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At least 955 records · Page 53

CRNT4SBML: a Python package for the detection of bistability in biochemical reaction networks

Motivation: Signaling pathways capable of switching between two states are ubiquitous within living organisms. They provide the cells with the means to produce reversible or irreversible decisions. Switchlike behavior of biological systems is realized through biochemical reaction networks capable of having two or more distinct steady states which are dependent on initial conditions. Investigation of whether a certain signaling pathway can confer bistability involves a substantial amount of hypothesis testing. The cost of direct experimental testing can be prohibitive. Therefore, constraining the hypothesis space is highly bene?cial. One such methodology is based on Chemical Reaction Network Theory which uses computational techniques to rule out pathways that are not capable of bistability regardless of kinetic constant values and molecule concentrations. Although useful, these methods are complicated from both pureandcomputationalmathematicsperspectives.Thus,theiradoptionisverylimitedamongstbiologists. Results: We brought Chemical Reaction Network Theory approaches closer to experimental biologists by automating all the necessary steps in CRNT4SMBL. The input is based on SBML format which is the community standard for biological pathway communication. The tool parses SBML and derives C-graph representations of the biological pathway with mass action kinetics. Next steps involve an ef?cient search for potential saddle-node bifurcation points using an optimization technique. This type of bifurcation is important as it has the potential of acting as a switching point between two steady states. Finally, if any bifurcation points are present, numerical continuation analysis extends the equilibria branches for generating the diagram. Presence of an S-shaped bifurcation diagram indicates that the pathway acts as a bistable switch for the given optimization parameters. Availability: CRNT4SBML is available via the Python Package Index. The documentation can be found at https://crnt4sbml.readthedocs.io. CRNT4SBML is licensed under the Apache Software License 2.0. Contact: vladislav.petyuk@pnnl.gov

Reyes, Brandon C.↗

Understanding Interfacial Electrochemical Reactions through in situ ec-STEM and IL-Cryo-STEM

A major criterion in the design of next generation materials for electrical energy storage applications is a comprehensive understanding of interfacial electrochemical reactions as well as correlating the structure and chemistry across site-specific electrode/electrolyte interfaces with electron, charge, and mass transport processes as they govern performance characteristics. Scanning transmission electron microscopy (STEM) based techniques have emerged as an indispensable materials characterization tool that provides high spatial resolution imaging and chemical analysis and has been effectively utilized to obtain an atomic to nanoscale view of the interfacial structure before and after electrochemical cycling. More recently, there have been several advances that now allows us to obtain more detailed mechanistic insight into evolving reactions through in situ ec-STEM and electrical biasing platforms such as in the understanding of the mechanisms of solid electrolyte interphase formation, lithium dendrite nucleation and growth mechanisms and ionic transport mechanisms within intercalation, conversion, and alloying electrode materials. Several major advantages of the in situ ec-STEM approach is the quantitative electrochemical measurement of charge passed during cycling with simultaneous analysis of the electrochemical processes with STEM imaging and diffraction. Here, while spectroscopic analysis of the electrochemical reactions products has been performed, there is the issue of beam sensitivity and therefore, Cryo-STEM imaging combined with electron energy loss spectroscopy (EELS) techniques have been employed to analyze the chemistry of the SEI and Li dendrites. In this talk, we discuss the potential for combining identical location (IL) STEM techniques with Cryo-EM. The advantage of using this approach is that the sample is placed on a conventional TEM grid and the exact same location of the specimen can be analyzed before and after quantitative electrochemical measurements. Moreover, since the sample is on the TEM grid, the grid itself can be prepared for further Cryo-TEM experiments by plunge freezing in liquid nitrogen then transferred to the Cryo-TEM under liquid nitrogen. Results obtain from these experiments can be used to enhance our scientific understanding of interfacial chemistry at electrode/electrolyte interfaces and may be useful in the design of new materials.

36 MATERIALS SCIENCE↗

The cross-section measurement for the 3 H($e, e'K^+)nnΛ$ reaction

The small binding energy of the hypertriton leads to predictions of the non-existence of bound hypernuclei for isotriplet three-body systems such as nnΛ. However, invariant mass spectroscopy at GSI has reported events that may be interpreted as the bound nnΛ state. The nnΛ state was sought by missing-mass spectroscopy via the (e, e'K + ) reaction at Jefferson Lab’s experimental Hall A. The present experiment has higher sensitivity to the nnΛ-state investigation in terms of better precision by a factor of about three. The analysis shown in this article focuses on the derivation of the reaction cross-section for the 3 H(γ*, K + )X reaction. Events that were detected in an acceptance, where a Monte Carlo simulation could reproduce the data well (|δp/p| < 4%), were analyzed to minimize the systematic uncertainty. No significant structures were observed with the acceptance cuts, and the upper limits of the production cross-section of the nnΛ state were obtained to be 21 and $31 nbsr -1 at the 90% confidence level when theoretical predictions of (-B Λ , Γ) = (0.25, 0.8) MeV and (0.55, 4.7) MeV, respectively, were assumed. The cross-section result provides valuable information for examining the existence of nnΛ.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

9 Li($\textit{d,p}$) reaction as a specific probe of 10 Li, the paradigm of parity-inverted nuclei around the $\textit{N}$ = 6 closed shell

In this work, we show, within the framework of renormalized nuclear field theory and of the induced reaction surrogate formalism, that the highly debated 10 Li structure, studied in a recent high statistics 9 Li ($\textit{d,p}$) 10 Li one-neutron transfer experiment, is consistent with, or better, requires, the presence of a virtual 1/2 + state of similar single-particle strength than that of the 1/2 – resonance at 0.45 ± 0.03 MeV. Based on continuum spectroscopy self-energy techniques, we find that the physical mechanism responsible for parity inversion in $^{10}_3$Li is the same as that at the basis of the similar phenomenon observed in $^{11}_4$Be and as that needed in 11 Li to have an important $\textit{s}$-wave ground-state component. In particular the strong dynamical coupling between the $s_{1/2}$ and the $d_{5/2}$ states, mediated by the quadrupole vibration of the core 9 Li. A phenomenon which also affects the strength distribution of the $d_{5/2}$ state, in particular, in the energy range of 3–4.5 MeV. Furthermore, this mechanism is also consistent with the (normal) sequence of the $1_{p_{1/2}}$ and $2_{s_{1/2}}$ levels in the $\textit{N}$ = 7 isotones $^{12}_5$B and $^{13}_6$C. The main aim of the present Rapid Communication is that of treating structure and reactions on equal footing and in a common language. In other words, the calculation of the 9 Li ($\textit{d,p}$) 10 Li reaction as a single conceptual step from individual single-particle motion and collective vibrations to absolute double differential cross sections of renormalized virtual and resonant final states, which can be directly compared with experiment.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Bayesian analysis of the Zn 70 ( d , He 3 ) Cu 69 transfer reaction

Transfer reactions provide information about the single-particle nature of nuclear levels. In particular, the differential cross sections from these measurements are sensitive to the angular momentum of the transferred particle and the spectroscopic factor of the populated level. However, the process of extracting these properties is subject to uncertainties, both from experimental and theoretical sources. By integrating the distorted wave Born approximation into a Bayesian model, we propagate these uncertainties through to the spectroscopic factors and orbital angular momentum values. We use previously reported data of the proton pickup reaction Zn 70 ( d , He 3 ) Cu 69 as an example. By accounting for uncertainties in the experimental data, optical model parameters, and reaction mechanism, we find that the extracted spectroscopic factors for low-lying states of 69 Cu are subject to large, asymmetric uncertainties ranging from 35 to 108%. Additionally, Bayesian model comparison is employed to assign probabilities to each of the allowed angular momentum transfers. This method confirms the assignments for many states, but suggests that the data for a state lying at 3.70 MeV are better characterized by an ℓ =3 transfer, rather than the previously reported ℓ =2 .

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Shell-model studies of the astrophysical r p -process reactions S 34 ( p , γ ) Cl 35 and Cl 34 g , m ( p , γ ) Ar 35

Background: Dust grains condensed in the outflows of presolar classical novae should have been present in the protosolar nebula. Candidates for such presolar nova grains have been found in primitive meteorites and can in principle be identified by their isotopic ratios, but the ratios predicted by state-of-the-art one-dimensional hydrodynamic models are uncertain due to nuclear-physics uncertainties. Purpose: To theoretically calculate the thermonuclear rates and uncertainties of the S 34 ( p , γ ) Cl 35 and Cl 34 g , m ( p , γ ) Ar 35 reactions and investigate their impacts on the predicted 34 S/ 32 S isotopic ratio for presolar nova grains. Method: A shell-model approach in a (0 +1 ) ℏ ω model space was used to calculate the properties of resonances in the 34 S(p ,γ ) 35 Cl and 34 g,m Cl (p ,γ ) 35 Ar reactions and their thermonuclear rates. Uncertainties were estimated using a Monte Carlo method. The implications of these rates and their uncertainties on sulfur isotopic nova yields were investigated using a postprocessing nucleosynthesis code. The rates for transitions from the ground state of 34 Cl as well as from the isomeric first excited state of 34 Cl were explicitly calculated. Results: At energies in the resonance region near the proton-emission threshold, many negative-parity states appear. Energies, spectroscopic factors, and proton-decay widths are reported. The resulting thermonuclear rates are compared with previous determinations. Conclusions: The shell-model calculations alone are sufficient to constrain the variation of the 34 S/ 32 S ratios to within about 30%. Uncertainties associated with other reactions must also be considered, but in general we find that the 34 S/ 32 S ratios are not a robust diagnostic to clearly identify presolar grains made from nova ejecta.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Evaluation of experimental constraints on the 44 Ti(α,p) 47 V reaction cross section relevant for supernovae

Due to its importance as an astronomical observable in core-collapse supernovae (CCSNe), the reactions producing and destroying 44 Ti must be well constrained. Generally, statistical model calculations such as Hauser-Feshbach are employed when experimental cross sections are not available, but the variation in such adopted rates can be large. Here, data from the literature is compared with statistical model calculations of the 44 Ti(α,p) 47 V reaction cross section and used to constrain the possible reaction rate variation over the temperatures relevant to CCSNe. Suggestions for targeted future measurements are given.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Clustering and α-capture reaction rate from ab initio 20 Ne

We introduce a new framework for studying clustering and for calculating α partial widths using ab initio wave functions. We demonstrate the formalism for 20 Ne, by calculating the overlap between the 16 O + α cluster configuration and states in 20 Ne computed in the ab initio symmetry-adapted no-core shell model. We present spectroscopic amplitudes and spectroscopic factors, and compare those to no-core symplectic shell-model results in larger model spaces, to gain insight into the underlying physics that drives α clustering. Specifically, we report on the α partial width of the lowest 1 – resonance in 20 Ne, which is found to be in good agreement with experiment.We also present first no-core shell-model estimates for asymptotic normalization coefficients for the ground state, as well as for the first excited 4 + state in 20 Ne that lies in a close proximity to the α + 16 O threshold. This outcome highlights the importance of correlations for developing cluster structures and for describing α widths. The widths can then be used to calculate α-capture reaction rates for narrow resonances of interest to astrophysics. Finally, we explore the reaction rate for the α-capture reaction 16 O(α, γ ) 20 Ne at astrophysically relevant temperatures and determine its impact on simulated x-ray burst abundances.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Experimental study of the isomeric state in 16 N using the 16 N$^{g,m}$($\textit{d}$, 3 He) reaction

Here, the isomeric state of 16 N was studied using the 16 N$^{g,m}$($\textit{d}$, 3 He) proton-removal reactions at 11.8 MeV/u in inverse kinematics. The 16 N beam, of which 24% was in the isomeric state, was produced using the Argonne Tandem-Linac Accelerator System (ATLAS) in-flight system and delivered to the Helical Orbit Spectrometer (HELIOS), which was used to analyze the 3 He ions from the ($\textit{d}$, 3 He) reactions. The simultaneous measurement of reactions on both the ground state and the isomeric states, reduced the systematic uncertainties from the experiment and in the analysis. A direct and reliable extraction of the relative spectroscopic factors was made based on a distorted-wave Born approximation approach. The experimental results suggest that the isomeric state of 16N is an excited neutron-halo state. The results can be understood through calculations using a Woods-Saxon potential model, which captures the effects of weak binding.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Role of low-lying resonances for the 10 Be(p,α) 7 Li reaction rate and implications for the formation of the Solar System

Evidence for the presence of short-lived radioactive isotopes when the Solar System formed is preserved in meteorites, providing insights into the conditions at the birth of our Sun. A low-mass core-collapse supernova had been postulated as a candidate for the origin of 10Be, reinforcing the idea that a supernova triggered the formation of the Solar System. We present a detailed study of the production of 10Be by the ν process in supernovae, which is very sensitive to the reaction rate of the major destruction channel, 10 Be(p,α) 7 Li. With data from recent nuclear experiments that show the presence of a resonant state in 11B at ≈193 keV, we derive new values for the 1 0 Be(p,α) 7 Li reaction rate, which are significantly higher than previous estimates. We show that, with the new 10 Be(p,α) 7 Li reaction rate, a low-mass CCSN is unlikely to produce enough 10 Be to explain the observed 10 Be/ 9 Be ratio in meteorites, even for a wide range of neutrino spectra considered in our models.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

New isotope 286 Mc produced in the 243 Am + 48 Ca reaction

In this paper, we present results of the second experiment on the synthesis of Mc isotopes in the 243 Am + 48 Ca reaction performed at the gas-filled separator DGFRS-2 of the SHE Factory at JINR. Here, the new isotope 286 Mc was synthesized, and its half-life of $20^{+98}_{–9}$ ms and α-particle energy of 10.71 ± 0.02 MeV were determined. A 286 Mc α–decay chain was recorded down to the spontaneous fission of 266 Db. The spontaneous fission of 279 Rg was observed for the first time in one of four new decay chains of 287 Mc. The excitation function of the reaction was measured at three 48 Ca energies of 242, 250, and 259 MeV; the latter resulted in the first observation of the 5$\textit{n}$–evaporation channel with a cross section of $0.5^{+1.3}_{–0.4}$ pb. The decay properties of 21 previously known odd–$\textit{Z}$ isotopes were improved. The potential for an electron-capture decay mode is discussed for 288 Mc and 284 Nh isotopes. The half-lives of spontaneously fissioning nuclei produced in the 48 Ca–induced reactions with actinide targets are compared with several theoretical predictions.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Relative population of states in 21 Mg from few-nucleon removal reactions

Nuclear reactions with intermediate-energy beams in which three, four, and five nucleons are removed are expected to proceed through a combination of nondissipative and statistical processes. In an experiment at the National Superconducting Cyclotron Laboratory, in-beam γ-ray spectroscopy was utilized to study few-nucleon removal reactions from incoming beams of 24 Mg, 25 Al, and 26 Si projectiles to the same reaction product, 21 Mg. Here, new γ-ray transitions and γ-γ coincidences in 21 Mg were established using the CsI(Na) array CAESAR and the inclusive cross section for three-neutron removal from 24 Mg was measured. Significant differences in the relative population of states in 21 Mg from 25 Al compared to 26 Si were observed and found to be correlated with the spins of the 21 Mg states. As a result, this intermediate regime between direct and statistical nucleon removal may have potential as a tool to deliver unique patterns of level populations in fast-beam experiments and alter isomer to ground state ratios in the production of exotic beams.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Absolute cross section of the C 12 ( p , γ ) N 13 reaction

Solar neutrino measurements have recently reached a level of sensitivity such that CNO fluxes can now be experimentally determined. While these first measurements are still only sensitive to the higher energy neutrinos resulting from the β + decays of 15 Ο produced by the 14 Ν ⁡( p ,$\gamma$)⁢ 15 O reaction, future measurements will work towards detection of neutrinos from the β + decay of 13 N from the 12 C ⁡( p ,$\gamma$)⁢ 13 N reaction. Here, this paper reports on a recent measurement of the 12 C ⁡( p ,$\gamma$)⁢ 13 N reaction covering a broad laboratory energy range between 1.0 and 2.5 MeV. The measurement was made to better determine the overall normalization of the absolute cross section and to explore the interference effects between the two broad, overlapping resonances at proton energies of 0.460 and 1.689 MeV and the direct capture to the ground state of 13 N in the framework of a multichannel R -matrix analysis. This work takes into account previous radiative capture as well as elastic 12 C ( p , p ) 12 C scattering data, making uncertainty estimations using a Bayesian framework, to determine a reliable extrapolation of the low energy S factor towards the stellar energy range of CNO hydrogen burning. These new experimental results, and a detailed investigation of the past literature data, suggest that the resonant component of the cross section should be 30% lower than previously accepted.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Deuterium-tritium fusion γ -ray spectrum at MeV energies with application to reaction-in-flight inertial confinement fusion measurements

In inertial confinement fusion implosions, tertiary reaction-in-flight processes create deuterium-tritium fusion reactions [ T ( d , n ) 4 He ] with an incident particle moving at MeV energies instead of the thermonuclear keV temperatures. Additional relativistic kinematic treatments were added to a nuclear resonance code, , and resulting calculations showed an upshifting of the deuterium-tritium fusion γ -ray pathway [ T ( d , γ ) 5 He ] for MeV interactions. Using the calculated spectra, a representative reaction-in-flight γ -ray emission for ICF implosions was estimated. Published by the American Physical Society 2024

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Tunable-fidelity wave functions for the ab initio description of scattering and reactions

Here, the no-core shell model (NCSM) is an ab initio method that solves the nuclear many-body problem by expanding the many-particle wave function into a (typically) harmonic oscillator basis and minimizing the energy to obtain the expansion coefficients. Extensions of the NCSM, such as its coupling with microscopic-cluster basis states, further allow for an ab initio treatment of light-ion nuclear reactions of interest for both astrophysics and nuclear technology applications. A downside of the method is the exponential scaling of the basis size with increasing number of nucleons and excitation quanta, which limits its applicability to mass A ≲ 16 nuclei, except for variants where the basis is further down-selected via some truncation scheme. We consider a basis selection method for the NCSM that was first introduced in the context of the large-scale shell model and captures the essential degrees of freedom of the nuclear wave function leading to a favorable complexity scaling for calculations and enabling ab initio reaction calculations in sd-shell nuclei. The particle configurations within the NCSM basis are ordered based on their contribution to the first moment of the Hamiltonian matrix that results from the projection onto the many-body basis. The truncation scheme then consists in retaining only the lowest-first-moment configurations, which typically contain only few many-body basis states (Slater determinants). As the energy threshold above which configurations are disregarded is increased, the size of the basis becomes an almost-continuous variable, allowing for tunable fidelity in the obtained wave functions. The resulting wave functions can then be used directly in ab initio reaction calculations. We present calculations for 7 Li and n + 12 C scattering using nucleon-nucleon interactions derived from chiral effective field theory and softened using the similarity renormalization group method. The obtained energy levels invariably demonstrate exponential convergence with the size of the basis, and we find improved convergence in scattering calculations. To demonstrate the possibilities enabled by the approach, we also present a first calculation for the scattering of neutrons from 24 Mg. The method presented in this work appears promising for future studies of nuclei with mass A > 16, opening multiple future research directions impacting both nuclear astrophysics and nuclear technology applications.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

First measurement in a magnetic confinement fusion experiment of the H 3 + H 3 → He 5 + n intermediate two-body resonant reaction

We report on the first experimental measurements made at a magnetic confinement fusion device of the tritium(T)-tritium(T) reaction T + T → He 4 + 2 n indicating the presence of the intermediate two-body resonant reaction T + T → He 5 + n . During the second deuterium-tritium campaign (DTE2) at the Joint European Torus, measurements of fusion plasmas with high tritium concentrations, n T / ( n T + n D ) ≈ 0.99 , heated with tritium neutral beam injection, were performed using the neutron time-of-flight (TOF) spectrometer TOFOR. We detect a peak in the neutron emission TOF spectrum consistent with the two-body resonant reaction. The TT neutron emission energy spectrum is modeled using an R -matrix framework where the distributions of the most likely model parameters given our experimental TOF data are determined utilizing a Markov chain Monte Carlo approach. We compare our best estimate of the T + T neutron emission energy spectrum with results obtained at inertial confinement fusion experiments at the OMEGA facility and find a spectral shape that is consistent with the energy dependency in the neutron spectrum observed at OMEGA. Published by the American Physical Society 2024

Physics↗

A high-temperature sample changer for parallelized in situ X-ray studies to efficiently explore reaction space

A sample environment for high-throughput X-ray scattering studies in transmission geometry to probe the mechanism and kinetics of moderate-temperature reactions in solution, molten fluxes and solids is described. This high-temperature sample changer enables efficient studies of reactions that are slow relative to the timescale of the X-ray scattering measurements by allowing up to 18 samples to be probed at the same temperature in parallel. This significantly enhances the throughput ofin situX-ray scattering studies as the sample changer effectively facilitates systematic studies that compare different reaction parameters (e.g.concentration, precursor, composition, additives), reference samples (e.g.background, pure precursors) and replicates (to demonstrate reproducibility) with enhanced consistency afforded by the quasi-simultaneous nature of the measurements. The large sample volumes, compared with those typically used for X-ray scattering measurements, are on a similar scale to those in the laboratory, making the results more directly comparable.

Chemistry↗

Effects of Peptide-Functionalized Surfaces on the Electrochemical Hydrogen Evolution Reaction

Abstract This review outlines the approaches and mechanisms through which peptides and amino acids functionalize electrocatalytically active surfaces to promote or inhibit the electrochemical hydrogen evolution reaction (HER). HER is important in many electrochemical systems. For example, HER is highly desired in water electrolysis, which if driven by renewable energy could serve as a green alternative to the fossil-fuel-driven steam methane-reforming process. However, HER is often an undesired side reaction and thus limits the selectivity of promising electrochemical technologies such as electrochemical nitrogen reduction or carbon dioxide reduction. In pursuing higher product selectivity and yield in emerging and existing electrochemical systems, amino acids and short-chain peptides are promising molecules for the modification of electrochemically active surfaces. Peptides are attractive because they are highly tunable, which allows for versatility in their applications. This short review article summarizes literature that illustrates the mechanisms through which electrode-bound peptides can affect HER including via modulating surface binding and adsorbate coverage, altering the surface composition, and controlling proton transfer rates. Our goal is to motivate additional studies utilizing electrode-bound peptides to modulate electrochemical hydrogen evolution reactions.

Electrochemistry↗