference in snowline locations of nitrogen-bearing molecules and of methanol, biasing the gas-phase observations toward fewer nitrogen-bearing molecules. Moreover, we find tentative evidence for enhancement of OCN$^-$, CH$_3$CN, and C$_2$H$_5$CN in warmer ices, although formation of these molecules likely starts along with methanol in the cold prestellar phase. Future surveys combining NIRSpec and MIRI, and additional laboratory spectroscopic measurements of C$_2$H$_5$CN ice, are necessary for robust detection and conclusions on the formation history of complex cyanides., Comment: Accepted for publication in A&A

We investigate the bright CO fundamental emission in the central regions of five protostars in their primary mass assembly phase using new observations from JWST's Near-Infrared Spectrograph (NIRSpec) and Mid-Infrared Instrument (MIRI). CO line emission images and fluxes are extracted for a forest of $\sim$150 ro-vibrational transitions from two vibrational bands, $v=1-0$ and $v=2-1$. However, ${}^{13}$CO is undetected, indicating that ${}^{12}$CO emission is optically thin. We use H$_2$ emission lines to correct fluxes for extinction and then construct rotation diagrams for the CO lines with the highest spectral resolution and sensitivity to estimate rotational temperatures and numbers of CO molecules. Two distinct rotational temperature components are required for $v=1$ ($\sim600$ to 1000 K and 2000 to $\sim 10^4$ K), while one hotter component is required for $v=2$ ($\gtrsim 3500$ K). ${}^{13}$CO is depleted compared to the abundances found in the ISM, indicating selective UV photodissociation of ${}^{13}$CO; therefore, UV radiative pumping may explain the higher rotational temperatures in $v=2$. The average vibrational temperature is $\sim 1000$ K for our sources and is similar to the lowest rotational temperature components. Using the measured rotational and vibrational temperatures to infer a total number of CO molecules, we find that the total gas masses range from lower limits of $\sim10^{22}$ g for the lowest mass protostars to $\sim 10^{26}$ g for the highest mass protostars. Our gas mass lower limits are compatible with those in more evolved systems, which suggest the lowest rotational temperature component comes from the inner disk, scattered into our line of sight, but we also cannot exclude the contribution to the CO emission from disk winds for higher mass targets., Comment: 31 pages, 7 figures, 4 tables, received to ApJ December 10 2023, accepted to ApJ August 4 2024

Complex organic molecules (COMs) detected in the gas phase are thought to be mostly formed on icy grains, but no unambiguous detection of icy COMs larger than CH3OH has been reported so far. Exploring this matter in more detail has become possible with the JWST the critical 5-10 $\mu$m range. In the JOYS+ program, more than 30 protostars are being observed with the MIRI/MRS. This study explores the COMs ice signatures in the low and high-mass protostar, IRAS 2A and IRAS 23385, respectively. We fit continuum and silicate subtracted observational data with IR laboratory ice spectra. We use the ENIIGMA fitting tool to find the best fit between the lab data and the observations and to performs statistical analysis of the solutions. We report the best fits for the spectral ranges between 6.8 and 8.6 $\mu$m in IRAS 2A and IRAS 23385, originating from simple molecules, COMs, and negative ions. The strongest feature in this range (7.7 $\mu$m) is dominated by CH4 and has contributions of SO2 and OCN-. Our results indicate that the 7.2 and 7.4 $\mu$m bands are mostly dominated by HCOO-. We find statistically robust detections of COMs based on multiple bands, most notably CH3CHO, CH3CH2OH, and CH3OCHO. The likely detection of CH3COOH is also reported. The ice column density ratios between CH3CH2OH and CH3CHO of IRAS 2A and IRAS 23385, suggests that these COMs are formed on icy grains. Finally, the derived ice abundances for IRAS 2A correlate well with those in comet 67P/GC within a factor of 5. Based on the MIRI/MRS data, we conclude that COMs are present in interstellar ices, thus providing additional proof for a solid-state origin of these species in star-forming regions. The good correlation between the ice abundances in comet 67P and IRAS 2A is in line with the idea that cometary COMs can be inherited from the early protostellar phases., Comment: Accepted for publication in A&A

Investigating Protostellar Accretion (IPA) is a JWST Cycle~1 GO program that uses NIRSpec IFU and MIRI MRS to obtain 2.9--28~$\mu$m spectral cubes of young, deeply embedded protostars with luminosities of 0.2 to 10,000~L$_{\odot}$ and central masses of 0.15 to 12~M$_{\odot}$. In this Letter, we report the discovery of a highly collimated atomic jet from the Class~0 protostar IRAS~16253$-$2429, the lowest luminosity source ($L_\mathrm{bol}$ = 0.2 $L_\odot$) in the IPA program. The collimated jet is detected in multiple [Fe~II] lines, [Ne~II], [Ni~II], and H~I lines, but not in molecular emission. The atomic jet has a velocity of about 169~$\pm$~15~km\,s$^{-1}$, after correcting for inclination. The width of the jet increases with distance from the central protostar from 23 to~60 au, corresponding to an opening angle of 2.6~$\pm$~0.5\arcdeg. By comparing the measured flux ratios of various fine structure lines to those predicted by simple shock models, we derive a shock {speed} of 54~km\,s$^{-1}$ and a preshock density of 2.0$\times10^{3}$~cm$^{-3}$ at the base of the jet. {From these quantities and using a suite of jet models and extinction laws we compute a mass loss rate between $0.4 -1.1\times10^{-10}~M_{\odot}$~yr~$^{-1}$.} The low mass loss rate is consistent with simultaneous measurements of low mass accretion rate ($2.4~\pm~0.8~\times~10^{-9}~M_{\odot}$~yr$^{-1}$) for IRAS~16253$-$2429 from JWST observations (Watson et al. in prep), indicating that the protostar is in a quiescent accretion phase. Our results demonstrate that very low-mass protostars can drive highly collimated, atomic jets, even during the quiescent phase., Comment: Accepted to ApJL. Comments and feedback welcome

(Abridged) We investigate the impact of radiative feedback from massive stars on their natal cloud and focus on the transition from the HII region to the atomic PDR (crossing the ionisation front (IF)), and the subsequent transition to the molecular PDR (crossing the dissociation front (DF)). We use high-resolution near-IR integral field spectroscopic data from NIRSpec on JWST to observe the Orion Bar PDR as part of the PDRs4All JWST Early Release Science Program. The NIRSpec data reveal a forest of lines including, but not limited to, HeI, HI, and CI recombination lines, ionic lines, OI and NI fluorescence lines, Aromatic Infrared Bands (AIBs including aromatic CH, aliphatic CH, and their CD counterparts), CO2 ice, pure rotational and ro-vibrational lines from H2, and ro-vibrational lines HD, CO, and CH+, most of them detected for the first time towards a PDR. Their spatial distribution resolves the H and He ionisation structure in the Huygens region, gives insight into the geometry of the Bar, and confirms the large-scale stratification of PDRs. We observe numerous smaller scale structures whose typical size decreases with distance from Ori C and IR lines from CI, if solely arising from radiative recombination and cascade, reveal very high gas temperatures consistent with the hot irradiated surface of small-scale dense clumps deep inside the PDR. The H2 lines reveal multiple, prominent filaments which exhibit different characteristics. This leaves the impression of a "terraced" transition from the predominantly atomic surface region to the CO-rich molecular zone deeper in. This study showcases the discovery space created by JWST to further our understanding of the impact radiation from young stars has on their natal molecular cloud and proto-planetary disk, which touches on star- and planet formation as well as galaxy evolution., Comment: 52 pages, 30 figures, submitted to A&A

Investigating Protostellar Accretion is a Cycle 1 JWST program using the NIRSpec+MIRI integral field units to obtain 2.9--28 $\mu$m spectral cubes of five young protostars with luminosities of 0.2-10,000 L$_{\odot}$ in their primary accretion phase. This paper introduces the NIRSpec 2.9--5.3 $\mu$m data of the inner 840-9000 au with spatial resolutions from 28-300 au. The spectra show rising continuum emission; deep ice absorption; emission from H$_{2}$, H~I, and [Fe~II]; and the CO fundamental series in emission and absorption. Maps of the continuum emission show scattered light cavities for all five protostars. In the cavities, collimated jets are detected in [Fe~II] for the four $< 320$~L$_{\odot}$ protostars, two of which are additionally traced in Br-$\alpha$. Knots of [Fe~II] emission are detected toward the most luminous protostar, and knots of [FeII] emission with dynamical times of $< 30$~yrs are found in the jets of the others. While only one jet is traced in H$_2$, knots of H$_2$ and CO are detected in the jets of four protostars. H$_2$ is seen extending through the cavities, showing that they are filled by warm molecular gas. Bright H$_2$ emission is seen along the walls of a single cavity, while in three cavities narrow shells of H$_2$ emission are found, one of which has an [Fe~II] knot at its apex. These data show cavities containing collimated jets traced in atomic/ionic gas surrounded by warm molecular gas in a wide-angle wind and/or gas accelerated by bow shocks in the jets., Comment: 26 pages, 12 figures

[Abridged] Most well-resolved disks observed with ALMA show signs of dust traps. These dust traps set the chemical composition of the planet forming material in these disks, as the dust grains with their icy mantles are trapped at specific radii and could deplete the gas and dust of volatiles at smaller radii. In this work we analyse the first detection of nitric oxide (NO) in a protoplanetary disk. We aim to constrain the nitrogen chemistry and the gas-phase C/O ratio in the highly asymmetric dust trap in the Oph-IRS 48 disk. We use ALMA observations of NO, CN, C$_2$H, and related molecules and model the effect of the dust trap on the physical and chemical structure using the thermochemical code DALI. Furthermore, we explore how ice sublimation contributes to the observed emission lines. NO is only observed at the location of the dust trap but CN and C$_2$H are not detected in the Oph-IRS 48 disk. This results in an CN/NO column density ratio of $< 0.05$ and thus a low C/O ratio at the location of the dust trap. The main gas-phase formation pathways to NO through OH and NH in the fiducial model predict NO emission that is an order of magnitude lower than is observed. The gaseous NO column density can be increased by factors ranging from 2.8 to 10 when the H$_2$O and NH$_3$ gas abundances are significantly boosted by ice sublimation. However, these models are inconsistent with the upper limits on the H$_2$O and OH column densities derived from observations. We propose that the NO emission in the Oph-IRS 48 disk is closely related to the nitrogen containing ices sublimating in the dust trap. The non-detection of CN constrains the C/O ratio both inside and outside the dust trap to be $< 1$ if all nitrogen initially starts as N$_2$ and $\leq 0.6$, consistent with the Solar value, if (part of) the nitrogen initially starts as N or NH$_3$., Comment: Accepted for publication in Astronomy and Astrophysics

The complex organic molecules (COMs) detected in star-forming regions are the precursors of the prebiotic molecules that can lead to the emergence of life. By studying COMs in more evolved protoplanetary disks we can gain a better understanding of how they are incorporated into planets. This paper presents ALMA band 7 observations of the dust and ice trap in the protoplanetary disk around Oph IRS 48. We report the first detection of dimethyl ether (CH3OCH3) in a planet-forming disk and a tentative detection of methyl formate (CH3OCHO). We determined column densities for the detected molecules and upper limits on non-detected species using the CASSIS spectral analysis tool. The inferred column densities of CH3OCH3 and CH3OCHO with respect to methanol (CH3OH) are of order unity, indicating unusually high abundances of these species compared to other environments. Alternatively, the 12CH3OH emission is optically thick and beam diluted, implying a higher CH3OH column density and a smaller emitting area than originally thought. The presence of these complex molecules can be explained by thermal ice sublimation, where the dust cavity edge is heated by irradiation and the full volatile ice content is observable in the gas phase. This work confirms the presence of oxygen-bearing molecules more complex than CH3OH in protoplanetary disks for the first time. It also shows that it is indeed possible to trace the full interstellar journey of COMs across the different evolutionary stages of star, disk, and planet formation., Comment: Accepted to A&A - 20th Jan 2022

Massive stars disrupt their natal molecular cloud material through radiative and mechanical feedback processes. These processes have profound effects on the evolution of interstellar matter in our Galaxy and throughout the Universe, from the era of vigorous star formation at redshifts of 1-3 to the present day. The dominant feedback processes can be probed by observations of the Photo-Dissociation Regions (PDRs) where the far-ultraviolet photons of massive stars create warm regions of gas and dust in the neutral atomic and molecular gas. PDR emission provides a unique tool to study in detail the physical and chemical processes that are relevant for most of the mass in inter- and circumstellar media including diffuse clouds, proto-planetary disks and molecular cloud surfaces, globules, planetary nebulae, and star-forming regions. PDR emission dominates the infrared (IR) spectra of star-forming galaxies. Most of the Galactic and extragalactic observations obtained with the James Webb Space Telescope (JWST) will therefore arise in PDR emission. In this paper we present an Early Release Science program using the MIRI, NIRSpec, and NIRCam instruments dedicated to the observations of an emblematic and nearby PDR: the Orion Bar. These early JWST observations will provide template datasets designed to identify key PDR characteristics in JWST observations. These data will serve to benchmark PDR models and extend them into the JWST era. We also present the Science-Enabling products that we will provide to the community. These template datasets and Science-Enabling products will guide the preparation of future proposals on star-forming regions in our Galaxy and beyond and will facilitate data analysis and interpretation of forthcoming JWST observations., Comment: Submitted to PASP

We present a protocol for the fully automated construction of quantum mechanical-(QM)-classical hybrid models by extending our previously reported approach on self-parametrizing system-focused atomistic models (SFAM) J. Chem. Theory Comput. 2020, 16, 1646]. In this QM/SFAM approach, the size and composition of the QM region is evaluated in an automated manner based on first principles so that the hybrid model describes the atomic forces in the center of the QM region accurately. This entails the automated construction and evaluation of differently sized QM regions with a bearable computational overhead that needs to be paid for automated validation procedures. Applying SFAM for the classical part of the model eliminates any dependence on pre-existing parameters due to its system-focused quantum mechanically derived parametrization. Hence, QM/SFAM is capable of delivering a high fidelity and complete automation. Furthermore, since SFAM parameters are generated for the whole system, our ansatz allows for a convenient re-definition of the QM region during a molecular exploration. For this purpose, a local re-parametrization scheme is introduced, which efficiently generates additional classical parameters on the fly when new covalent bonds are formed (or broken) and moved to the classical region., Comment: 38 pages, 9 figures

We propose a stable Petrov-Galerkin discretization of a kinetic Fokker-Planck equation constructed in such a way that uniform inf-sup stability can be inferred directly from the variational formulation. Inspired by well-posedness results for parabolic equations, we derive a lower bound for the dual inf-sup constant of the Fokker-Planck bilinear form by means of stable pairs of trial and test functions. The trial function of such a pair is constructed by applying the kinetic transport operator and the inverse velocity Laplace-Beltrami operator to a given test function. For the Petrov-Galerkin projection we choose an arbitrary discrete test space and then define the discrete trial space using the same application of transport and inverse Laplace-Beltrami operator. As a result, the spaces replicate the stable pairs of the continuous level and we obtain a well-posed numerical method with a discrete inf-sup constant identical to the inf-sup constant of the continuous problem independently of the mesh size. We show how the specific basis functions can be efficiently computed by low-dimensional elliptic problems, and confirm the practicability and performance of the method with numerical experiments.

Computational studies of chemical reactions in complex environments such as proteins, nanostructures, or on surfaces require accurate and efficient atomistic models applicable to the nanometer scale. In general, an accurate parametrization of the atomistic entities will not be available for arbitrary system classes, but demands a fast automated system-focused parametrization procedure to be quickly applicable, reliable, flexible, and reproducible. Here, we develop and combine an automatically parametrizable quantum chemically derived molecular mechanics model with machine-learned corrections under autonomous uncertainty quantification and refinement. Our approach first generates an accurate, physically motivated model from a minimum energy structure and its corresponding Hessian matrix by a partial Hessian fitting procedure of the force constants. This model is then the starting point to generate a large number of configurations for which additional off-minimum reference data can be evaluated on the fly. A $\Delta$-machine learning model is trained on these data to provide a correction to energies and forces including uncertainty estimates. During the procedure, the flexibility of the machine learning model is tailored to the amount of available training data. The parametrization of large systems is enabled by a fragmentation approach. Due to their modular nature, all model construction steps allow for model improvement in a rolling fashion. Our approach may also be employed for the generation of system-focused electrostatic molecular mechanics embedding environments in a quantum-mechanical/molecular-mechanical hybrid model for arbitrary atomistic structures at the nanoscale., Comment: 53 pages, 12 figures, 2 tables

We consider ultraweak variational formulations for (parametrized) linear first order transport equations in time and/or space. Computationally feasible pairs of optimally stable trial and test spaces are presented, starting with a suitable test space and defining an optimal trial space by the application of the adjoint operator. As a result, the inf-sup constant is one in the continuous as well as in the discrete case and the computational realization is therefore easy. In particular, regarding the latter, we avoid a stabilization loop within the greedy algorithm when constructing reduced models within the framework of reduced basis methods. Several numerical experiments demonstrate the good performance of the new method.

In this paper we introduce a new hierarchical model reduction framework for the Fokker-Planck equation. We reduce the dimension of the equation by a truncated basis expansion in the velocity variable, obtaining a hyperbolic system of equations in space and time. Unlike former methods like the Legendre moment models, the new framework generates a suitable problem-dependent basis of the reduced velocity space that mimics the shape of the solution in the velocity variable. To that end, we adapt the framework of [M. Ohlberger and K. Smetana. A dimensional reduction approach based on the application of reduced basis methods in the framework of hierarchical model reduction. SIAM J. Sci. Comput., 36(2):A714-A736, 2014] and derive initially a parametrized elliptic partial differential equation (PDE) in the velocity variable. Then, we apply ideas of the Reduced Basis method to develop a greedy-algorithm that selects the basis from solutions of the parametrized PDE. Numerical experiments demonstrate the potential of this new method., Comment: In proceedings of ALGORITMY 2016

The formation of inorganic dust in circumstellar environments of evolved stars is poorly understood. Spectra of molecules thought to be most important for the nucleation, i.e. AlO, TiO, and TiO2, have been recently detected in the red supergiant VY CMa. These molecules are effectively formed in VY CMa and the observations suggest that non-equilibrium chemistry must be involved in their formation and nucleation into dust. In addition to exploring the recent observations of VY CMa, we briefly discuss the possibility of detecting these molecules in the dust-poor circumstellar environment of Betelgeuse., Comment: contribution to Betelgeuse Workshop 2012: "The physics of Red Supergiants: recent advances and open questions", 26-29 Nov 2012 Paris (France)