Building Biominerals: finding the tools that shape biogenic calcite and its signatures

Lead Research Organisation: University College London
Department Name: Chemistry

Abstract

In paleoclimatological studies, where the climate and Earth's surface environment are reconstructed throughout the geological past, information is often obtained from signals in fossil shells, corals and other biologically formed minerals (biominerals). These signals, or proxies, are for example trace metal concentrations or isotope ratios measured in fossils, that tell us what sea surface temperature the organism experienced during the building of its shell, or how much nutrients were available; even how much polar ice was present can be reconstructed. However, reliable application of these proxies to reconstruct past environments and climate requires sound knowledge of the processes that lead to the recording of these proxies by biominerals

The first step in the uptake of trace metals by minerals occurs at the surface of those minerals and crucial in this step is the structure of that surface. Some trace metals prefer to attach to very "open" sites, while others prefer more "closed" sites. This preference for particular surface sites is one of the many factors that can affect the signal ultimately interpreted as a proxy. Organisms are highly capable of controlling the shape of the biominerals they build. By controlling this shape, they control the structure of the surface through which trace metals incorporate.

We know that organic compounds such as amino acids are used by organisms as tools to shape their biominerals. In order to understand the effects these organic compounds have on the growing biomineral surface, and on the process of recording proxies during biomineral growth, I will conduct both experimental and theoretical research.

The experimental line of research focuses on determining the interaction between amino acids and selected trace metals during mimicked calcite biomineralisation. Among others, I will grow calcite crystals in the presence of amino acids and trace metals. The results will quantify the extent to which biological regulation of crystal morphology may explain variations in trace metal signatures of biogenic calcites.

The theoretical line of research focuses on understanding the mechanisms behind the interactions observed experimentally. Atomic-scale simulation techniques developed for calcite within the host institute are the ideal tool to obtain detailed insight into the interaction of the calcite surface with trace metals and organic molecules. Previous geochemical models I developed for calcite will be used to bridge the macroscopic, microscopic and atomic-scale results. Ultimately, all results will be merged with current physiological biomineralisation concepts into a state-of-the-art biomineralisation model.

The outcome of my ambitious research project bridges between molecular level surface chemistry and macroscale geochemical modelling, validated at all stages by experimental data. Specific applications of the project are in the fields of biomineralisation and paleoclimatology.

Planned Impact

The results of this project will be important for understanding the underlying mechanisms for a variety of processes, including carbon mineral sequestration, currently one of the most viable routes to lower atmospheric CO2 levels and the uptake of contaminants by the host rock of carbonaceous subsoils, aquifers and linings of waste repositories. The beneficiaries of this project range from (i) the general public, (ii) environmental protection agencies in the UK and abroad, and (iii) the Government and public sector, to potentially (iv) a variety of industries, as well as (v) academic colleagues, as outlined in the Academic Beneficiaries section.

(i) General Public
We are all aware of the threat from the potentially disastrous effects of climate change, such as rising sea levels and extreme weather conditions. Improved methods for the reduction of atmospheric CO2 levels will therefore benefit all humans as well as the natural environment.
In addition, any progress made in understanding immobilisation of contaminants by calcite, limestone and calcareous materials also benefits us all, whether by providing new routes to regenerate contaminated land to make it suitable for housing or for leisure/recreational purposes.
(ii) Environmental Protection Agencies
Detailed understanding of tailored mineral growth and trace metal uptake will aid in improving various remediation methods such as in situ precipitation of solids to form reactive barriers against ground water contaminant transport, and improving CO2 sequestration methods.
(iii) Government and public sector
In addition to improved carbon mineral sequestration routes to lower atmospheric CO2 levels, reliable (paleo)climate models for the quantitative prediction of future climate change are clearly of prime importance to policy makers and legislators. Reliable paleoclimate modelling and reconstruction depends up valid indicators of the past climate and environment, which in their turn rely on sound knowledge of the processes that lead to the formation of these indicators. In this sense, the proposed research is fundamental both in approach and application. Moreover, the prediction of the effects of Ocean Acidification on the production and stability of marine calcium carbonate minerals requires, among others, more realistic, pH dependent, simulations of the calcite surface, which will be facilitated tools provided in this project.
(iv) Industries
In particular manufacturers of tailored (nano)crystals may gain from understanding the morphological effect of combined application of trace elements and surface-active amino acids.
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Publications

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Islam H (2013) In Situ XAS of the Solvothermal Decomposition of Dithiocarbamate Complexes in Journal of Physics: Conference Series

 
Title Materials Research Exchange Event 
Description Some of my recent work (electromicroscopy images) was among the display material at the Materials Research Exchange Event, Coventry, February 2014, showcasing UK materials research to facilitate closer collaboration between industry and UK materials research base. 
Type Of Art Image 
Year Produced 2014 
Impact None yet. 
URL http://www.iom3.org/event/2014-materials-research-exchange
 
Description We used computational chemistry methods to determine fundamental properties of calcite (lime scale mineral) and quantify its reactivity to impurities and its rate of growth. We observed large variations with surface topography (roughness). Our results help to predict different mineral growth rates for differently sized and shaped particles and biominerals. We also determined how sensitive the calcite in the shells of tiny marine organisms is to changes in salt concentration of the sea. This helps to look into past changes of salinity and therefore upland rainfall and climate change, when looking at fossil calcite shells in seafloor sediments.
Exploitation Route Knowing how, how fast or why limescale (calcite) forms or does not form is important for engineering efforts such as descaling drinking water, or preventing clogging up of (oil) pipelines, industrial and household appliances. Besides, inducing calcite and it's magnesium-rich "brother" magnesite formation is currently one of the most viable ways for long-term storage of CO2. Improved control on the formation of these minerals will improve the efficiency of such engineering efforts.
Sectors Chemicals,Construction,Energy,Environment

 
Description My results have been used by peers, in particular to better understand paleoclimate signals in fossil (shells) and stalagmite calcite (lime scale) archives. Better tools to study the past climate will ultimately help to better understand how Earth responds to changes in increasing CO2 in the atmosphere and to better predict what we can expect in the current global climate change.
First Year Of Impact 2014
Sector Chemicals,Education,Environment
Impact Types Societal

 
Description Palace Symposium, Amsterdam, the Netherlands
Geographic Reach National 
Policy Influence Type Participation in a national consultation
URL http://www.paleisamsterdam.nl/nieuws/2015/06/25/25-juni-paleissymposium-getting-from-where-we-are-to...
 
Description ESRF beamtime on Calcite nucleation
Amount £30,000 (GBP)
Funding ID ESRF code 26-02-698 
Organisation Netherlands Organisation for Scientific Research (NWO) 
Department Dutch-Belgian Beamline
Sector Public
Country Netherlands
Start 03/2014 
End 04/2014
 
Description ESRF beamtime on In situ electrochemical studies of carbon loaded greigite reactivity with carbon dioxide
Amount £28,000 (GBP)
Funding ID 26-01-975 
Organisation Netherlands Organisation for Scientific Research (NWO) 
Department Dutch-Belgian Beamline
Sector Public
Country Netherlands
Start 02/2013 
End 05/2013
 
Description ESRF beamtime on Reactive oxygen species formation with pyrite under anoxic conditions
Amount £38,000 (GBP)
Funding ID 26-01-986 
Organisation Netherlands Organisation for Scientific Research (NWO) 
Department Dutch-Belgian Beamline
Sector Public
Country Netherlands
Start 08/2013 
End 10/2013
 
Title Calcite surface model incorporated in geochemical freeware modelling software 
Description This software can be used to simulate geochemical conditions and material properties. 
Type Of Material Computer model/algorithm 
Year Produced 2012 
Provided To Others? Yes  
Impact Scientists can better calculate chemical reactivity of a widespread mineral: calcite. 
URL https://vminteq.lwr.kth.se/
 
Description Collaboration Munster/Granada 
Organisation University of Granada
Department Department of Mineralogy and Petrology
Country Spain 
Sector Academic/University 
PI Contribution We have performed experiments together, using a flow-through set-up for macroscale experiments (Granada) and microscale using the Atomic Force Microscope (Munster). I planned the experiments, after generating the research question, specified the experimental conditions and collaborated on the microscale experiments.
Collaborator Contribution In Granada, experiments were conducted to verify microscale results. They provided the chemicals for these experiments and performed solution analyses. Munster provided the Atomic Force Microscope, flow-though cell, chemical and solution analyses for the microscale experiments.
Impact Thus far, output in conference abstracts only, including an invited talks at the Goldschmidt conference, Prague, Czech Republic.
Start Year 2014
 
Description Collaboration Munster/Granada 
Organisation University of Münster
Department Institute of Mineralogy
Country Germany 
Sector Academic/University 
PI Contribution We have performed experiments together, using a flow-through set-up for macroscale experiments (Granada) and microscale using the Atomic Force Microscope (Munster). I planned the experiments, after generating the research question, specified the experimental conditions and collaborated on the microscale experiments.
Collaborator Contribution In Granada, experiments were conducted to verify microscale results. They provided the chemicals for these experiments and performed solution analyses. Munster provided the Atomic Force Microscope, flow-though cell, chemical and solution analyses for the microscale experiments.
Impact Thus far, output in conference abstracts only, including an invited talks at the Goldschmidt conference, Prague, Czech Republic.
Start Year 2014
 
Description Collaboration QMUL 
Organisation Queen Mary University of London
Department School of Biological and Chemical Science QMUL
Country United Kingdom 
Sector Academic/University 
PI Contribution Sharing of codes and discussion of computational results
Collaborator Contribution Sharing of codes and discussion of computational results
Impact Wolthers M., D. Di Tommaso, Z. Du and N.H de Leeuw, 2013. Variations in calcite growth kinetics with surface topography: Molecular Dynamics simulations and process-based growth kinetics modelling. CrystEngComm 15, 5506-5514. (IF 4.1; 13 citations) Wolthers M., D. Di Tommaso, Z. Du and N.H de Leeuw, 2012. Calcite surface structure and reactivity: molecular dynamics simulations and macroscopic surface modelling of the calcite-water interface. Phys. Chem. Chem. Phys., 14, 15145-15157.
Start Year 2012
 
Title Modelling the impact of surface roughness on reactivity of materials 
Description Numerical tool to calculate the impact of the roughness of a material surface on its reactivity (to dissolve or grow). 
Type Of Technology New/Improved Technique/Technology 
Year Produced 2013 
Impact Better prediction of calcite reactivity under a wide variety of conditions. Various research groups now use this tool. 
URL http://pubs.rsc.org/en/Content/ArticleLanding/2013/CE/c3ce40249e#!divAbstract
 
Description Media Interest 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact Fact check on Himalaya salt.

No further impact as yet.
Year(s) Of Engagement Activity 2015
URL http://www.nrc.nl/next/van/2015/mei/01/himalayazout-komt-niet-uit-de-himalaya-de-rode-1490103
 
Description Media Interest 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact Enhanced insight into the properties of kidney stones.

No further impacts noted as yet.
Year(s) Of Engagement Activity 2015
URL http://www.volkskrant.nl/dossier-inzicht/nierstenen-van-kristal~a4056893/
 
Description Palace Symposium, the Netherlands 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Policymakers/politicians
Results and Impact I participated in the paleissymposium discussion 'Getting from where we are to where we want to be in clean energy' between scientists, industry and top consortia for knowledge and innovation, hosted by the Royal Family at the Royal Palace Amsterdam, the NL.

After this symposium, I have been in contact with the CEO of the NAM (Dutch Gas) and directors of Shell Netherlands and BASF Netherlands to look for future opportunities.
Year(s) Of Engagement Activity 2015
URL http://www.paleisamsterdam.nl/en/programme/symposia