Use and development of molecular modelling techniques for the study of minerals, materials and interactions at their interfaces

EdChemLogo

Screenshot 2020-02-05 at 16.56.57

 

Panel 1

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 techniques for the study of dynamic processes involving minerals, materials and interactions at their interfaces.

The group and our collaborators have a very 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 are of direct benefit to our society.

The applications of our research are vast, from abiogenetic origins of life, enhanced oil recovery, crystal growth inhibition, modifications of materials for desired functionality, soil and water pollution remediation,  separation of polymeric matrices, and always a pinch of software development.


OUR AREAS of research

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 are interested on the surface-supported the abiogenetic formation of proto-biomolecules in early Earth and extraterrestrial conditions, as well as the preservation of potential bosignatures.

Pollution Remediation

MMT TC Ca2+/Mg2+
Two co-joined systems featuring tetracycline and clay layers in of Ca2+ (left) vs Mg2+ (right) brine

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

BIOCHARS

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

Biochar is a remarkable material! Made from pyrolysis of biomass, byproduct of human waste, they have been used for soil amendment, carbon deposition and, more recently for sequestration of pollutants. With a poorly defined structure and featuring large variety of chemical structures and functional groups, creating a representative molecular model of biochar is not a simple task. We are working on developing these models to become available for the biochar research community.

Enhanced Oil Recovery

jp-2016-00187q_0024

Organic molecules in the hydrated pore of kaolinite clay mineral

EOR has become commonplace in order to maximise oil field production. Our work elucidates the mechanisms behind this process with series of clay – oil simulations.

Continue reading “Research”

Panel 2

Group

CURRENT Members

Dr Valentina Erastova

Chancellor’s Fellow

Further information and contact details here

Rosie

Rosie Wood – E4 DTP PhD Student (since 2020)

I am a PhD student working on the molecular modelling of biochars. The goal of my research is to better understand the interfacial interactions of biochars and ultimately offer insights into how to improve their performance as adsorbents in water treatment. I did my undergraduate degree in chemistry at the University of Bristol and, as part of the E4 DTP, I will be taking courses across many different areas of environmental science.

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.

Kacper Patej – Summer Student (2021)

Kacper is a third-year undergraduate student at the School of Chemistry at the University of Edinburgh. Kacper was awarded a prestigious Carnegie Trust Vacation Scholarship for his project titled ‘In search of interstellar glycine – characterisation of spectroscopic properties under extreme conditions via computational simulation‘. Kacper will be working between our group and In Silico Photochemistry Group of Basile Curchod at Durham University, bringing together molecular dynamics and quantum chemical calculations.

Sarah Stewart – Summer Student (2021)

Sarah is an undergraduate student at the end of her 3rd year of MChem degree at the University of Edinburgh and has won Afton Chemical Summer Internship to join our group. Sarah is working with Hannah studying interactions between glycine and Martian clays.

Szymon Kosc – Summer Student (2021)

Szymon is finishing his 3rd year of chemistry undergraduate degree and joined our group with the EPSRC Vacation Scholarship. Szymon is working with Rosie testing the models of biochar adsorption materials for the uptake of pharmaceutical pollutants.

Ioana Papa – Summer Student (2021)

Ioana has just completed her second year of degree in chemistry at the UoE and was awarded extremely competitive Undergraduate Research Bursary by the Royal Society of Chemistry for her project with the title ‘Prebiotic Molecules of Icy Moons: Molecular Modelling for Characterisation of Interactions in the Extreme Environments’. Ioana has joined forces with Eoin, together looking at the galactic ices.

Benjamin Carpenter – Summer Student (2021)

Ben is at the fourth year of computational physics degree at the University of Edinburgh, and have joined our group on the E4 Research Experience Placement and working with Hannah on the development of analysis tools for quantification of adsorption/desorption dynamics on mineral surfaces.

Boyang Wang – PGT project student (summer 2021)


Visiting the Group

Our group is a host for HPC-EuropaPan-European Research Infrastructure on High-Performance Computing. If you are interested in a collaboration, please get in touch with Valentina about EPCC visit through the Transnational Access Program.

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”
Panel 3

News

NERC Research Experience Placements this Summer

We are looking for a motivated UG student from the UK university to join our group with the NERC funded placement. Bringing Atomic-level insights to Caesium Decontamination by Clay Minerals The student will investigate the adsorption of Cs-137 onto montmorillonite and vermiculite clays at atomic-level resolution. They will use molecular dynamics (MD) simulations, a theoretical … Continue reading NERC Research Experience Placements this Summer

Panel 4 Placeholder