Publications by Jonathan Jones

Mapping Mutations in Legislation: A Bioinformatics Approach


RM Dixon, JA Jones

Practical pulse engineering: Gradient ascent without matrix exponentiation


G Bhole, JA Jones

Superconducting Super Motor and Generator


M Kawamura, JA Jones

Quantum correlations which imply causation.

Scientific reports 5 (2015) 18281-

JF Fitzsimons, JA Jones, V Vedral

In ordinary, non-relativistic, quantum physics, time enters only as a parameter and not as an observable: a state of a physical system is specified at a given time and then evolved according to the prescribed dynamics. While the state can, and usually does, extend across all space, it is only defined at one instant of time. Here we ask what would happen if we defined the notion of the quantum density matrix for multiple spatial and temporal measurements. We introduce the concept of a pseudo-density matrix (PDM) which treats space and time indiscriminately. This matrix in general fails to be positive for measurement events which do not occur simultaneously, motivating us to define a measure of causality that discriminates between spatial and temporal correlations. Important properties of this measure, such as monotonicity under local operations, are proved. Two qubit NMR experiments are presented that illustrate how a temporal pseudo-density matrix approaches a genuinely allowed density matrix as the amount of decoherence is increased between two consecutive measurements.

Conspiracist ideation as a predictor of climate-science rejection: an alternative analysis.

Psychological science 26 (2015) 664-666

RM Dixon, JA Jones

Composite pulses for interferometry in a thermal cold atom cloud

PHYSICAL REVIEW A 90 (2014) ARTN 033608

A Dunning, R Gregory, J Bateman, N Cooper, M Himsworth, JA Jones, T Freegarde

Experimental heat-bath cooling of spins


G Brassard, Y Elias, JM Fernandez, H Gilboa, JA Jones, T Mor, Y Weinstein, L Xiao

Designing short robust NOT gates for quantum computation

PHYSICAL REVIEW A 87 (2013) ARTN 052317

JA Jones

Nested composite NOT gates for quantum computation

PHYSICS LETTERS A 377 (2013) 2860-2862

JA Jones

Further analysis of some symmetric and antisymmetric composite pulses for tackling pulse strength errors.

J Magn Reson 230 (2013) 145-154

S Husain, M Kawamura, JA Jones

Composite pulses have found widespread use in both conventional Nuclear Magnetic Resonance experiments and in experimental quantum information processing to reduce the effects of systematic errors. Here we describe several families of time symmetric and antisymmetric fully compensating composite pulses, inspired by the previous Fn, Gn and BB1 families family developed by Wimperis. We describe families of composite 180° pulses (not gates) which exhibit unprecedented tolerance of pulse strength errors without unreasonable sensitivity to off-resonance errors, and related families with more exotic tailored responses. Next we address the problem of extending these methods to other rotation angles, and discuss numerical results for 90° pulses. Finally we demonstrate the performance of some 90° and 180° pulses in NMR experiments.

Implementing quantum logic gates with gradient ascent pulse engineering: principles and practicalities.

Philos Trans A Math Phys Eng Sci 370 (2012) 4636-4650

B Rowland, JA Jones

We briefly describe the use of gradient ascent pulse engineering (GRAPE) pulses to implement quantum logic gates in nuclear magnetic resonance quantum computers, and discuss a range of simple extensions to the core technique. We then consider a range of difficulties that can arise in practical implementations of GRAPE sequences, reflecting non-idealities in the experimental systems used.

Entanglements of two and three coupled two-level systems in a cavity QED setup including inter atomic interactions

Nonlinear Optics Quantum Optics 44 (2012) 65-87

J Jones, A Joshi

Generic models of two and three coupled two-level system (TLS) entangled through their interaction with a single mode field sustained in an ideal cavity, including other interactions among TLS, exhibit violation of Bell's and Mermin's inequality periodically in the interaction time of theTLS with the field mode. The effect of the initial states of TLS on the violation of these inequalities are discussed. The entanglement measure in terms of concurrence for these systems is also calculated which matches very well with the violation of Bell's inequality results. These systems can be employed for quantum logic gate implementations useful in quantum computing. © 2012 Old City Publishing, Inc.

A mode-matching analysis of dielectric-filled resonant cavities coupled to terahertz parallelplate waveguides

Optics Express 20 (2012) 21766-21772

V Astley, KS Reichel, J Jones, R Mendis, DM Mittleman

We use the mode-matching technique to study parallel-plate waveguide resonant cavities that are filled with a dielectric. We apply the generalized scattering matrix theory to calculate the power transmission through the waveguide-cavities. We compare the analytical results to experimental data to confirm the validity of this approach. © 2012 Optical Society of America.

Terahertz multichannel microfluidic sensor based on parallel-plate waveguide resonant cavities

Applied Physics Letters 100 (2012)

V Astley, KS Reichel, J Jones, R Mendis, DM Mittleman

We demonstrate a terahertz multichannel microfluidic sensor based on a parallel-plate waveguide geometry with two independent integrated resonant cavities. The resonant frequency of each cavity exhibits an approximately linear dependence on the index of refraction of the material inside the cavity and each cavity is demonstrated to respond independently with no measurable crosstalk. The sensitivities of the two cavities in terms of the change in resonant wavelength per refractive index unit (RIU) are measured to be 1.21 × 106nm/RIU and 6.77 × 105nm/RIU. © 2012 American Institute of Physics.

Quantum information, computation and communication

, 2012

JA Jones, D Jaksch

© J. A. Jones and D. Jaksch 2012. Quantum physics allows entirely new forms of computation and cryptography, which could perform tasks currently impossible on classical devices, leading to an explosion of new algorithms, communications protocols and suggestions for physical implementations of all these ideas. As a result, quantum information has made the transition from an exotic research topic to part of mainstream undergraduate courses in physics. Based on years of teaching experience, this textbook builds from simple fundamental concepts to cover the essentials of the field. Aimed at physics undergraduate students with a basic background in quantum mechanics, it guides readers through theory and experiment, introducing all the central concepts without getting caught up in details. Worked examples and exercises make this useful as a self-study text for those who want a brief introduction before starting on more advanced books. Solutions are available online at

Quantum computing with NMR.

Prog Nucl Magn Reson Spectrosc 59 (2011) 91-120

JA Jones

Terahertz multichannel microfluidic sensor based on parallel-plate waveguide resonant cavities

IRMMW-THz 2011 - 36th International Conference on Infrared, Millimeter, and Terahertz Waves (2011)

KS Reichel, V Astley, J Jones, R Mendis, DM Mittleman

We demonstrate a terahertz multichannel microfluidic sensor based on a parallel-plate waveguide geometry with two independent integrated resonant cavities. © 2011 IEEE.

Group epitope mapping considering relaxation of the ligand (GEM-CRL): including longitudinal relaxation rates in the analysis of saturation transfer difference (STD) experiments.

J Magn Reson 203 (2010) 1-10

S Kemper, MK Patel, JC Errey, BG Davis, JA Jones, TDW Claridge

In the application of saturation transfer difference (STD) experiments to the study of protein-ligand interactions, the relaxation of the ligand is one of the major influences on the experimentally observed STD factors, making interpretation of these difficult when attempting to define a group epitope map (GEM). In this paper, we describe a simplification of the relaxation matrix that may be applied under specified experimental conditions, which results in a simplified equation reflecting the directly transferred magnetisation rate from the protein onto the ligand, defined as the summation over the whole protein of the protein-ligand cross-relaxation multiplied by with the fractional saturation of the protein protons. In this, the relaxation of the ligand is accounted for implicitly by inclusion of the experimentally determined longitudinal relaxation rates. The conditions under which this "group epitope mapping considering relaxation of the ligand" (GEM-CRL) can be applied were tested on a theoretical model system, which demonstrated only minor deviations from that predicted by the full relaxation matrix calculations (CORCEMA-ST) [7]. Furthermore, CORCEMA-ST calculations of two protein-saccharide complexes (Jacalin and TreR) with known crystal structures were performed and compared with experimental GEM-CRL data. It could be shown that the GEM-CRL methodology is superior to the classical group epitope mapping approach currently used for defining ligand-protein proximities. GEM-CRL is also useful for the interpretation of CORCEMA-ST results, because the transferred magnetisation rate provides an additional parameter for the comparison between measured and calculated values. The independence of this parameter from the above mentioned factors can thereby enhance the value of CORCEMA-ST calculations.

Magnetic field sensors using 13-spin cat states

PHYSICAL REVIEW A 82 (2010) ARTN 022330

S Simmons, JA Jones, SD Karlen, A Ardavan, JJL Morton

Preparing pseudopure states with controlled-transfer gates

PHYSICAL REVIEW A 82 (2010) ARTN 032315

M Kawamura, B Rowland, JA Jones