Molecular modelling and machine learning for high-throughput screening of metal-organic frameworks for hydrogen storage

ABSTRACT

Hydrogen is an appealing energy storage solution for electric vehicles due to its low environmental impact and faster recharge times compared to batteries. However, there are many engineering challenges involved in safely storing a sufficient amount of hydrogen onboard a vehicle with a reasonable volumetric density. Nanoporous materials such as metal–organic frameworks (MOFs) have the potential to store hydrogen at high density and only moderate pressure. Considerable research has been devoted to finding new MOFs for hydrogen storage in recent years; however, a MOF that provides sufficient hydrogen density and is suitable to commercial applications has not yet been found. Much of this research makes use of molecular modelling to screen thousands of materials in a high-throughput way. Computational screening can be an effective tool for gaining insight into structure-performance relationships as well as finding specific candidates for an application. Recently, some research groups have also used machine learning to analyze data more effectively and accelerate the screening process. In this review, we discuss some recent advances in using molecular modelling and machine learning to find materials for hydrogen storage. We also discuss and compare some popular models for the hydrogen molecule and the accuracy of different equations of state, which are important considerations for accurate molecular simulations.     

Influences of lithium doping and fullerene impregnation on hydrogen storage in metal organic frameworks

Using the grand canonical ensemble Monte Carlo method, two similar metal organic frameworks (isoreticular MOFs [IRMOF]-12 and -14) and their modified structures by doping lithium (Li) atoms above the organic units and/or impregnating with fullerenes in their cavities have been employed to investigate the capacities of H₂ storage. Our simulations show that the H₂ uptakes of Li-C₆₀@Li-IRMOF-12 and Li-C₆₀@Li-IRMOF-14 achieve the U.S. Department of Energy targets before 2017 both in gravimetric density and in volumetric density at 243 K and 100 bar. Combining the results of IRMOF-10-based structures, we further study the relationships between the H₂ uptakes and the physical properties of the materials to identify the influence factors on the H₂ storage at room temperature.     

RecA-mediated homology search as a nearly optimal signal detection system

Homologous recombination facilitates the exchange of genetic material between homologous DNA molecules. This crucial process requires detecting a specific homologous DNA sequence within a huge variety of heterologous sequences. The detection is mediated by RecA in E. coli, or members of its superfamily in other organisms. Here, we examine how well the RecA-DNA interaction is adjusted to its task. By formulating the DNA recognition process as a signal detection problem, we find the optimal value of binding energy that maximizes the ability to detect homologous sequences. We show that the experimentally observed binding energy is nearly optimal. This implies that the RecA-induced deformation and the binding energetics are fine-tuned to ensure optimal sequence detection. Our analysis suggests a possible role for DNA extension by RecA, in which deformation enhances detection. The present signal detection approach provides a general recipe for testing the optimality of other molecular recognition systems.     

Acetate as a carbon source for hydrogen production by photosynthetic bacteria

Hydrogen is a clean energy alternative to fossil fuels. Photosynthetic bacteria produce hydrogen from organic compounds by an anaerobic light-dependent electron transfer process. In the present study hydrogen production by three photosynthetic bacterial strains (Rhodopseudomonas sp., Rhodopseudomonas palustris and a non-identified strain), from four different short-chain organic acids (lactate, malate, acetate and butyrate) was investigated. The effect of light intensity on hydrogen production was also studied by supplying two different light intensities, using acetate as the electron donor. Hydrogen production rates and light efficiencies were compared. Rhodopseudomonas sp. produced the highest volume of H2. This strain reached a maximum H2 production rate of 25 ml H2 l(-1) h(-1), under a light intensity of 680 micromol photons m(-2) s(-1), and a maximum light efficiency of 6.2% under a light intensity of 43 micromol photons m(-2) s(-1). Furthermore, a decrease in acetate concentration from 22 to 11 mM resulted in a decrease in the hydrogen evolved from 214 to 27 ml H2 per vessel.     

Terrestrial organic carbon storage in a British moorland

Accurate estimates for the size of terrestrial organic carbon (C) stores are needed to determine their importance in regulating atmospheric CO₂ concentrations. The C stored in vegetation and soil components of a British moorland was evaluated in order to: (i) investigate the importance of these ecosystems for C storage and (ii) test the accuracy of the United Kingdom's terrestrial C inventory. The area of vegetation and soil types was determined using existing digitized maps and a Geographical Information System (GIS). The importance of evaluating C storage using 2D area projections, as opposed to true surface areas, was investigated and found to be largely insignificant. Vegetation C storage was estimated from published results of productivity studies at the site supplemented by field sampling to evaluate soil C storage. Vegetation was found to be much less important for C storage than soil, with peat soils, particularly Blanket bog, containing the greatest amounts of C. Whilst the total amount of C in vegetation was similar to the UK national C inventory's estimate for the same area, the national inventory estimate for soil C was over three times higher than the value derived in the current study. Because the UK's C inventory can be considered relatively accurate compared to many others, the results imply that current estimates for soil C storage, at national and global scales, should be treated with caution.     

Statistical approach in search for optimal signal in simple olfactory neuronal models

Several models (concentration detectors and a flux detector) for coding of odor intensity in olfactory sensory neurons are investigated. Behavior of the system is described by different stochastic processes of binding the odorant molecules to the receptors and their activation. Characteristics how well the odorant concentration can be estimated from the knowledge of response, the number of activated neurons, are studied. The approach is based on the Fisher information and analogous measures. These measures of optimality are computed and applied to locate the odorant concentration which is most suitable for coding. The results are compared with the classical deterministic approach which judges the optimal odorant concentration via steepness of the input-output function.     

1997-2006年中国城市建成区有机碳储量的估算

随着城市区域碳排放的增加,城市碳循环在全球碳循环中的地位越来越重要,而城市碳排放和碳储量的估算是城市碳循环研究的基础.本研究利用统计资料,参考国内外相关研究成果,对1997-2006年中国城市建成区有机碳储量进行估算.结果表明:1997-2006年,中国城市建成区总有机碳储量呈上升趋势,由0.13 ～0.19 Pg C(平均值为0.16 Pg C)增加到0.28 ～0.41 Pg C(平均值为0.34 Pg C);建成区有机碳密度由9.86 ～ 14.03 kg C·m-2 (平均值为11.95 kg C·m-2)增加到10.54～15.54 kg C·m-2(平均值为13.04 kg C·m-2).建成区的有机碳主要储存在土壤中,其次是建筑物和绿地,居民有机体的碳储量可忽略不计.1997和2006年,土壤、建筑物、绿地和居民有机体在总碳库中的比例分别为78％、12％、9％、1％和73％、16％、10％、1％.     

Need for relevant timescales when crediting temporary carbon storage

Purpose

Earth faces an urgent need for climate change mitigation, and carbon storage is discussed as an option. Approaches for assessing the benefit of temporary carbon storage in relation to carbon footprinting exist, but many are based on a 100-year accounting period, disregarding impacts after this time. The aim of this paper is to assess the consequences of using such approaches that disregard the long timescale on which complete removal of atmospheric CO₂ occurs. Based on these findings, an assessment is made on what are relevant timescales to consider when including the value of temporary carbon storage in carbon footprinting.

Methods

Implications of using a 100-year accounting period is evaluated via a literature review study of the global carbon cycle, as well as by analysing the crediting approaches that are exemplified by the PAS 2050 scheme for crediting temporary carbon storage.

Results and discussion

The global carbon cycle shows timescales of thousands of years for the transport of carbon from the atmosphere to pools beyond the near-surface layers of the Earth, from where it will not readily be re-emitted as a response to change in near-surface conditions. Compared to such timescales, the use of the 100-year accounting period appears hard to justify. We illustrate how the use of the 100-year accounting period can cause long-term global warming impacts to be hidden by short-term storage solutions that may not offer real long-term climate change mitigation. Obtaining long-term climatic benefits is considered to require storage of carbon for at least thousand years. However, it has been proposed that there may exist tipping points for the atmospheric CO₂ concentration beyond which irreversible climate changes occur. To reduce the risk of passing such tipping points, fast mitigation of the rise in atmospheric greenhouse gas concentration is required and in this perspective, shorter storage times may still provide climatic benefits.

Conclusions

Both short- and long-term perspectives should be considered when crediting temporary carbon storage, addressing both acute effects on the climate and the long-term climate change. It is however essential to distinguish between short- and long-term mitigation potential by treating them separately and avoid that short-term mitigation is used to counterbalance long-term climate change impacts from burning of fossil fuels.     

Enhancing soil carbon storage for carbon remediation: potential contributions and constraints by microbes

Terrestrial carbon sequestration represents an important option for partially mitigating anthropogenic CO(2) emissions. Evidence suggests that terrestrial ecosystems can be managed for carbon sequestration, but it is not certain to what extent the microbes within them can be manipulated. Challenges include identifying which specific microbes and mechanisms contribute to sequestered carbon; understanding how microbial communities respond over large spatial and long temporal scales to crucial environmental variables; and developing management strategies suitable for large spatial and long temporal scales. The growing recognition that microbes produce proteins that limit organic matter degradation suggests targets for basic research. Directly manipulating microbes to sequester CO(2) through other processes such as mineral formation offers intriguing alternatives that merit further attention, but at present the prospects for practical implementation appear remote.     

Decomposition of seawater-irrigated halophytes: implications for potential carbon storage

Plants were cultivated in a nutrient solution containing increasing cadmium concentrations (i.e. 0.001–25 µM), under strictly controlled growth conditions. Changes in both growth parameters and enzyme activities, directly or indirectly related to the cellular free radical scavenging systems, were studied in roots and leaves of 14-day-old maize plants (Zea mays L., cv. Volga) as a result of Cd uptake. A decrease in both shoot length and leaf dry biomass was found to be significant only when growing on 25 µM Cd, whereas concentrations of chlorophyll pigments in the 4th leaf decreased from 1.7 µM Cd on. Changes in enzyme activities occurred at lower Cd concentrations in solution leading to lower threshold values for Cd contents in plants than those observed for growth parameters. Peroxidase (POD; E.C. 1.11.1.7) activity increased in the 3rd and 4th leaf, but not in roots. In contrast, glucose-6-phosphate dehydrogenase (G6PDH; E.C. 1.1.1.49), isocitrate dehydrogenase (ICDH; E.C. 1.1.1.42) and malic enzyme (ME; E.C. 1.1.1.40) activities decreased in the 3rd leaf. According to the relationship between the POD activity and the Cd content, a toxic critical value was set at 3 mg Cd per kg dry matter in the 3rd leaf and 5 mg Cd per kg dry matter in the 4th. Anionic POD were determined both in root and leaf protein extracts; however, no changes in the isoperoxidase pattern were detected in case of Cd toxicity. Results show that in contrast with growth parameters, the measurement of enzyme activities may be included as early biomarkers in a plant bioassay to assess the phytotoxicity of Cd-contaminated soils on maize plants.     

Evaluation of methods for storage of marine macroorganisms with optimal recovery of bacteria

Marine macroorganisms are a potential source for new bioactive substances. In many cases marine microorganisms--especially bacteria--associated with these macroorganisms are actually producing the bioactive substances. One often is not able to immediately isolate microorganisms from collected macroorganismic materials; we therefore evaluated different methods for storage of such material, e.g., on board research vessels. These methods were the following: storage of macerates in sintered glass beads and 5% trehalose at -20 degrees C (SGT method); storage of sections in 5% dimethyl sulfoxide at -70 degrees C (SD method); storage of macerates at -20 degrees C using the commercial ROTI-STORE system (RS method); storage of macerates at -20 degrees C in 50% glycerol (GC method); and storage of macerates covered by mineral oil at 4 degrees C (MO method). The SGT and SD methods resulted in numbers of and especially diversity of recoverable bacteria that were higher than for the other methods. Data for the RS method indicated its potential usefulness, too. The MO method resulted in growth during storage, thereby enriching a few selected microorganisms; the GC method resulted in a survival and diversity of recovered bacteria that was too low.     

An optimal policy for the metabolism of storage materials in unicellular algae.

The perturbation theory provides an explanation of the trans-membrane electric field effects on the polarizability of the photosynthetic pigments.In the photosynthetic membranes, the photo-induced effect is linear despite the spectroscopic properties of the carotenoids that should produce a quadratic effect. Consequently, the hypothesis previously assumed of a permanent field in the membrane is confirmed.Our calculation shows that the effect includes two terms, but only one is often taken into account in the literature.This one varies as the first derivative of the polarizability and corresponds to the induced shift of the electronic levels. The other one varies as the polarizability itself; this term is often omitted, and it corresponds to the variation of transition probability. Taking into account both these terms, the carotenoid shift can be interpreted without further hypothesis, as the one consisting in assuming that only one part of the carotenes is sensitive to the field.Finally, this approach allows a quantitative interpretation of the light-induced change measurements with polarized measuring light, which demonstrate the participation of the pigments orientation in the electric field effects.     

Litter quality in a north European transect versus carbon storage potential

Newly shed foliar plant litter often has a decomposition rate of ca 0.1–0.2% day^–1, which decreases greatly with time and may reach 0.0001 to 0.00001% day^–1 or lower in litter material in the last stages of decay. The decrease in decomposability (substrate quality) varies among species and is complex, involving both direct chemical changes in the substrate itself and the succession in microorganisms able to compete for substrate with a given chemical composition. In late stages, the decomposition appears very little affected by climate, suggesting that climate change will have little effect on late-stages decomposition rates. Here, we apply a model for the late stages of litter decomposition to address the question of climate-change effects on soil-C storage. Decomposition of litter turning into soil organic matter (SOM) is determined by the degradation rate of lignin. In the last phases of decay, raised N concentrations have a rate-retarding effect on lignin degradation and thus on the decomposition of far-decomposed litter and litter in near-humus stages. The retardation of the decomposition rate in late stages may be so strong that decomposition reaches a limit value at which total mass losses virtually stop. At such a stage the remaining litter would be close to that of stabilized SOM. The estimated limit values for different species range from about 45 to 100% decomposition indicating that between 0 and 55% should either be stabilized or decompose extremely slowly. For no less than 106 long-term studies on litter decomposition, encompassing 21 litter types, limit values were significantly and negatively related to N concentration, meaning that the higher the N concentration in the newly shed litter (the lower the C/N ratio) the more litter was left when it reached its limit value. Trees growing under warmer and wetter climates (higher actual evapotranspiration, AET) tend to shed foliar litter more rich in N than those growing under colder and drier climates. A change in climate resulting in higher AET would thus mean that within species, e.g., Scots pine, a higher N level in the foliar litter may result. Further, within the boreal system deciduous species appear to have foliar litter richer in N than have conifers and within the conifers group, Norway spruce has needle litter more rich in N than, e.g., Scots pine. Thus, a change of species (e.g., by planting) from pine to spruce or from spruce to a deciduous species such as birch may result in a higher N level in the litter fall at a given site. In both cases the result would be a lower limit value for decomposition. The paper presents an hypothesis, largely based on available data that a change in climate of 4° higher annual average temperature and 40% higher precipitation in the Baltic basin would result in higher N levels in litter, lower decomposition and thus a considerable increase in humus accumulation.     

Janospira - an Ordovician microfossil in search of a Phylum

Janospira is described from early Ordovician (Arenig) rocks of northern Spitsbergen. It is a curious microfossil, probably calcareous, about 1 mm in length, made up of an initial coil which expands distally into a straight tube, at the same time as producing a narrower tube almost in line with the first but in the opposite direction. Although showing some similarities to Foraminifera, molluscs and polychaetes, there are objections to its inclusion in any of these groups, and it is equally probable that it belongs to an unknown group with a planktic early growth stage.     

Kinetic evidence for a role of heme geometry on the modulation of carbon monoxide reactivity in human hemoglobin

Kinetics of CO binding to human hemoglobin (Hb) has been followed below neutrality. With respect to the behavior observed at pH 7.0, CO binding to deoxy-Hb at pH 2.3 displays a much faster second-order combination rate constant (1.2 x 10(-7) M-1 s-1) and loss of the autocatalytic character of the kinetic progress curve. The spectroscopic features of the transient deoxy-Hb at pH 2.75 indicate the phenomenon to be related to the cleavage of the proximal histidine N epsilon-Fe bond, as reported for monomeric hemoproteins (Coletta, M., Ascenzi, P., Traylor, T. G., and Brunori, M. (1985) J. Biol. Chem. 260, 4151-4155). The faster CO binding rate constant, higher than that characteristic of the R state, cannot be attributed to either (i) an enhanced dimerization of deoxy-Hb at low pH, or (ii) a quaternary switch of the unliganded form to the R0 state. The data indicate that interaction(s) of the heme on the proximal side is crucial in accounting for the difference in the CO binding rate constant between the two quaternary conformations of hemoglobin.