CURRENT GROUP MEMBERS

 BSc Project Students

1. Lauren Coller (BSc Math), University of Lincoln, UK. Project: “Applications of Fractal Shapes analysis in Science.”
2. William Liyayi (BSc Chemistry), University of Lincoln, UK. Project: “Mathematical modelling and simulation analysis of electrolysers.”
3. William Hawkridge (BSc Phys), University of Lincoln, UK. Project:” The Mathematical Basis of the Brain Function: The Hodgkin-Huxley Model and its applications.”

ALUMNI MEMBERS

1. Prof Karen C. Weber. Associate professor at the Federal University of Paraiba, Brazil. Postdoctoral training research period 2019-2020.
2. Dr Susruta Samanta (Manipal University Jaipur, India).
3. Dr Rajni Verma (Wichita State University, USA).
4. Dr Samira Hezaveh (Technische Universität Hamburg, Germany).
5. Dr Khadga Karki (Guangdong Technion-Israel Institute of Technology, China).
6. Dr Edita Sarukhanyan (University of Wuerzburg Germany).
7. Dr Zhenwei Li (R&D Bontac Bioengineering, China).
8. Dr Amol Shivange (Novozymes, India).
9. Dr Ronny Martinez-moya (Universidad de La Serena, Chile).
10. Dr Aamir Shehzad (KAUST, Pakistan).
11. Mr Alaa Othman (University of Zurich, Switzerland).
12. Miss Andrea Scacioc (Max Planck Institute Gottingen, Germany).

STUDENT MENTORING ACTIVITY

As PhD advisor

1. Rajni Verma. (BMBF molzyme/EU Oxygreen grant, 2009-2012). PhD defence on 14/12/2012. Thesis: “Development and Application of Novel Bioinformatics and Computational Modeling Tools for Protein Engineering.”
2. Susruta Samanta. (DFG grant, 2009-2012). PhD defence on 18/12/2012. Thesis: Theoretical Study of the Interaction of Amphiphilic Block Copolymers with Biological Interfaces and Small Molecules.
3. Samira Hezaveh. (DFG grant, 2009-2012). PhD defence on 21/5/2012. Thesis: Study of Interaction Mechanisms of Block Copolymers with Biological Interfaces.
4. Khadga Karki. PhD defence on 16/12/2011. Thesis: Molecular Modeling and Investigation of Ultrafast Dynamics in Nanosystems. Awarded with distinction.

As PhD Students Co-advisor

1. Edita Sarukhanyan (Ph.D. 2013). Thesis: Multi-scale Simulation Studies of Interactions of Carbon Nanotubes with Biopolymers and Lipid Bilayer. Joint international PhD program between University of Salerno and Jacobs University Bremen. Co-supervised with Dr G. Milano (University of Salerno, Italy).
2. Zhenwei Li (Ph.D. 2012). Thesis: Directed subtilisin E evolution into a chaotolerant protease. Co-supervised with Prof U. Schwaneberg (RWTH University, Aachen).
3. Amol Shivange (PhD 2010, with distinction).  Thesis: Rational and Evolutive Reengineering of Phosphatase: from Method Development to Understanding of properties. Co-supervised with Prof U. Schwaneberg (RWTH University, Aachen).
4. Ronny Martinez-moya (PhD 2010 with distinction). Thesis: Directed evolution of Bacillus gibsonii Alkaline Protease towards Washing Applications: A Study of Protein Adaptation. Co-supervised with Prof U. Schwaneberg (RWTH University, Aachen).
5. Kan Lang Tee (PhD 2007 with distinction). Thesis: Directed evolution of P450 BM-3 for epoxidation of styrene and characterisation of tolerance towards ionic liquids. Co-supervised with Prof U. Schwaneberg (RWTH University, Aachen).
6. Jovana Razor (PhD 2007). Thesis: Alternative Cofactor Systems Driving P450 BM3. Co-supervised with Prof U. Schwaneberg (RWTH University, Aachen).
7. S. Wong (PhD 2006, with distinction). Thesis: Expanding the toolbox of directed evolution for understanding protein structure-function relationships. Co-supervised with Prof U. Schwaneberg (RWTH University, Aachen).
8. Andrea Scacioc (during the Sesam Biotech granted period, 2009-2011).
9. Aamir Shehzad (with Prof U. Schwaneberg RTWH Aachen, PhD Biotechnology).
10. Alaa Othman (with Prof U. Schwaneberg RTWH Aachen, during the BMBF Bioindustry2021 (Molzym) granted period).

Supervised MSc Thesis

1. Lauren Bartie (MSc Mathematics, 2022), University of Lincoln, UK. MSc Project: “Mathematical Modelling of Fish Biomechanics.”
2. Kanchan Devkota (MSc Biotechnology, 2010), Jacobs University Germany. Project: “Study on a novel light triggered release system based on engineering Channel protein FhuA D1-160.”
3. Upakul Deka (MSc Chemistry 2008), Jacobs University Bremen, Germany. Co-supervised with Prof Rayan Richards (Colorado Mines University, USA). Project: “Study of the properties of acetophenone molecules and derivatives in the presence of MgO(111) surfaces by Quantum Mechanics and Molecular Dynamics calculations.”
4. Hande Karaöse (MSc Chemistry 2009), Jacobs University Bremen, Germany. Co-supervised with Prof N. Khunert (Jacobs University Bremen). Project: “Profiling and Characterization of Chlorogenic Acids.”
5. Kadgha Karki (MSc Physics 2007), Jacobs University Bremen, Germany. Co-supervised with Prof Anrulf Materny (Jacobs University Bremen). Project: “Molecular Dynamics of Pigment Molecules in Inorganic Interfaces.” 

Supervised BSc Final Projects

1. Ellis Page (BSc Math, 2021/2022), University of Lincoln, UK. Project: “The Radon Transform and Its Applications. “
2. Jessica Norridge (BSc Math, 2021/2022), University of Lincoln, UK. Project: “Fractal Properties of Natural Systems.”
3. Silvana L. Lamb (BSc Math, 2021/2022), University of Lincoln, UK. Project:” Mathematical modelling of Patterns in Nature: From Turing to recent theories.”
4. Oluwadamilola Ajiboye (BSc Math, 20/212021), University of Lincoln, UK. Project: “Principal Component Analysis in Computer Simulations of Molecular Systems.”
5. George Lightfoot (BSc Math, 2020/2021), University of Lincoln, UK. Project: “The Mathematical Basis of Morphogenesis: study of the Meinhardt’s branching model.”
6. Jack Dandy (BSc Math, 2020/2021), University of Lincoln, UK. Project: “Patterns in Nature: A Geometry View, A Study into The Fractal Nature of Lightning Discharges”
7. Lezley A. Dawes (BSc Math, 2019/2020), University of Lincoln, UK. Project: “The Mathematical Basis of Morphogenesis: study of Meinhardt’s activator-inhibitor systems model.”
8. Andrew Tompkins (BSc Math, 2018/2019), University of Lincoln, UK. Project: “Fractal Properties of Natural Systems: Generation of 2D fractal trees.”
9. Ruth Denham (BSc Math, 2018/2019), University of Lincoln, UK. Project: “Pattern in Nature: A Geometry View.”
10. Shannon Woolis (BSc Math, 2017/2018), University of Lincoln, UK. Project: “Pattern in Nature: A Geometry View of the Seashell shape.”
11. Eloise Bowden (BSc Math, 2017/2018), University of Lincoln, UK. Project:”Fractal Sets: a computational study of Mandelbrot and Julia sets.”
12. Kristina Alushi (BSc Chemistry 2010), Jacobs University Bremen, Germany. Project: “Molecular dynamics study of 2,3-diazabicyclo [2.2.2]oct-2-ene in water, n-pentane and diethyl-ether.”
13. Marian Breuer (Bsc Chemistry 2010), Jacobs University Bremen, Germany. Project: “Optical properties of the LH2 complex in rps. Acidophila.”
14. Bora Qesja (Bsc Bioinformatics and computational biology 2010), Jacobs University Bremen, Germany. Project: “Optical properties of the LH2 complex in rps. Acidophila.”
15. Yaw Fordjour (BSc Biotechnology 2008/2007), Jacobs University Bremen, Germany. Project: “Investigation of domain closure the aspartate amino transferase enzyme using molecular dynamics simulations.”
16. Samuel Wilberforce (BSc Biotechnology 2005/2006), Jacobs University Bremen, Germany. Project: “Molecular dynamics simulation study of a 6-mer peptide in water and 2,2,2-trifluoroethanol/water mixtures”.

Supervised visiting and trainee students

University of Oxford/Jacobs University student exchange program

1. Oliver Crossley (from University of Oxford, UK), from 24/6/2014-9/7/2014. Project: “Study using Molecular dynamics simulations of the interaction of Polyoxometalates with proteins.”

Supervised Students from the International Association for the Exchange of Students for Technical Experience (IAESTE/DAAD, Germany)

1. Dushyant Kshatriya (from Institute of Chemical Technology Mumbai, India), from 10/6/2014-24/7/2014. Project: “Study using Molecular dynamics simulations of the interaction of Melittin peptide with polymers.
2. Mojmir Mutni (from University of Edinburgh, UK), from 26/7/2013-16/9/2013. Project: “Study using Molecular dynamics simulations of the Bacteriochlorophyll in solution and adsorbed on carbon-based nanomaterials.”
3. Thais Luiza Donega e Souza (from Fundação Educacional do Municipio de Assis University, Brazil): from 15/6/2012-14/9/2012. Project: “Porting of the Molecular Dynamics Docking algorithm on Gromacs.”
4. Justyna Lenda (from University of Krakow, Poland), from 1/7/2011 to 25/9/2011. Project: “Parameterization Xanthophylls models for Molecular dynamics simulations study in solution”

 

CURRENT/PAST COLLABORATIONS

     WITH ACADEMICS

1. Dr Kadgha Karki (Guangdong Technion-Israel Institute of Technology). Experimental and computational study of photosynthetic pigments.
2. Prof Karen C. Weber associate professor in Physical Chemistry at the Federal University of Paraiba (UFPB). Project: Metabotropic glutamate receptor 5.
3. Dr Richard Ngomba (University of Lincoln, UK). Project: Metabotropic glutamate receptor 5.
4. Dr Steven Hayward (University of East Anglia, UK). Project: Study of the ligand-induced domain motion in proteins.
5. Dr Enrico Ferrari (University of Lincoln, UK). Project: Interaction of proteins with gold and silica nanoparticles
6. Prof Christy A. Hunter (University of Lincoln, UK). Project. EU Marie Skłodowska-Curie Innovative Training Networks grant, DIRNANO.
7. Jyh-Yeuan Lee (University of Ottawa, CAN). Project “Structure-governed design of neutralizing antibodies against SARS-CoV-2”. Submitted a joint application for NSERC Applied Research Rapid Response to COVID-19 grant.
8. Prof Ronen Zangi, PhD (IKERBASQUE. Basque Foundation for Science, Spain). Project: Properties of solvents monolayer on a graphene surface.
9. Prof Dr Ulrich Schwaneberg. (RWTH Aachen, Germany). Different projects on computational protein engineering and structural modelling.
10. Prof Dr Giorgio Colombo. (University of Pavia and Instituto di Riconoscimento Molecolare CNR, Milano, Italy). MD studies of peptide folding and dynamics in solution.
11. Prof Dr Martin Zacharias (Technische Universität München, Germany). Different theoretical study of protein dynamics.
12. Prof Dr Giuseppe Milano (University of Salerno, Italy). Study of the interaction of nanomaterials with biological systems.
13. Prof Alfredo Di Nola (University of Rome “La Sapienza”, Italy). Several MD studies on proteins and peptides dynamics.
14. Prof Dr Massimiliano Aschi (University of L’Aquila, Italy). Different theoretical studies of proteins dynamics and spectroscopy
15. Dr Tuck S. Wong (University of Sheffield, UK). Developing tools for protein engineering and directed evolution of proteins.
16. Dr Kang Lan Tee (University of Sheffield, UK). Study of the solvent effects on P450 BM3.
17. Dr Andrea Amadei (University of Rome “Tor Vergata”, Italy). Different theoretical study of protein folding and dynamics.
18. Prof Dr Alan Mark (The University of Queensland, Australia). Studies of peptide dynamics in non-aqueous solution and domain motion.
19. Prof Dr Herman J.C. Berendsen (University of Groningen, The Netherlands). Studies of peptide dynamics and protein docking.

   WITH BIOTECH COMPANIES

1. SeSaM Biotech, Aachen, Germany. 2009-2011. Project: Advancements in Step 1 and 2 of SeSaM (Sequence Saturation Mutagenesis).
2. BASF AG, Ludwigshafen, Germany. 2007-2010. Project: Optimierung einer Phosphatase.
3. BRAIN AG (Biotechnology Research and Information Network Aktiengesellschaft), Zwingenberg, Germany. project: Modelling of a sugar Isomerase with different substrates.
4. EVONIK (DEGUSA AG Direkt Company Funding), Marl, Germany. Project: In silico modelling of Hydrolases. 2007. Project: Optimierung einer Malonyl-CoA-Dehydrogenase.