Publications

Please feel free to email me for reprints of any of the articles mentioned below, and specify if you preferred an electronic one in pdf format to the printed version.

The list of papers is also visible at my ResearcherID Profile, including citation information or in my Mendeley profile.

2012

R. Webster, S. Maxwell, H. Spearman, K. Tai, O. Beckstein, M.S.P. Sansom, and D. Beeson. A novel congenital myasthenic syndrome due to decreased acetylcholine receptor ion channel conductance. Brain (2012). doi:10.1093/brain/aws016.
See also the commentary Diverse aspects of vulnerability at the neuromuscular junction by C. Slater in the same issue.
O. Beckstein and B.I. Iorga. Prediction of hydration free energies for aliphatic and aromatic chloro derivatives using molecular dynamics simulations with the OPLS-AA force field. J Comp Aid Mol Design. (2012) doi:10.1007/s10822-011-9527-9.
P. Pongprayoon, O. Beckstein, and M.S.P. Sansom. Biomimetic Design of a Brush-Like Nanopore: Simulation Studies. J Phys Chem B 116 (2012) 462–468. doi:10.1021/jp206754w.

2011

N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, O. Beckstein. MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations J. Comp. Chem. 32 (2011) 2319–2327. doi:10.1002/jcc.21787.
Please see MDAnalysis Errata for corrected Python examples from the paper (which got mangled during type-setting).
J. R. Perilla, O. Beckstein, E. J. Denning, and T. B. Woolf. Computing ensembles of transitions from stable states: Dynamic importance sampling. J. Comp. Chem. 32 (2011), 196–209. doi:10.1002/jcc.21564.
S. Weyand, T. Shimamura, O. Beckstein, M. S. P. Sansom, S. Iwata, P. J. F. Henderson, and A. D. Cameron. The alternating access mechanism of transport as observed in the sodium-hydantoin transporter Mhp1. J. Synchrotron Rad., 18 (2011), 20–23. doi:10.1107/S0909049510032449.

2010

T. Shimamura*, S. Weyand*, O. Beckstein*, N. G. Rutherford, J. M. Hadden, D. Sharples, M. S. P. Sansom, S. Iwata, P. J. F. Henderson, and A. D. Cameron. Molecular Basis of Alternating Access Membrane Transport by the Sodium-Hydantoin Transporter, Mhp1. Science 328 (2010), 470–473. doi:10.1126/science.1186303.
See also media coverage and a animated cartoon of the mechanism.
J. Domański, P. Stansfeld, M.S.P. Sansom, and O. Beckstein. Lipidbook: A public repository for force field parameters used in membrane simulations. J. Membrane Biol. 236 (2010), 255–258. doi:10.1007/s00232-010-9296-8. URL:http://lipidbook.bioch.ox.ac.uk. preprint (pdf)
S. Weyand, P. Ma, M. Saidijam, J. Baldwin, O. Beckstein, S. Jackson, S. Suzuki, S. G. Patching, T. Shimamura, M. S. P. Sansom, S. Iwata, A. D. Cameron, S. A. Baldwin, and P. J. F. Henderson. The nucleobase-cation-symport-1 family of membrane transport proteins (met 268). In Albrecht Messerschmidt, editor, Handbook of Metalloproteins. Wiley, 2010.

2009

P. Pongprayoon, O. Beckstein, C.-L. Wee, and M. S. P. Sansom. Simulations of anion transport through OprP reveal the molecular basis for high affinity and selectivity for phosphate. Proc. Natl. Acad. Sci. USA 106 (2009), 21614–21618. doi:10.1073/pnas.0907315106
O. Beckstein*, E. J. Denning*, J. R. Perilla, and T. B. Woolf. Zipping and Unzipping of Adenylate Kinase: Atomistic Insights into the Ensemble of Open ↔ Closed Transitions. J Mol Biol 394 (2009), 160–176, doi:10.1016/j.jmb.2009.09.009 (local preprint pdf, supplementary information (pdf), movies)
O. Beckstein. New and Notable: Teaching old coefficients new tricks: new insight into the meaning of the osmotic and diffusive permeation coefficients. Biophys J 96 (2009), 763–764. doi:10.1016/j.bpj.2008.10.048
S. E. Rogers, K. Tai, O. Beckstein, M. S. P. Sansom. Opening a hydrophobic gate: the nicotinic acetylcholine receptor as an example. arXiv:0902.1417v1 [q-bio.BM].

2008

S. Furini, O. Beckstein, and C. Domene. Permeation of water through the KcsA K⁺ channel. Proteins 74 (2008), 437–448. doi:10.1002/prot.22163
C. Millar, R. Madathil, O.Beckstein, M. S. P. Sansom, S. Roy, and A. Asenov. Brownian simulation of charge transport in α-haemolysin. J. Comput. Electron. 7 (2008), 28–33.

2007

C. Millar, S. Roy, O. Beckstein, M. S. P. Sansom, and A. Asenov, Continuum vs particle simulations of model nano-pores, J. Comput. Electr. 6 (2007), 367–371

2006

O. Beckstein and M. S. P. Sansom, A Hydrophobic Gate in an Ion Channel: The Closed State of the Nicotinic Acetylcholine Receptor, Phys. Biol. 3 (2006), 147–159; preprint arXiv:q-bio.BM/0509018
(See also the image of the density of water in an Ion channel in the nervous system and a short movie (9.2 MB) of water in the gate of nAChR. The paper made the journal cover and was included in IoP Select.)

2005

Shiva Amiri, Kaihsu Tai, Oliver Beckstein, Philip C Biggin and Mark S P Sansom, The α7 nicotinic acetylcholine receptor: molecular modelling, electrostatics, and energetics, Molec. Memb. Biol. 22 (2005), 151–162

2004

O. Beckstein, Doctoral Thesis: Principles of Gating Mechanisms of Ion Channels, University of Oxford. (pdf and movies)
O. Beckstein, K. Tai, and M. S. P. Sansom, Not ions alone: Barriers to ion permeation in nanopores and channels, J. Am. Chem. Soc. 126 (2004), 14694–14695 and Supporting Material.
O. Beckstein and M. S. P. Sansom, The influence of geometry, surface character and flexibility on the permeation of ions and water through biological pores, Phys. Biol. 1 (2004), 42–52. doi:10.1088/1478-3967/1/1/005; preprint q-bio.SC/0402041
(This is the most cited paper in Physical Biology and earned the 2008 Physical Biology Citations Award.)

2003

O. Beckstein, P.C. Biggin, P. Bond, J.N. Bright, C. Domene, A. Grottesi, J. Holyoake, and M.S.P. Sansom, Ion channel gating: insights via molecular simulations, FEBS Letters 555 (2003), 85–90
Yalini Arinaminpathy, Oliver Beckstein, Philip C. Biggin, Peter J. Bond, Carmen Domene, Andrew Pang and Mark S.P. Sansom*, Large Scale Biomolecular Simulations: Current Status and Future Prospects, 901–907. In Proc. UK e-Science All Hands Meeting 2003, ed. Simon J. Cox (2003), Swindon: EPSRC, ISBN 1-904425-11-9
O. Beckstein and Mark S. P. Sansom, Liquid-vapor oscillations of water in hydrophobic nanopores, Proc. Natl. Acad. Sci. USA. 100 (2003), 7063–7068. doi:10.1073/pnas.1136844100. preprint physics/0303096.
(This article received some media coverage.)

2002

Mark S. P. Sansom, Peter Bond, Oliver Beckstein, Philip C. Biggin, Jose Faraldo-Gomez, Richard J. Law, George Patargias, D. Peter Tieleman, Water in ion channels and pores—simulation studies, in Novartis Foundation Symposia 245 (2002), 66–83

2001

O. Beckstein, Philip C. Biggin and Mark S. P. Sansom, A hydrophobic gating mechanism for nanopores, J. Phys. Chem. B 105 (2001), 12902-12905
J. E. Klepeis, O. Beckstein, O. Pankratov, G. L. W. Hart, Chemical bonding, elasticity, and valence force field models: a case study for α-Pt₂Si and PtSi, Phys. Rev. B 64 (2001), 155110
O. Beckstein, J. E. Klepeis, G. L. W. Hart, and O. Pankratov, First-principles elastic constants and electronic structure of α-Pt₂Si and PtSi, Phys. Rev. B 63 (2001), 134112

Last modified: 2012-01-23 by Oliver Beckstein