DLTKcat: deep learning-based prediction of temperature-dependent enzyme turnover rates.

The enzyme turnover rate, ${k}_{cat}$, quantifies enzyme kinetics by indicating the maximum efficiency of enzyme catalysis. Despite its importance, ${k}_{cat}$ values remain scarce in databases for most organisms, primarily because of the cost of experimental measurements. To predict ${k}_{cat}$ and account for its strong temperature dependence, DLTKcat was developed in this study and demonstrated superior performance (log10-scale root mean squared error = 0.88, R-squared = 0.66) than previously published models. Through two case studies, DLTKcat showed its ability to predict the effects of protein sequence mutations and temperature changes on ${k}_{cat}$ values. Although its quantitative accuracy is not high enough yet to model the responses of cellular metabolism to temperature changes, DLTKcat has the potential to eventually become a computational tool to describe the temperature dependence of biological systems.

The S1 to S2 and S2 to S3 state transitions in plant photosystem II: relevance to the functional and structural heterogeneity of the water oxidizing complex.

In Photosystem II, light-induced water splitting occurs via the S state cycle of the CaMn4O5-cluster. To understand the role of various possible conformations of the CaMn4O5-cluster in this process, the temperature dependence of the S1 → S2 and S2 → S3 state transitions, induced by saturating laser flashes, was studied in spinach photosystem II membrane preparations under different conditions. The S1 → S2 transition temperature dependence was shown to be much dependent on the type of the cryoprotectant and presence of 3.5% methanol, resulting in the variation of transition half-inhibition temperature by 50 K. No similar effect was observed for the S2 → S3 state transition, for which we also show that both the low spin g = 2.0 multiline and high spin g = 4.1 EPR configurations of the S2 state advance with similar efficiency to the S3 state, both showing a transition half-inhibition temperature of 240 K. This was further confirmed by following the appearance of the Split S3 EPR signal. The results are discussed in relevance to the functional and structural heterogeneity of the water oxidizing complex intermediates in photosystem II.

Temperature dependence of pollen germination and tube growth in conifers relates to their distribution along an elevational gradient in Washington State, USA.

BACKGROUND AND AIMS: Pollen germination and tube growth are essential processes for successful fertilization. They are among the most temperature-vulnerable stages and subsequently affect seed production and determine population persistence and species distribution under climate change. Our study aims to investigate intra- and inter-specific variations in the temperature dependence of pollen germination and tube length growth and to explore how these variations differ for pollen from elevational gradients. METHODS: We focused on three conifer species, Pinus contorta, Picea engelmannii, and Pinus ponderosa, with pollen collected from 350 to 2200m elevation in Washington State, USA. We conducted pollen viability tests at temperatures from 5 to 40°C in 5°C intervals. After testing for four days, we took images of these samples under a microscope to monitor pollen germination percentage (GP) and tube length (TL). We applied the Gamma function to describe the temperature dependence of GP and TL and estimated key parameters, including the optimal temperature for GP (Topt_GP) and TL (Topt_TL). KEY RESULTS: Results showed that pollen from three species and different elevations within a species have different GP, TL, Topt_GP, and Topt_TL. The population with a higher Topt_GP would also have a higher Topt_TL, while Topt_TL was generally higher than Topt_GP, i.e., a positive but not one-to-one relationship. However, only Pinus contorta showed that populations from higher elevations have lower Topt_GP and Topt_TL and vice versa. The variability in GP increased at extreme temperatures, whereas the variability in TL was greatest near Topt_TL. CONCLUSIONS: Our study demonstrates the temperature dependences of three conifers across a wide range of temperatures. Pollen germination and tube growth are highly sensitive to temperature conditions and vary among species and elevations, affecting their reproduction success during warming. Our findings can provide valuable insights to advance our understanding of how conifer pollen responds to rising temperatures.

Temperature-dependent excitonic emission characteristics of highly crystallized carbon nitride nanosheets.

Highly-crystallized carbon nitride (HCCN) nanosheets exhibit significant potential for advancements in the field of photoelectric conversion. However, to fully exploit their potential, a thorough understanding of the fundamental excitonic photophysical processes is crucial. Here, the temperature-dependent excitonic photoluminescence (PL) of HCCN nanosheets and amorphous polymeric carbon nitride (PCN) is investigated using steady-state and time-resolved PL spectroscopy. The exciton binding energy of HCCN is determined to be 109.26 meV, lower than that of PCN (207.39 meV), which is attributed to the ordered stacking structure of HCCN with a weaker Coulomb interaction between electrons and holes. As the temperature increases, a noticeable reduction in PL lifetime is observed on both the HCCN and PCN, which is ascribed to the thermal activation of carrier trapping by the enhanced electron-phonon coupling effect. The thermal activation energy of HCCN is determined to be 102.9 meV, close to the value of PCN, due to their same band structures. Through wavelength-dependent PL dynamics analysis, we have identified the PL emission of HCCN as deriving from the transitions:σ*-LP,π*-π, andπ*-LP, where theπ*-LP transition dominants the emission because of the high excited state density of the LP state. These results demonstrate the impact of high-crystallinity on the excitonic emission of HCCN materials, thereby expanding their potential applications in the field of photoelectric conversion.

Polyparameter Linear Free Energy Relationships for Partitioning of Neutral Organic Compounds to Storage Lipids.

Storage lipids are an important compartment in the bioaccumulation of neutral organic compounds. Reliable models for predicting storage lipid-water and storage lipid-air partition coefficients (Kislip/w and Kislip/a), as well as their temperature dependence, are considered useful. Polyparameter linear free energy relationships (PP-LFERs) are accurate, general, and mechanistically clear models for predicting partitioning-related physicochemical quantities. About a decade ago, PP-LFERs were calibrated for Kislip/w at the physiological temperature of 37 °C. However, to date, a comprehensive collection and sufficiently reliable PP-LFERs for Kislip/w and Kislip/a at the most common standard temperature of 25 °C are still lacking. In this study, experimentally based Kislip/w and/or Kislip/a values at 25 °C for 278 compounds were extensively collected or converted from the literature. Subsequently, PP-LFERs were calibrated for Kislip/w and Kislip/a at 25 °C, performing well over 10 orders of magnitude with root-mean-square errors of 0.17-0.21 log units for compounds with reliable descriptors. Furthermore, standard internal energy changes of transfer from water or air to storage lipids for 158 compounds were derived and used to calibrate PP-LFERs for estimating the temperature dependence of Kislip/w or Kislip/a. Additionally, using PP-LFERs, low-density polyethylene was confirmed to be a better storage lipid analogue than silicone and polyoxymethylene in the equilibrium passive sampling of nonpolar and H-bond acceptor polar compounds.

Investigating Temperature-Dependent Microscopic Deformation in Tough and Self-Healing Hydrogel Using Time-Resolved USAXS.

Tough and self-healing hydrogels are typically sensitive to loading rates or temperatures due to the dynamic nature of noncovalent bonds. Understanding the structure evolution under varying loading conditions can provide valuable insights for developing new tough soft materials. In this study, polyampholyte (PA) hydrogel with a hierarchical structure is used as a model system. The evolution of the microscopic structure during loading is investigated under varied loading temperatures. By combining ultra-small angle X-ray scattering (USAXS) and Mooney-Rivlin analysis, it is elucidated that the deformation of bicontinuous hard/soft phase networks is closely correlated with the relaxation dynamics or strength of noncovalent bonds. At high loading temperatures, the gel is soft and ductile, and large affine deformation of the phase-separated networks is observed, correlated with the fast relaxation dynamics of noncovalent bonds. At low loading temperatures, the gel is stiff, and nonaffine deformation occurs from the onset of loading due to the substantial breaking of noncovalent bonds and limited chain mobility as well as weak adaptation of phase deformation to external stretch. This work provides an in-depth understanding of the relationship between structure and performance of tough and self-healing hydrogels.

Temperature Dependence of the Number of Defect-Structures in Poly(vinylidene fluoride).

Poly(vinylidene fluoride) (PVDF) is predominantly characterized by alternating CH2 and CF2 units in a polymer backbone, originating from the head-to-tail addition of monomers or regular propagation. Due, to a small extent, to inverse monomer addition, so-called defect structures occur which influence the macroscopic properties of PVDF significantly. The amount of defect structures in the material is determined by the polymerization conditions. Here, the temperature dependence of the fraction of defect structures in PVDF obtained from polymerizations between 45 and 90 °C is reported. We utilized 19F-NMR spectroscopy to determine the fraction of defect structures as a function of temperature. To derive kinetic data, the polymerization of VDF is considered a quasi-copolymerization described by the Terminal Model involving four different propagation reactions. Based on the experimentally determined temperature-dependent fractions of defect structures, the known overall propagation rate coefficient, and taking into account the self-healing behavior of the macroradical, the Arrhenius parameters of the individual propagation rate coefficients were determined using the Monte Carlo methods.

The Temperature Dependence of Hydrogen Bonds Is More Uniform in Stable Proteins: An Analysis of NMR h3JNC' Couplings in Four Different Protein Structures.

Long-range HNCO NMR spectra for proteins show crosspeaks due to 1JNC', 2JNC', 3JNCγ, and h3JNC' couplings. The h3JNC' couplings are transmitted through hydrogen bonds and their sizes are correlated to hydrogen bond lengths. We collected long-range HNCO data at a series of temperatures for four protein structures. P22i and CUS-3i are six-stranded beta-barrel I-domains from phages P22 and CUS-3 that share less than 40% sequence identity. The cis and trans states of the C-terminal domain from pore-forming toxin hemolysin ΙΙ (HlyIIC) arise from the isomerization of a single G404-P405 peptide bond. For P22i and CUS-3i, hydrogen bonds detected by NMR agree with those observed in the corresponding domains from cryoEM structures of the two phages. Hydrogen bond lengths derived from the h3JNC' couplings, however, are poorly conserved between the distantly related CUS-3i and P22i domains and show differences even between the closely related cis and trans state structures of HlyIIC. This is consistent with hydrogen bond lengths being determined by local differences in structure rather than the overall folding topology. With increasing temperature, hydrogen bonds typically show an apparent increase in length that has been attributed to protein thermal expansion. Some hydrogen bonds are invariant with temperature, however, while others show apparent decreases in length, suggesting they become stabilized with increasing temperature. Considering the data for the three proteins in this study and previously published data for ubiquitin and GB3, lowered protein folding stability and cooperativity corresponds with a larger range of temperature responses for hydrogen bonds. This suggests a partial uncoupling of hydrogen bond energetics from global unfolding cooperativity as protein stability decreases.

Modeling the temperature dependence of the fluorescence properties of Indole in aqueous solution.

In a recent paper, we proposed a scheme to describe the relaxation mechanism of the excited Indole in aqueous solution, involving the fluctuations among the diabatic electronic states 1Lb, 1La and 1πσ∗. Such a theoretical and computational model reproduced accurately the available experimental data at room temperature. Following these results, in the present work, we model the complex temperature dependence of the fluorescence properties of Indole in aqueous solution, with results further validating the proposed relaxation scheme. This scheme is able to explain the temperature effects on the fluorescence behavior indicating the water fluctuations as the main cause of (i) the stabilization of the dark state (1πσ∗) and (ii) the increase in temperature of the kinetics of the irreversible transition towards such a state.

Temperature dependence of the dielectric function and critical points of monolayer WSe2.

Monolayer materials typically display intriguing temperature-dependent dielectric and optical properties, which are crucial for improving the structure and functionality of associated devices. Due to its unique photoelectric capabilities, monolayer WSe2 has recently received a lot of attention in the fields of atomically thin electronics and optoelectronics. In this work, we focus on the evolution of the temperature-dependent dielectric function (ε = ε1 + i ε2) of monolayer WSe2 over energies from 0.74 to 6.40 eV and temperatures from 40 to 350 K. We analyze the second derivatives of ε with respect to energy to accurately locate the critical points (CP). The dependence of the observed CP energies on temperature is consistent with the alternative domination of the declining exciton binding energy as the temperature increases.

Temperature Dependence of Platelet Metabolism.

Temperature plays a fundamental role in biology, influencing cellular function, chemical reaction rates, molecular structures, and interactions. While the temperature dependence of many biochemical reactions is well defined in vitro, the effect of temperature on metabolic function at the network level is poorly understood, and it remains an important challenge in optimizing the storage of cells and tissues at lower temperatures. Here, we used time-course metabolomic data and systems biology approaches to characterize the effects of storage temperature on human platelets (PLTs) in a platelet additive solution. We observed that changes to the metabolome with storage time do not simply scale with temperature but instead display complex temperature dependence, with only a small subset of metabolites following an Arrhenius-type relationship. Investigation of PLT energy metabolism through integration with computational modeling revealed that oxidative metabolism is more sensitive to temperature changes than glycolysis. The increased contribution of glycolysis to ATP turnover at lower temperatures indicates a stronger glycolytic phenotype with decreasing storage temperature. More broadly, these results demonstrate that the temperature dependence of the PLT metabolic network is not uniform, suggesting that efforts to improve the health of stored PLTs could be targeted at specific pathways.

Prediction of Thermo-Mechanical Properties of 8-Harness Satin-Woven C/C Composites by Asymptotic Homogenization.

The elasticity matrix and the coefficients of thermal expansion (CTEs) of 8-harness satin-woven (8HS) carbon-fiber-reinforced carbon matrix (C/C) composites at high temperatures were obtained by the asymptotic homogenization method (AHM) and finite element method (FEM). By analyzing the microstructure of the 8HS C/C composites, a representative volume element (RVE) model considering a braided structure was established. The effects of the temperature and component volume fraction on the elasticity matrix and CTEs of the composites were investigated. The sensitivity of model parameters, including the size of RVE model and mesh sensitivity, were studied. The optimal calculation model was employed. In addition, the effects of the 4HS methods and 8HS methods on the elastic constants of the composites were compared. The temperature and variation in the carbon fiber volume fraction were found to have a significant impact on the elasticity matrix and CTEs of composite materials. At the same volume fraction of carbon fibers, some elastic coefficients of the 4HS composite material were slightly lower than those of 8HS composite material. This research affords a computational strategy for the accurate prediction of the themo-mechanical properties of satin-woven C/C composites.

Beyond a deterministic representation of the temperature dependence of soil respiration.

Soil CO2 efflux represents a complex interplay of biological and physical processes that result in the production and transfer of CO2 from soils to the atmosphere. Temperature has been widely recognized as a critical factor regulating soil CO2 efflux and is commonly utilized in deterministic empirical models to predict this important flux for the carbon cycle. This study introduces the Bernstein copula-based cosimulation (BCC) as a data-driven probabilistic approach to model the temperature-soil CO2 efflux relationship. The BCC accounts for the joint probability distribution and temporal dependence of soil CO2 efflux, which are often overlooked in deterministic models. The BCC was implemented as a proof of concept using two years of data on soil CO2 efflux conditioned by soil temperature in a temperate forest. The BBC accurately reproduced the original probability distribution, temporal dependency, and temperature-soil CO2 efflux relationship. Our findings show that a deterministic method, such as the commonly employed exponential relationship between soil CO2 efflux and temperature, is limited for comprehensively capturing the intricate nature of the temperature-soil CO2 efflux relationship. This is due to the confounding and interacting effects of environmental drivers beyond temperature, which are not fully accounted for in such a deterministic approach. Furthermore, the BCC revealed that the probability density between the joint cumulative probability of temperature and soil CO2 efflux is not constant, which raises the concern that deterministic approaches introduce incorrect assumptions for estimating temperature-soil CO2 relationship. In conclusion, we propose that probabilistic approaches hold promise for effectively depicting dependency relationships for soil CO2 efflux modeling, and for improving predictions of the effects of weather variability and climate change.

Analytical Calculation of Relationship Temperature and Fatigue and Creep Strength Based on Thermal Activation.

The purpose of this study was to formulate a mathematical expression for the temperature dependence of adhesive strength using various parameters. Adhesive structures are typically exposed to a broad temperature range, spanning from low to high temperatures; therefore, understanding how their strength depends on temperature is crucial. The strength was measured through tensile, fatigue, and creep tests at temperatures ranging from -60 °C to 135 °C. The properties of these test types were thoroughly investigated by analyzing the strength of the test results from a thermal activity perspective. The results demonstrate that there is a clear relationship between temperature and strength. The intensity decreased with temperature according to the exponential function and could be accurately represented using the parameters of thermal activity. The temperature at which the strength begins to decrease in the fatigue test was higher than in the static tests. Consequently, we were able to accurately express the relationship between the temperature and intensity using certain parameters. Few studies successfully developed a precise nonlinear relationship between temperature and intensity using approximate expressions.

Aluminum/Graphene Thermal Interface Materials with Positive Temperature Dependence.

Graphene is widely used in excellent thermal interface materials (TIMs), thanks to its remarkably high in-plane thermal conductivity (k∥). However, the poor through-plane thermal conductivity (k⊥) limits its further application. Here, we developed a simple in situ growth method to prepare graphene-based thermal interface composites with positively temperature-dependent thermal conductivity, which loaded aluminum (Al) nanoparticles onto graphene nanoplatelets (GNPs). To evaluate the variations in thermal performance, we determined the thermal diffusivity and specific heat capacity of the composites using a laser-flash analyzer and a differential scanning calorimeter, respectively. The Al nanoparticles act as bridges between the nanoplatelets, enhancing the k⊥ of the 1.3-Al/GNPs composite to 11.70 W·m-1·K-1 at 25 °C. Even more remarkably, those nanoparticles led to a unique increase in k⊥ with temperature, reaching 20.93 W·m-1·K-1 at 100 °C. Additionally, we conducted an in-depth investigation of the thermal conductivity mechanism of the Al/GNPs composites. The exceptional heat transport property enabled the composites to exhibit a superior heat dissipation performance in simulated practical applications. This work provides valuable insights into utilizing graphene in composites with Al nanoparticles, which have special thermal conductivity properties, and offers a promising pathway to enhance the k⊥ of graphene-based TIMs.

The temperature dependence of the Hildebrand solubility parameters of selected hydrocarbon polymers and hydrocarbon solvents: a molecular dynamics investigation.

CONTEXT: To determine the miscibility of liquids at high temperatures using the concept of Hildebrand solubility parameter δ , the current practice is to examine the difference in δ between two liquids at room temperature, assuming that δ is not sensitive to temperature. However, such an assumption may not be valid for certain polymer blends and solutions. Therefore, a knowledge of the δ values of the liquids of interest at high temperatures is desirable. The determination of δ at high temperatures, especially for high-molecular-weight polymers, is impossible, as polymers have vapor pressures of zero. To this end, molecular dynamics (MD) simulations provide a practical means for determining δ over a wide range of temperatures. In this work, we study the temperature dependence of δ of five hydrocarbon polymers: polyethylene (PE), isotactic and atactic polypropylene (i-PP and a-PP), polyisobutylene (PIB), and polyisoprene (PI) in five hydrocarbon solvents: n-pentane, n-hexane, n-dodecane, isobutene, and cyclohexane. The polymers are modeled as monodisperse chains with 100 repeat units. The average δ values of PE, i-PP, a-PP, PIB, and PI at 300 K are determined as 18.6, 14.9, 14.6, 14.3, and 16.4 MPa1/2, respectively, in a good agreement with experimental data. The δ values of these polymers at various temperatures are also determined. The temperature dependence of δ is fitted to two linear equations, one above and the other below the polymer's glass transition temperature Tg. The δ values are more sensitive to temperature at T ≥ Tg. The Tg values of the polymers, determined based upon their specific volumes and δ values agree with the experiment qualitatively. The determination of the temperature dependence of δ has a great potential for industrial applications, such as determining miscibility, developing polymeric organogelators as flocculants and oil spill treating agents, and identifying potential solvents and ideal processing temperatures. METHODS: The MD simulations are performed using the GROMACS 2022.3 package with optimized potential for liquid simulations-all atom (OPLS-AA) force field parameters. All polymers are built as extended chains using CHARMM-GUI Polymer Builder.

Temperature dependence mechanism of high-temperature oxidation of transition metal silicide MoSi2.

Transition metal silicides represented by MoSi2have excellent oxidation resistance and are widely used as high-temperature anti-oxidation coatings in hot end components of power equipment. However, the mechanism of temperature-dependent growth of MoSi2oxidation products has not been revealed. Therefore, this study investigated the formation characteristics of oxide film and silicide-poor compound on MoSi2at temperatures of 1000 °C-1550 °C through high-temperature oxidation experiments, combined with microscopic Raman spectroscopy, scanning electron microscope, and x-ray diffraction (XRD) characterizations. The result showed that MoSi2underwent high-temperature selective oxidation reactions at 1000 °C-1200 °C, forming MoO2and SiO2oxide film on the substrate. As the oxidation temperature increased to 1550 °C, after 100 h of oxidation, along with the disappearance of MoO2and the phase transformation of SiO2, a continuous Mo5Si3layer with a thickness of approximately 47µm was formed at the SiO2-MoSi2interface. Thermodynamics and kinetic calculations further revealed the mechanism of temperature-dependent growth of oxidation products (MoO2and Mo5Si3) during high-temperature oxidation process of MoSi2. As the temperature increased, the diffusion flux ratio of O and Si decreased, leading to a decrease in oxygen concentration at the interface and promoting the growth of the Mo5Si3layer. Its thickness is an important indicator for evaluating the oxidation resistance of MoSi2coatings during service. This study provides experimental and mechanistic insights into the temperature-dependent growth behavior of Mo5Si3during the high-temperature oxidation of MoSi2coating, and provides guidance for predicting the service life and improving the oxidation resistance of silicide coatings.

A cost-effective enzyme kinetics and inhibition model for biochemistry education and research.

Enzyme kinetics and inhibition studies are crucial in biochemistry education and research. Conventional methods often require expensive equipment and reagents, potentially limiting their accessibility in limited resource settings. Our approach sought to develop a cost-effective experimental design for studying enzyme kinetics and inhibition. Lactase was chosen as a protein model and its activity was investigated by measuring glucose production from lactose hydrolysis. In the study, commercially available lactase pills were used as an enzyme source, while milk was used as a substrate. Instead of scientific equipment, glucometers were used to measure lactase activity. Enzyme kinetics were evaluated using Michaelis-Menten and Lineweaver-Burk plots. In the study, the effects of temperature, pH, and inhibitors were also investigated. The results of our study aligned with established enzyme kinetics theories and previous studies. Lactase showed temperature and pH-dependent activity, with decreased activity observed at both low and high extremes. Results also showed that galactose acts as a competitive inhibitor of lactase. The approach presented here offers a cost-effective procedure for studying enzyme kinetics and inhibition. It can act as a valuable tool for educational purposes and for preliminary research in settings with limited resources.

Biomimicking TRPM8: A Conversely Temperature-Dependent Nonionic Retrorse Nanochannel for Ion Flow Control.

Ion channels play a crucial role in the transmembrane transport and signal transmission of substances. In animals, transient receptor potential vanilloid 1 (TRPV1) and transient receptor potential melastatin 8 (TRPM8) serve as temperature-sensing units in sensory nerve endings. TRPV1 allows cells to sense heat, while TRPM8 enables them to detect cold, both serving to protect living organisms from harmful substances and environments. However, almost all studies on artificial nanochannels have mainly focused on TRPV1-like "forward nanochannels" thus far, which are incapable of "backward" responding to heat. So, we constructed an innovational TRPM8-inspired "retrorse nanochannel" through internal modification of poly(acrylamide-co-acrylonitrile) [P(AAm-co-AN)] with an upper critical solution temperature (UCST). Our results demonstrated that the internally modified nanochannels exhibited rapid, stable, and reversible heat-closing capability and converse temperature dependence within the typical temperature range of 25-40 °C. The biomimetic ion channel can effectively function as a facile, precise, and reversible thermal gate for controlling the transport of ions and substances. It also offers a promising microscopic technology for managing thermal effects on the substance, fluid, energy, and even signal delivery.

Motility Assay to Probe the Calcium Sensitivity of Myosin and Regulated Thin Filaments.

Calcium-dependent activation of the thin filament mediated by the troponin-tropomyosin complex is key in the regulation of actin-myosin based muscle contraction. Perturbations to this system, either physiological (e.g., phosphorylation of myosin light chains) or pathological (e.g., mutations that cause familial cardiomyopathies), can alter calcium sensitivity and thus have important implications in human health and disease. The in vitro motility assay provides a quantitative and precise method to study the calcium sensitivity of the reconstituted myosin-thin filament motile system. Here we present a simple and robust protocol to perform calcium-dependent motility of ß-cardiac myosin and regulated thin filaments. The experiment is done on a multichannel microfluidic slide requiring minimal amounts of proteins. A complete velocity vs. calcium concentration curve is produced from one experiment in under 1 h.