Laboratory Time Scale Research Articles

Reconsidering Museums’ Climate and Seasonal Adjustment for Vulnerable Artifacts

ABSTRACT The paper provides new experimental evidence for vulnerable artifacts on the dependence of failure strain on the loading rate corresponding to typical environmental loads lasting between hours and months. Animal glue-based ground was chosen for this study as an easily available, hygroscopic and brittle material as well as due to its abundance in collections and its relevance when discussing the risk of mechanical damage to objects. Gesso specimens were tested using dynamic mechanical analysis and tensile testing at different frequencies, under a variety of loading rates and temperatures. The time-temperature superposition principle was used to predict the material response to slow deformations (lasting hours to months) that are otherwise inaccessible on laboratory timescales. The results demonstrate that brittle materials such as animal glue-based grounds do not benefit from longer cycles of applied loads as failure strain is not time-dependent within the investigated timescale.

Behavior of helium diffusion sinks in apatite: Evidence from continuous ramped heating analysis of borehole and well-characterized samples

Diffusion sinks have been proposed to explain the complex high-temperature 4He release often seen in Continuous Ramped Heating (CRH) analysis of apatites, which often correlates with over-dispersed and anomalously old (U-Th)/He ages. In this work, we first conducted CRH experiments with various ramping rates and cycled CRH experiments that confirm that the high-temperature 4He release from diffusion sinks is systematically temperature sensitive at laboratory time scales. We then analyzed apatite grains from the KTB borehole (German Continental Deep Drilling program) that have well-constrained thermal histories to test whether different thermal histories could alter the trapping of 4He at geologic time scales. The KTB samples show large intra-sample single-grain age dispersion, with most ages being older than predictions from a 4He radiation-damage diffusion model RDAAM. Individual grains from shallower depths show complex 4He outgassing behaviors, including the expected low-temperature volume-diffusion loss, sudden release spikes, and a higher- temperature-dependent component. Grains from the current partial retention zone and greater depths retain considerable helium and exhibit exclusively complex outgassing behavior dominated by high-temperature release in the laboratory. KTB samples show a systematic difference with depth in the proportion of low- and high-temperature gas-release gas components. Deeper samples, having long open-system thermal histories, contain a greater proportion of 4He that appears to have been trapped compared to the simpler volume-diffusion behavior exhibited by shallower samples that experienced a simpler monotonic cooling history. While greatly reduced, the high-temperature component is still present in the highest-temperature samples analyzed, well hotter than the partial retention zone. These observations confirm that in apatite trapping and release of helium from sinks is temperature dependent at geological time scales as well. This supports the suggestion that additional thermal-history information from apatites might be obtained using 4He/3He analysis, with laboratory release of 3He providing information about trap distribution and kinetics and 4He providing information about the geologic thermal history.

Autotrophic growth of Escherichia coli is achieved by a small number of genetic changes.

Synthetic autotrophy is a promising avenue to sustainable bioproduction from CO2. Here, we use iterative laboratory evolution to generate several distinct autotrophic strains. Utilising this genetic diversity, we identify that just three mutations are sufficient for Escherichia coli to grow autotrophically, when introduced alongside non-native energy (formate dehydrogenase) and carbon-fixing (RuBisCO, phosphoribulokinase, carbonic anhydrase) modules. The mutated genes are involved in glycolysis (pgi), central-carbon regulation (crp), and RNA transcription (rpoB). The pgi mutation reduces the enzyme's activity, thereby stabilising the carbon-fixing cycle by capping a major branching flux. For the other two mutations, we observe down-regulation of several metabolic pathways and increased expression of native genes associated with the carbon-fixing module (rpiB) and the energy module (fdoGH), as well as an increased ratio of NADH/NAD+ - the cycle's electron-donor. This study demonstrates the malleability of metabolism and its capacity to switch trophic modes using only a small number of genetic changes and could facilitate transforming other heterotrophic organisms into autotrophs.

Low Temperature Magnetic Properties of Variably Oxidized Natural and Synthetic Siderite

AbstractSiderite (FeCO3) is an important ferrous iron carbonate in the geochemical cycling of iron, as it is a sink for iron under reducing conditions. However, its detection is not straightforward with classical analytical approaches because in natural samples it is often fine‐grained and/or occurs in low concentrations. In this study, we explore the analytical potential of low‐temperature magnetometry. Synthetic siderites with a limited amount of associated ferric iron of up to 5 mol% and some natural siderites were subjected to investigation. Maxima in the cooling curves in a 5 T magnetic field shows that the Néel temperature of siderite is at 37 K in agreement with literature data. Those maxima appear at a higher temperature in the synthetic siderites with associated/sorbed ferric iron; it is 45 K for the 5 mol% Fe3+ synthesis. With the increasing amount of ferric iron, the synthetic siderites show an increasingly prominent remanence tail beyond the nominal Néel temperature in field‐cooled (FC) and zero‐field‐cooled (ZFC) warming curves of the remanent magnetization acquired in 5 T at 5 K. Fine‐grained siderite alters in air on laboratory time scales which is manifested by more pronounced remanence tails up to higher temperatures. Siderite's presence is best diagnosed by evaluating a combination of FC warming curves and a FC/ZFC remanence ratio >3 at 5 K. Standard addition experiments of FC warming curves enable the determination of siderite down to 0.1 wt%.

Divergent directed evolution of a TetR-type repressor towards aromatic molecules.

Reprogramming cellular behaviour is one of the hallmarks of synthetic biology. To this end, prokaryotic allosteric transcription factors (aTF) have been repurposed as versatile tools for processing small molecule signals into cellular responses. Expanding the toolbox of aTFs that recognize new inducer molecules is of considerable interest in many applications. Here, we first establish a resorcinol responsive aTF-based biosensor in Escherichia coli using the TetR-family repressor RolR from Corynebacterium glutamicum. We then perform an iterative walk along the fitness landscape of RolR to identify new inducer specificities, namely catechol, methyl catechol, caffeic acid, protocatechuate, L-DOPA, and the tumour biomarker homovanillic acid. Finally, we demonstrate the versatility of these engineered aTFs by transplanting them into the model eukaryote Saccharomyces cerevisiae. This work provides a framework for efficient aTF engineering to expand ligand specificity towards novel molecules on laboratory timescales, which, more broadly, is invaluable across a wide range of applications such as protein and metabolic engineering, as well as point-of-care diagnostics.

Long-Time Dynamics of Selected Molecular-Motor Components Using a Physics-Based Coarse-Grained Approach.

Molecular motors are essential for the movement and transportation of macromolecules in living organisms. Among them, rotatory motors are particularly efficient. In this study, we investigated the long-term dynamics of the designed left-handed alpha/alpha toroid (PDB: 4YY2), the RBM2 flagellum protein ring from Salmonella (PDB: 6SD5), and the V-type Na+-ATPase rotor in Enterococcus hirae (PDB: 2BL2) using microcanonical and canonical molecular dynamics simulations with the coarse-grained UNRES force field, including a lipid-membrane model, on a millisecond laboratory time scale. Our results demonstrate that rotational motion can occur with zero total angular momentum in the microcanonical regime and that thermal motions can be converted into net rotation in the canonical regime, as previously observed in simulations of smaller cyclic molecules. For 6SD5 and 2BL2, net rotation (with a ratcheting pattern) occurring only about the pivot of the respective system was observed in canonical simulations. The extent and direction of the rotation depended on the initial conditions. This result suggests that rotatory molecular motors can convert thermal oscillations into net rotational motion. The energy from ATP hydrolysis is required probably to set the direction and extent of rotation. Our findings highlight the importance of molecular-motor structures in facilitating movement and transportation within living organisms.

Long-time scale simulations of virus-like particles from three human-norovirus strains.

The dynamics of the virus like particles (VLPs) corresponding to the GII.4 Houston, GII.2 SMV, and GI.1 Norwalk strains of human noroviruses (HuNoV) that cause gastroenteritis was investigated by means of long-time (about 30 μs in the laboratory timescale) molecular dynamics simulations with the coarse-grained UNRES force field. The main motion of VLP units turned out to be the bending at the junction between the P1 subdomain (that sits in the VLP shell) and the P2 subdomain (that protrudes outside) of the major VP1 protein, this resulting in a correlated wagging motion of the P2 subdomains with respect to the VLP surface. The fluctuations of the P2 subdomain were found to be more pronounced and the P2 domain made a greater angle with the normal to the VLP surface for the GII.2 strain, which could explain the inability of this strain to bind the histo-blood group antigens (HBGAs).

Potential impacts of chemical weathering on feldspar luminescence dating properties

Abstract. Chemical weathering alters the chemical composition of mineral grains. As a result, trapped-charge dating signals of primary silicates may be progressively modified. In this study, we treated three feldspar specimens to understand the effect of proton- and ligand-promoted dissolution on their luminescence properties. We conducted kinetic experiments over 720 h using two solutions: (1) oxalic acid (pH 3, 20 ∘C), an organic acid with chelating abilities, and (2) aqua regia (pH < 1, 40 ∘C), a mixture of strong acids creating aggressive acid hydrolysis conditions. These two solutions were chosen to provoke, on laboratory timescales, some of the changes that may occur on geological timescales as minerals weather in nature. The effect of the extracting solutions on mineral dissolution was investigated by monitoring the concentration of dissolved elements, while changes in feldspar surface morphology were assessed by scanning electron microscopy (SEM). Subsequent changes in feldspar luminescence in the near-UV (∼ 340 nm) and blue (∼ 410 nm) thermoluminescence (TL) and infrared stimulated luminescence (IRSL) emission bands were assessed at the multi- and/or single-grain levels to gain insight into the emission spectra, dose response, saturation, and anomalous fading characteristics of the feldspars. In all experiments, only minor feldspar dissolution was observed after 720 h. In general, aqua regia, the more chemically aggressive solution, had a larger effect on feldspar dissolution compared to that of oxalic acid. Additionally, our results showed that although the TL and IRSL intensities changed slightly with increasing artificial weathering time, the feldspar luminescence properties were otherwise unmodified. This suggests that chemical alteration of feldspar surfaces may not affect luminescence dating signals obtained from natural samples.

Simple and convenient mapping of molecular dynamics mechanical property predictions of bisphenol-F epoxy for strain rate, temperature, and degree of cure.

It is well-known that all-atom molecular dynamics (MD) predictions of mechanical properties of thermoset resins suffer from multiple accuracy issues associated with their viscoelastic nature. The nanosecond simulation times of MD simulations do not allow for the direct simulation of the molecular conformational relaxations that occur under laboratory time scales. This adversely affects the prediction of mechanical properties at realistic strain rates, intermediate degrees of cure, and elevated temperatures. While some recent studies have utilized a time-temperature superposition approach to relate MD predictions to expected laboratory observations, such an approach becomes prohibitively difficult when simulating thermosets with a combination of strain rates, intermediate degrees of cure, and temperatures. In this study, a phenomenological approach is developed to map the predictions of Young's modulus and Poisson's ratio for a DGEBF/DETDA epoxy system to the corresponding laboratory-based properties for intermediate degrees of cure and temperatures above and below the glass transition temperature. The approach uses characterization data from dynamical mechanical analysis temperature sweep experiments. The mathematical formulation and experimental characterization of the mapping is described, and the resulting mapping of computationally-predicted to experimentally-observed elastic properties for various degrees of cure and temperatures are demonstrated and validated. This mapping is particularly important to mitigate the strain-rate effect associated with MD predictions, as well as to accurately predict mechanical properties at elevated temperatures and intermediate degrees of cure to facilitate accurate and efficient composite material process modeling.

Evolutionary jumps in bacterial GC content.

Genomic GC (Guanine-Cytosine) content is a fundamental molecular trait linked with many key genomic features such as codon and amino acid use. Across bacteria, GC content is surprisingly diverse and has been studied for many decades; yet its evolution remains incompletely understood. Since it is difficult to observe GC content evolve on laboratory time scales, phylogenetic comparative approaches are instrumental; but this dimension is rarely studied systematically in the case of bacterial GC content. We applied phylogenetic comparative models to analyze GC content evolution in multiple bacterial groups across 2 major bacterial phyla. We find that GC content diversifies via a combination of gradual evolution and evolutionary “jumps.” Surprisingly, unlike prior reports that solely focused on reductions in GC, we found a comparable number of jumps with both increased and decreased GC content. Overall, many of the identified jumps occur in lineages beyond the well-studied peculiar examples of endosymbiotic and AT-rich marine bacteria and do not support the predicted role of oxygen dependence. Our analysis of rapid and large shifts in GC content thus identifies new clades and novel contexts to further understand the ecological and evolutionary drivers of this important genomic trait.

Many-body localization in a tilted potential in two dimensions

Thermalization in many-body systems can be inhibited by the application of a linearly increasing potential, which is known as Stark many-body localization. Here we investigate the fate of this phenomenon on a two-dimensional disorder-free lattice with up to $24\ifmmode\times\else\texttimes\fi{}6$ sites. Similar to the one-dimensional case, ``density-polarized'' regions can act as bottlenecks for transport and thermalization on laboratory timescales. However, compared to the one-dimensional case, a substantially stronger potential gradient is needed to prevent thermalization when an extra spatial dimension is involved. The origin of this difference and implications for experiments are discussed. We argue that delocalization is generally favored for typical states in two-dimensional Stark many-body systems, although nonergodicity can still be observed for a specific choice of initial states, such as those probed in experiments.

SUPERFACT: A Model Fuel for Studying the Evolution of the Microstructure of Spent Nuclear Fuel during Storage/Disposal.

The transmutation of minor actinides (in particular, Np and Am), which are among the main contributors to spent fuel α-radiotoxicity, was studied in the SUPERFACT irradiation. Several types of transmutation UO2-based fuels were produced, differing by their minor actinide content (241Am, 237Np, Pu), and irradiated in the Phénix fast reactor. Due to the high content in rather short-lived alpha-decaying actinides, both the archive, but also the irradiated fuels, cumulated an alpha dose during a laboratory time scale, which is comparable to that of standard LWR fuels during centuries/millenaries of storage. Transmission Electron Microscopy was performed to assess the evolution of the microstructure of the SUPERFACT archive and irradiated fuel. This was compared to conventional irradiated spent fuel (i.e., after years of storage) and to other 238Pu-doped UO2 for which the equivalent storage time would span over centuries. It could be shown that the microstructure of these fluorites does not degrade significantly from low to very high alpha-damage doses, and that helium bubbles precipitate.

Rheological stratification in impure rock salt during long-term creep: morphology, microstructure, and numerical models of multilayer folds in the Ocnele Mari salt mine, Romania

Abstract. At laboratory timescales, rock salt samples with different composition and microstructure show variance in steady-state creep rates, but it is not known if and how this variance is manifested at low strain rates and corresponding deviatoric stresses. Here, we aim to quantify this from the analysis of multilayer folds that developed in rock salt over geological timescale in the Ocnele Mari salt mine in Romania. The formation is composed of over 90 % of halite, while distinct multiscale layering is caused by variation in the fraction of impurities. Regional tectonics and mine-scale fold structure are consistent with deformation in a shear zone after strong shearing in a regional detachment, forming over 10 m scale chevron folds of a tectonically sheared sedimentary layering, with smaller folds developing on different scales in the hinges. Fold patterns at various scales clearly indicate that during folding, the sequence was mechanically stratified. The dark layers contain more impurities and are characterised by a more regular layer thickness compared to the bright layers and are thus inferred to have higher viscosities. Optical microscopy of gamma-decorated samples shows a strong shape-preferred orientation of halite grains parallel to the foliation, which is reoriented parallel to the axial plane of the folds studied. Microstructures indicate dislocation creep, together with extensive fluid-assisted recrystallisation and strong evidence for solution–precipitation creep. This provides support for linear (Newtonian) viscous rheology as a dominating deformation mechanism during the folding. Deviatoric stress during folding was lower than during shearing in the detachment at around 1 MPa. We investigate fold development on various scales in a representative multilayer package using finite-element numerical models, constrain the relative layer thicknesses in a selected outcrop, and design a numerical model. We explore the effect of different Newtonian viscosity ratios between the layers on the evolving folds on different scales. By comparing the field data and numerical results, we estimate that the effective viscosity ratio between the layers was larger than 10 and up to 20. Additionally, we demonstrate that the considerable variation of the layer thicknesses is not a crucial factor to develop folds on different scales. Instead, unequal distribution of the thin layers, which organise themselves into effectively single layers with variable thickness, can control deformation on various scales. Our results show that impurities can significantly change the viscosity of rock salt deforming at low deviatoric stress and introduce anisotropic viscosity, even in relatively pure layered rock.

Inductive Rectilinear Frame Dragging and Local Coupling to the Gravitational Field of the Universe

There is a drag force on objects moving in the background cosmological metric, known from galaxy cluster dynamics. The force is quite small over laboratory timescales, yet it applies in principle to all moving bodies in the universe. The drag force can be understood as inductive rectilinear frame dragging because it also exists in the rest frame of a moving object, and it arises in that frame from the off-diagonal components induced in the boosted-frame metric. Unlike the Kerr metric or other typical frame-dragging geometries, cosmological inductive dragging occurs at uniform velocity, along the direction of motion, and dissipates energy. Proposed gravito-magnetic invariants formed from contractions of the Riemann tensor do not capture inductive dragging effects, and this might be the first identification of inductive rectilinear dragging. The existence of this drag force proves it is possible for matter in motion through a finite region to exchange momentum and energy with the gravitational field of the universe. The cosmological metric can in principle be determined through this force from local measurements on moving bodies, at resolutions similar to that of the Pound–Rebka experiment.

On the relation of structural disorder and thermoelastic properties in ZnGa2O4 and Zn1−xMgxGa2O4 (x ≈ 0.33)

The cation distribution at room temperature, as well as elastic properties and thermal expansion of single crystal ZnGa2O4 (ZGO) and Zn1−xMgxGa2O4 (x ≈ 0.33; ZMGO) with spinel-type structure were studied in a wide temperature range using single crystal X-ray diffraction, neutron powder diffraction, inductive gauge dilatometry and resonant ultrasound spectroscopy. ZGO adopts an almost normal spinel structure, whereas ZMGO is significantly disordered. At room temperature, the elastic properties of ZMGO mostly fall between those of ZGO and MgGa2O4 (MGO). The temperature dependences of the thermoelastic properties of ZGO and ZMGO, as well as thermal expansion of ZGO reveal distinct signatures of glass-like transitions, which separate states in which the cation dynamics are fast enough to relax the cation order in response to temperature change in laboratory timescales from those in which they are not. In equilibrium, thermal expansion is increased in ZMGO, whereas the thermoelastic coefficients are decreased in both ZGO and ZMGO. The temperature range of the transition is significantly larger in ZGO compared to ZMGO and MGO. Trends within the elastic properties, thermoelastic properties, thermal expansion and the glass-like transition in the (Zn,Mg)Ga2O4 solid solution series are discussed based on the impact of inversion, structural disorder, bond character and in comparison to other spinels.

Physical aging of selenium glass: Assessing the double mechanism of equilibration and the crystallization process

This work focuses on the study of the physical aging of a selenium glass by differential scanning calorimetry (DSC) and fast scanning calorimetry (FSC). Aged samples of 30 and 40 years old at room temperature were analysed by classical DSC, and their enthalpies of recovery were calculated, showing that the glass has reached its thermodynamic equilibrium and is stable over time. The study of accelerated physical aging by using FSC on a rejuvenated sample allows reproducing the way by which this glass has reached its thermodynamic equilibrium at the laboratory time scale. We evidence that the glass reaches its equilibrium state in one or two steps, depending on the gap between the aging temperature and the glass transition temperature, resulting from the difference in the mechanisms governing the relaxation process. Furthermore, a second phenomenon is evidenced, consisting in the crystallization of the glass once the equilibrium has been reached for aging temperatures close to the glass transition temperature.

Application of surface complexation modeling on adsorption of uranium at water-solid interface: A review.

Precise prediction of uranium adsorption at water-mineral interface is of great significance for the safe disposal of radionuclides in geologic environments. Surface complexation modeling (SCM) as a very useful tool has been extensively investigated for simulating adsorption behavior of metals/metalloids at water-mineral interface. Numerous studies concerning the fitting of uranium adsorption on various adsorbents using SCM are well documented, but the systematic and comprehensive review of uranium adsorption using various SCM is not available. In this review, we briefly summarized the rationale of SCM, including constant-capacitance-model (CCM), diffuse-layer-model (DLM), triple-layer-model (TLM); The recent progress in the application of SCM on the fitting of uranium adsorption towards metal (hydr)oxides, clay minerals and soil/sediments was reviewed in details. This review hopefully provides the beneficial guidelines for predicting the transport and fate of uranium in geologic environments beyond laboratory timescales.

Punin Ripening and the Classification of Solution-Mediated Recrystallization Mechanisms

Ripening (also called recrystallization) is a process that occurs commonly in nature and industry that shifts the size distribution of an ensemble of crystals toward a smaller number of larger crystals. Ostwald ripening is by far the best known recrystallization mechanism and sometimes is mistakenly considered as the only mechanism for shifting the crystal size distribution. Ostwald ripening accounts for recrystallization under thermodynamic control and is driven only by the well-known size dependence of solubility. There are, however, other recrystallization mechanisms that can be observed on laboratory timescales for crystals of any size under certain conditions. Internal stress dispersion is a thermodynamic ripening mechanism that depends not on surface energies but rather on crystal defects. In addition, there are two other mechanisms that are kinetic in nature. The most efficient is driven by the size dependence of growth and dissolution rates at low supersaturation. Finally, a mechanism proposed by Punin is driven by the difference between growth and dissolution rates due to crystal defects. All the four mechanisms can be at work simultaneously. The efficiency of ripening can be enhanced by temperature oscillations, but only the thermodynamic mechanisms can work at constant temperature. In this paper, we discuss the fundamentals of these four ripening mechanisms and revisit in detail Punin’s mechanism because it is the least well articulated in the literature.

Connecting molecular simulations and laboratory experiments for the study of time-resolved cation-exchange process in the interlayer of swelling clay minerals

In the context of element migration in clay-rich media, self-diffusion coefficients of interlayer cations in swelling clay minerals obtained from molecular simulations are rarely used by macroscopic models predicting cation-exchange processes. Based on experiments and simulations, this study aims at (i) making a connection between molecular and sample scale processes to predict the dynamics of cation-exchange reactions between the interlayer space of millimetre disks of vermiculite and aqueous reservoirs, and (ii) assessing the role played by both self-diffusion and selectivity coefficients on this process.Time-resolved cation exchange experiments were performed using Ca-saturated vermiculite disks immersed in aqueous reservoirs with different NaCl or SrCl2 salinities. The results were reproduced via a finite-volume model constrained by (i) cation self-diffusion coefficients calculated by molecular dynamics simulations and (ii) interlayer selectivity coefficients drawn from “batch” cation-exchange isotherms.Results showed that considering the averaged values for both the cation-exchange selectivity coefficients and self-diffusion coefficients of the slowest interlayer cation led to good agreement between the experiments and simulations, validating the modelling strategy for the connection between the molecular and laboratory time scales. A sensitivity test regarding the influence of the two input parameters on the overall results was then performed. This study underlined a constrained upscaling strategy to better assess the role played by different intrinsic parameters of the clay/water systems (molecular self-diffusion coefficients in the interlayer space vs. selectivity coefficient) on the diffusion of cations during cation-exchange reaction in clay-rich media.

Scalable continuous evolution for the generation of diverse enzyme variants encompassing promiscuous activities

Enzyme orthologs sharing identical primary functions can have different promiscuous activities. While it is possible to mine this natural diversity to obtain useful biocatalysts, generating comparably rich ortholog diversity is difficult, as it is the product of deep evolutionary processes occurring in a multitude of separate species and populations. Here, we take a first step in recapitulating the depth and scale of natural ortholog evolution on laboratory timescales. Using a continuous directed evolution platform called OrthoRep, we rapidly evolve the Thermotoga maritima tryptophan synthase β-subunit (TmTrpB) through multi-mutation pathways in many independent replicates, selecting only on TmTrpB’s primary activity of synthesizing l-tryptophan from indole and l-serine. We find that the resulting sequence-diverse TmTrpB variants span a range of substrate profiles useful in industrial biocatalysis and suggest that the depth and scale of evolution that OrthoRep affords will be generally valuable in enzyme engineering and the evolution of biomolecular functions.