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 aluminosilicate zeolite "molecular sieve" framework structures. I work particularly on physically-based methods to achieve realistic and informative all-atom simulations of flexible motion in proteins, using desktop computing resources. With Dr. Sartbaeva (Department of Chemistry) I have an ongoing research program investigating the physics and flexibility of zeolite frameworks.
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 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
- Dynamic disorder in polyhedral framework mineral structures, including zeolites, manganites and glasses
- 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., 2013. Forthcoming. Geometric simulation of flexible motion in proteins. In: Livesay, D. R., ed. Protein Dynamics. Humana Press.
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-Verlag.
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.
