We update the capabilities of the open-knowledge software instrument Modules for Experiments in Stellar Astrophysics (MESA). RSP is a new functionality in MESAstar that models the nonlinear radial stellar pulsations that characterize RR Lyrae, Cepheids, and other classes of variable stars. We significantly enhance numerical energy conservation capabilities, including during mass changes. For example, this enables calculations through the He flash that conserve energy to better than 0.001%. To improve the modeling of rotating stars in MESA, we introduce a new approach to modifying the pressure and temperature equations of stellar structure, as well as a formulation of the projection effects of gravity darkening. A new scheme for tracking convective boundaries yields reliable values of the convective core mass and allows the natural emergence of adiabatic semiconvection regions during both core hydrogen- and helium-burning phases. We quantify the parallel performance of MESA on current-generation multicore architectures and demonstrate improvements in the computational efficiency of radiative levitation. We report updates to the equation of state and nuclear reaction physics modules. We briefly discuss the current treatment of fallback in core-collapse supernova models and the thermodynamic evolution of supernova explosions. We close by discussing the new MESA Testhub software infrastructure to enhance source code development.

https://iopscience.iop.org/article/10.3847/1538-4365/ab2241/pdf

Modules for Experiments in Stellar Astrophysics (MESA): Pulsating Variable Stars, Rotation, Convective Boundaries, and Energy Conservation

We update the capabilities of the open-knowledge software instrument Modules for Experiments in Stellar Astrophysics (MESA). RSP is a new functionality in MESAstar that models the non-linear radial stellar pulsations that characterize RR Lyrae, Cepheids, and other classes of variable stars. We significantly enhance numerical energy conservation capabilities, including during mass changes. For example, this enables calculations through the He flash that conserve energy to better than 0.001 %. To improve the modeling of rotating stars in MESA, we introduce a new approach to modifying the pressure and temperature equations of stellar structure, and a formulation of the projection effects of gravity darkening. A new scheme for tracking convective boundaries yields reliable values of the convective-core mass, and allows the natural emergence of adiabatic semiconvection regions during both core hydrogen- and helium-burning phases. We quantify the parallel performance of MESA on current generation multicore architectures and demonstrate improvements in the computational efficiency of radiative levitation. We report updates to the equation of state and nuclear reaction physics modules. We briefly discuss the current treatment of fallback in core-collapse supernova models and the thermodynamic evolution of supernova explosions. We close by discussing the new MESA Testhub software infrastructure to enhance source-code development.

Considerable progress has been made in identifying the molecular composition of complex signaling networks controlling cell proliferation, differentiation, and survival. However, to discover general building principles and predict the dynamic behavior of signaling networks, it is necessary to develop quantitative models based on experimental observations. Here we report a mathematical model of the core module of the Janus family of kinases (JAK)–signal transducer and activator of transcription (STAT) signaling pathway based on time-resolved measurements of receptor and STAT5 phosphorylation. Applying the fitted model, we can determine the quantitative behavior of STAT5 populations not accessible to experimental measurement. By in silico investigations, we identify the parameters of nuclear shuttling as the most sensitive to perturbations and verify experimentally the model prediction that inhibition of nuclear export results in a reduced transcriptional yield. The model reveals that STAT5 undergoes rapid nucleocytoplasmic cycles, continuously coupling receptor activation and target gene transcription, thereby forming a remote sensor between nucleus and receptor. Thus, dynamic modeling of signaling pathways can promote functional understanding at the systems level.

/pdf/identification-of-nucleocytoplasmic-cycling-as-a-remote-3tsndnslh4.pdf

Identification of nucleocytoplasmic cycling as a remote sensor in cellular signaling by databased modeling

This contribution addresses the identification of metabolic fluxes and metabolite concentrations in mammalian cells from transient (13)C-labeling experiments. Whilst part I describes experimental set-up and acquisition of required metabolite and (13)C-labeling data, part II focuses on setting up network models and the estimation of intracellular fluxes. Metabolic fluxes were determined in glycolysis, pentose-phosphate pathway (PPP), and citric acid cycle (TCA) in a hepatoma cell line grown in aerobic batch cultures. In glycolytic and PPP metabolite pools isotopic stationarity was observed within 30 min, whereas in the TCA cycle the labeling redistribution did not reach isotopic steady state even within 180 min. In silico labeling dynamics were in accordance with in vivo (13)C-labeling data. Split ratio between glycolysis and PPP was 57%:43%; intracellular glucose concentration was estimated at 101.6 nmol per 10(6) cells. In contrast to isotopic stationary (13)C-flux analysis, transient (13)C-flux analysis can also be applied to industrially relevant mammalian cell fed-batch and batch cultures.

Identification of metabolic fluxes in hepatic cells from transient 13C-labeling experiments: Part II. Flux estimation.

This review surveys quantum scattering calculations on chemical reactions of polyatomic molecules in the gas phase published in the last ten years. These calculations are useful because they provide highly accurate information on the dynamics of chemical reactions which can be compared in detail with experimental results. They also serve as quantum mechanical benchmarks for testing approximate theories which can more readily be applied to more complicated reactions. This review includes theories for calculating quantities such as rate constants which have many important scientific applications.

/pdf/recent-advances-in-quantum-scattering-calculations-on-268dxi3er9.pdf

C.J.F. Ridders

Papers

Accurate computation of F′(x) and F′(x) F″(x)

Two algorithms for the calculation of F′(x) = D