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At least 559 records · Page 31

How microscopic epistasis and clonal interference shape the fitness trajectory in a spin glass model of microbial long-term evolution

The adaptive dynamics of evolving microbial populations takes place on a complex fitness landscape generated by epistatic interactions. The population generically consists of multiple competing strains, a phenomenon known as clonal interference. Microscopic epistasis and clonal interference are central aspects of evolution in microbes, but their combined effects on the functional form of the population’s mean fitness are poorly understood. Here, we develop a computational method that resolves the full microscopic complexity of a simulated evolving population subject to a standard serial dilution protocol. Through extensive numerical experimentation, we find that stronger microscopic epistasis gives rise to fitness trajectories with slower growth independent of the number of competing strains, which we quantify with power-law fits and understand mechanistically via a random walk model that neglects dynamical correlations between genes. We show that increasing the level of clonal interference leads to fitness trajectories with faster growth (in functional form) without microscopic epistasis, but leaves the rate of growth invariant when epistasis is sufficiently strong, indicating that the role of clonal interference depends intimately on the underlying fitness landscape. The simulation package for this work may be found at https://github.com/nmboffi/spin_glass_evodyn .

59 BASIC BIOLOGICAL SCIENCES↗

How microscopic epistasis and clonal interference shape the fitness trajectory in a spin glass model of microbial long-term evolution

The adaptive dynamics of evolving microbial populations takes place on a complex fitness landscape generated by epistatic interactions. The population generically consists of multiple competing strains, a phenomenon known as clonal interference. Microscopic epistasis and clonal interference are central aspects of evolution in microbes, but their combined effects on the functional form of the population’s mean fitness are poorly understood. Here, we develop a computational method that resolves the full microscopic complexity of a simulated evolving population subject to a standard serial dilution protocol. Through extensive numerical experimentation, we find that stronger microscopic epistasis gives rise to fitness trajectories with slower growth independent of the number of competing strains, which we quantify with power-law fits and understand mechanistically via a random walk model that neglects dynamical correlations between genes. We show that increasing the level of clonal interference leads to fitness trajectories with faster growth (in functional form) without microscopic epistasis, but leaves the rate of growth invariant when epistasis is sufficiently strong, indicating that the role of clonal interference depends intimately on the underlying fitness landscape. The simulation package for this work may be found at https://github.com/nmboffi/spin_glass_evodyn .

59 BASIC BIOLOGICAL SCIENCES↗

Analytical Modeling of Biomass Transport and Feeding Systems

The processing of biomass solids in a biorefinery consists of pretreatment, enzyme hydrolysis / concurrent fermentation of sugars to ethanol, product recovery, and drying. Sustainable operation requires a front end that transforms wet solids into a pumpable slurry. Otherwise the biorefinery will suffer unscheduled shut-downs and inefficient operation due to solids that obstruct pumps and other equipment and resist mixing in a bioreactor. Downtime in pioneer biorefineries due to interruptions from materials handling problems has been 50% or more, leading to unsustainable manufacturing processes. This work addresses new technology, predictive computational models, and definition of operational conditions that result in formation of slurries of corn stover at up to 300 g/L using low enzyme loadings (1 to 3 FPU cellulase/g) before the biomass (corn stover) enters the pretreatment step. A team of researchers from Purdue University, Idaho National Laboratory (INL), Forest Concepts, AdvanceBio, Argonne National Laboratory, and DOE BETO have combined their knowledge in agricultural and biological engineering, bioprocess engineering, mechanical engineering, chemical engineering, agricultural economics, materials engineering and enzyme and microbial technology to address the challenge of making lignocellulose flow. This team effort has resulted in the development and validation of conditions that employ low levels of commercial enzyme in an agitated bioreactor to which corn stover pellets are added resulting in formation of slurries at high solids loadings, before pretreatment. This approach overcomes challenges caused by handling of dry, particulate biomass materials at the front end of the biorefinery. The subsequent materials handling issues cause obstruction at pumps, pipes and valves. Formation of high loadings slurries with low yield stress, as reported here, significantly decreases the potential for process interruption and enhances plant operability. Key advances in the knowledge of how slurry formation occurs is reported here and in recently published journal papers. We found that pellets are needed to achieve high solids loading, and that commercial enzymes are effective in forming slurries of corn stover particles from pellets that have not been pretreated. Our work has resulted in models that predict solids behavior for formation of compressed solids and pellets that in turn facilitate slurries made of high concentrations of corn stover particles. A computational model was developed that gives mechanistic insights into properties of particles and mixing process that gives the slurry rheology needed to facilitate pumping. Hence, the corn stover may be pumped into a pretreatment reactor in place of auguring in solids against high pressure which is a root cause of interruptions at the front end of a biorefinery. Subsequent mixing in enzyme and microbial bioreactors results in conversion of lignocellulose to sugars in a biorefinery in agitated bioreactors, with flows in and out of the vessels being less likely to be interrupted due to plugging or materials handling problems. The obtained data coupled to process models, techno-economic assessment (TEA) and Life Cycle Analysis (LCA) were used to assess whether this approach is practical. These results are based on a foundation of laboratory characterization and pilot runs. The NREL biochemical sugar model was utilized to carry out techno-economic analysis of enzyme catalyzed liquefaction followed by enzyme hydrolysis. The minimum sugar selling price was between 17.5 and 18.3 ¢/pound or about the same as calculated by the NREL model for dilute acid pretreatment followed by enzyme hydrolysis. Life cycle analysis (LCA) based on Argonne’s Greet Model showed the enzyme catalyzed route had the lowest greenhouse gas emissions of the three combinations studied (i.e., enzyme, enzyme mimetic, and enzyme + mimetic combined). GHG emissions for enzyme-based corn stover liquefaction step, alone, were about 21 g CO 2 -equivalent/kg of liquefied slurry. We believe this approach will further enhance operability of a pioneer biorefinery, and bring large-scale conversion of lignocellulosic biomass to low carbon footprint biofuels closer to implementation.

09 BIOMASS FUELS↗

First Principle based Thermal Conductivity Modeling of Metal Alloys with Applications on Uranium Alloys

Thermal conductivity is an important materials property related to heat transport, which is essential to many applications, ranging from thermoelectrics to nuclear reactor materials. High- quality thermal conductivity data is critical to these materials and their associated technologies, including the nuclear fuel materials like traditional oxide fuels and metallic uranium (U) fuels, e.g. U-Zr and U-Mo alloys. And thermal conductivity modeling is widely used to interpolate or extrapolate experimental data, to obtain high-quality thermal conductivity data over wide temperature and composition range, and to understand the impacts of different factors including defects and microstructures. However, a general thermal conductivity model for metal alloys which can work regrading different phase components is still missing. Also, for U alloys, a thermal conductivity model working with different phases is needed. Therefore, in this work, we developed thermal conductivity models for metal alloys, based on ab-initio calculations, semi-classical physics rules, and limited experimental data. The goals of these models are to help obtain high- quality thermal conductivity data within a little experimental input as possible, have models that are extendable to varying microstructures, including different types of irradiation effects, and provide mechanistic understanding of heat transfer in the modeled alloys. In this work, our model solves several challenges in the development. The DFT-BTE approach is applied to decrease the reliance on experimental data and make the model extendable to composition changes and defects. A practical and efficient way to combine the DFT inputs with physics rules is pointed out in this work too. A staged approach, which starts from simple cases of elemental metals, then extends to solid solutions, different compound phases, and multi-phase mixtures, is presented to work with the metal alloys in different phase components. Our models are demonstrated respectively on aU for elemental metal model, on U-Zr and U-Mo alloys in aU temperature range for multi-phase mixture model, on high-temperature U-Zr, U-Nb, and U-Mo alloys in the body-centered cubic phase for concentrated solid solution model, and on irradiated U-Mo alloys for irradiated metal alloy model. All models show great agreement with experimental data. In these demonstrations, our model shows its advantages compared to previous empirical fitting model. Our model requires fewer experimental data, due to the inputs from DFT. The quantitative insights into the different physical factors are provided in our model, as it incorporates the electron and phonon scattering mechanisms. Our model also can be extended to incorporate the contributions of point defects, grain boundaries, and noble gas bubbles, to integrate their effects on heat transfer. This model can serve as both a foundation for understanding the more complex thermal conductivity of realistic U alloy fuels and a useful tool to guide further modeling of thermal conductivity to aid materials and device design.

11 - NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Thermochemical Modeling of Radionuclide Vapor-Liquid Equilibria in Sodium Pools for SFR Mechanistic Source Term Analysis

Mechanistic source term (MST) analysis of sodium fast reactors (SFR) requires understanding of various radionuclide (RN) transport phenomena influencing potential releases from the fuel to the environment. One such phenomenon includes the retention or release of RNs from the sodium coolant pool, representing the step after possible fuel failures and influencing transport to the cover gas region. Thermodynamic vapor-liquid equilibria (VLE) calculations were performed on systems representing SFR sodium pools containing oxygen impurities and radionuclide (RN) inventories. First, an assessment and recreation of a previously developed thermodynamic database was completed, including updates to thermodynamic parameters. The RN inventories used in VLE calculations represented hypothetical source terms that might be released to the pool during previously analyzed fuel failure scenarios. The calculations were performed for all possible combinations of sodium pool size (i.e., total oxygen) and number of failed fuel pins (i.e., total RNs). In this way, multiple ratios of the RN relative to the oxygen impurity (RN:O) were compared for their impact on RN volatility, which is discussed in terms of the vapor fraction (VF), defined as the fraction of the RN that is calculated to exist in the vapor phase at equilibrium above condensed phases of that element. Similar trends in VLE behavior are seen in the equilibrium calculation results for elements of similar chemistry, and for some element types, it was found that the RN:O ratio can be important due to oxide formation, which typically exist in the condensed phase.

Shahbazi, Shayan↗

Personalized whole-brain neural mass models reveal combined Aβ and tau hyperexcitable influences in Alzheimer's disease.

Neuronal dysfunction and cognitive deterioration in Alzheimer's disease (AD) are likely caused by multiple pathophysiological factors. However, mechanistic evidence in humans remains scarce, requiring improved non-invasive techniques and integrative models. We introduce personalized AD computational models built on whole-brain Wilson-Cowan oscillators and incorporating resting-state functional MRI, amyloid-β (Aβ) and tau-PET from 132 individuals in the AD spectrum to evaluate the direct impact of toxic protein deposition on neuronal activity. This subject-specific approach uncovers key patho-mechanistic interactions, including synergistic Aβ and tau effects on cognitive impairment and neuronal excitability increases with disease progression. The data-derived neuronal excitability values strongly predict clinically relevant AD plasma biomarker concentrations (p-tau217, p-tau231, p-tau181, GFAP) and grey matter atrophy obtained through voxel-based morphometry. Furthermore, reconstructed EEG proxy quantities show the hallmark AD electrophysiological alterations (theta band activity enhancement and alpha reductions) which occur with Aβ-positivity and after limbic tau involvement. Microglial activation influences on neuronal activity are less definitive, potentially due to neuroimaging limitations in mapping neuroprotective vs detrimental activation phenotypes. Mechanistic brain activity models can further clarify intricate neurodegenerative processes and accelerate preventive/treatment interventions.

60 APPLIED LIFE SCIENCES↗

Recent Trends in Global Ocean Chlorophyll

Recent analyses of SeaWiFS data have shown that global ocean chlorophyll has increased more than 5% since 1998. The North Pacific ocean basin has increased nearly 19%. To understand the causes of these trends we have applied the newly developed NASA Ocean Biogeochemical Assimilation Model (OBAM), which is driven in mechanistic fashion by surface winds, sea surface temperature, atmospheric iron deposition, sea ice, and surface irradiance. The mode1 utilizes chlorophyll from SeaWiFS in a daily assimilation. The model has in place many of the climatic variables that can be expected to produce the changes observed in SeaWiFS data. Th~s enables us to diagnose the model performance, the assimilation performance, and possible causes for the increase in chlorophyll.

Gregg, Watson↗

Microbial inoculants and invasions: a call to action

Microbial inoculants are increasingly used for beneficial purposes in agriculture, bioremediation, and medicine, but they can carry risks of generating invasive microbes. Here, we present a roadmap for guarding against these invasions, proposing developing (i) coherent mechanistic understandings of how microbial inoculants can effect invasions, (ii) predictive models forecasting microbial invasion risks, and (iii) effective management strategies. To guide mechanistic understandings, we distill 17 guiding hypotheses. For predictive modeling, we highlight data collection needs and qualitative approaches. For management strategies, we stress the importance of accurately weighing the risks against benefits. The unified approach presented here provides a route toward an effective research and management infrastructure for microbial inoculants in order to avoid potentially catastrophic microbial invasions.

invasive species↗

Applicability of 1D site response analysis to shallow sedimentary basins: A critical evaluation through physics-based 3D ground motion simulations

One-dimensional site response analysis (1D SRA) remains the standard practice in considering the effect of local soil deposits and predicting site-specific ground motions, although its range of applicability to realistic seismic wavefields is still in question. In this 1D approach, horizontal and vertical ground shaking are assumed to be induced by vertically propagating shear and compressional waves, respectively. A recent study based on analytical two-dimensional (2D) plane waves and simple point source earthquake simulations has shown two mechanistic limitations in this 1D modelling technique for general inclined seismic waves, that is, systematic over-prediction of the vertical motion and wave trapping in the 1D soil column. In this article, we evaluate in detail the applicability of this 1D modelling approach to realistic three-dimensional (3D) simulated seismic wavefields in shallow sedimentary basins. Linear-viscoelastic 1D SRA predictions using two types of input motions that are commonly used in practice—rock outcrop and in-column motions, are compared with the reference true site response results from 3D earthquake simulations in terms of various measures in the frequency and time domain. It is shown that the horizontal motion in the 3D seismic wavefield exhibits dominant shear wave propagation phenomenon, while the vertical motion is a combined effect of compressional and shear waves and can be over-predicted by the 1D approach when the incident seismic waves are inclined. Direct evidence of the wave refraction process that leads to the vertical motion over-prediction is provided. 1D SRA with in-column inputs can yield motions that have significantly longer duration compared to the true 3D site response solution due to trapped waves, casting in doubt the frequent need for increased soil damping in existing site studies to compensate for wave attenuation due to scattering alone. Sensitivity investigation on the increase of soil profile damping by a multiplier D mul shows D mul values compatible with those found in the literature for both horizontal and vertical motions. It is shown that the level of D mul optimized for a best match of the spectral acceleration is dependent on the characteristic of the input motion and a larger D mul is typically required for the vertical component. In contrast, 1D SRA with outcrop motions predicts motions with shorter significant duration due to its inability to capture the basin-edge generated surface waves. A suite of ground motion simulations was performed to assess the sensitivity of the observations to the basin geologic structure including the velocity gradient, rock-basin impedance contrast and basin depth. The analysis results show that the accuracy of the simplified 1D procedure is dependent on the wavefield composition of both the input motions and the true 3D site response solution. While the horizontal motions in shallow sedimentary basins can, to the first order, be reasonably captured by the simplified 1D approach, 1D SRA for the vertical component is in general not reliable and contributions from inclined shear waves should be accounted for in site-specific evaluation of the vertical design ground motion.

1D assumption↗

Sequential oxidation-depolymerization strategies for lignin conversion to low molecular weight aromatic chemicals

Lignin is the largest source of bio-derived aromatic chemicals, and oxidative conversion of this polymeric material can generate valuable oxygenated aromatic compounds. Oxidative depolymerization of lignosulfonate feedstocks under alkaline conditions is used commercially for vanillin production. Recent studies have led to other oxidation methods that access different aromatic products from lignin in good yields. A particularly effective strategy that accesses some of the highest yields of aromatic monomers to date features a two-step process in which the oxidation of specific alcohol groups in lignin is followed by an oxidative, reductive, or redoxneutral step that cleaves the polymer into aromatic monomers and oligomers. Studies of model compounds have provided crucial mechanistic insights and contributed to the development of effective lignin depolymerization methods. Furthermore, this review provides a general overview of lignin depolymerization methods, followed by a survey of oxidation-depolymerization methods that access oxygenated aromatic monomers in good yields.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Selective phosphate removal with manganese oxide composite anion exchange membranes in membrane capacitive deionization

The discharge of excessive phosphorous into water bodies can lead to serious eutrophication threatening aquatic ecosystem. Membrane capacitive deionization (MCDI) is an effective platform for deionizing aqueous streams; however, conventional MCDI is unable to selectively remove targeted ions from a liquid mixture. Here, in this work, we fabricated manganese oxide composite anion exchange membranes (AEMs) for MCDI to enhance phosphate removal selectivity from sodium chloride-sodium dihydrogen phosphate (10:1 M ratio) aqueous mixtures. We systematically investigated several critical factors, such as constant current or voltage operation, applied voltage amount, process stream pH, and manganese oxide (Mn 2 O 3 ) content in the AEM, on phosphate removal efficiency and phosphate selectivity. A trade-off was observed between phosphate removal and selectivity when increasing the cell voltage. Under the best conditions, a MCDI unit with a 20 wt% Mn 2 O 3 composite AEM and a bipolar membrane facilitated high phosphate removal efficiency of ≥ 31.8 % and a phosphate over chloride selectivity of 1.1 while showing stability for at least 30 cycles. To help understand how Mn 2 O 3 composite AEM boosts phosphate selectivity, static electronic structure calculations were performed, and they revelated that hydrogen phosphate absorption on Mn 2 O 3 composite AEM was 314 kcal/mol more exothermic than that on pristine AEM while chloride adsorption on Mn 2 O 3 composite AEM was 2.2 kcal/mol less exothermic than that on a pristine AEM. Overall, this work presents an effective strategy for selectively removing phosphate from model wastewater solutions and the mechanistic understanding that governs ion selectivity in composite ion-exchange membranes used in MCDI.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Mechanisms of Three-Dimensional Solid-Phase Epitaxial Crystallization of Strontium Titanate

Strontium titanate (SrTiO 3 , STO) is a complex metal oxide with a cubic perovskite crystal structure. Due to its easily described and understood crystal structure in the cubic phase, STO is an ideal model system for exploring the mechanistic details of solid-phase epitaxy (SPE) in complex oxides. SPE is a crystallization approach that aims to guide crystal growth at low homologous temperatures to achieve targeted microstructures. Beyond planar thin films, SPE can also exploit the addition of a chemically inert, noncrystallizing, amorphous obstacle in the path of crystallization to generate complex three-dimensional structures. The introduction of this mask fundamentally alters the SPE process, inducing a transition from two- to three-dimensional geometries and from vertical to lateral crystal growth under the influence of the crystal/mask/amorphous boundary. Using a combination of molecular dynamics simulations and experiments, we identify several unique phenomena in the nanoscale growth behaviors in both conventional (unmasked) and masked SPE. Examining conventional SPE of STO, we find that crystallization at the interface is strongly correlated to, and potentially driven by, density fluctuations in the region of the amorphous STO near the crystalline/amorphous interface with a strong facet dependence. In the masked case, we find that the crystalline growth front becomes nonplanar near contact with the mask. We also observe a minimum vertical growth requirement prior to lateral crystallization. Both phenomena depend on the relative bulk and interfacial free energies of the three-phase (crystal/mask/amorphous) system.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Real-Space Constrained Density Functional Theory Investigation of Site-Specific, Interfacial Charge Recombination Dynamics Across the Au Nanoparticle/TiO 2 Heterojunction

Au nanoparticle (NP)/TiO 2 heterojunction is a representative system to study interfacial charge transfer in photocatalysis and photovoltaics, where suppressing recombination from TiO 2 to Au can enhance hot carrier extraction. We apply real-space constrained density functional theory (CDFT) with Marcus theory to quantify charge recombination time scales across Au/TiO 2 . This approach enables direct control and visualization of charge-separated states, aligning with site-specific probes like time-resolved X-ray photoelectron spectroscopy (trXPS). We find that the charge-separated state features a bipolaron, with recombination dominated by TiO 2 LUMO to Au HOMO transitions, primarily at interfacial Au sites. Marcus rate predictions are benchmarked with surface hopping methods, quantifying differences in time scales and computational efficiency. Lastly, we examine how the Au cluster size affects the free energy change (ΔG) and reorganization energy (λ), explaining trends in closed-shell systems and highlighting challenges for open-shell extrapolations. Overall, CDFT + Marcus theory provides efficient, mechanistically transparent interfacial charge transfer modeling, and we clearly defined its applicability and limitation.

Glenna, Drew M. [Univ. of Idaho, Idaho Falls, ID (↗

Optically Pure C 1 -Symmetric Cyclic(alkyl)(amino)carbene Ruthenium Complexes for Asymmetric Olefin Metathesis

An expedient access to the first optically pure ruthenium complexes containing C 1 -symmetric cyclic (alkyl)(amino)carbene (CAAC) ligands is reported. Furthermore, they demonstrate excellent catalytic performances in asymmetric olefin metathesis with high enantioselectivities (up to 92% ee). Preliminary mechanistic insights provided by DFT models highlight the origin of the enantioselectivity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Dynamic conformational switching underlies TFIIH function in transcription and DNA repair and impacts genetic diseases

Transcription factor IIH (TFIIH) is a protein assembly essential for transcription initiation and nucleotide excision repair (NER). Yet, understanding of the conformational switching underpinning these diverse TFIIH functions remains fragmentary. TFIIH mechanisms critically depend on two translocase subunits, XPB and XPD. To unravel their functions and regulation, we build cryo-EM based TFIIH models in transcription- and NER-competent states. Using simulations and graph-theoretical analysis methods, we reveal TFIIH’s global motions, define TFIIH partitioning into dynamic communities and show how TFIIH reshapes itself and self-regulates depending on functional context. Our study uncovers an internal regulatory mechanism that switches XPB and XPD activities making them mutually exclusive between NER and transcription initiation. By sequentially coordinating the XPB and XPD DNA-unwinding activities, the switch ensures precise DNA incision in NER. Mapping TFIIH disease mutations onto network models reveals clustering into distinct mechanistic classes, affecting translocase functions, protein interactions and interface dynamics.

59 BASIC BIOLOGICAL SCIENCES↗

Thermally driven surface phase separation in intermetallic alloys

Intermetallic compounds are widely recognized for their high-temperature phase stability and resistance to composition and structural changes. However, we reveal athermally activated bulk-to-surface mass exchange mechanism that drives surface phase separation, resulting in the formation of surface precipitates with distinct composition andstructure from the bulk matrix. Using the archetypal β-NiAl system, we show that asymmetries in vacancy formation energies between Ni and Al atoms induce preferential Ni segregation to the surface, forming Ni-rich γ'-Ni 3 Al precipitates. By integrating in-situ electron microscopy, synchrotron X-ray absorption spectroscopy and first-principles computational modeling, we establish a direct mechanistic connection between bulk thermal defect dynamics, surface compositional evolution, and phase segregation behavior. This bulk-surface coupling mechanism can be a driver of surface phase separation in multicomponent alloys under thermal stress. In conclusion, these results refine the thermodynamic boundaries of intermetallic stability and provide insights into managingthe performance and durability of intermetallic alloys for demanding high-temperature applications.

36 MATERIALS SCIENCE↗

Challenges for density functional theory: calculation of CO adsorption on electrocatalytically relevant metals

Density Functional Theory (DFT) is currently the most tractable choice of theoretical model used to understand the mechanistic pathways for electrocatalytic processes such as CO 2 or CO reduction. In this work, we assess the performance of two DFT functionals designed specifically to describe surface interactions, RTPSS and RPBE, as well as two popular meta-GGA functionals, SCAN and B97M-rV, that have not been a priori optimized for better interfacial properties. We assess all four functionals against available experimental data for prediction of bulk and bare surface properties on four electrocatalytically relevant metals, Au, Ag, Cu, and Pt, and for binding CO to surfaces of these metals. To partially mitigate issues such as thermal and anharmonic corrections associated with comparing computations with experiments, molecular benchmarks against high level quantum chemistry are reported for CO complexes with Au, Ag, Cu and Pt atoms, as well as the CO–water complex and the water dimer. Overall, we find that the surface modified RPBE functional performs reliably for many of the benchmarks examined here, and the meta-GGA functionals also show promising results. Specifically B97M-rV predicts the correct site preference for CO binding on Ag and Au (the only functional tested here to do so), while RTPSS performs well for surface relaxations and binding of CO on Pt and Cu.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗