development and implementation of molecular modelling techniques for the advancement of natural materials in environmental applications

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Research

Amino acids and Peptides Intercalated by LDH
From amino acids (top) to peptides (bottom) within a mineral  interlayer

Our research focus is on the use and development of molecular models and computational techniques for the study of processes involving natural materials, minerals and interactions at their interfaces.

We have unique multidisciplinary background, bringing together knowledge from theoretical and experimental chemistry, material and environmental sciences, geosciences and astrobiology. We aspire for our work to foster a step-change in computational modelling, ensuring that the work we do is of direct benefit to our society.

The applications of our research are vast from the origins of life,  biosignature identification, soil and water pollution remediation, nuclear waste storage, enhanced oil recovery and fuel additives, all supported through ongoing software development


MAterials of interest

Our passion is in studying how the finest changes naturally occurring in natural materials affect their properties and interactions with other species in the environment. To this end, we must ensure that the material models used in the simulation are truthfully representative of their experimental counterparts. 

BIOCHAR MATERIALS 

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Model of biochar, highlighting the cyclic structures, coloured by the number of carbons

Biochar is a remarkable material! Made from pyrolysis of biomass (byproduct of anthropogenic waste) they have been used for soil amendment, carbon deposition and, more recently, for sequestration of pollutants. With a poorly defined overall structure, semi-amorphous, comprised of a variety of chemical structures and functional groups, means that creating a representative molecular model of biochar is not a simple task. Our group has been working on developing these models, with the goal of ensuring they are available for the biochar research community. Recently, we have shared an approach to creating representative structures of biochars based on experimentally determined descriptors. We then extended this approach to integrate the control of microporosity, a key factor influencing biochar performance, into the models. 

CLAY & Layered MINERALS

For many years we have been working with clay minerals. While they are comprised of silicate layers, the smallest substitutions in the structure result in dramatic changes to its properties, so studying these minerals is very rewarding!

 

Yet, many models of clay minerals seen in published works (including our earlier ones) do not incorporate these finest structural variations and, therefore, are unable to represent their structures and properties truthfully. To facilitate the construction of clay models and aid in their high-throughput simulations and analysis, we have created ClayCode software.

Thanks to ClayCode, we were able to study how the effects of even the smallest changes in clay structures impact the retention and preservation of protobiomolecules, or mobility of natural organic molecules in soils

ICES

While hexagonal ice is common on Earth, this is not the same across the universe. To this end, molecular modelling (coupling classical MD and QM) can aid in understanding the interactions in the interstellar medium or icy moons and planets.

 

Glycine (neutral and zwitterionic forms) on low-density amorphous ice

 

Applications

Origins of Life

Upon dehydration, the N- and C-termini of adsorbed amino acids co-align, allowing the formation of a peptidic bond. The newly formed di-peptide remains tethered via C-terminus only. The bond formation leads to the loss of the charge, facilitating introduction of a new amino acid. The N-terminal of amino acid is then able to form a bond with the C-terminal of di-peptide, thus triggering further peptide growth.
Proposed mechanism for LDH-supported peptide bond formation

The origins of life have been the subject of much research, but fundamental questions still remain unanswered. We have a long interest in investigating the surface-supported abiogenetic formation of proto-biomolecules in early Earth and extraterrestrial conditions, as well as the preservation of potential biosignatures.

 

Pollution Remediation

The rise of densely populated environments brings new challenges to our society. One of many is the management and disposal of increasingly diverse pollutants. Our work aims to identify the key properties making naturally occurring materials capable of adsorbing small organic pollutants.

Biochars produced at low (450C) and high (800C) temperatures show a noticeable difference in Mn2+ uptake from solution.

Shale Oil characteristics

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Organic molecules in the hydrated pore of kaolinite clay mineral

Enhanced oil recovery has become commonplace in order to maximise oil field production. Through our work we aim to elucidate the mechanisms behind this process and to understand the interactions within the shales.

Unraveling Slow Motions in Crystalline Materials

The applicability of molecular dynamics is limited by accessible timescales, often leading to simulations that only describe static states and omit information on the transition rates and pathways. My work focuses on the development of methods to describe slow dynamics in solids, coupling the information to the solid-state NMR observables.

 

Production of High surface materials 

Modeling pipeline for identification of graphene dispersion agent

Layered materials, such as graphene, clays, layered double hydroxides, can be found in a wealth of technological applications. Often, the performance of these materials depends on the accessibility of their large surfaces. The increase of the surface area is often obtained via post-production treatment with a range of organic solvents. The hunt for a perfect solvent is the focus of thousands of hours in the laboratories. Working with experimental and industrial collaborators, we use our computational pipelines to rationalise the key interactions behind specific delimitations, helping to find that perfect solvent for the material in mind.

Crystallisation in Fuels

Wax formation in petroleum impacts the ease of its transportation and use. There are numerous wax crystal inhibitors on the market, but their mode of action is still poorly understood. Multi-scale computer simulations allow elucidating mechanisms of wax formation and inhibition, guiding further development of cold flow additives.

 

Mixing and Separation in PolymerIC matriCes

Many of our daily products rely on polymeric systems. For instance, the shelf life of products containing adhesives is determined by the rates of their component mixing and separation. These often are slow processes not tractable by atomistic or even coarse-grained molecular dynamics, requiring the usage of enhanced sampling techniques and additional methods. While a lot of the work we have done is embargoes, to facilitate the set-up of complex polymeric systems we have developed software Assemble! 

 

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Group

Dr Valentina Erastova

Chancellor’s Fellow

Lecturer

Further information and contact details here

CURRENT Members

Hannah Pollak – PhD Student (since 2021)

In my PhD project I am studying interactions between clays and organic pollutants such as pharmaceuticals. I am using molecular modelling techniques in order to gain atomic-level understanding about retention and release of contaminants by minerals in soils. These insights should enable the design of effective materials to be used in drug pollution remediation.

During my bachelor’s studies in chemistry, and my master’s studies in theoretical chemistry and computational modelling I focused on the experimental and theoretical study of biological systems. I believe that my expertise in these fields provides me with a good foundation for my current research.

Audrey Ngambia – PhD student (since 2021)

Audrey was awarder prestigious Edinburgh Doctoral College Scholarship to do her PhD on modelling of biochars, and is co-supervised by Prof Ondrej Masek at the UK Biochar Research Center.

Sarah Stewart – PhD student (since 2023)

Having worked with us for her internship in the summer of 2021, Sarah became interested in using and developing molecular modelling for astrobiology research. She then secured a competitive E4 DTP for her project Understanding Preservation of Potential Biosignatures by Martian Soils, co-supervised by Dr Sean McMahon and Prof Charles Cockell at the UK Center for Astrobiology.

Jonathan Reid – PhD student (since 2023)

Jon’s PhD focuses on connecting molecular modelling and experiment to enable the Understanding interactions between minerals and small biopolymers under extreme conditions. Jon is co-supervised by Dr Sean McMahon and Prof Charles Cockell at the UK Center for Astrobiology.

Rosa Braeuer – BSc student (2024-2025)

Rosa is our current honours project student, investigating the interaction between GABA and STx using molecular modelling.

Anar Nuruzada – remote UG project student (2023-2024)

Anar is a student at French-Azerbaijani University and also an undergraduate research assistant in Environmental Mineralogy and Geochemistry Research Group at Khazar University.

Joining the Group

If you are interested in joining the group as a PostDoc, PhD, Masters or an Intern for more details and funding opportunities see here.

Continue reading “Group”
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News

Here you will find:

Accounts article on the Layered Minerals in the context of Origin of Life

Our recent article, published in the ACS Accounts of Chemical Research, overviews mechanisms through which layered minerals could have facilitated the formation of the first molecules of life and molecules looking like the first molecules of life. We discuss how one could tell those apart based on their composition, local environment and the encapsulating layered … Continue reading Accounts article on the Layered Minerals in the context of Origin of Life

Imagining Aliens

I have recently been approached for some comments by Sarah Wells, who was writing a news article about aliens for Live Science (article can be found here https://www.livescience.com/space/extraterrestrial-life/what-could-aliens-look-like) When asked to imagine an alien, straight after green glowing bipeds with dragonfly eyes, a rather different specie comes to my mind – a fungi. Knowing that … Continue reading Imagining Aliens