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Mathematical Model of ATM Activation and Chromatin Relaxation by Ionizing Radiation
We propose a comprehensive mathematical model to study the dynamics of ionizing radiation induced Ataxia-telangiectasia mutated (ATM) activation that consists of ATM activation through dual mechanisms: the initiative activation pathway triggered by the DNA damage-induced local chromatin relaxation and the primary activation pathway consisting of a self-activation loop by interplay with chromatin relaxation. The model is expressed as a series of biochemical reactions, governed by a system of differential equations and analyzed by dynamical systems techniques. Radiation induced double strand breaks (DSBs) cause rapid local chromatin relaxation, which is independent of ATM but initiates ATM activation at damage sites. Key to the model description is how chromatin relaxation follows when active ATM phosphorylates KAP-1, which subsequently spreads throughout the chromatin and induces global chromatin relaxation. Additionally, the model describes how oxidative stress activation of ATM triggers a self-activation loop in which PP2A and ATF2 are released so that ATM can undergo autophosphorylation and acetylation for full activation in relaxed chromatin. In contrast, oxidative stress alone can partially activate ATM because phosphorylated ATM remains as a dimer. The model leads to predictions on ATM mediated responses to DSBs, oxidative stress, or both that can be tested by experiments.
Low- and intermediate-temperature oxidation of dimethyl ether up to 100 atm in a supercritical pressure jet-stirred reactor
Understanding the low- and intermediate-temperature oxidation chemistry of oxygenated fuels like dimethyl ether (DME) at high pressure is paramount to the development of advanced engines with low carbon emissions. The supercritical pressure jet-stirred reactor (SP-JSR) recently developed at Princeton provides a new platform for conducting kinetic studies at low and intermediate temperatures at extremely high pressures with a uniform temperature distribution and a short flow residence time. This paper uses the SP-JSR to investigate DME oxidation at equivalence ratios of 0.175, 1.0, and 1.72, for pressures of 10 and 100 atm, and temperatures ranging from 400 to 900 K. The results demonstrate weakened NTC behavior at 100 atm relative to 10 atm due to increased flux through QOOH + O 2 = O 2 QOOH relative to QOOH = 2 CH 2 O + OH at 100 atm. Furthermore, the intermediate-temperature oxidation window is shifted to lower temperatures at 100 atm. The experimental data are compared with several chemical kinetic models from the literature. The existing models are seen to agree quite well with the experimental data at 10 atm. However, the models fail to properly capture the NTC behavior at 100 atm. Reaction pathway analyses indicate that both the low- and intermediate-temperature chemistries are controlled by RO 2 consumption pathways. The reaction rates for several of the important reactions, such as DME + OH = CH 3 OCH 2 + H 2 O, H 2 O 2 (+M) = 2 OH (+M), and 2 HO 2 = 2 OH + O 2 are updated in this work. Furthermore, the updated model improves the predictability for all key species compared to the original model.
Methanol oxidation up to 100 atm in a supercritical pressure jet-stirred reactor
Methanol (CH 3 OH) has attracted considerable attention as a renewable fuel or fuel additive with low greenhouse gas emissions. Methanol oxidation was studied using a recently developed supercritical pressure jet-stirred reactor (SP-JSR) at pressures of 10 and 100 atm, at temperatures from 550 to 950 K, and at equivalence ratios of 0.1, 1.0, and 9.0 in experiments and simulations. Here, the experimental results show that the onset temperature of CH 3 OH oxidation at 100 atm is around 700 K, which is more than 100 K lower than the onset at 10 atm and this trend cannot be predicted by the existing kinetics models. Furthermore, a negative temperature coefficient (NTC) behavior was clearly observed at 100 atm at fuel rich conditions for methanol for the first time. To understand the observed temperature shift in the reactivity and the NTC effect, we updated some key elementary reaction rates of relevance to high pressure CH 3 OH oxidation from the literature and added some new low-temperature reaction pathways such as CH 2 O + HO 2 = HOCH 2 O 2 (RO 2 ), RO 2 + RO 2 = HOCH 2 O (RO) + HOCH 2 O (RO) + O 2 , and CH 3 OH + RO 2 = CH 2 OH + HOCH 2 O 2 H (ROOH). Although the model with these updates improves the prediction somewhat for the experimental data at 100 atm and reproduces well high-temperature ignition delay times and laminar flame speed data in the literature, discrepancies still exist for some aspects of the 100 atm low-temperature oxidation data. In addition, it was found that the pressure-dependent HO 2 chemistry shifts to lower temperature as the pressure increases such that the NTC effect at fuel-lean conditions is suppressed. Therefore, as shown in the experiments, the NTC phenomenon was only observed at the fuel-rich condition where fuel radicals are abundant and the HO 2 chemistry at high pressure is weakened by the lack of oxygen resulting in comparatively little HO 2 formation.
Studies of Low and Intermediate Temperature Oxidation of Propane up to 100 Atm in a Supercritical-Pressure Jet-Stirred Reactor
Here, the low and intermediate temperature oxidation of propane has been investigated by using a novel supercritical pressure jet stirred reactor (SP-JSR) with and without 20% CO 2 additions at fuel lean and rich conditions at 10 and 100 atm and 500–1000 K. The mole fractions of C 3 H 8 , O 2 , CO, CO 2 , CH 2 O, C 2 H 4 , CH 3 CHO, and C 3 H 6 were quantified by using a micro-gas chromatograph (µ-GC). The experiment showed that different from that of 10 atm, at 100 atm only a weak negative temperature coefficient (NTC) behavior was observed because of the significant shift of the intermediate temperature HO 2 chemistry to lower temperature. In addition, at 100 atm, existing models in literatures could successfully capture the onset temperatures of the low and intermediate chemistry, while under-predict the fuel oxidation quantitatively and fail to capture the NTC behavior between 650 and 780 K at both fuel lean and rich conditions. Similar discrepancy was observed in studies of n-butane and dimethyl ether (DME) oxidations in literatures, implying that there existed large uncertainties in hierarchy model development of fuels with low temperature chemistries at extremely high pressures. Reaction pathways and sensitivity analyses showed that RO 2 competing reactions through (P1) RO 2 = QOOH, (P2) RO 2 = C 3 H 6 + HO 2 , (P3) RO 2 + CH 2 O/HO 2 = RO 2 H + HCO / O 2 dominated the low and intermediate temperature chemistries, followed by HO 2 / H 2 O 2 chemistry at 100 atm, which differed from the dominant pathway through QOOH consumption reactions at lower pressures. Especially, P3 is a new pathway of RO 2 consumption at high pressures, which was not observed in importance at low pressures. Special attention should be paid to the accurate computations of n-C 3 H 7 O 2 / i-C 3 H 7 O 2 + CH 2 O and n-C 3 H 7 O 2 / i-C 3 H 7 O 2 + in the P3 pathway and n-C 3 H 7 O 2 / i-C 3 H 7 O 2 decomposition reactions in the P2 pathway at high pressures.
High pressure ammonia/methanol oxidation up to 100 atm
Here, high pressure ammonia/methanol oxidation and NOx formations were investigated using a recently developed supercritical pressure jet-stirred reactor (SP-JSR) at 20 and 100 atm with temperatures between 550 and 950 K and equivalence ratios of 0.138 and 1.15. The experimental results show that NH 3 oxidation at high pressure is significantly accelerated by the active OH radicals produced from CH 3 OH oxidation. Furthermore, the kinetic interactions between NH 3 and CH 3 OH are governed mainly by the reactions CH 3 OH + NH 2 = CH 2 OH + NH 3 , CH 3 OH + NH 2 = CH 3 O + NH 3 , and CH 2 O + NH 2 = HCO + NH 3 . A HP-Mech model for high-pressure NH 3 /CH 3 OH oxidation was developed in this study. It consists of the most recent NH 3 and CH 3 OH models including some new reactions and updated rate constants from the literature as well as NH 3 -CH 3 OH interactions where rate constants of CH 3 OH + NH 2 = CH 2 OH + NH 3 , CH 3 OH + NH 2 = CH 3 O + NH 3 , NH 2 + CH 2 O = NH 3 + HCO, and NH 2 + CH 2 O = NH 2 CHO + H were theoretically calculated in this study. Our model with these updates improves the prediction for the measured N 2 O/NO x temperature dependence at 100 atm. In addition, the reaction pathway and sensitivity analysis show that N 2 O/NO x /HONO interactions with HO 2 are very important, especially for a fuel-lean mixture at 100 atm. The HONO mole fraction for the fuel-lean mixture at 100 atm was then measured by off-axis integrated cavity output spectroscopy (ICOS) at wavenumber of 6638.26 cm -1 . The experimental data show a significant HONO formation at intermediate temperature that is strongly underpredicted by numerical simulation at 100 atm. Therefore, the HONO related reactions with notable uncertainty at high pressure such as NO + OH (+M) = HONO (+M) and H 2 NO + NO 2 = HONO + HNO need deeper exploration in the future.
Determination of the Diffusion Coefficients of Binary CH4 and C2H6 in a Supercritical CO2 Environment (500–2000 K and 100–1000 atm) by Molecular Dynamics Simulations
The self-diffusion coefficients of carbonaceous fuels in a supercritical CO2 environment provide transport information that can help us understand the Allam Cycle mechanism at a high pressure of 300 atm. The diffusion coefficients of pure CO2 and binary CO2/CH4 and CO2/C2H6 at high temperatures (500 K~2000 K) and high pressures (100 atm~1000 atm) are determined by molecular dynamics simulations in this study. Increasing the temperature leads to an increase in the diffusion coefficient, and increasing the pressure leads to a decrease in the diffusion coefficients for both methane and ethane. The diffusion coefficient of methane at 300 atm is approximately 0.012 cm2/s at 1000 K and 0.032 cm2/s at 1500 K. The diffusion coefficient of ethane at 300 atm is approximately 0.016 cm2/s at 1000 K and 0.045 cm2/s at 1500 K. The understanding of diffusion coefficients potentially leads to the reduction in fuel consumption and minimization of greenhouse gas emissions in the Allam Cycle.
TChem-atm (v2.0.0): scalable performance-portable multiphase atmospheric chemistry
We present TChem-atm, a performance-portable approach that enables efficient simulation of chemically detailed and multiphase atmospheric chemistry on modern heterogeneous computing architectures. Unlike previous efforts that rely on architecture-specific code or focus exclusively on gas-phase chemistry, TChem-atm supports fully coupled gas–aerosol systems with execution across CPUs, NVIDIA GPUs, and AMD GPUs through the Kokkos programming model. It integrates the flexible multiphase capabilities of the Community Atmospheric Model Chemistry Package (CAMP) with the high-performance kinetic routines of TChem, and includes automatic Jacobian construction with support for a range of stiff ODE solvers. In a proof-of-concept integration with the particle-resolved model PartMC, TChem-atm reproduces the existing PartMC–CAMP implementation within solver tolerances and delivers substantial GPU speedups, especially for large particle populations. Performance benchmarks reveal substantial speedups on GPU platforms, particularly for large particle populations, with consistent results across hardware backends. TChem-atm enables performance-portable execution across CPUs and GPUs, though optimal efficiency may require modest architecture-specific tuning (e.g., team and vector sizes), with up to a twofold improvement on the NVIDIA H100. It directly supports sectional and particle-resolved host models, while modal aerosol schemes require minor adaptation to provide particle-scale quantities such as representative diameters. By enabling chemically detailed, multiphase simulations with performance portability and host-model flexibility, TChem-atm facilitates the incorporation of advanced chemistry into atmospheric models.
Lasing in 15 atm CO 2 cell optically pumped by a Fe:ZnSe laser
10 µm lasing is studied in a compact CO 2 -He cell pressurized up to 15 atm when optically pumped by a ∼50 mJ Fe:ZnSe laser tunable around 4.3 µm. The optimal pump wavelength and partial pressure of CO 2 for generating 10 µm pulses are found to be ∼4.4 µm and 0.75 atm, respectively. Without cavity optimization, the optical-to-optical conversion efficiency reached ∼10% at a total pressure of 7 atm. The gain lifetime is measured to be ∼1 µs at pressures above 10 atm, indicating the feasibility of using high-pressure optically pumped CO 2 for the efficient amplification of picosecond 10 µm pulses.
Simultaneous inhibition of ATM, ATR, and DNA-PK causes synergistic lethality
Here, in this paper, we report that simultaneous inhibition of the three primary DNA damage recognition PI3 kinase-like kinases (PIKKs) —ATM, ATR, and DNA-PK— induces severe combinatorial synthetic lethality in mammalian cells. Utilizing Chinese hamster cell lines CHO and V79 and their respective PIKK mutants, we evaluated effects of inhibiting these three kinases on cell viability, DNA damage response, and chromosomal integrity. Our results demonstrate that while single or dual kinase inhibition increased cytotoxicity, inhibition of all three PIKKs results in significantly higher synergistic lethality, chromosomal aberrations, and DNA double-strand break (DSB) induction as calculated by their synergy scores. These findings suggest that the overlapping redundancy of ATM, ATR, and DNA-PK functions is critical for cell survival, and their combined inhibition greatly disrupts DNA damage signaling and repair processes, leading to cell death. This study provides insights into the potential of multi-targeted DDR kinase inhibition as an effective anticancer strategy, necessitating further research to elucidate underlying mechanisms and therapeutic applications.
Study on ammonia and dimethyl ether oxidation and kinetic interaction up to 100 atm
NH 3 and DME dual fuel oxidation and kinetic coupling are experimentally studied by using a supercritical pressure jet-stirred reactor (SP-JSR) at 20 and 100 atm, over a temperature range of 500–900 K, and at fuel-lean and stoichiometric conditions with NH 3 to DME molar ratios of 4 and 0.62, respectively. An HP-Mech model for high-pressure NH3/DME oxidation is developed based on our previous studies and it shows generally better performance than other models in the literature on high-pressure oxidation experiments. Due to DME’s strong low-temperature reactivity, it dramatically enhances the oxidation of NH3 at low temperature. However, the effect of NH 3 on DME oxidation varies with temperature. At low temperatures, NH 3 inhibits low-temperature reactivity by consuming OH radicals. In addition, the NH 2 and NO x formation from NH 3 further suppresses the low-temperature DME reactivity by reducing alkylperoxyl and O 2 QOOH radicals via RO 2 + NH 2 = RO + H 2 NO, RO 2 + NO = RO + NO 2 and O 2 QOOH + NO = 2CH 2 O + HO 2 + NO 2 . At intermediate temperatures, due to enhanced kinetic coupling of NH 2 /NO x /HO 2 chemistry, DME oxidation is significantly promoted. It is found that there are two major NH 2 /NO x /HO 2 coupling pathways for OH radical production brought by NH 3 : (1) NH 2 + HO 2 = H 2 NO + OH and (2) NH 2 + NO 2 = H 2 NO + NO with NO + HO 2 = OH + NO 2 . Moreover, the resulting H 2 NO will further contribute to OH production via the H 2 NO/NO x /HONO coupling pathways: H 2 NO + NO 2 = HNO + HONO, HNO + NO 2 = HONO + NO, and HONO (+M) = OH + NO (+M). These new NH 2 /NO x /HO 2 and H 2 NO/NO x /HONO pathways play a critical role in promoting DME oxidation at intermediate temperatures. Novelty and Significance Statement: Blending NH 3 with DME can significantly enhance the reactivity of NH 3 and facilitate its practical application in advanced internal combustion engines. NH 3 /DME oxidation is studied in a novel supercritical pressure jet-stirred reactor up to 100 atm, a much higher pressure than previous studies. An interesting non-monotonic effect of NH3 addition on fuel oxidation has been found. Unique kinetic couplings of NH2/HO2/NOx and H2NO/NOx/HONO brough by NH3 and DME blending are identified to play important roles in radical generation and reactivity promotion. The valuable experimental data and key kinetics revealed in the current work can tremendously improve our understanding of NH 3 /DME oxidation via NO x /RO 2 and NH 2 / H 2 NO/HO 2 /NO x kinetic couplings at low to intermediate temperatures.
ATM signaling modulates cohesin behavior in meiotic prophase and proliferating cells
Cohesins are ancient and ubiquitous regulators of chromosome architecture and function, but their diverse roles and regulation remain poorly understood. During meiosis, chromosomes are reorganized as linear arrays of chromatin loops around a cohesin axis. This unique organization underlies homolog pairing, synapsis, double-stranded break induction, and recombination. We report that axis assembly in Caenorhabditis elegans is promoted by DNA-damage response (DDR) kinases that are activated at meiotic entry, even in the absence of DNA breaks. Downregulation of the cohesin-destabilizing factor WAPL-1 by ATM-1 promotes axis association of cohesins containing the meiotic kleisins COH-3 and COH-4. ECO-1 and PDS-5 also contribute to stabilizing axis-associated meiotic cohesins. Further, our data suggest that cohesin-enriched domains that promote DNA repair in mammalian cells also depend on WAPL inhibition by ATM. Thus, DDR and Wapl seem to play conserved roles in cohesin regulation in meiotic prophase and proliferating cells.
ATM–dependent phosphorylation of CHD7 regulates morphogenesis-coupled DSB stress response in fetal radiation exposure
Following radiation exposure, unrepaired DNA double-strand breaks (DSBs) persist to some extent in a subset of cells as residual damage; they can exert adverse effects, including late-onset diseases. In search of the factor(s) that characterize(s) cells bearing such damage, we discovered ataxia-telangiectasia mutated (ATM)-dependent phosphorylation of the transcription factor chromodomain helicase DNA binding protein 7 (CHD7). CHD7 controls the morphogenesis of cell populations derived from neural crest cells during vertebrate early development. Indeed, malformations in various fetal bodies are attributable to CHD7 haploinsufficiency. Following radiation exposure, CHD7 becomes phosphorylated, ceases promoter/enhancer binding to target genes, and relocates to the DSB-repair protein complex, where it remains until the damage is repaired. Thus, ATM-dependent CHD7 phosphorylation appears to act as a functional switch. As such stress responses contribute to improved cell survival and canonical nonhomologous end joining, we conclude that CHD7 is involved in both morphogenetic and DSB-response functions. Thus, we propose that higher vertebrates have evolved intrinsic mechanisms underlying the morphogenesis-coupled DSB stress response. In fetal exposure, if the function of CHD7 becomes primarily shifted toward DNA repair, morphogenic activity is reduced, resulting in malformations.
TChem-atm v1.0
SAND2024-11300O TChem-atm is a software library that was developed to solve complex kinetic models for atmospheric chemistry applications. TChem-atm interface employs a hierarchical parallelism design to exploit the massive parallelism available from modern computing platforms. It also supports gas atmospheric chemistry applications, e.g., the energy exascale earth system model. TChem can be used as a box model or coupled with a climate model to compute the time evolution of gas tracer species. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.
Methyl formate oxidation kinetics up to 100 atm
Methyl formate (MF, CH3OCHO), the simplest ester, is a representative oxygenated fuel with high oxygen content, and low sooting tendency. However, its oxidation behavior under high-pressure and intermediate-temperature conditions remains insufficiently understood, especially where low-temperature peroxy radical chemistry, methanol chemistry, and pressure-dependent reaction pathways play a critical role. In this study, MF oxidation experiments were conducted in the Princeton supercritical-pressure jet-stirred reactor (SP-JSR) at 20 and 100 atm over the temperature range of 400–950 K under both fuel-lean and fuel-rich conditions. Based on the experimental results, an updated HP-Mech was developed by incorporating previous MF sub-mechanisms, expanded low-temperature peroxy pathways, and evaluated pressure-dependent decomposition kinetics. The newly updated HP-Mech shows greatly improved performance in predicting the onset temperature, the key intermediate species fractions, methanol formation, and the progression of MF oxidation across all the experimental conditions. Path flux analysis indicates that MF consumption at the onset stage is dominated by H-abstraction at the methyl site, forming CH2OCHO radicals that lead to the formation and isomerization of O2CH2OCHO, driving low-temperature chain propagation. Moreover, H-abstraction at the formate site forms CH3OCO radicals that preferentially decompose to CH3, initiating the methanol formation pathway linked to CH3O2 and HO2 chemistry. At the same time, HO2 formation is strongly coupled to MF oxidation through multiple MF-derived radical pathways. HCO originates from MF oxidation and acts as a key coupling species linking fuel consumption to HO2 buildup, especially under high-pressure and intermediate-temperature conditions. In addition to this dominant channel, supplementary HO2 formation pathways involving CH3, CH3O, CH2OH, and CH3O2 reacting with O2 further connect methanol chemistry and oxygenated radical chemistry to the HO2 pool, indicating the central role of HO2 in governing MF oxidation. Sensitivity analysis identifies MF with OH/HO2/CH3O2 reactions and the HO2/H2O2/OH sequence as the key factors controlling reactivity in the high-pressure and intermediate-temperature regime. MF directly reacts with OH/HO2/CH3O2 to consume the fuel and produce reactive radicals like CH2OCHO and CH3OCO that undergo subsequent oxidation pathways. Moreover, HO2 recombination suppresses oxidation at lower temperatures, while thermal decomposition of H2O2 accelerates OH production and promotes fuel consumption as temperature increases. The direct formation of active OH from HO2 radicals further completes the mechanism, improving its prediction especially during the oxidation onset stage.
ATM Variants in Breast Cancer: Implications for Breast Radiation Therapy Treatment Recommendations
Advances in germline genetic testing have led to a surge in identification of ataxia-telangiectasia mutated (ATM) variant carriers among breast cancer patients, raising numerous questions regarding use of breast radiation therapy (RT) in this population.
RbB 3 Si 3 : An Alkali Metal Borosilicide that is Metastable and Superconducting at 1 atm
The stability, electronic structure and potential superconductivity in AB 3 Si 3 (A = Na, K, Rb, and Cs) compounds that assume the clathrate-based sodalite structure whose frameworks consists of covalent B-Si bonds is investigated via first-principles calculations. This structure type has recently been predicted in a number of high temperature superconducting hydrides, but these are only stable under megabar pressures. Herein, we predict a novel superconducting phase, RbB 3 Si 3 , that could be synthesized under pressures that are a factor of ten smaller, ~10 GPa, and quenched to atmospheric conditions. Electron-phonon coupling calculations predict that RbB 3 Si 3 possesses a superconducting critical temperature, T c , of 14 K at 1 atm. Here, the dynamic stability of RbB 3 Si 3 and CsB 3 Si 3 at ambient pressure can be explained by considering the chemical pressure exerted on the B-Si framework that is caused by the size effect of the alkali metal atom.
Self-organization in 1 atm DC glows with liquid anodes: current understanding and potential applications
Self-organization refers to the spontaneous generation of spatially or temporally organized patterns in an otherwise disordered system. Self-organization is ubiquitous in plasma physics particularly in the low-pressure regime as observed in astrophysical jets or plasma loaded flux loops that form on the surface of the Sun. In recent times, self-organization in atmospheric pressure plasmas has captured the attention of researchers. Its occurrence has been observed in DBD discharges as well as DC 1 atm glows with liquid electrodes. The mechanism of pattern formation is still not well understood. In this work, we briefly review the current understanding of pattern formation in DC glows with liquid anode, surveying past work, application areas, theories on mechanisms of formation from the context of reaction diffusion systems, current experimental work and computational progress towards predicting pattern formation.