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Molecular Modeling for Design of Biochar Materials

  • Full or part time
  • Application Deadline
    Thursday, January 09, 2020
  • Competition Funded PhD Project (European/UK Students Only)
    Competition Funded PhD Project (European/UK Students Only)

Project Description

The project brings molecular modeling into biochar research, providing atomistic details to the key properties of biochar, and through this enabling the informed design and optimization of biochar for desirable functionality.


Biochar is a low-cost environmental carbon-rich porous material produced through pyrolysis of biomass, a waste organic material resulting from diverse human activities. Depending on the biomass composition and production conditions, biochar will express a range of physical and chemical properties, tunable to suit many applications. Examples of its use can be found in water conservation and desalination, pollution remediation, heavy metal sequestration, carbon dioxide capture, and soil nutrient management. A full understanding of the mechanisms behind biochar functionality is critical for the targeted design and optimisation of its properties, currently obtained through trial-and-error.

Molecular dynamics (MD) is a modelling technique providing atomic-level insights into physicochemical interactions. Here, MD is of a particular use to characterise energetics and dynamics of the adsorption and release processes occurring between biochar surfaces and adsorbate (metal ions, pollutants, nutrients, gasses). Modelling delivers key descriptors behind behaviours observed in laboratory and field experiments. Furthermore, MD allows us to design and test hypothetical biochar models, aiming at desired functionality, prior to engaging in biochar production for its successful modification.

Biochar is a complex system, and to date there is no realistic model of it. The aim of this project is to create a tool for generating realistic biochar models ready for MD simulations, based upon analytical insights (exposed surfaces, interlinking, porosity, functional groups, their surface density, etc). This tool will allow scientists without strong computing backgrounds to perform theoretical studies of systems of interest. Overall, the project is a key stepping stone to bringing molecular modelling to the extensive biochar research community, enabling scientists to better understand and design this important material.

AIM 1: Create the first realistic molecular model of biochar guided by experimental observables.
AIM 2: Leveraging molecular simulation, rationalize interactions within biochar and guide design for specific applications:
- What physicochemical characteristic of biochar determines its property?
- How can we modify its physicochemical structure for optimal performance under given environmental conditions?

This project combines computational chemistry and software development to study systems of relevance to geoenvironmental material sciences.
Collaboration with the group of Dr Ondrej Masek allows us to cross validate predictions and refine molecular models. Furthermore, the project benefits from the feed of information between theoretical and laboratory work, allowing to rationalise observables and guide experiments for material design.
The computational work will be performed using bond order potentials (such as Tersoff, EDIP or ReaxFF) using LAMMPS molecular dynamics engine. Currently, available potentials are comparable via, knowledge-base website.

During the research project, the student will be able to learn and apply computational techniques, such as molecular dynamics. Through interactions with the UK Biochar Research Centre and its wide network of contacts the student will gain knowledge in material sciences and environmental applications. The student will also further develop skills in software engineering (Python/Bash) and high-performance computing. Overall, through the project the student will build a unique and highly desirable profile in the growing and influential areas of computer sciences and geoenvironmental research. This will make the graduate competitive on the job market at both industrial and academic level.
Specific training activities: CCP5 summers school, CECAM workshops, software development and high performance computing courses offered through ARCHER.

- A highly motivated student with an interest in computer science and geoenvironmental research.
- Essential software development skills (preferentially Python) are required.
- Understanding of chemistry and physics would be highly beneficial.
- Furthermore, experience in either molecular modelling, or usage of high-performance computing would be advantageous.

More information about research in the group, see
For more details on the project, contact Dr Valentina Erastova valentina.erastova [ at ]


Funding Notes

RCUK eligibility rules apply
a. Eligible for a full funding: UK/EU citizens or settled overseas students only, who have worked and/or studied in the UK for at least three years before the programme starts.
b. Eligible for fees-only: UK/EU citizens who do not comply with the 3-year UK residency criteria. The award includes fees and research costs but not stipend. Students have to find match funding to cover their living costs for 3 years minimum.
c. Non Eligible: Overseas students who are currently on a Tier 4 Visa or would need a Visa to come to the UK.

How good is research at University of Edinburgh in Chemistry?
(joint submission with University of St Andrews)

FTE Category A staff submitted: 43.30

Research output data provided by the Research Excellence Framework (REF)

Click here to see the results for all UK universities

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