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Homepage of Dr. S. A. Wells

Position

I am currently a Leverhulme Early Career Research Fellow.

Research

My principal research theme is rapid simulation of protein flexible motion. I use a combination of rigidity analysis, geometric simulation and elastic-network modelling to investigate the intrinsic capacity for flexible motion in protein structure.

At Warwick, I collaborate with Prof. Rudo Roemer and with Prof. Robert Freedman. We have two students, Mr. J. Emilio Jimenez-Roldan and Mr. Jack Heal, working on projects in protein rigidity and flexible motion.

I collaborate with my wife, Dr. Asel Sartbaeva, at the University of Oxford, studying the intrinsic flexibility of framework mineral structures, particularly aluminosilicate zeolites. We also collaborate with Prof. Edwards on scientific issues surrounding the concept of the "hydrogen economy".

Teaching

I currently teach the PX260 Maths Methods course for second-year physics students. The module home page has links to the old lecture notes and to my new notes as I upload them.

Software

I am an author on the copyrighted software FIRST and developed the "FRODA" module for modelling protein flexible motion using rigidity-based coarse graining. This software is available from the "Flexweb" site at Arizona State University; it is free to academic collaborators and is commercially available under licence for industrial use.

In my mineral research I use my own code, "GASP", which is available on request to academics for research.

Career and qualifications

M.Sci. and B.A., Natural Sciences (Physics), St. John's College, University of Cambridge, 1999.

PhD, Dept. of Earth Sciences, University of Cambridge, 2003 (Mineral Physics).

Researcher, Royal Institution, London, 2002-2004.

Researcher, Dept. of Physics, Arizona State University, Tempe, AZ, 2004-2007.

Researcher (with teaching responsibilities), Dept. of Physics and Centre for Scientific Computing, University of Warwick, 2007-2010.

Leverhulme Early Career Research Fellow (Rapid simulations of protein motion), Dept. of Physics and Centre for Scientific Computing, University of Warwick, 2010-present.

 

Publications

 

Book chapters

A Sartbaeva, SA Wells, V Kuznetsov, PP Edwards
"Hydrogen: an end-state solution for transportation?", in "Energy, Transport and the Environment", O. Inderwildi and Sir D. King (ed.s), Springer. In press.
 
SA Wells, A Sartbaeva, V Kuznetsov, PP Edwards
"Hydrogen economy" in "Energy Production and Storage: Inorganic Chemical Strategies for a Warming World". Robert H. Crabtree (ed.), Wiley-VCN, ISBN: 978-0-470-74986-9 (2010).

 

Publications in preparation

H Li, SA Wells et al.
"Protein flexibility is key to cisplatin cross-linking in calmodulin"
In preparation for submission to Journal of Proteome Research.
 
A Sartbaeva, SA Wells, J Haines et al.
"Flexibility windows and compression of monoclinic and orthorhombic silicalites"
Submitted to PRL.
 
CT Shih, SA Wells, CL Hsu, YY Cheng and RA Roemer
" The interplay of mutations and electronic properties in disease-related genes"
Submitted to Nature Scientific Reports

 

Peer-reviewed publications  

JE Jimenez-Roldan, RB Freedman, RA Roemer and SA Wells
"Protein flexibility explored with normal modes and geometric simulation"
ACCEPTED 1 December 2011 to Physical Biology.
 
JW Heal, JE Jimenez-Roldan, SA Wells, RB Freedman and RA Roemer
"Inhibition of HIV-1 protease: the rigidity perspective"
ACCEPTED 3 December 2011 to Bioinformatics.
 
N Burkoff, C Varnai, SA Wells and DL Wild
"Exploring the energy landscapes of protein folding simulations with Bayesian computation"
ACCEPTED December 2011 to Bioinformatics.
 
SA Wells, A Sartbaeva and GD Gatta
"Flexibility windows and phase transitions of ordered and disordered ANA framework zeolites"
Euro Physics Letters 94, 56001 (2011).
[Selected for highlight in Euro Physics News, June 2011.]
 
JE Jimenez-Roldan, SA Wells, RB Freedman and RA Roemer
"Integration of FIRST, FRODA and NMM in a coarse grained method to study Protein Disulphide Isomerase conformational change."
Proceedings of IOP Condensed Matter and Materials Physics "CMMP10".
Journal of Physics: Conference Series 286, 01 2002 (2011).
 
JW Heal, SA Wells, JE Jimenez-Roldan, RB Freedman and RA Roemer
"Rigidity analysis of HIV-1 protease."
Proceedings of IOP Condensed Matter and Materials Physics "CMMP10".
Journal of Physics: Conference Series 286, 01 2006 (2011).
 
CT Shih, YY Cheng, SA Wells, CL Hsu and RA Roemer
"Charge transport in cancer-related genes and early carcinogenesis"
Computer Physics Communications 182, Issue 1, 36-38 (2011).
 
A Sartbaeva, SA Wells, M Sommariva, MJT Lodge, MO Jones, AJ Ramirez-Cuesta, G Li and PP Edwards
"Formation of crystalline sodium hydride nanoparticles encapsulated within an amorphous framework."
Journal of Cluster Science 21, Issue 3, 543-549 (2010).
 
SA Wells, JE Jimenez and RA Roemer
"Comparative analysis of rigidity across protein families."
Physical Biology 6, 046005 (2009).
 
SA Wells, CT Shih and RA Roemer
"Modelling charge transport in DNA using transfer matrices with diagonal terms."
Proceedings of the 32nd International Workshop on Condensed Matter Theories,
International Journal of Modern Physics B 23, 4138-4149 (2009).
 

M Lei, AMR de Graff, MF Thorpe, SAWells and A Sartbaeva
"Uncovering the intrinsic geometry from the atomic pair distribution function of nanomaterials." Physical Review B 80, 024118, 2009.

GD Gatta, A Sartbaeva, SA Wells
"Compression behaviour and flexibility window of the analcime-like feldspathoids: experimental and theoretical findings." EUROPEAN JOURNAL OF MINERALOGY 21, Issue 3, 571--580, 2009.


A Sartbaeva, V Kuznetsov, SA Wells and PP Edwards
"Hydrogen nexus in a sustainable energy future." Energy and Environmental Science 1, 79--85, 2008. Invited Paper.

A Sartbaeva, GD Gatta, SA Wells
"Flexibility window controls pressure-induced phase transition in analcime." EuroPhysics Letters 83, 26002 (2008)

ES Bozin, A Sartbaeva, H Zheng, SA Wells, JF Mitchell, Th Proffen, MF Thorpe and SJL Billinge "Structure of CaMnO3 in the range 10K -- 550K from neutron time-of-flight total scattering." Journal of Physics and Chemistry of Solids 69, 2146-2150, 2008.

CC Jolley, SA Wells, P Fromme and MF Thorpe
"Fitting low-resolution cryo-EM maps of proteins using constrained geometric simulations." Biophysical Journal 94, 1613-1621, 2008

AM Walker et al.
"The origin of the compressibility anomaly in amorphous silica: a molecular dynamics study." JPCM 19, 275210, 2007.

A Sartbaeva, SA Wells, MF Thorpe, ES Bozin and SJL Billinge
“Quadrupolar ordering of LaMnO3 revealed from scattering data and geometric modeling.” PRL 99,155503 (2007).
 
A Sartbaeva, SA Wells, A Huerta and MF Thorpe
“Local structural variability and the intermediate phase window in network glasses.”, Phys. Rev. B 75, article 224204 (2007).
 
A Sartbaeva, SA Wells, MMJ Treacy and MF Thorpe
“The flexibility window in zeolites.” Nature Materials 5, 962-965 (2006).
 
A Sartbaeva, SA Wells, MF Thorpe, ES Bozin and SJL Billinge
“Geometric modeling of perovskite frameworks with Jahn-Teller distortions: application to cubic manganites.” Physical Review Letters 97, 065501 (2006).
 
CC Jolley, SA Wells, BM Hespenheide, MF Thorpe and P Fromme
“Docking of Photosystem I subunit C using a constrained geometric simulation.” JACS 128, 8803-8812 (2006).
 
SA Wells, MD Foster and MMJ Treacy
“A Simple Geometric Structure Optimizer for Accelerated Detection of Infeasible Zeolite Graphs.” Microporous and Mesoporous Materials 93, 151-157 (2006).
 
GD Gatta and SA Wells
“Structural evolution of zeolite levyne under hydrostatic and non-hydrostatic pressure: geometric modelling.” Phys. Chem. Minerals 33, 243-255 (2006).

MG Tucker, AL Goodwin, MT Dove, DA Keen, SA Wells and J Evans
“Negative thermal expansion in ZrW2O8: Mechanisms, rigid unit modes, and neutron total scattering.” Physical Review Letters 95, 255501 (2005).
 
S Flores, N Echols, D Milburn, BM Hespenheide, K Keating, J Lu, SA Wells, EZ Yu, MF Thorpe and M Gerstein
“The database of macromolecular motions: new features added at the decade mark.” Nucleic Acid Research 34, D296-D301 (2005).
 
SA Wells, S Menor, BM Hespenheide and MF Thorpe
“Constrained geometric simulation of diffusive motion in proteins.”
Physical Biology 2 S127-S136 (2005).
 
MA Zwijnenburg, A Simperler, SA Wells and RG Bell
“Tetrahedral distortion and energetic packing penalty in “zeolite” frameworks: linked phenomena?” J. Phys. Chem. B 10, 1021 ( 2005)
(Highlighted in Science 309, 990 (2005))
 
SA Wells et al.
“Ab-initio simulations of magnetic iron sulphides.” Molecular Simulations 31, 379-384 (2005)
 
MT Dove, SA Wells, K Wright et al.
“The eMinerals collaboratory: tools and experience” Molecular Simulations 31, 329-337 (2005)
 
Q Hui, MG Tucker, MT Dove, SA Wells and DA Keen
“Total scattering and reverse Monte Carlo study of the 105 K displacive phase transition in strontium titanate.” Journal of Physics: Condensed Matter 17, S111-S124. (2005)
 
A Sartbaeva, SA Wells, SAT Redfern, RW Hinton and SJB Reed
"Ionic diffusion in quartz studied by transport measurement, SIMS and atomistic simulations." Journal of Physics: Condensed Matter 17, 1099-1112. (2005)
 
A Sartbaeva, SA Wells, SAT Redfern
"Li+ motion in quartz and beta-eucryptite studied by dielectric spectroscopy and atomistic simulations." Journal of Physics: Condensed Matter 16, 8173-8189. (2004)
 
MT Dove, SA Wells, K Wright et al.
“Collaborative tools in support of the eMinerals Virtual Organisation”.
Proceedings of the "All Hands" UK national e-science conference (2004).
M Alfredsson et al.
"Science outcomes from the use of grid tools in the eMinerals project."
Proceedings of the "All Hands" UK national e-science conference (2004).


GD Gatta and SA Wells
"Rigid Unit Modes at high pressure: an explorative study of a fibrous zeolite-like framework with EDI topology." Phys. Chem. Minerals 31, 465-474. (2004)
 
SA Wells, MT Dove, MG Tucker
"Reverse Monte Carlo with geometric analysis- RMC+GA."
J. Appl. Crystall. 37, 536-544. (2004)
 
SA Wells
"Real-space Rigid Unit analysis of framework structures using Geometric Algebra".
Ph.D. Thesis, Department of Earth Sciences, Cambridge University. (2003)
 
MT Dove, MG Tucker, SA Wells, DA Keen
"Reverse Monte Carlo methods". EMU Notes in Mineralogy 4, 59-82. (2002)
SA Wells, MT Dove, MG Tucker, K Trachenko.
"Real-space rigid unit mode analysis of dynamic disorder in quartz, cristobalite and amorphous silica". Journal of Physics: Condensed Matter 14, 4645-4657. (2002)
 
SA Wells, MT Dove, G Tucker
"Finding best-fit polyhedral rotations with geometric algebra".
Journal of Physics: Condensed Matter 14, 4567-4584. (2002)

S A Wells picture

Email: s.a.wells AT warwick.ac.uk