Department of Chemistry

Stephen Wells

 

1 South 0.15
Email: s.a.wells@bath.ac.uk

Phone: 01225 386893

 

Dr Stephen Wells

Profile

My research is principally directed at modelling the rigidity and intrinsic flexibility of atomic framework structures, especially proteins considered as molecular frameworks, and framework mineral structures such as zeolites. I work on physically-based methods to achieve realistic and informative all-atom simulations of flexible motion in proteins, using desktop computing resources. I have recently joined the "M4" project on metastable materials, and am extending my methods to model organic and hybrid frameworks such as MOFs and ZIFs.

I studied Natural Sciences at St. John's College, Cambridge, obtaining an M.Sci in physics, and a Ph.D. in mineral physics from the Department of Earth Sciences, Cambridge. I have postdoctoral research experience at the Royal Institution, London, as part of the national eMinerals initiative; at Arizona State University, where my "FRODA" software for protein flexible motion simulation was successfully commercialised with uptake by pharmaceutical companies; and at the University of Warwick, where I held a Leverhulme Early Career fellowship. I have lectured mathematical methods and physics at Warwick and at Bath.

I maintain and develop the "GASP" code for geometric analysis and simulation in framework mineral structures, which can be freely used by academics.

Research interests

  • Template-based geometric simulation of flexible motion in frameworks. Geometric simulation and analysis using "GASP" (geometric analysis of structural polyhedra).
  • Framework flexibility, compression mechanisms and the "flexibility window" in zeolite frameworks and MOFs.
  • Rapid simulations of flexible motion in proteins, using a combination of template-based geometric simulation (FRODA), elastic network modelling (ElNemo), and "pebble-game" rigidity analysis (FIRST).
  • Large-amplitude flexible motion in proteins; mainchain flexibility; conformational flexibility; protein structural biology; protein structural biophysics.

 

Publications

Wells, S. A., Leung, K. M., Edwards, P. P., Tucker, M. and Sartbaeva, A., 2017. Forthcoming. Defining the flexibility window in ordered aluminosilicate zeolites. Royal Society Open Science, 4, 170757.

Jones, H. B.L., Wells, S. A., Prentice, E. J., Kwok, A., Liang, L. L., Arcus, V. L. and Pudney, C. R., 2017. A complete thermodynamic analysis of enzyme turnover links the free energy landscape to enzyme catalysis. FEBS Journal

Fokas, A. S., Cole, D. J., Hine, N. D.M., Wells, S. A., Payne, M. C. and Chin, A. W., 2017. Evidence of Correlated Static Disorder in the Fenna-Matthews-Olson Complex. Journal of Physical Chemistry Letters, 8 (10), pp. 2350-2356.

Chen, Y.-C., Smith, T., Hicks, R. H., Doekhie, A., Koumanov, F., Wells, S. A., Edler, K. J., van den Elsen, J., Holman, G. D., Marchbank, K. J. and Sartbaeva, A., 2017. Thermal stability, storage and release of proteins with tailored fit in silica. Scientific Reports, 7, 46568.

Fletcher, R. E., Wells, S., Leung, K. M., Edwards, P. P. and Sartbaeva, A., 2015. Intrinsic flexibility of porous materials:theory, modelling and the flexibility window of the EMT zeolite framework. Acta Crystallographica Section B-Structural Science, 71 (Part 6), 641–647.

Wells, S. A., Van Der Kamp, M. W., Mcgeagh, J. D. and Mulholland, A. J., 2015. Structure and Function in Homodimeric Enzymes:Simulations of Cooperative and Independent Functional Motions. PLoS ONE, 10 (8), e0133372.

Wells, S. A. and Sartbaeva, A., 2015. GASP:software for geometric simulations of flexibility in polyhedral and molecular framework structures. Molecular Simulation, 41 (16-17), pp. 1409-1421.

Wells, S. A., Leung, K. M., Edwards, P. P. and Sartbaeva, A., 2015. Flexibility windows in faujasite with explicit water and methanol extra-framework content. Dalton Transactions, 44 (13), pp. 5978-5984.

Heal, J. W., Wells, S. A., Blindauer, C. A., Freedman, R. B. and Roemer, R. A., 2015. Flexibility-based predictions of folding cores:characterization of the cyclophilin A - cyclosporin A complex. Biophysical Journal, 108 (7), pp. 1739-1746.

Erskine, P., Fokas, A., Muriithi, C., Rehman, H., Yates, L., Bowyer, A., Findlow, I., Hagan, R., Miles, J., Wallace, B., Wells, S., Wood, S. and Cooper, J., 2015. X-ray, spectroscopic and normal-mode dynamics of calexcitin:structure–function studies of a neuronal calcium-signalling protein. Acta Crystallographica Section D-Biological Crystallography, 71 (3), pp. 615-631.

Wells, S. A., Crennell, S. J. and Danson, M. J., 2014. Structures of mesophilic and extremophilic citrate synthases reveal rigidity and flexibility for function. Proteins: Structure, Function, and Bioinformatics, 82 (10), pp. 2657-2670.

Wells, S. A., 2013. Geometric simulation of flexible motion in proteins. In: Livesay, D. R., ed. Protein Dynamics.Vol. II. New York: Humana Press, pp. 173-192.

Amin, N. T., Wallis, A. K., Wells, S. A., Rowe, M. L., Williamson, R. A., Howard, M. J. and Freedman, R. B., 2013. High-resolution NMR studies of structure and dynamics of human ERp27 indicate extensive inter-domain flexibility. Biochemical Journal, 450 (2), pp. 321-332.

Sartbaeva, A. and Wells, S., 2012. Framework flexibility and rational design of new zeolites for catalysis. Applied Petrochemical Research, 2 (3-4), pp. 69-72.

Li, H., Wells, S. A., Jimenez-Roldan, J.E., Römer, R.A., Zhao, Y., Sadler, P.J. and O'Connor, P.B., 2012. Protein flexibility is key to cisplatin crosslinking in calmodulin. Protein Science, 21 (9), pp. 1269-1279.

Wells, S. and Sartbaeva, A., 2012. Template-based geometric simulation of flexible frameworks. Materials, 5 (3), pp. 415-431.

Burkoff, N.S., Várnai, C., Wild, D.L. and Wells, S.A., 2012. Exploring the energy landscapes of protein folding simulations with Bayesian computation. Biophysical Journal, 102 (4), pp. 878-886.

Sartbaeva, A., Haines, J., Cambon, O., Santoro, M., Gorelli, F., Levelut, C., Garbarino, G. and Wells, S., 2012. Flexibility windows and compression of monoclinic and orthorombic silicalites. Physical Review B, 85 (6), 064109.

Heal, J.W., Jimenez-Roldan, J.E., Wells, S.A., Freedman, R.B. and Römer, R.A., 2012. Inhibition of HIV-1 protease:The rigidity perspective. Bioinformatics, 28 (3), pp. 350-357.

Jimenez-Roldan, J.E., Freedman, R.B., Römer, R.A. and Wells, S. A., 2012. Rapid simulation of protein motion: merging flexibility, rigidity and normal mode analyses. Physical Biology, 9 (1), 016008.

Shih, C.-T., Wells, S. A., Hsu, C.-L., Cheng, Y.-Y. and Römer, R.A., 2012. The interplay of mutations and electronic properties in disease-related genes. Scientific Reports, 2, 272.

Sartbaeva, A., Wells, S., Kuznetsov, V. L. and Edwards, P. P., 2012. Hydrogen: An end-state solution for transportation? In: Inderwildi, O. and King, D., eds. Energy, Transport, & the Environment. London: Springer.

Wells, S.A., Sartbaeva, A. and Gatta, G.D., 2011. Flexibility windows and phase transitions of ordered and disordered ANA framework zeolites. EPL (Europhysics Letters), 94 (5), 56001.

Heal, J. W., Wells, S. A., Jimenez-roldan, E., Freedman, R. F. and Römer, R. A., 2011. Rigidity analysis of HIV-1 protease. Journal of Physics: Conference Series, 286 (1), 012006.

Shih, C.-T., Cheng, Y.-Y., Wells, S.A., Römer, R.A. and Hsu, C.-L., 2011. Charge transport in cancer-related genes and early carcinogenesis. Computer Physics Communications, 182 (1), pp. 36-38.

Jimenez-Roldan, J.E., Wells, S.A., Roemer, R.A. and Freedman, R.B., 2011. Integration of FIRST, FRODA and NMM in a coarse grained method to study Protein Disulphide Isomerase conformational change. Journal of Physics: Conference Series, 286 (1), 012002.

Sartbaeva, A., Wells, S., Sommariva, M., Lodge, M. J.T., Jones, M. O., Ramirez-Cuesta, T., Lee, G. and Edwards, P. P., 2010. Formation of crystalline Sodium Hydride nanoparticles encapsulated within an amorphous framework. Journal of Cluster Science, 21, pp. 543-549.

Wells, S., Sartbaeva, A., Kuznetsov, V. L. and Edwards, P. P., 2010. Hydrogen economy. In: Crabtree, R., ed. Energy Production and Storage. Chichester: Wiley.

Wells, S. A., Jimenez-Roldan, J. E. and Römer, R. A., 2009. Comparative analysis of rigidity across protein families. Physical Biology, 6 (4), 046005.

Wells, S. A., Shih, C.-t. and Römer, R. A., 2009. Modelling charge transport in data DNA using transfer matrices with diagonal terms. International Journal of Modern Physics B, 23 (20n21), pp. 4138-4149.

Lei, M., De Graff, A.M.R., Thorpe, M.F., Wells, S.A. and Sartbaeva, A., 2009. Uncovering the intrinsic geometry from the atomic pair distribution function of nanomaterials. Physical Review B, 80 (2), 024118.

Gatta, D., Sartbaeva, A. and Wells, S., 2009. Compression behaviour and flexibility window of the analcime like feldspathoids: experimental and theoretical findings. European Journal of Mineralogy, 21 (3), pp. 571-580.

Božin, E.S., Billinge, S.J.L., Sartbaeva, A., Wells, S.A., Thorpe, M.F., Zheng, H., Mitchell, J.F. and Proffen, T., 2008. Structure of CaMnO3 in the range 10 K ≤ T ≤ 550 K from neutron time-of-flight total scattering. Journal of Physics and Chemistry of Solids, 69 (9), pp. 2146-2150.

Sartbaeva, A., Gatta, G.D. and Wells, S.A., 2008. Flexibility window controls pressure-induced phase transition in analcime. EPL (Europhysics Letters), 83 (2), 26002.

Jolley, C.C., Wells, S., Fromme, P. and Thorpe, M.F., 2008. Fitting low-resolution cryo-EM maps of proteins using constrained geometric simulations. Biophysical Journal, 94 (5), pp. 1613-1621.

Sartbaeva, A., Kuznetsov, V.L., Edwards, P.P. and Wells, S.A., 2008. Hydrogen nexus in a sustainable energy future. Energy & Environmental Science, 1 (1), pp. 79-85.

This list was generated on Thu Oct 19 12:05:45 2017 IST.

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