Rock–water–carbon interactions germane to serpentinization in hydrothermal vents have occurred fo... more Rock–water–carbon interactions germane to serpentinization in hydrothermal vents have occurred for over 4 billion years, ever since there was liquid water on Earth. Serpentinization converts iron(II) containing minerals and water to magnetite (Fe3O4) plus H2. The hydrogen can generate native metals such as awaruite (Ni3Fe), a common serpentinization product. Awaruite catalyzes the synthesis of methane from H2 and CO2 under hydrothermal conditions. Native iron and nickel catalyze the synthesis of formate, methanol, acetate, and pyruvate—intermediates of the acetyl-CoA pathway, the most ancient pathway of CO2 fixation. Carbon monoxide dehydrogenase (CODH) is central to the pathway and employs Ni0 in its catalytic mechanism. CODH has been conserved during 4 billion years of evolution as a relic of the natural CO2-reducing catalyst at the onset of biochemistry. The carbide-containing active site of nitrogenase—the only enzyme on Earth that reduces N2—is probably also a relic, a biologic...
Thermochemical processing methods such as pyrolysis are of growing interest as a means of convert... more Thermochemical processing methods such as pyrolysis are of growing interest as a means of converting biomass into fuels and commodity chemicals in a sustainable manner. Macroalgae, or seaweed, represent a novel class of feedstock for pyrolysis that, owing to the nature of the environments in which they grow coupled with their biochemistry, naturally possess high metal contents. Although the impact of metals upon the pyrolysis of terrestrial biomass is well documented, their influence on the thermochemical conversion of marine-derived feeds is largely unknown. Furthermore, these effects are inherently difficult to study, owing to the heterogeneous character of natural seaweed samples. The work described in this paper uses copper(II) alginate, together with alginic acid and sodium alginate as model compounds for exploring the effects of metals upon macroalgae thermolysis. A thermogravimetric analysis-Fourier transform infrared spectroscopic study revealed that, unusually, Cu(2+) ions ...
We report chiral differences in the effects of D-and L-histidine on the interlayer spacing of ver... more We report chiral differences in the effects of D-and L-histidine on the interlayer spacing of vermiculite clays that are relevant in assessing the role of clays in the origin of bio-homochirality.
We present a joint experimental and theoretical investigation into the adsorption of polycationic... more We present a joint experimental and theoretical investigation into the adsorption of polycationic quaternary ammonium polymers on the clay mineral kaolinite. Within the cement and concrete manufacturing industries such polymers are used to improve the final product by inerting the adsorption capacity of the clay minerals for more expensive additives. The adsorption of the presently used polymer (FL22) was compared with both a similar variant, but without a hydroxyl group (Fl22mod) and uncharged polyvinyl alcohol (PVA). Experimental results show that adsorption of FL22 is higher than that of FL22mod at both pH 6 and at pH > 10 and that the adsorption of PVA is the highest. Theoretical density functional theory (DFT) results and simplified models consisting of the basal surfaces of kaolinite, with monomers of FL22, FL22mod and PVA gave monomer coverage per unit surface area of kaolinite, a comparison of the configurations of the relaxed models, formation energies and Mulliken charges. These results show that the polycationic polymers interact with the basal surfaces of kaolinite electrostatically, explaining the high affinity of these polymers for kaolinite surfaces in the experimental results. The hydroxyl groups of FL22 and PVA form hydrogen bonds with the basal surfaces of kaolinite in conditions of pH 6. The joint experimental and theoretical results suggest that, due to the presence of the hydroxyl group, the conformation of FL22 changes under pH, where at neutral pH it lies relatively flat to the kaolinite surfaces, but at higher pH, conformational changes of the polymer occur, thereby increasing the adsorbed quantity of FL22.
We present a joint experimental and theoretical investigation into the adsorption of polycationic... more We present a joint experimental and theoretical investigation into the adsorption of polycationic quaternary ammonium polymers on the clay mineral kaolinite. Within the cement and concrete manufacturing industries such polymers are used to improve the final product by inerting the adsorption capacity of the clay minerals for more expensive additives. The adsorption of the presently used polymer (FL22) was compared with both a similar variant, but without a hydroxyl group (Fl22mod) and uncharged polyvinyl alcohol (PVA). Experimental results show that adsorption of FL22 is higher than that of FL22mod at both pH 6 and at pH > 10 and that the adsorption of PVA is the highest. Theoretical density functional theory (DFT) results and simplified models consisting of the basal surfaces of kaolinite, with monomers of FL22, FL22mod and PVA gave monomer coverage per unit surface area of kaolinite, a comparison of the configurations of the relaxed models, formation energies and Mulliken charges. These results show that the polycationic polymers interact with the basal surfaces of kaolinite electrostatically, explaining the high affinity of these polymers for kaolinite surfaces in the experimental results. The hydroxyl groups of FL22 and PVA form hydrogen bonds with the basal surfaces of kaolinite in conditions of pH 6. The joint experimental and theoretical results suggest that, due to the presence of the hydroxyl group, the conformation of FL22 changes under pH, where at neutral pH it lies relatively flat to the kaolinite surfaces, but at higher pH, conformational changes of the polymer occur, thereby increasing the adsorbed quantity of FL22.
... Full details of how the LAMMPS code was employed in the molecular dynamics simulations and of... more ... Full details of how the LAMMPS code was employed in the molecular dynamics simulations and of the procedure used to prepare the claypolymer composites are given in Boulet et al.1,3. ... PEO-Mac (M w 375 g mol −1 ), 1.70, 1.77, 1.79. 1.74. ...
Preparation of industrially useful clay-polymer nanocomposite materials often requires the disper... more Preparation of industrially useful clay-polymer nanocomposite materials often requires the dispersal of clay particles within a polymer matrix. The degree to which the clay particles may be dispersed has an effect on the resultant properties of the material, and the clay is often rendered organophilic using alkylammonium species to facilitate incorporation of polymer. The use of a low molecular weight poly(propylene) oxide diamine is investigated as a reagent for controlling the separation between layers in smectite clays and therefore the extent to which the clay tactoid may be dispersed. The arrangement and interactions of the amine species in the interlayer region are investigated through analysis by both experimental methods and computer simulation, which gives insight into coordination mechanisms within the organoclay. Infrared spectroscopy indicates the presence of extensive hydrogen bonding within the amine-clay interlayer. Some of the amine species were found to intercalate in a nonprotonated state, resulting in strong hydrogen-bonding interactions between amine and ammonium groups. Large-scale classical molecular dynamics simulation shows that the amine groups do not interact strongly with the clay sheets, in contradistinction to ammonium groups. The effect of simulation cell size was considered, and in the limit of zero finite size effects, physically realistic undulations are observed within the individual clay sheets.
North Sea oil is overwhelmingly generated in shales of the Upper Jurassic e basal Cretaceous Kimm... more North Sea oil is overwhelmingly generated in shales of the Upper Jurassic e basal Cretaceous Kimmeridge Clay Formation. Once generated, the oil is expelled and ultimately migrates to accumulate in sandstone or carbonate reservoirs. The source rock shales, however, still contain the portion of the oil that was not expelled. As a consequence such shales and juxtaposed non-source lithofacies can form the targets for the exploration of 'unconventional oil'.
Thermochemical processing methods such as pyrolysis are of growing interest as a means of convert... more Thermochemical processing methods such as pyrolysis are of growing interest as a means of converting biomass into fuels and commodity chemicals in a sustainable manner. Macroalgae, or seaweed, represent a novel class of feedstock for pyrolysis that, owing to the nature of the environments in which they grow coupled with their biochemistry, naturally possess high metal contents. Although the impact of metals upon the pyrolysis of terrestrial biomass is well documented, their influence on the thermochemical conversion of marine-derived feeds is largely unknown. Furthermore, these effects are inherently difficult to study, owing to the heterogeneous character of natural seaweed samples. The work described in this paper uses copper(II) alginate, together with alginic acid and sodium alginate as model compounds for exploring the effects of metals upon macroalgae thermolysis. A thermogravimetric analysis-Fourier transform infrared spectroscopic study revealed that, unusually, Cu(2+) ions ...
Biofuels production from microalgae attracts much attention but remains an unproven technology. W... more Biofuels production from microalgae attracts much attention but remains an unproven technology. We explore routes to enhance production through modifications to a range of generic microalgal physiological characteristics. Our analysis shows that biofuels production may be enhanced ca fivefold through genetic modification (GM) of factors affecting growth rate, respiration, photoacclimation, photosynthesis efficiency and the minimum cell quotas for nitrogen and phosphorous (N : C and P : C). However, simulations indicate that the ideal GM microalgae for commercial deployment could, on escape to the environment, become a harmful algal bloom species par excellence, with attendant risks to ecosystems and livelihoods. In large measure, this is because an organism able to produce carbohydrate and/or lipid at high rates, providing stock metabolites for biofuels production, will also be able to attain a stoichiometric composition that will be far from optimal as food for the support of zoopl...
Electronic Materials: Science and Technology, 2007
Clay minerals belong to a wider class of solids known as layered materials, which may be defined ... more Clay minerals belong to a wider class of solids known as layered materials, which may be defined as ‘crystalline materials wherein the atoms in the layers are cross-linked by chemical bonds, while the atoms of adjacent layers interact by physical forces’ [1]. Both clay sheets and interlayer space have one dimension in the nanometre range. Cationic clays are the predominant
ABSTRACT The role of mineral surfaces in the adsorption, transport, formation, and degradation of... more ABSTRACT The role of mineral surfaces in the adsorption, transport, formation, and degradation of natural organic matter (NOM) in the biosphere remains an active research area owing to the difficulties in identifying proper working models of both NOM and mineral phases present in the environment. The variety of aqueous chemistries encountered in the subsurface (e. g., oxic vs. anoxic, variable pH) further complicate this field of study. Recently, the advent of nanoscale probes such as X-ray adsorption spectroscopy and surface vibrational spectroscopy applied to study such complicated interfacial systems have enabled new insight into NOM-mineral interfaces. Additionally, due to increasing capabilities in computational chemistry, it is now possible to simulate molecular processes of NOM at multiple scales, from quantum methods for electron transfer to classical methods for folding and adsorption of macroparticles. In this review, we present recent developments in interfacial properties of NOM adsorbed on mineral surfaces from a computational point of view that is informed by recent experiments.
ABSTRACT In this study we investigate the fundamentals of a problem pertinent to the cement and c... more ABSTRACT In this study we investigate the fundamentals of a problem pertinent to the cement and concrete manufacturing industries, where clay minerals are pollutants of sands due to their capacity to adsorb additives designed to improve concrete workability. In this density functional theory (DFT) investigation we examine the adsorption of a selection of organic monomers, (e.g., CH3CH2CHOHCH3 and (CH3)3N+CH2CHOHCH2CH3,Cl−) on kaolinite (Al2Si2O5(OH)4) to determine the nature of the basal surface/monomer interactions and, also, to determine whether the presence of an additional clay layer and separately water changes the nature of these interactions. We gauge these effects by examining their formation energies, structural configurations post relaxation, Mulliken charges, and molecular orbitals occupancies. The results show that interactions are predominantly electrostatic for charged monomers and H-bonding for noncharged and also that increasing the complexity of these systems does not change the nature of these interactions, but that it does change the strength of them as well as the potential chemical reactivity of these clay/monomer environments.
... Performance Computing Facility (HPCF) at Cambridge. Some of the initial optimizations were co... more ... Performance Computing Facility (HPCF) at Cambridge. Some of the initial optimizations were completed on 4 processors of a 16 processor (400 MHz processor speed) SGI Onyx2 machine at Queen Mary, University of London. ...
One of the fundamental difficulties when considering the origin of life on Earth is the identific... more One of the fundamental difficulties when considering the origin of life on Earth is the identification of an emergent system that not only replicated, but also had the capacity to undergo discrete mutation in such a way that following generations might inherit and pass on the mutation. We speculate that the layered double hydroxide (LDH) minerals are plausible candidates for a proto-RNA molecule. We describe a hypothetical LDH-like system which, when intercalated with certain anions, forms crystals with a high degree of internal order giving rise to novel information storage structures in which replication fidelity is maintained, a concept we use to propose an explanation for interstratification in terephthalate LDHs. The external surfaces of these hypothetical crystals provide active sites whose structure and chemistry is dictated by the internal information content of the LDH. Depending on the LDH polytype, the opposing external surfaces of a crystal may give rise to reactive sites that are either complementary or mirror images of each other, and so may be chiral. We also examine similarities between these proposed "proto-RNA" structures and the DNA that encodes the hereditary information in life today, concluding with a hypothetical scenario wherein these proto-RNA molecules predated the putative RNA-world.
Preparation of industrially useful clay-polymer nanocomposite materials often requires the disper... more Preparation of industrially useful clay-polymer nanocomposite materials often requires the dispersal of clay particles within a polymer matrix. The degree to which the clay particles may be dispersed has an effect on the resultant properties of the material, and the clay is often rendered organophilic using alkylammonium species to facilitate incorporation of polymer. The use of a low molecular weight poly(propylene) oxide diamine is investigated as a reagent for controlling the separation between layers in smectite clays and therefore the extent to which the clay tactoid may be dispersed. The arrangement and interactions of the amine species in the interlayer region are investigated through analysis by both experimental methods and computer simulation, which gives insight into coordination mechanisms within the organoclay. Infrared spectroscopy indicates the presence of extensive hydrogen bonding within the amine-clay interlayer. Some of the amine species were found to intercalate in a nonprotonated state, resulting in strong hydrogen-bonding interactions between amine and ammonium groups. Large-scale classical molecular dynamics simulation shows that the amine groups do not interact strongly with the clay sheets, in contradistinction to ammonium groups. The effect of simulation cell size was considered, and in the limit of zero finite size effects, physically realistic undulations are observed within the individual clay sheets.
We present the results of large-scale molecular simulations, run over several tens of nanoseconds... more We present the results of large-scale molecular simulations, run over several tens of nanoseconds, of 25-mer sequences of single-stranded ribonucleic acid (RNA) in bulk water and at the surface of three hydrated positively charged MgAl layered double hydroxide (LDH) minerals. The three LDHs differ in surface charge density, through varying the number of isomorphic Al substitutions. Over the course of the simulations, RNA adsorbs tightly to the LDH surface through electrostatic interactions between the charged RNA phosphate groups and the alumina charge sites present in the LDH sheet. The RNA strands arrange parallel to the surface with the base groups aligning normal to the surface and exposed to the bulk aqueous region. This templating effect makes LDH a candidate for amplifying the population of a known RNA sequence from a small number of RNAs. The structure and interactions of RNA at a positively charged, hydroxylated LDH surface were compared with those of RNA at a positively charged calcium montmorillonite surface, allowing us to establish the comparative effect of complexation and water structure at hydroxide and silicate surfaces. The systems were studied by computing radial distribution functions, atom density plots, and radii of gyration, as well as visualization. An observation pertinent to the role of these minerals in prebiotic chemistry is that, for a given charge density on the mineral surface, different genetic sequences of RNA adopt different configurations.
Journal of Theoretical Biology - J THEOR BIOL, 2010
A mechanistic model of microalgae is used to explore the implications of modifying microalgal chl... more A mechanistic model of microalgae is used to explore the implications of modifying microalgal chlorophyll content and photosynthetic efficiency with an aim to optimising commercial biomass production. The models show the potential for a 10 fold increase in microalgae productivity in genetically modified versus unmodified configurations, while also enabling the use of bioreactors of greater optical depth operating at lower dilution rates. Analysis suggests that natural selection of a trait benefiting the individual (high Chl:Cmax, i.e., high antennae size) conflicts with artificial selection of a trait (low Chl:Cmax) of most benefit to production at the population level. The implication is that GM strains rather than strains selected from nature will be most beneficial for commercial algal biofuels production. Further, escaped GM algae populations may, depending on the specific nature of the modification, be quickly out-competed by the natural forms because individually a high Chl:C is beneficial in low light environments. However, it remains possible that changes in biochemical composition associated with genetic modification of photosystem competence, or with other selection processes to enhance commercial gain, may adversely affect the value of such organisms as prey for zooplankton, leading to the unwanted generation of future harmful algae.
Layered double hydroxides (LDHs) have been shown to form staged intermediate structures in experi... more Layered double hydroxides (LDHs) have been shown to form staged intermediate structures in experimental studies of intercalation. However, the mechanism by which staged structures are produced remains undetermined. Using molecular dynamics simulations, we show that LDHs are flexible enough to deform around bulky intercalants such as deoxyribonucleic acid (DNA). The flexibility of layered materials has previously been shown to affect the pathway by which staging occurs. We explore three possible intermediate structures which may form during intercalation of DNA into Mg2Al LDHs and study how the models differ energetically. When DNA strands are stacked directly on top of each other, the LDH system has a higher potential energy than when they are stacked in a staggered or interstratified structure. It is generally thought that staged intercalation occurs through a Daumas-Herold or a Rudorff model. We find, on average, greater diffusion coefficients for DNA strands in a Daumas-Herold configuration compared to a Rudorff model and a stage-1 structure. Our simulations provide evidence for the presence of peristaltic modes of motion within Daumas-Herold configurations. This is confirmed by spectral analysis of the thickness variation of the basal spacing. Peristaltic modes are more prominent in the Daumas-Herold structure compared to the Rudorff and stage-1 structures and support a mechanism by means of which bulky intercalated molecules such as DNA rapidly diffuse within an LDH interlayer.
Rock–water–carbon interactions germane to serpentinization in hydrothermal vents have occurred fo... more Rock–water–carbon interactions germane to serpentinization in hydrothermal vents have occurred for over 4 billion years, ever since there was liquid water on Earth. Serpentinization converts iron(II) containing minerals and water to magnetite (Fe3O4) plus H2. The hydrogen can generate native metals such as awaruite (Ni3Fe), a common serpentinization product. Awaruite catalyzes the synthesis of methane from H2 and CO2 under hydrothermal conditions. Native iron and nickel catalyze the synthesis of formate, methanol, acetate, and pyruvate—intermediates of the acetyl-CoA pathway, the most ancient pathway of CO2 fixation. Carbon monoxide dehydrogenase (CODH) is central to the pathway and employs Ni0 in its catalytic mechanism. CODH has been conserved during 4 billion years of evolution as a relic of the natural CO2-reducing catalyst at the onset of biochemistry. The carbide-containing active site of nitrogenase—the only enzyme on Earth that reduces N2—is probably also a relic, a biologic...
Thermochemical processing methods such as pyrolysis are of growing interest as a means of convert... more Thermochemical processing methods such as pyrolysis are of growing interest as a means of converting biomass into fuels and commodity chemicals in a sustainable manner. Macroalgae, or seaweed, represent a novel class of feedstock for pyrolysis that, owing to the nature of the environments in which they grow coupled with their biochemistry, naturally possess high metal contents. Although the impact of metals upon the pyrolysis of terrestrial biomass is well documented, their influence on the thermochemical conversion of marine-derived feeds is largely unknown. Furthermore, these effects are inherently difficult to study, owing to the heterogeneous character of natural seaweed samples. The work described in this paper uses copper(II) alginate, together with alginic acid and sodium alginate as model compounds for exploring the effects of metals upon macroalgae thermolysis. A thermogravimetric analysis-Fourier transform infrared spectroscopic study revealed that, unusually, Cu(2+) ions ...
We report chiral differences in the effects of D-and L-histidine on the interlayer spacing of ver... more We report chiral differences in the effects of D-and L-histidine on the interlayer spacing of vermiculite clays that are relevant in assessing the role of clays in the origin of bio-homochirality.
We present a joint experimental and theoretical investigation into the adsorption of polycationic... more We present a joint experimental and theoretical investigation into the adsorption of polycationic quaternary ammonium polymers on the clay mineral kaolinite. Within the cement and concrete manufacturing industries such polymers are used to improve the final product by inerting the adsorption capacity of the clay minerals for more expensive additives. The adsorption of the presently used polymer (FL22) was compared with both a similar variant, but without a hydroxyl group (Fl22mod) and uncharged polyvinyl alcohol (PVA). Experimental results show that adsorption of FL22 is higher than that of FL22mod at both pH 6 and at pH > 10 and that the adsorption of PVA is the highest. Theoretical density functional theory (DFT) results and simplified models consisting of the basal surfaces of kaolinite, with monomers of FL22, FL22mod and PVA gave monomer coverage per unit surface area of kaolinite, a comparison of the configurations of the relaxed models, formation energies and Mulliken charges. These results show that the polycationic polymers interact with the basal surfaces of kaolinite electrostatically, explaining the high affinity of these polymers for kaolinite surfaces in the experimental results. The hydroxyl groups of FL22 and PVA form hydrogen bonds with the basal surfaces of kaolinite in conditions of pH 6. The joint experimental and theoretical results suggest that, due to the presence of the hydroxyl group, the conformation of FL22 changes under pH, where at neutral pH it lies relatively flat to the kaolinite surfaces, but at higher pH, conformational changes of the polymer occur, thereby increasing the adsorbed quantity of FL22.
We present a joint experimental and theoretical investigation into the adsorption of polycationic... more We present a joint experimental and theoretical investigation into the adsorption of polycationic quaternary ammonium polymers on the clay mineral kaolinite. Within the cement and concrete manufacturing industries such polymers are used to improve the final product by inerting the adsorption capacity of the clay minerals for more expensive additives. The adsorption of the presently used polymer (FL22) was compared with both a similar variant, but without a hydroxyl group (Fl22mod) and uncharged polyvinyl alcohol (PVA). Experimental results show that adsorption of FL22 is higher than that of FL22mod at both pH 6 and at pH > 10 and that the adsorption of PVA is the highest. Theoretical density functional theory (DFT) results and simplified models consisting of the basal surfaces of kaolinite, with monomers of FL22, FL22mod and PVA gave monomer coverage per unit surface area of kaolinite, a comparison of the configurations of the relaxed models, formation energies and Mulliken charges. These results show that the polycationic polymers interact with the basal surfaces of kaolinite electrostatically, explaining the high affinity of these polymers for kaolinite surfaces in the experimental results. The hydroxyl groups of FL22 and PVA form hydrogen bonds with the basal surfaces of kaolinite in conditions of pH 6. The joint experimental and theoretical results suggest that, due to the presence of the hydroxyl group, the conformation of FL22 changes under pH, where at neutral pH it lies relatively flat to the kaolinite surfaces, but at higher pH, conformational changes of the polymer occur, thereby increasing the adsorbed quantity of FL22.
... Full details of how the LAMMPS code was employed in the molecular dynamics simulations and of... more ... Full details of how the LAMMPS code was employed in the molecular dynamics simulations and of the procedure used to prepare the claypolymer composites are given in Boulet et al.1,3. ... PEO-Mac (M w 375 g mol −1 ), 1.70, 1.77, 1.79. 1.74. ...
Preparation of industrially useful clay-polymer nanocomposite materials often requires the disper... more Preparation of industrially useful clay-polymer nanocomposite materials often requires the dispersal of clay particles within a polymer matrix. The degree to which the clay particles may be dispersed has an effect on the resultant properties of the material, and the clay is often rendered organophilic using alkylammonium species to facilitate incorporation of polymer. The use of a low molecular weight poly(propylene) oxide diamine is investigated as a reagent for controlling the separation between layers in smectite clays and therefore the extent to which the clay tactoid may be dispersed. The arrangement and interactions of the amine species in the interlayer region are investigated through analysis by both experimental methods and computer simulation, which gives insight into coordination mechanisms within the organoclay. Infrared spectroscopy indicates the presence of extensive hydrogen bonding within the amine-clay interlayer. Some of the amine species were found to intercalate in a nonprotonated state, resulting in strong hydrogen-bonding interactions between amine and ammonium groups. Large-scale classical molecular dynamics simulation shows that the amine groups do not interact strongly with the clay sheets, in contradistinction to ammonium groups. The effect of simulation cell size was considered, and in the limit of zero finite size effects, physically realistic undulations are observed within the individual clay sheets.
North Sea oil is overwhelmingly generated in shales of the Upper Jurassic e basal Cretaceous Kimm... more North Sea oil is overwhelmingly generated in shales of the Upper Jurassic e basal Cretaceous Kimmeridge Clay Formation. Once generated, the oil is expelled and ultimately migrates to accumulate in sandstone or carbonate reservoirs. The source rock shales, however, still contain the portion of the oil that was not expelled. As a consequence such shales and juxtaposed non-source lithofacies can form the targets for the exploration of 'unconventional oil'.
Thermochemical processing methods such as pyrolysis are of growing interest as a means of convert... more Thermochemical processing methods such as pyrolysis are of growing interest as a means of converting biomass into fuels and commodity chemicals in a sustainable manner. Macroalgae, or seaweed, represent a novel class of feedstock for pyrolysis that, owing to the nature of the environments in which they grow coupled with their biochemistry, naturally possess high metal contents. Although the impact of metals upon the pyrolysis of terrestrial biomass is well documented, their influence on the thermochemical conversion of marine-derived feeds is largely unknown. Furthermore, these effects are inherently difficult to study, owing to the heterogeneous character of natural seaweed samples. The work described in this paper uses copper(II) alginate, together with alginic acid and sodium alginate as model compounds for exploring the effects of metals upon macroalgae thermolysis. A thermogravimetric analysis-Fourier transform infrared spectroscopic study revealed that, unusually, Cu(2+) ions ...
Biofuels production from microalgae attracts much attention but remains an unproven technology. W... more Biofuels production from microalgae attracts much attention but remains an unproven technology. We explore routes to enhance production through modifications to a range of generic microalgal physiological characteristics. Our analysis shows that biofuels production may be enhanced ca fivefold through genetic modification (GM) of factors affecting growth rate, respiration, photoacclimation, photosynthesis efficiency and the minimum cell quotas for nitrogen and phosphorous (N : C and P : C). However, simulations indicate that the ideal GM microalgae for commercial deployment could, on escape to the environment, become a harmful algal bloom species par excellence, with attendant risks to ecosystems and livelihoods. In large measure, this is because an organism able to produce carbohydrate and/or lipid at high rates, providing stock metabolites for biofuels production, will also be able to attain a stoichiometric composition that will be far from optimal as food for the support of zoopl...
Electronic Materials: Science and Technology, 2007
Clay minerals belong to a wider class of solids known as layered materials, which may be defined ... more Clay minerals belong to a wider class of solids known as layered materials, which may be defined as ‘crystalline materials wherein the atoms in the layers are cross-linked by chemical bonds, while the atoms of adjacent layers interact by physical forces’ [1]. Both clay sheets and interlayer space have one dimension in the nanometre range. Cationic clays are the predominant
ABSTRACT The role of mineral surfaces in the adsorption, transport, formation, and degradation of... more ABSTRACT The role of mineral surfaces in the adsorption, transport, formation, and degradation of natural organic matter (NOM) in the biosphere remains an active research area owing to the difficulties in identifying proper working models of both NOM and mineral phases present in the environment. The variety of aqueous chemistries encountered in the subsurface (e. g., oxic vs. anoxic, variable pH) further complicate this field of study. Recently, the advent of nanoscale probes such as X-ray adsorption spectroscopy and surface vibrational spectroscopy applied to study such complicated interfacial systems have enabled new insight into NOM-mineral interfaces. Additionally, due to increasing capabilities in computational chemistry, it is now possible to simulate molecular processes of NOM at multiple scales, from quantum methods for electron transfer to classical methods for folding and adsorption of macroparticles. In this review, we present recent developments in interfacial properties of NOM adsorbed on mineral surfaces from a computational point of view that is informed by recent experiments.
ABSTRACT In this study we investigate the fundamentals of a problem pertinent to the cement and c... more ABSTRACT In this study we investigate the fundamentals of a problem pertinent to the cement and concrete manufacturing industries, where clay minerals are pollutants of sands due to their capacity to adsorb additives designed to improve concrete workability. In this density functional theory (DFT) investigation we examine the adsorption of a selection of organic monomers, (e.g., CH3CH2CHOHCH3 and (CH3)3N+CH2CHOHCH2CH3,Cl−) on kaolinite (Al2Si2O5(OH)4) to determine the nature of the basal surface/monomer interactions and, also, to determine whether the presence of an additional clay layer and separately water changes the nature of these interactions. We gauge these effects by examining their formation energies, structural configurations post relaxation, Mulliken charges, and molecular orbitals occupancies. The results show that interactions are predominantly electrostatic for charged monomers and H-bonding for noncharged and also that increasing the complexity of these systems does not change the nature of these interactions, but that it does change the strength of them as well as the potential chemical reactivity of these clay/monomer environments.
... Performance Computing Facility (HPCF) at Cambridge. Some of the initial optimizations were co... more ... Performance Computing Facility (HPCF) at Cambridge. Some of the initial optimizations were completed on 4 processors of a 16 processor (400 MHz processor speed) SGI Onyx2 machine at Queen Mary, University of London. ...
One of the fundamental difficulties when considering the origin of life on Earth is the identific... more One of the fundamental difficulties when considering the origin of life on Earth is the identification of an emergent system that not only replicated, but also had the capacity to undergo discrete mutation in such a way that following generations might inherit and pass on the mutation. We speculate that the layered double hydroxide (LDH) minerals are plausible candidates for a proto-RNA molecule. We describe a hypothetical LDH-like system which, when intercalated with certain anions, forms crystals with a high degree of internal order giving rise to novel information storage structures in which replication fidelity is maintained, a concept we use to propose an explanation for interstratification in terephthalate LDHs. The external surfaces of these hypothetical crystals provide active sites whose structure and chemistry is dictated by the internal information content of the LDH. Depending on the LDH polytype, the opposing external surfaces of a crystal may give rise to reactive sites that are either complementary or mirror images of each other, and so may be chiral. We also examine similarities between these proposed "proto-RNA" structures and the DNA that encodes the hereditary information in life today, concluding with a hypothetical scenario wherein these proto-RNA molecules predated the putative RNA-world.
Preparation of industrially useful clay-polymer nanocomposite materials often requires the disper... more Preparation of industrially useful clay-polymer nanocomposite materials often requires the dispersal of clay particles within a polymer matrix. The degree to which the clay particles may be dispersed has an effect on the resultant properties of the material, and the clay is often rendered organophilic using alkylammonium species to facilitate incorporation of polymer. The use of a low molecular weight poly(propylene) oxide diamine is investigated as a reagent for controlling the separation between layers in smectite clays and therefore the extent to which the clay tactoid may be dispersed. The arrangement and interactions of the amine species in the interlayer region are investigated through analysis by both experimental methods and computer simulation, which gives insight into coordination mechanisms within the organoclay. Infrared spectroscopy indicates the presence of extensive hydrogen bonding within the amine-clay interlayer. Some of the amine species were found to intercalate in a nonprotonated state, resulting in strong hydrogen-bonding interactions between amine and ammonium groups. Large-scale classical molecular dynamics simulation shows that the amine groups do not interact strongly with the clay sheets, in contradistinction to ammonium groups. The effect of simulation cell size was considered, and in the limit of zero finite size effects, physically realistic undulations are observed within the individual clay sheets.
We present the results of large-scale molecular simulations, run over several tens of nanoseconds... more We present the results of large-scale molecular simulations, run over several tens of nanoseconds, of 25-mer sequences of single-stranded ribonucleic acid (RNA) in bulk water and at the surface of three hydrated positively charged MgAl layered double hydroxide (LDH) minerals. The three LDHs differ in surface charge density, through varying the number of isomorphic Al substitutions. Over the course of the simulations, RNA adsorbs tightly to the LDH surface through electrostatic interactions between the charged RNA phosphate groups and the alumina charge sites present in the LDH sheet. The RNA strands arrange parallel to the surface with the base groups aligning normal to the surface and exposed to the bulk aqueous region. This templating effect makes LDH a candidate for amplifying the population of a known RNA sequence from a small number of RNAs. The structure and interactions of RNA at a positively charged, hydroxylated LDH surface were compared with those of RNA at a positively charged calcium montmorillonite surface, allowing us to establish the comparative effect of complexation and water structure at hydroxide and silicate surfaces. The systems were studied by computing radial distribution functions, atom density plots, and radii of gyration, as well as visualization. An observation pertinent to the role of these minerals in prebiotic chemistry is that, for a given charge density on the mineral surface, different genetic sequences of RNA adopt different configurations.
Journal of Theoretical Biology - J THEOR BIOL, 2010
A mechanistic model of microalgae is used to explore the implications of modifying microalgal chl... more A mechanistic model of microalgae is used to explore the implications of modifying microalgal chlorophyll content and photosynthetic efficiency with an aim to optimising commercial biomass production. The models show the potential for a 10 fold increase in microalgae productivity in genetically modified versus unmodified configurations, while also enabling the use of bioreactors of greater optical depth operating at lower dilution rates. Analysis suggests that natural selection of a trait benefiting the individual (high Chl:Cmax, i.e., high antennae size) conflicts with artificial selection of a trait (low Chl:Cmax) of most benefit to production at the population level. The implication is that GM strains rather than strains selected from nature will be most beneficial for commercial algal biofuels production. Further, escaped GM algae populations may, depending on the specific nature of the modification, be quickly out-competed by the natural forms because individually a high Chl:C is beneficial in low light environments. However, it remains possible that changes in biochemical composition associated with genetic modification of photosystem competence, or with other selection processes to enhance commercial gain, may adversely affect the value of such organisms as prey for zooplankton, leading to the unwanted generation of future harmful algae.
Layered double hydroxides (LDHs) have been shown to form staged intermediate structures in experi... more Layered double hydroxides (LDHs) have been shown to form staged intermediate structures in experimental studies of intercalation. However, the mechanism by which staged structures are produced remains undetermined. Using molecular dynamics simulations, we show that LDHs are flexible enough to deform around bulky intercalants such as deoxyribonucleic acid (DNA). The flexibility of layered materials has previously been shown to affect the pathway by which staging occurs. We explore three possible intermediate structures which may form during intercalation of DNA into Mg2Al LDHs and study how the models differ energetically. When DNA strands are stacked directly on top of each other, the LDH system has a higher potential energy than when they are stacked in a staggered or interstratified structure. It is generally thought that staged intercalation occurs through a Daumas-Herold or a Rudorff model. We find, on average, greater diffusion coefficients for DNA strands in a Daumas-Herold configuration compared to a Rudorff model and a stage-1 structure. Our simulations provide evidence for the presence of peristaltic modes of motion within Daumas-Herold configurations. This is confirmed by spectral analysis of the thickness variation of the basal spacing. Peristaltic modes are more prominent in the Daumas-Herold structure compared to the Rudorff and stage-1 structures and support a mechanism by means of which bulky intercalated molecules such as DNA rapidly diffuse within an LDH interlayer.
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Papers by H Greenwell