Jim Al-Khalili

Prof. Jim Al-Khalili

Department of Physics, University of Surrey, Guildford, Surrey, GU2 7XH, UK

Research Focus & Metrics

Academic Career Length

28Years (1999-Present)

(Calculated once Scilit publication data is synced: current year − year of first publication + 1)

Representative Publications

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26 January 2021 in Quantum Reports
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YKYoungchan Kim
Youngchan Kim
FBFederico Bertagna
Federico Bertagna
EDEdeline M. D’souza
Edeline M. D’souza
DHDerren Heyes
Derren Heyes
LJLinus O. Johannissen
Linus O. Johannissen
JMJohnjoe Mcfadden
Johnjoe Mcfadden
Understanding the rules of life is one of the most important scientific endeavours and has revolutionised both biology and biotechnology. Remarkable advances in observation techniques allow us to investigate a broad range of complex and dynamic biological processes in which living systems could exploit quantum behaviour to enhance and regulate biological functions. Recent evidence suggests that these non-trivial quantum mechanical effects may play a crucial role in maintaining the non-equilibrium state of biomolecular systems. Quantum biology is the study of such quantum aspects of living systems. In this review, we summarise the latest progress in quantum biology, including the areas of enzyme-catalysed reactions, photosynthesis, spin-dependent reactions, DNA, fluorescent proteins, and ion channels. Many of these results are expected to be fundamental building blocks towards understanding the rules of life.

12 December 2018 in Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences
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JMJohnjoe Mcfadden
Johnjoe Mcfadden
Jim Al-KhaliliJim Al-Khalili
Jim Al-Khalili
Quantum biology is usually considered to be a new discipline, arising from recent research that suggests that biological phenomena such as photosynthesis, enzyme catalysis, avian navigation or olfaction may not only operate within the bounds of classical physics but also make use of a number of the non-trivial features of quantum mechanics, such as coherence, tunnelling and, perhaps, entanglement. However, although the most significant findings have emerged in the past two decades, the roots of quantum biology go much deeper—to the quantum pioneers of the early twentieth century. We will argue that some of the insights provided by these pioneering physicists remain relevant to our understanding of quantum biology today.

5 May 2022 in Communications Physics
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LSLouie Slocombe
Louie Slocombe
Marco SacchiMarco Sacchi
Marco Sacchi
Jim Al-KhaliliJim Al-Khalili
Jim Al-Khalili
One of the most important topics in molecular biology is the genetic stability of DNA. One threat to this stability is proton transfer along the hydrogen bonds of DNA that could lead to tautomerisation, hence creating point mutations. We present a theoretical analysis of the hydrogen bonds between the Guanine-Cytosine (G-C) nucleotide, which includes an accurate model of the structure of the base pairs, the quantum dynamics of the hydrogen bond proton, and the influence of the decoherent and dissipative cellular environment. We determine that the quantum tunnelling contribution to the proton transfer rate is several orders of magnitude larger than the classical over-the-barrier hopping. Due to the significance of the quantum tunnelling even at biological temperatures, we find that the canonical and tautomeric forms of G-C inter-convert over timescales far shorter than biological ones and hence thermal equilibrium is rapidly reached. Furthermore, we find a large tautomeric occupation probability of 1.73 × 10−4, suggesting that such proton transfer may well play a far more important role in DNA mutation than has hitherto been suggested. Our results could have far-reaching consequences for current models of genetic mutations.
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1 June 1999 in BioSystems
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JMJohnjoe Mcfadden
Johnjoe Mcfadden
Jim Al-KhaliliJim Al-Khalili
Jim Al-Khalili

20 April 2015 in Physical Chemistry Chemical Physics
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AGA. D. Godbeer
A. D. Godbeer
Jim Al-KhaliliJim Al-Khalili
Jim Al-Khalili
Paul StevensonPaul Stevenson
Paul Stevenson
The energies of the canonical (standard, amino-keto) and tautomeric (non-standard, imino-enol) charge-neutral forms of the adenine–thymine base pair (A–T and A*–T*, respectively) are calculated using density functional theory. The reaction pathway is then computed using a transition state search to provide the asymmetric double-well potential minima along with the barrier height and shape, which are combined to create the potential energy surface using a polynomial fit. The influence of quantum tunnelling on proton transfer within a base pair H-bond (modelled as the DFT deduced double-well potential) is then investigated by solving the time-dependent master equation for the density matrix. The effect on a quantum system by its surrounding water molecules is explored via the inclusion of a dissipative Lindblad term in the master equation, in which the environment is modelled as a heat bath of harmonic oscillators. It is found that quantum tunnelling, due to transitions to higher energy eigenstates with significant amplitudes in the shallow (tautomeric) side of the potential, is unlikely to be a significant mechanism for the creation of adenine–thymine tautomers within DNA, with thermally assisted coupling of the environment only able to boost the tunnelling probability to a maximum of 2 × 10−9. This is barely increased for different choices of the starting wave function or when the geometry of the potential energy surface is varied.

5 November 2022 in Communications Chemistry
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LSLouie Slocombe
Louie Slocombe
MWMax Winokan
Max Winokan
Jim Al-KhaliliJim Al-Khalili
Jim Al-Khalili
Marco SacchiMarco Sacchi
Marco Sacchi
Proton transfer between the DNA bases can lead to mutagenic Guanine-Cytosine tautomers. Over the past several decades, a heated debate has emerged over the biological impact of tautomeric forms. Here, we determine that the energy required for generating tautomers radically changes during the separation of double-stranded DNA. Density Functional Theory calculations indicate that the double proton transfer in Guanine-Cytosine follows a sequential, step-like mechanism where the reaction barrier increases quasi-linearly with strand separation. These results point to increased stability of the tautomer when the DNA strands unzip as they enter the helicase, effectively trapping the tautomer population. In addition, molecular dynamics simulations indicate that the relevant strand separation time is two orders of magnitude quicker than previously thought. Our results demonstrate that the unwinding of DNA by the helicase could simultaneously slow the formation but significantly enhance the stability of tautomeric base pairs and provide a feasible pathway for spontaneous DNA mutations.
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