Philosophical Transactions of the Royal Society A

Mathematical, Physical and Engineering Sciences

VOLUME 370 2012

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Phil. Trans. R. Soc. A (2012) Contents

No. 1958 13 January 2012

Sensor network algorithms and applications PAPERS OF A THEME ISSUE COMPILED AND EDITED BY NIKI TRIGONI AND BHASKAR KRISHNAMACHARI Editorial Philosophical Transactions A: looking forward to 2012 By C. D. Garner 3

Introduction Sensor network algorithms and applications By N. Trigoni and B. Krishnamachari 5

Articles Distributed algorithms for sensor networks By C. Lenzen and R. Wattenhofer 11 Geometric algorithms for sensor networks By J. Gao and L. Guibas 27 Energy management in sensor networks By J. A. Stankovic and T. He 52 Operating systems and network protocols for wireless sensor networks By P. Dutta and A. Dunkels 68 Wireless sensor node localization By Á. Lédeczi and M. Maróti 85 Distributed inference in wireless sensor networks By V. V. Veeravalli and P. K. Varshney 100 Signal compression in wireless sensor networks By M. F. Duarte, G. Shen, A. Ortega and R. G. Baraniuk 118 Sensing data centres for energy efﬁciency By J. Liu and A. Terzis 136 Underwater sensor networks: applications, advances and challenges By J. Heidemann, M. Stojanovic and M. Zorzi 158 Human-centric sensing By M. Srivastava, T. Abdelzaher and B. Szymanski 176

No. 1959 28 January 2012

The peaks and troughs of wave energy: the dreams and the reality PAPERS OF A THEO MURPHY MEETING ISSUE ORGANIZED AND EDITED BY FRANCIS FARLEY,ROD RAINEY AND JOHN CHAPLIN Preface The peaks and troughs of wave energy, the dreams and the reality By F. J. M. Farley 201

Phil. Trans. R. Soc. A (2012) iii iv Contents

Introduction Opening remarks and the power spectrum of ocean waves By F. J. M. Farley 203

Articles Hydrodynamic principles of wave power extraction By C. C. Mei 208 A review of oscillating water columns By T. V. Heath 235 Heaving buoys, point absorbers and arrays By J. Falnes and J. Hals 246 Far-ﬁeld theory of wave power capture by oscillating systems By F. J. M. Farley 278 Discrete control of resonant wave energy devices By A. H. Clément and A. Babarit 288 Wave energy extraction by coupled resonant absorbers By D. V. Evans and R. Porter 315 Nearshore oscillating wave surge converters and the development of Oyster By T. Whittaker and M. Folley 345 Pelamis: experience from concept to connection By R. Yemm, D. Pizer, C. Retzler and R. Henderson 365 Rubber tubes in the sea By F. J. M. Farley, R. C. T. Rainey and J. R. Chaplin 381 Laboratory testing the Anaconda By J. R. Chaplin, V. Heller, F. J. M. Farley, G. E. Hearn and R. C. T. Rainey 403 Key features of wave energy By R. C. T. Rainey 425 What can wave energy learn from offshore oil and gas? By E. R. Jefferys 439 The lessons learned from the development of the wind energy industry that might be applied to marine industry renewables By A. Garrad 451 Wave energy technology in China By Y. You, S. Sheng, B. Wu and Y. He 472 Wave energy: a Paciﬁc perspective By R. Paasch, K. Ruehl, J. Hovland and S. Meicke 481 Assessing wave energy effects on biodiversity: the Wave Hub experience By M. J. Witt, E. V. Sheehan, S. Bearhop, A. C. Broderick, D. C. Conley, S. P. Cotterell, E. Crow, W. J. Grecian, C. Halsband, D. J. Hodgson, P. Hosegood, R. Inger, P. I. Miller, D. W. Sims, R. C. Thompson, K. Vanstaen, S. C. Votier, M. J. Attrill and B. J. Godley 502

No. 1960 13 February 2012

The physics, chemistry and dynamics of explosions PAPERS OF A THEME ISSUE COMPILED AND EDITED BY ELAINE S. ORAN AND FORMAN A. WILLIAMS

Phil. Trans. R. Soc. A (2012) Contents v

Preface The physics, chemistry and dynamics of explosions By E. S. Oran and F. A. Williams 533

Introduction The physics, chemistry and dynamics of explosions By E. S. Oran and F. A. Williams 534

Articles Large vapour cloud explosions, with particular reference to that at Buncefield By D. Bradley, G. A. Chamberlain and D. D. Drysdale 544 Gas-phase detonation propagation in mixture composition gradients By D. A. Kessler, V. N. Gamezo and E. S. Oran 567 Analytical studies of the dynamics of gaseous detonations By P. Clavin and F. A. Williams 597 Combustion waves in hydraulically resisted systems By I. Brailovsky, L. Kagan and G. Sivashinsky 625 Explosion propagation in inert porous media By G. Ciccarelli 647 Stability of detonation in a circular pipe with porous walls By C. Chiquete and A. Tumin 668 Autoignitions and detonations in engines and ducts By D. Bradley 689 Some observations on the initiation and onset of detonation By G. Thomas 715 Plasma-assisted ignition and deflagration-to-detonation transition By A. Starikovskiy, N. Aleksandrov and A. Rakitin 740 Astrophysical explosions: from solar flares to cosmic gamma-ray bursts By J. C. Wheeler 774

No. 1961 28 February 2012

Physics at the high-energy frontier: the Large Hadron Collider project PAPERS OF A DISCUSSION MEETING ISSUE ORGANIZED AND EDITED BY GEORGE KALMUS,ROBERT BROWN,DAVID EVANS,VALERIE GIBSON AND RICHARD NICKERSON Preface Physics at the high-energy frontier: the Large Hadron Collider project By G. Kalmus 803

Articles The Standard Model By T. Shears 805 Outstanding questions: physics beyond the Standard Model By J. Ellis 818 The Large Hadron Collider By L. Evans 831 Large Hadron Collider commissioning and ﬁrst operation By S. Myers 859

Phil. Trans. R. Soc. A (2012) vi Contents

Physics requirements for the design of the ATLAS and CMS experiments at the Large Hadron Collider By T. S. Virdee 876 Characteristics of the ATLAS and CMS detectors By A. Seiden 892 Flavour physics and the Large Hadron Collider beauty experiment By V. Gibson 907 Heavy-ion physics with the ALICE experiment at the CERN Large Hadron Collider By J. Schukraft 917 Early physics results By P. Jenni 933 The data acquisition and reduction challenge at the Large Hadron Collider By S. Cittolin 950 The Large Hadron Collider and Grid computing By N. Geddes 965 The Large Hadron Collider project: organizational and ﬁnancial matters (of physics at the terascale) By J. Engelen 978 The future of the Large Hadron Collider and CERN By R.-D. Heuer 986 The Large Hadron Collider: lessons learned and summary By C. Llewellyn Smith 995

No. 1962 13 March 2012

Climate predictions: the inﬂuence of nonlinearity and randomness PAPERS OF A THEME ISSUE COMPILED AND EDITED BY J. M. T. THOMPSON AND J. SIEBER Introduction Climate predictions: the inﬂuence of nonlinearity and randomness By J. M. T. Thompson and J. Sieber 1007

Articles How does the Earth system generate and maintain thermodynamic disequilibrium and what does it imply for the future of the planet? By A. Kleidon 1012 A new modelling framework for statistical cumulus dynamics By R. S. Plant 1041 Data-based stochastic subgrid-scale parametrization: an approach using cluster-weighted modelling By F. Kwasniok 1061 Model complexity versus ensemble size: allocating resources for climate prediction By C. A. T. Ferro, T. E. Jupp, F. H. Lambert, C. Huntingford and P. M. Cox 1087 On the visualization, veriﬁcation and recalibration of ternary probabilistic forecasts By T. E. Jupp, R. Lowe, C. A. S. Coelho and D. B. Stephenson 1100 ELPIS-JP: a dataset of local-scale daily climate change scenarios for Japan By T. Iizumi, M. A. Semenov, M. Nishimori, Y. Ishigooka and T. Kuwagata 1121 Oscillators and relaxation phenomena in Pleistocene climate theory By M. Cruciﬁx 1140

Phil. Trans. R. Soc. A (2012) Contents vii

Tipping points in open systems: bifurcation, noise-induced and rate-dependent examples in the climate system By P. Ashwin, S. Wieczorek, R. Vitolo and P. Cox 1166 Early warning of climate tipping points from critical slowing down: comparing methods to improve robustness By T. M. Lenton, V. N. Livina, V. Dakos, E. H. van Nes and M. Scheffer 1185 Nonlinear softening as a predictive precursor to climate tipping By J. Sieber and J. M. T. Thompson 1205 Change-point analysis as a tool to detect abrupt climate variations By C. Beaulieu, J. Chen and J. L. Sarmiento 1228 Robustness of estimators of long-range dependence and self-similarity under non-Gaussianity By C. L. E. Franzke, T. Graves, N. W. Watkins, R. B. Gramacy and C. Hughes 1250

No. 1963 28 March 2012

Structure and biological activity of glasses and ceramics PAPERS OF A THEME ISSUE COMPILED AND EDITED BY ANTONIO TILOCCA AND ALASTAIR N. CORMACK Introduction Structure and biological activity of glasses and ceramics By A. N. Cormack and A. Tilocca 1271

Articles Surface characterization of silicate bioceramics By M. Cerruti 1281 Coordination chemistry of Ca sites at the surface of nanosized hydroxyapatite: interaction with H2O and CO By V. Bolis, C. Busco, G. Martra, L. Bertinetti, Y. Sakhno, P. Ugliengo, F. Chiatti, M. Corno and N. Roveri 1313 High-resolution three-dimensional probes of biomaterials and their interfaces By K. Grandﬁeld, A. Palmquist and H. Engqvist 1337 Titanium-containing bioactive phosphate glasses By A. Kiani, N. J. Lakhkar, V. Salih, M. E. Smith, J. V. Hanna, R. J. Newport, D. M. Pickup and J. C. Knowles 1352 Local structures of mesoporous bioactive glasses and their surface alterations in vitro: inferences from solid-state nuclear magnetic resonance By P. N. Gunawidjaja, R. Mathew, A. Y. H. Lo, I. Izquierdo-Barba, A. García, D. Arcos, M. Vallet-Regí and M. Edén 1376 Structure and functionalization of mesoporous bioceramics for bone tissue regeneration and local drug delivery By M. Vallet-Regí, I. Izquierdo-Barba and M. Colilla 1400 Characterizing the hierarchical structures of bioactive sol–gel silicate glass and hybrid scaffolds for bone regeneration By R. A. Martin, S. Yue, J. V. Hanna, P. D. Lee, R. J. Newport, M. E. Smith and J. R. Jones 1422 Molecular modelling of protein adsorption on the surface of titanium dioxide polymorphs By G. Raffaini and F. Ganazzoli 1444 Disentangling protein–silica interactions By L. Giussani, G. Tabacchi, E. Gianotti, S. Coluccia and E. Fois 1463

Phil. Trans. R. Soc. A (2012) viii Contents

Ab initio modelling of protein–biomaterial interactions: inﬂuence of amino acid polar side chains on adsorption at hydroxyapatite surfaces By A. Rimola, M. Corno, J. Garza and P. Ugliengo 1478

No. 1964 13 April 2012

Nonlinear water waves PAPERS OF A THEME ISSUE COMPILED AND EDITED BY ADRIAN CONSTANTIN Introduction Nonlinear water waves By A. Constantin 1501

Articles Seismically generated tsunamis By D. Arcas and H. Segur 1505 Theoretical and experimental study of particle trajectories for nonlinear water waves propagating on a sloping bottom By Y.-Y. Chen, M.-S. Li, H.-C. Hsu and C.-O. Ng 1543 Note on the velocity and related ﬁelds of steady irrotational two-dimensional surface gravity waves By D. Clamond 1572 On the open sea propagation of water waves generated by a moving bed By A. Constantin and P. Germain 1587 Regularity of rotational travelling water waves By J. Escher 1602 Regularity for steady periodic capillary water waves with vorticity By D. Henry 1616 Experimental study of the particle paths in solitary water waves By H.-C. Hsu, Y.-Y. Chen and H.-H. Hwung 1629 Models for the formation of a critical layer in water wave propagation By R. S. Johnson 1638 Trajectories of ﬂuid particles in a periodic water wave By H. Okamoto and M. Shoji¯ 1661 Synthetic tsunamis along the Israeli coast By J. Tobias and M. Stiassnie 1677 Eulerian–Lagrangian analysis for particle velocities and trajectories in a pure wave motion using particle image velocimetry By M. Umeyama 1687 Equivalence of weak formulations of the steady water waves equations By E. Varvaruca and A. Zarnescu 1703

No. 1965 28 April 2012

Geometry and mechanics of layered structures and materials PAPERS OF A THEME ISSUE COMPILED AND EDITED BY C. J. BUDD,R.BUTLER AND G. W. HUNT Preface Geometry and mechanics of layered structures and materials By G. Hunt, R. Butler and C. Budd 1723

Phil. Trans. R. Soc. A (2012) Contents ix

Articles Stripe patterns and a projection-valued formulation of the eikonal equation By M. A. Peletier and M. Veneroni 1730 Multi-layered folding with voids By T. J. Dodwell, G. W. Hunt, M. A. Peletier and C. J. Budd 1740 Compressive strength of delaminated aerospace composites By R. Butler, A. T. Rhead, W. Liu and N. Kontis 1759 Bending strength of delaminated aerospace composites By M. Kinawy, R. Butler and G. W. Hunt 1780 Folding in power-law viscous multi-layers By S. M. Schmalholz and D. W. Schmid 1798 Geometric modelling of kink banding in laminated structures By M. A. Wadee, C. Völlmecke, J. F. Haley and S. Yiatros 1827 The role of delamination in failure of fibre-reinforced composites By M. R. Wisnom 1850 On longitudinal compressive failure of carbon-fibre-reinforced polymer: from unidirectional to woven, and from virgin to recycled By S. T. Pinho, R. Gutkin, S. Pimenta, N. V. De Carvalho and P. Robinson 1871 Effects of imperfections on localized bulging in inflated membrane tubes By Y. B. Fu and Y. X. Xie 1896 On the influence of delamination on laminated paperboard creasing and folding By L. A. A. Beex and R. H. J. Peerlings 1912 Numerical optimization approach to modelling delamination and buckling of geometrically constrained structures By G. Mullineux, B. J. Hicks and C. Berry 1925 Non-smooth mode I fracture of fibre-reinforced composites: an experimental, numerical and analytical study By P. Davidson and A. M. Waas 1942 Localized and chaotic folding: the role of axial plane structures By B. E. Hobbs and A. Ord 1966 Compliant shell mechanisms By K. A. Seffen 2010

No. 1966 13 May 2012

River history PAPERS OF A THEME ISSUE COMPILED AND EDITED BY CLAUDIO VITA-FINZI Introduction River history By C. Vita-Finzi 2029

Articles 210Pb geochronology of ﬂood events in large tropical river systems By R. Aalto and C. A. Nittrouer 2040 Historical sources and watershed evolution By S. W. Trimble 2075 River sediments By M. Williams 2093 Modelling river history and evolution By T. J. Coulthard and M. J. Van De Wiel 2123

Phil. Trans. R. Soc. A (2012) x Contents

The ﬂuvial record of climate change By M. G. Macklin, J. Lewin and J. C. Woodward 2143 River history and tectonics By C. Vita-Finzi 2173 The ﬂuvial history of Mars By M. H. Carr 2193 Indo-Gangetic river systems, monsoon and malaria By E. Whitcombe 2216 Geomorphic histories for river and catchment management By R. J. Wasson 2240 No. 1967 28 May 2012

Biosensors: surface structures and materials PAPERS OF A THEME ISSUE COMPILED AND EDITED BY BHARAT BHUSHAN Preface Biosensors: surface structures and materials By B. Bhushan 2267

Articles Theory, fabrication and applications of microﬂuidic and nanoﬂuidic biosensors By S. Prakash, M. Pinti and B. Bhushan 2269 Measurement of slip length on superhydrophobic surfaces By A. Maali and B. Bhushan 2304 Bioadhesion: a review of concepts and applications By M. L. B. Palacio and B. Bhushan 2321 Designing nanostructured block copolymer surfaces to control protein adhesion By S. R. Schricker, M. L. B. Palacio and B. Bhushan 2348 Biofouling: lessons from nature By G. D. Bixler and B. Bhushan 2381 Towards biodegradable wireless implants By C. M. Boutry, H. Chandrahalim, P. Streit, M. Schinhammer, A. C. Hänzi and C. Hierold 2418 Monitoring the progression of metastatic breast cancer on nanoporous silica chips By J. Fan, X. Deng, J. W. Gallagher, H. Huang, Y. Huang, J. Wen, M. Ferrari, H. Shen and Y. Hu 2433 A new approach to gas sensing with nanotechnology By S. Sharma and M. Madou 2448 ImmunoFET feasibility in physiological salt environments By P. Casal, X. Wen, S. Gupta, T. Nicholson III, Y. Wang, A. Theiss, B. Bhushan, L. Brillson, W. Lu and S. C. Lee 2474 No. 1968 13 June 2012

Water in the gas phase PAPERS OF A THEO MURPHY MEETING ISSUE COMPILED AND EDITED BY JONATHAN TENNYSON AND KEITH P. SHINE Preface Water in the gas phase By J. Tennyson and K. P. Shine 2491

Phil. Trans. R. Soc. A (2012) Contents xi

Articles Pressure effects on water vapour lines: beyond the Voigt profile By N. H. Ngo, H. Tran, R. R. Gamache and J. M. Hartmann 2495 Spectroscopic measurement of the vapour pressure of ice By K. Bielska, D. K. Havey, G. E. Scace, D. Lisak and J. T. Hodges 2509 Development and recent evaluation of the MT_CKD model of continuum absorption By E. J. Mlawer, V. H. Payne, J.-L. Moncet, J. S. Delamere, M. J. Alvarado and D. C. Tobin 2520 Water vapour foreign-continuum absorption in near-infrared windows from laboratory measurements By I. V. Ptashnik, R. A. McPheat, K. P. Shine, K. M. Smith and R. G. Williams 2557 The water vapour self- and water–nitrogen continuum absorption in the 1000 and 2500 cm−1 atmospheric windows By Yu. I. Baranov and W. J. Lafferty 2578 Absolute high spectral resolution measurements of surface solar radiation for detection of water vapour continuum absorption By T. D. Gardiner, M. Coleman, H. Browning, L. Tallis, I. V. Ptashnik and K. P. Shine 2590 Airborne and satellite remote sensing of the mid-infrared water vapour continuum By S. M. Newman, P. D. Green, I. V. Ptashnik, T. D. Gardiner, M. D. Coleman, R. A. McPheat and K. M. Smith 2611 Recent advances in measurement of the water vapour continuum in the far-infrared spectral region By P. D. Green, S. M. Newman, R. J. Beeby, J. E. Murray, J. C. Pickering and J. E. Harries 2637 An adiabatic model for calculating overtone spectra of dimers such as (H2O)2 By J. Tennyson, M. J. Barber and R. E. A. Kelly 2656 Infrared shifts of the water dimer from the fully flexible ab initio HBB2 potential By C. Leforestier 2675 − H2O N2 collision-induced absorption band intensity in the region of the N2 fundamental: ab initio investigation of its temperature dependence and comparison with laboratory data By Yu. I. Baranov, I. A. Buryak, S. E. Lokshtanov, V. A. Lukyanchenko and A. A. Vigasin 2691 State-resolved spectroscopy of high vibrational levels of water up to the dissociative continuum By P. Maksyutenko, M. Grechko, T. R. Rizzo and O. V. Boyarkin 2710 Global spectroscopy of the water monomer By O. L. Polyansky, N. F. Zobov, I. I. Mizus, L. Lodi, S. N. Yurchenko, J. Tennyson, A. G. Császár and O. V. Boyarkin 2728 Water in exoplanets By G. Tinetti, J. Tennyson, C. A. Griffith and I. Waldmann 2749 Models of very-low-mass stars, brown dwarfs and exoplanets By F. Allard, D. Homeier and B. Freytag 2765 Water in star- and planet-forming regions By E. A. Bergin and E. F. van Dishoeck 2778

Corrections Correction to Theme Issue ‘The physics, chemistry and dynamics of explosions’ compiled and edited by Elaine S. Oran and Forman A. Williams 2803

Phil. Trans. R. Soc. A (2012) xii Contents

No. 1969 28 June 2012

Beyond crystals: the dialectic of materials and information PAPERS OF A THEME ISSUE COMPILED AND EDITED BY JULYAN H. E. CARTWRIGHT AND ALAN L. MACKAY Introduction Beyond crystals: the dialectic of materials and information By J. H. E. Cartwright and A. L. Mackay 2807 Dedication Happy birthday Alan: a Festschrift for Alan Mackay By J. H. E. Cartwright 2823 Articles Using shape for self-assembly By L. Cademartiri, K. J. M. Bishop, P. W. Snyder and G. A. Ozin 2824 Tubular precipitation structures: materials synthesis under non-equilibrium conditions By R. Makki, L. Roszol, J. J. Pagano and O. Steinbock 2848 Crystal growth as an excitable medium By J. H. E. Cartwright, A. G. Checa, B. Escribano and C. I. Sainz-Díaz 2866 Decoding the energy landscape: extracting structure, dynamics and thermodynamics By D. J. Wales 2877 Unusual co-crystal of isonicotinamide: the structural landscape in crystal engineering By S. Tothadi and G. R. Desiraju 2900 A glimpse of quantum phenomena in optical lattices By S. Vishveshwara 2916 The memory of surfaces: epitaxial growth on quasi-crystals By R. McGrath, H. R. Sharma, J. A. Smerdon and J. Ledieu 2930 Structures of pseudo-decagonal approximants in Al−Co−Ni By S. Hovmöller, L. Hovmöller Zou, X. Zou and B. Grushko 2949 DNA information: from digital code to analogue structure By A. A. Travers, G. Muskhelishvili and J. M. T. Thompson 2960 DNA, dichotomic classes and frame synchronization: a quasi-crystal framework By S. Giannerini, D. L. Gonzalez and R. Rosa 2987 Peptide and RNA contributions to iron–sulphur chemical gardens as life’s ﬁrst inorganic compartments, catalysts, capacitors and condensers By S. E. McGlynn, I. Kanik and M. J. Russell 3007 Spatial and temporal organization of multi-protein assemblies: achieving sensitive control in information-rich cell-regulatory systems By V. M. Bolanos-Garcia, Q. Wu, T. Ochi, D. Y. Chirgadze, B. L. Sibanda and T. L. Blundell 3023

No. 1970 13 July 2012

Astrophysical processes on the Sun Papers of a Theme Issue compiled and edited by Clare E. Parnell Introduction Astrophysical processes on the Sun By C. E. Parnell 3043

Phil. Trans. R. Soc. A (2012) Contents xiii

Articles The solar dynamo By M. S. Miesch 3049 Magneto-convection By R. F. Stein 3070 Magnetic flux emergence and associated dynamic phenomena in the Sun By V. Archontis 3088 Numerical models of sunspot formation and fine structure By M. Rempel 3114 The quiet-Sun photosphere and chromosphere By R. J. Rutten 3129 The Sun’s global magnetic field By D. H. Mackay 3151 Theory of magnetic reconnection in solar and astrophysical plasmas By D. I. Pontin 3169 Magnetohydrodynamic waves and coronal seismology: an overview of recent results By I. De Moortel and V. M. Nakariakov 3193 A contemporary view of coronal heating By C. E. Parnell and I. De Moortel 3217 Solar flares and energetic particles By N. Vilmer 3241 Retractions Green waxes, adhesives and lubricants By W. Li, X. H. Kong, M. Ruan, F. M. Ma, Y. F. Jiang, M. Z. Liu, Y. Chen and X. H. Zuo 3269

No. 1971 28 July 2012

The foundations of computation, physics and mentality: the Turing legacy PAPERS OF A THEME ISSUE COMPILED AND EDITED BY BARRY COOPER AND SAMSON ABRAMSKY Preface The foundations of computation, physics and mentality: the Turing legacy By S. B. Cooper and S. Abramsky 3273 Articles Formalism and intuition in computability By R. I. Soare 3277 Programs = data = ﬁrst-class citizens in a computational world By N. D. Jones and J. G. Simonsen 3305 From Turing machines to computer viruses By J.-Y. Marion 3319 Honest universality By N. Dershowitz and E. Falkovich 3340 The physical Church–Turing thesis and non-deterministic computation over the real numbers By G. Dowek 3349 Axiomatizing physical experiments as oracles to algorithms By E. J. Beggs, J. F. Costa and J. V. Tucker 3359

Phil. Trans. R. Soc. A (2012) xiv Contents

The operator tensor formulation of quantum theory By L. Hardy 3385 Turing, ciphers and quanta By A. Ekert, A. Kay and J. Pope 3418 Certiﬁable quantum dice By U. Vazirani and T. Vidick 3432 On the computational content of convergence proofs via Banach limits By U. Kohlenbach and L. Leu¸stean 3449 Rice sequences of relations By A. Montalbán 3464 Universality probability of a preﬁx-free machine By G. Barmpalias and D. L. Dowe 3488 Uniform derandomization from pathetic lower bounds By E. Allender, V. Arvind, R. Santhanam and F. Wang 3512 Turing’s three philosophical lessons and the philosophy of information By L. Floridi 3536 Symbolic functions from neural computation By P. Smolensky 3543 Computability-theoretic learning complexity By J. Case and T. Kötzing 3570 A Turing test for free will By S. Lloyd 3597

No. 1972 13 August 2012

Quantum-coherent energy transfer: implications for biology and new energy technologies PAPERS OF A THEO MURPHY MEETING ISSUE ORGANIZED AND EDITED BY ALEXANDRA OLAYA-CASTRO,AHSAN NAZIR AND GRAHAM R. FLEMING Preface Quantum-coherent energy transfer: implications for biology and new energy technologies By A. Olaya-Castro, A. Nazir and G. R. Fleming 3613 Dedication Robert Silbey 1940–2011 By G. R. Fleming and R. A. Harris 3618 Articles Theoretical description of quantum effects in multi-chromophoric aggregates By E. N. Zimanyi and R. J. Silbey 3620 Coherence and decoherence in biological systems: principles of noise-assisted transport and the origin of long-lived coherences By A. W. Chin, S. F. Huelga and M. B. Plenio 3638 Non-Markovianity: initial correlations and nonlinear optical measurements By A. G. Dijkstra and Y. Tanimura 3658 Microscopic quantum coherence in a photosynthetic-light-harvesting antenna By J. M. Dawlaty, A. Ishizaki, A. K. De and G. R. Fleming 3672 Peak shape analysis of diagonal and off-diagonal features in the two-dimensional electronic spectra of the Fenna–Matthews–Olson complex By D. Hayes and G. S. Engel 3692

Phil. Trans. R. Soc. A (2012) Contents xv

Coherent nonlinear optical studies of elementary processes in biological complexes: diagrammatic techniques based on the wave function versus the density matrix By J. D. Biggs, J. A. Voll and S. Mukamel 3709 Measures and implications of electronic coherence in photosynthetic light-harvesting By C. Smyth, F. Fassioli and G. D. Scholes 3728 Exciton diffusion length in complex quantum systems: the effects of disorder and environmental ﬂuctuations on symmetry-enhanced supertransfer By D. F. Abasto, M. Mohseni, S. Lloyd and P. Zanardi 3750 A critical view on transport and entanglement in models of photosynthesis By M. Tiersch, S. Popescu and H. J. Briegel 3771 Energy transfer processes along a supramolecular chain of π-conjugated molecules By S. A. Schmid, R. Abbel, A. P. H. J. Schenning, E. W. Meijer and L. M. Herz 3787 Excitation energy migration processes in various multi-porphyrin assemblies By J. Yang and D. Kim 3802 Learning from photosynthesis: how to use solar energy to make fuels By R. J. Cogdell, A. T. Gardiner and L. Cronin 3819

No. 1973 28 August 2012

Ultra-precision engineering: from physics to manufacturing PAPERS OF A DISCUSSION MEETING ISSUE ORGANIZED AND EDITED BY XIANGQIAN JANE JIANG,PAUL SHORE,PAT MCKEOWN AND DAVID WHITEHOUSE Preface Preface By X. J. Jiang, P. Shore, P. McKeown, D. J. Whitehouse and P. C. Rufﬂes 3829

Introduction Ultra-precision engineering: from physics to manufacturing By X. J. Jiang, P. Shore, P. McKeown, D. J. Whitehouse and P. C. Rufﬂes 3831

Articles Precision engineering: an evolutionary perspective By C. J. Evans 3835 Precision engineering for astronomy: historical origins and the future revolution in ground-based astronomy By C. Cunningham and A. Russell 3852 The engineering needed for particle physics By S. Myers 3887 Precision manufacturing for clinical-quality regenerative medicines By D. J. Williams, R. J. Thomas, P. C. Hourd, A. Chandra, E. Ratcliffe, Y. Liu, E. A. Rayment and J. R. Archer 3924 Ultra-precision engineering in lithographic exposure equipment for the semiconductor industry By R.-H. Munnig Schmidt 3950 Micro-machining By E. Brinksmeier and W. Preuss 3973 Ultra-precision: enabling our future By P. Shore and P. Morantz 3993 Lithography for enabling advances in integrated circuits and devices By C. M. Garner 4015

Phil. Trans. R. Soc. A (2012) xvi Contents

Surface geometry, miniaturization and metrology By D. J. Whitehouse 4042 Mathematics for modern precision engineering By P. J. Scott and A. B. Forbes 4066 Precision surface measurement By X. Jiang 4089 The National Ignition Facility: the path to a carbon-free energy future By C. J. Stolz 4115 Precision engineering for future propulsion and power systems: a perspective from Rolls-Royce By S. Beale 4130

Discussion Precision metrology By X. Jiang and D. J. Whitehouse 4154

No. 1974 13 September 2012

Geoengineering: taking control of our planet’s climate? PAPERS OF A DISCUSSION MEETING ISSUE ORGANIZED AND EDITED BY ANDY RIDGWELL,CHRIS FREEMAN AND RICHARD LAMPITT Preface Geoengineering: taking control of our planet’s climate? By A. Ridgwell, C. Freeman and R. Lampitt 4163

Articles Geoengineering the climate: an overview and update By J. G. Shepherd 4166 Exploring early public responses to geoengineering By N. Pidgeon, A. Corner, K. Parkhill, A. Spence, C. Butler and W. Poortinga 4176 The runaway greenhouse: implications for future climate change, geoengineering and planetary atmospheres By C. Goldblatt and A. J. Watson 4197 Marine cloud brightening By J. Latham, K. Bower, T. Choularton, H. Coe, P. Connolly, G. Cooper, T. Craft, J. Foster, A. Gadian, L. Galbraith, H. Iacovides, D. Johnston, B. Launder, B. Leslie, J. Meyer, A. Neukermans, B. Ormond, B. Parkes, P. Rasch, J. Rush, S. Salter, T. Stevenson, H. Wang, Q. Wang and R. Wood 4217 Lifting options for stratospheric aerosol geoengineering: advantages of tethered balloon systems By P. Davidson, C. Burgoyne, H. Hunt and M. Causier 4263 Regional climate change mitigation with crops: context and assessment By J. S. Singarayer and T. Davies-Barnard 4301 Ocean acidiﬁcation in a geoengineering context By P. Williamson and C. Turley 4317 Interactions between reducing CO2 emissions, CO2 removal and solar radiation management By N. E. Vaughan and T. M. Lenton 4343 Cumulative carbon as a policy framework for achieving climate stabilization By H. D. Matthews, S. Solomon and R. Pierrehumbert 4365

Phil. Trans. R. Soc. A (2012) Contents xvii

An air–liquid contactor for large-scale capture of CO2 from air By G. Holmes and D. W. Keith 4380 Peatland geoengineering: an alternative approach to terrestrial carbon sequestration By C. Freeman, N. Fenner and A. H. Shirsat 4404

No. 1975 28 September 2012

Decoherence PAPERS OF A THEME ISSUE COMPILED AND EDITED BY AMIT HAGAR Introduction Decoherence By A. Hagar 4425

Articles Environmental decoherence versus intrinsic decoherence By P. C. E. Stamp 4429 Decoherence without dissipation By W. G. Unruh 4454 Temperature of a decoherent oscillator with strong coupling By W. G. Unruh 4460 Decoherence and the conditions for the classical control of quantum systems By G. J. Milburn 4469 Mesoscopic systems: classical irreversibility and quantum coherence By B. Barbara 4487 Decoherence in the chemical compass: the role of decoherence for avian magnetoreception By M. Tiersch and H. J. Briegel 4517 Key ideas in quantum error correction By R. Raussendorf 4541 Emergence of a classical Universe from quantum gravity and cosmology By C. Kiefer 4566 Decoherence and its role in the modern measurement problem By D. Wallace 4576 Decoherence: the view from the history and philosophy of science By A. Hagar 4594

No. 1976 13 October 2012

Quantum information processing in NMR: theory and experiment PAPERS OF A THEME ISSUE COMPILED AND EDITED BY IVAN S. OLIVEIRA AND ROBERTO M. SERRA Preface Preface By I. S. Oliveira and R. M. Serra 4613

Introduction Nuclear magnetic resonance quantum information processing By R. M. Serra and I. S. Oliveira 4615

Phil. Trans. R. Soc. A (2012) xviii Contents

Articles Recent advances in nuclear magnetic resonance quantum information processing By B. Criger, G. Passante, D. Park and R. Laﬂamme 4620 Implementing quantum logic gates with gradient ascent pulse engineering: principles and practicalities By B. Rowland and J. A. Jones 4636 Control aspects of quantum computing using pure and mixed states By T. Schulte-Herbrüggen, R. Marx, A. Fahmy, L. Kauffman, S. Lomonaco, N. Khaneja and S. J. Glaser 4651 Geometric aspects of composite pulses By T. Ichikawa, M. Bando, Y. Kondo and M. Nakahara 4671 Solid-state multiple quantum NMR in quantum information processing: exactly solvable models By E. B. Fel’dman, A. N. Pyrkov and A. I. Zenchuk 4690 Storage of quantum coherences as phase-labelled local polarization in solid-state nuclear magnetic resonance By M. B. Franzoni, R. H. Acosta, H. M. Pastawski and P. R. Levstein 4713 Experimental study of quantum simulation for quantum chemistry with a nuclear magnetic resonance simulator By D. Lu, N. Xu, B. Xu, Z. Li, H. Chen, X. Peng, R. Xu and J. Du 4734 Robust dynamical decoupling By A. M. Souza, G. A. Álvarez and D. Suter 4748 Quantum information processing by nuclear magnetic resonance on quadrupolar nuclei By J. Teles, E. R. DeAzevedo, J. C. C. Freitas, R. S. Sarthour, I. S. Oliveira and T. J. Bonagamba 4770 Controlling and exploiting phases in multi-spin systems using electron spin resonance and nuclear magnetic resonance By S. Simmons, H. Wu and J. J. L. Morton 4794 Classical to quantum in large-number limit By K. Modi, R. Fazio, S. Pascazio, V. Vedral and K. Yuasa 4810 On the quantumness of correlations in nuclear magnetic resonance By D. O. Soares-Pinto, R. Auccaise, J. Maziero, A. Gavini-Viana, R. M. Serra and L. C. Céleri 4821

No. 1977 28 October 2012

The new science of oxide interfaces PAPERS OF A DISCUSSION MEETING ISSUE ORGANIZED AND EDITED BY MARK BLAMIRE, DAVE BLANK AND JUDITH DRISCOLL Preface The new science of oxide interfaces By M. Blamire, J. Driscoll and D. Blank 4839

Articles Magnetoelectric interfaces and spin transport By J. D. Burton and E. Y. Tsymbal 4840 Emergent phenomena at multiferroic heterointerfaces By P. Yu, Y. H. Chu and R. Ramesh 4856 Reliable polarization switching of BiFeO3 By S. H. Baek and C. B. Eom 4872

Phil. Trans. R. Soc. A (2012) Contents xix

Insights from the study of high-temperature interface superconductivity By J. Pereiro, A. T. Bollinger, G. Logvenov, A. Gozar, C. Panagopoulos and I. Bozovi´ˇ c 4890 Termination control of electronic phases in oxide thin films and interfaces: LaAlO3/SrTiO3(001) By R. Pentcheva, R. Arras, K. Otte, V. G. Ruiz and W. E. Pickett 4904 Cationic-vacancy-induced room-temperature ferromagnetism in transparent, conducting anatase Ti1−x Tax O2 (x ∼ 0.05) thin films By A. Rusydi, S. Dhar, A. Roy Barman, Ariando, D.-C. Qi, M. Motapothula, J. B. Yi, I. Santoso, Y. P. Feng, K. Yang, Y. Dai, N. L. Yakovlev, J. Ding, A. T. S. Wee, G. Neuber, M. B. H. Breese, M. Ruebhausen, H. Hilgenkamp and T. Venkatesan 4927 Giant flexoelectric effect through interfacial strain relaxation By D. Lee and T. W. Noh 4944 Towards electrical spin injection into LaAlO3–SrTiO3 By M. Bibes, N. Reyren, E. Lesne, J.-M. George, C. Deranlot, S. Collin, A. Barthélémy and H. Jaffrès 4958 Phase engineering in oxides by interfaces By M. Fiebig 4972

No. 1978 13 November 2012

+ Chemistry, astronomy and physics of H3 PAPERS OF A THEO MURPHY MEETING ISSUE ORGANIZED AND EDITED BY TAKESHI OKA Introduction + Chemistry, astronomy and physics of H3 By T. Oka 4991

Articles + Progress in calculating the potential energy surface of H3 By L. Adamowicz and M. Pavanello 5001 + Spectroscopy of H3 based on a new high-accuracy global potential energy surface By O. L. Polyansky, A. Alijah, N. F. Zobov, I. I. Mizus, R. I. Ovsyannikov, J. Tennyson, L. Lodi, T. Szidarovszky and A. G. Császár 5014 + Visible transitions from ground state H3 measured with high-sensitivity action spectroscopy By M. Berg, A. Wolf and A. Petrignani 5028 Transfer of a proton between H2 and O2 By L. Kluge, S. Gärtner, S. Brünken, O. Asvany, D. Gerlich and S. Schlemmer 5041 + The ortho : para ratio of H3 in laboratory and astrophysical plasmas By K. N. Crabtree and B. J. McCall 5055 + Stabilization of H −H2 collision complexes between 11 and 28 K By R. Plašil, I. Zymak, P. Jusko, D. Mulin, D. Gerlich and J. Glosík 5066 The Jahn–Teller effect in the 3pe Rydberg state of H3: review of experimental and ab initio determinations By Ch. Jungen, M. Jungen and S. T. Pratt 5074 + Storage ring measurements of the dissociative recombination of H3 By H. Kreckel, A. Petrignani, O. Novotný, K. Crabtree, H. Buhr, B. J. McCall and A. Wolf 5088

Phil. Trans. R. Soc. A (2012) xx Contents

+ Binary recombination of para- and ortho-H3 with electrons at low temperatures By P. Dohnal, M. Hejduk, J. Varju, P. Ruboviˇc, Š. Rouˇcka, T. Kotrík, R. Plašil, R. Johnsen and J. Glosík 5101 + Kinetic processes in recombining H3 plasmas By R. Johnsen 5109 + Dissociative recombination of H3 : 10 years in retrospect By M. Larsson 5118 + H3 at the interface between astrochemistry and astroparticle physics By J. H. Black 5130 The distribution of cosmic-ray ionization rates in diffuse molecular clouds as probed + by H3 By N. Indriolo 5142 + Exploring the central molecular zone of the Galaxy using spectroscopy of H3 and CO By T. R. Geballe 5151 Hot, metastable hydronium ion in the Galactic centre: formation pumping in X-ray-irradiated gas? By D. C. Lis, P. Schilke, E. A. Bergin, M. Emprechtinger and the HEXOS Team 5162 Hydride spectroscopy of the diffuse interstellar medium: new clues on the gas fraction in + molecular form and cosmic ray ionization rate in relation to H3 By M. Gerin, F. Levrier, E. Falgarone, B. Godard, P. Hennebelle, F. Le Petit, M. De Luca, D. Neufeld, P. Sonnentrucker, P. Goldsmith, N. Flagey, D. C. Lis, C. M. Persson, J. H. Black, J. R. Goicoechea and K. M. Menten 5174 + Using deuterated H3 and other molecular species to understand the formation of stars and planets By F. F. S. van der Tak 5186 + H2,H3 and the age of molecular clouds and prestellar cores By L. Pagani, P. Lesaffre, E. Roueff, M. Jorﬁ, P. Honvault, T. González-Lezana and A. Faure 5200 Temperature changes and energy inputs in giant planet atmospheres: what we are + learning from H3 By T. S. Stallard, H. Melin, S. Miller, J. O’Donoghue, S. W. H. Cowley, S. V. Badman, A. Adriani, R. H. Brown and K. H. Baines 5213 + To be or not to be: the early history of H3 and H3 By H. Kragh 5225

No. 1979 28 November 2012

Principles and applications of quantum control engineering PAPERS OF A THEO MURPHY MEETING ISSUE ORGANIZED AND EDITED BY JOHN GOUGH Preface Principles and applications of quantum control engineering By J. E. Gough 5239

Introduction Principles and applications of quantum control engineering By J. E. Gough 5241

Articles Stabilizing entangled states with quasi-local quantum dynamical semigroups By F. Ticozzi and L. Viola 5259

Phil. Trans. R. Soc. A (2012) Contents xxi

Specification of photonic circuits using quantum hardware description language By N. Tezak, A. Niederberger, D. S. Pavlichin, G. Sarma and H. Mabuchi 5270 Qubit purification speed-up for three complementary continuous measurements By R. Ruskov, J. Combes, K. Mølmer and H. M. Wiseman 5291 Asymptotic inference in system identification for the atom maser By C. C˘atan˘a, M. van Horssen and M. Gu¸t˘a 5308 Pure Gaussian state generation via dissipation: a quantum stochastic differential equation approach By N. Yamamoto 5324 The quantum trajectory approach to quantum feedback control of an oscillator revisited By A. C. Doherty, A. Szorkovszky, G. I. Harris and W. P. Bowen 5338 Robust stability of uncertain linear quantum systems By I. R. Petersen, V. Ugrinovskii and M. R. James 5354 Quantum measurements in continuous time, non-Markovian evolutions and feedback By A. Barchielli and M. Gregoratti 5364 Quantum system characterization with limited resources By D. K. L. Oi and S. G. Schirmer 5386 Quantum demolition filtering and optimal control of unstable systems By V. P. Belavkin 5396 Single photon quantum filtering using non-Markovian embeddings By J. E. Gough, M. R. James and H. I. Nurdin 5408 On structure-preserving transformations of the Ito¯ generator matrix for model reduction of quantum feedback networks By H. I. Nurdin and J. E. Gough 5422 Non-abelian Weyl commutation relations and the series product of quantum stochastic evolutions By D. G. Evans, J. E. Gough and M. R. James 5437

No. 1980 13 December 2012

Prospectus for UK marine science PAPERS OF A THEME ISSUE COMPILED AND EDITED BY HARRY L. BRYDEN, CAROL ROBINSON AND GWYN GRIFFITHS Preface A strategy for UK marine science for the next 20 years By H. L. Bryden, C. Robinson and G. Grifﬁths 5455

Introduction A strategy for UK marine science for the next 20 years By J. G. Field 5457

Articles Changing currents: a strategy for understanding and predicting the changing ocean circulation By H. L. Bryden, C. Robinson and G. Grifﬁths 5461 A perspective on the future of physical oceanography By A. C. N. Garabato 5480 Ice sheets viewed from the ocean: the contribution of marine science to understanding modern and past ice sheets By C. Ó Cofaigh 5512

Phil. Trans. R. Soc. A (2012) xxii Contents

Palaeoceanography: motivations and challenges for the future By L. F. Robinson and M. Siddall 5540 Aspects of marine geoscience: a review and thoughts on potential for observing active processes and progress through collaboration between the ocean sciences By N. C. Mitchell 5567 Pressures on the marine environment and the changing climate of ocean biogeochemistry By A. P. Rees 5613 Challenges for implementing the Marine Strategy Framework Directive in a climate of macroecological change By A. McQuatters-Gollop 5636 Oceanographers’ contribution to climate modelling and prediction: progress to date and a future perspective By E. F. Shuckburgh 5656 Oceans of opportunity or rough seas? What does the future hold for developments in European marine policy? By T. Potts, T. O’Higgins and E. Hastings 5682

No. 1981 28 December 2012

Emergent magnetic monopoles in frustrated magnetic systems PAPERS OF A THEO MURPHY MEETING ISSUE ORGANIZED AND EDITED BY WILL BRANFORD

Introduction Emergent magnetic monopoles in frustrated magnetic systems By W. R. Branford 5702

Articles Magnetic monopoles in field theory and cosmology By A. Rajantie 5705 Magnetic charge and ordering in kagome spin ice By G.-W. Chern and O. Tchernyshyov 5718 Generalized longitudinal susceptibility for magnetic monopoles in spin ice By S. T. Bramwell 5738 Artificial kagome spin ice: dimensional reduction, avalanche control and emergent magnetic monopoles By R. V. Hügli, G. Duff, B. O’Conchuir, E. Mengotti, A. F. Rodríguez, F. Nolting, L. J. Heyderman and H. B. Braun 5767 Magnetic dipole configurations on honeycomb lattices: effect of finite size and boundaries By A. Schumann and H. Zabel 5783 Domain wall interactions at a cross-shaped vertex By L. O’Brien, A. Beguivin, D. Petit, A. Fernandez-Pacheco, D. Read and R. P. Cowburn 5794 Gauge fields in real and momentum spaces in magnets: monopoles and skyrmions By N. Nagaosa, X. Z. Yu and Y. Tokura 5806

Phil. Trans. R. Soc. A (2012) RSTA_370_1981_cover.qxd 2/11/12 8:31 PM Page 2

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Typeset in India by Techset Composition Limited, Salisbury, UK. Printed in the UK by Cambrian Printers. This paper meets the requirements of ISO 9706:1994(E) and ANSI/NISO Z39:48-1992 (Permanence of Paper) effective with volume 338, issue 1649, 1992. Phil. Trans. R. Soc. A (ISSN 1364-503X) is published twice a month for US$4283 per year by the Royal Society, and is distributed in the USA by Agent named Air Business, C/O Worldnet Shipping USA Inc., 149-35 177th Street, Jamaica, New York, NY11434, USA. US Postmaster: Send address changes to Phil. Trans. R. Soc. A, C/O Air Business Ltd, C/O Worldnet Shipping USA Inc., 149-35 177th Street, Jamaica, New York, NY11414. volume 370 volume 370 number 1981 pages 5701–5819 ISSN 1364-503X ISSN 28 December 2012 Emergent magnetic monopoles in frustrated magnetic monopoles Emergent systems magnetic Branford and edited by Will Murphy Meeting Issue organized Papers of a Theo The world’s ﬁrst science journal The world’s

Phil. Trans. R. Soc. A | vol. 370 no. 1981 pp. 5701–5819 | 28 December 2012 Emergent magnetic monopoles in frustrated magnetic systems 5783 5806 rsta.royalsocietypublishing.org Published in Great Britain by the Royal Society, 6–9 Carlton House Terrace, London SW1Y 5AG 28 December 2012 28 December volume 370 1981 · number · pages 5701–5819 Volume title page and table of contents Founded in 1660, the Royal Society is the independent scientific academy of the UK, dedicated to promoting excellence in science Registered Charity No 207043 Domain wall interactions at a cross-shaped vertex Domain wall interactions at a cross-shaped D. Read & R. P. Cowburn L. O’Brien, A. Beguivin, D. Petit, A. Fernandez-Pacheco, in magnets: monopoles and Gauge fields in real and momentum spaces skyrmions N. Nagaosa, X. Z. Yu & Y. Tokura 5794 R. V. Hügli, G. Duff, B. O’Conchuir, E. Mengotti, A. F. Rodríguez, F. Nolting, R. V. Hügli, G. Duff, B. O’Conchuir, E. Mengotti, L. J. Heyderman & H. B. Braun lattices: effect of finite Magnetic dipole configurations on honeycomb size and boundaries A. Schumann & H. Zabel Magnetic monopoles in field theory and cosmology Magnetic monopoles A. Rajantie spin ice Magnetic charge and ordering in kagome G.-W. Chern & O. Tchernyshyov for magnetic monopoles in spin ice Generalized longitudinal susceptibility S. T. Bramwell reduction, avalanche control and Artificial kagome spin ice: dimensional emergent magnetic monopoles 5738 5705 5718 5767 Introduction systems monopoles in frustrated magnetic Emergent magnetic W. R. Branford Articles 5702 Papers of a Theo Murphy Meeting Issue organized and edited by Will Branford and edited by Will Murphy Meeting Issue organized Papers of a Theo Emergent magnetic monopoles in frustrated magnetic monopoles in Emergent magnetic systems RSTA_370_1981_cover.qxd 2/11/12 8:31 PM Page 1 PM Page 8:31 2/11/12 RSTA_370_1981_cover.qxd