Search

The misincorporation of a noncomplementary DNA base in the polymerase active site is a critical source of replication errors that can lead to genetic mutations. In this work, we model the mechanism of wobble mispairing and the subsequent rate of misincorporation errors by coupling first-principles quantum chemistry calculations to an open quantum systems master equation. This methodology allows us to accurately calculate the proton transfer between bases, allowing the misincorporation and formation of mutagenic tautomeric forms of DNA bases. Our calculated rates of genetic error formation are in excellent agreement with experimental observations in DNA. Furthermore, our quantum mechanics/molecular mechanics model predicts the existence of a short-lived "tunnelling-ready" configuration along the wobble reaction pathway in the polymerase active site, dramatically increasing the rate of proton transfer by a hundredfold, demonstrating that quantum tunnelling plays a critical role in determining the transcription error frequency of the polymerase.

The adenine-thymine tautomer (A*-T*) has previously been discounted as a spontaneous mutagenesis mechanism due to the energetic instability of the tautomeric configuration. We study the stability of A*-T* while the nucleobases undergo DNA strand separation. Our calculations indicate an increase in the stability of A*-T* as the DNA strands unzip and the hydrogen bonds between the bases stretch. Molecular Dynamics simulations reveal the timescales and dynamics of DNA strand separation and statistical ensemble of opening angles present in a biological environment. Our results demonstrate that the unwinding of DNA, an inherently out-of-equilibrium process facilitated by helicase, will change the energy landscape of the adenine-thymine tautomerisation reaction. We propose that DNA strand separation allows the stable tautomerisation of adenine-thymine, providing a feasible pathway for genetic point mutations via proton transfer between the A-T bases.

Proton transfer along the hydrogen bonds of DNA can lead to the creation of short-lived, but biologically relevant point mutations that can further lead to gene mutation and, potentially, cancer. In this work, the energy landscape of the canonical A-T and G-C base pairs (standard, amino-keto) to tautomeric A*-T* and G*-C* (non-standard, imino-enol) Watson-Crick DNA base pairs is modelled with density functional theory and machine-learning nudge-elastic band methods. We calculate the energy barriers and tunnelling rates of hydrogen transfer between and within each base monomer (A, T, G and C). We show that the role of tunnelling in A-T tautomerisation is statistically unlikely due to the presence of a small reverse reaction barrier. On the contrary, the thermal populations of the G*-C* point mutation could be non-trivial and propagate through the replisome. For the direct intramolecular transfer, the reaction is hindered by a substantial energy barrier. However, our calculations indicate that tautomeric bases in their monomeric form have remarkably long lifetimes.

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.

Prof. Jim-Al-Khalili explains the emerging field of quantum biology and discusses how this new discipline has developed from its inception in the 1920s until fruition in the late 1990s with the discovery of quantum effects in magnetoreception, olfaction, enzyme catalysis, and photosynthesis.

Model uncertainties arising due to suppression of target excitations in the description of deuteron scattering and resulting in a modification of the two-body interactions in a three-body system are investigated for several ( d , p ) reactions serving as indirect tools for studying the astrophysical ( p , γ ) reactions relevant to r p process. The three-body nature of the deuteron-target potential is treated within the adiabatic distorted-wave approximation (ADWA) which relies on a dominant contribution from the components of the three-body deuteron-target wave function with small n - p separations. This results in a simple prescription for treating the explicit energy dependence of two-body optical potentials in a three-body system requiring nucleon optical potentials to be evaluated at a shifted energy with respect to the standard value of half the deuteron incident energy. In addition, the ADWA allows for leading-order multiple-scattering effects to be estimated, which leads to a simple renormalization of the adiabatic potential's imaginary part by a factor of two. These effects are assessed using both nonlocal and local optical potential systematics for Al 26 , P 30 , Cl 34 , and Ni 56 targets at a deuteron incident energy of 12 MeV, which is typical for experiments with radioactive beams in inverse kinematics. The model uncertainties induced by the three-body nature of deuteron-target scattering are found to be within 40 % both in the main peak of angular distributions and in total ( d , p ) cross sections. At higher deuteron energies, around 60 MeV, model uncertainties can reach 100% in the total cross sections. A few examples of application to astrophysically interesting proton resonances in Si 27 and Cu 57 obtained using ( d , p ) reactions and mirror symmetry are given.

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.

The contribution of a three-nucleon (3N) force, acting between the neutron and proton in the incoming deuteron with a target nucleon, to the deuteron-target potential in the entrance channel of the $A(d,p)B$ reaction has been calculated within the adiabatic distorted wave approximation (ADWA). Four different 3N interaction sets from local chiral effective field theory ($\ensuremath{\chi}\mathrm{EFT}$) at next-to-next-to-leading order were used. Strong sensitivity of the adiabatic deuteron-target potential to the choice of the 3N force format has been found, which originates from the enhanced sensitivity to the short-range physics of nucleon-nucleon and 3N interactions in the ADWA. Such a sensitivity is reduced when a Watanabe folding model is used to generate the $d\text{\ensuremath{-}}A$ potential instead of ADWA. The impact of the 3N force contribution on $(d,p)$ cross sections depends on assumptions made about the $p\text{\ensuremath{-}}A$ and $n\text{\ensuremath{-}}A$ optical potentials used to calculate the distorted $d\text{\ensuremath{-}}A$ potential in the entrance channel. It is different for local and nonlocal optical potentials and depends on whether the induced three-body force arising due to neglect of target excitations is included or not.

Understanding the behaviour of a quantum system coupled to its environment is of fundamental interest in the general field of quantum technologies. It also has important repercussions on foundational problems in physics, such as the process of decoherence and the so-called quantum measurement problem. There have been many approaches to explore Markovian and non-Markovian dynamics within the framework of open quantum systems, but the richness of the ensuing dynamics is still not fully understood. In this paper we develop a non-Markovian extension of the standard Caldeira-Leggett model, based on expanding the dynamics of the reduced system at high temperature in inverse powers of the high-frequency cut-off of the Ohmic spectral density of the environment, and derive a non-Markovian master equation for the reduced density matrix for the case of a general potential. We also obtain a fully analytical solution in the free particle case. While the short-time behaviour of this solution does not diverge substantially from the Markovian behaviour, at intermediate times we find a resurgence of coherence, which we name lateral coherence. We identify this with a corresponding transient negative entropy production rate, which is understood to be characteristic of non-Markovian dynamics. We also analyze the positivity of the reduced density matrix, and derive the corresponding Fokker-Planck equation in the classical limit., Comment: 11 pages, 6 figures

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.

This paper reviews the state of knowledge in the field of optics, mainly in catoptrics and dioptrics, before the birth of modern science and the well-documented contributions of men such as Kepler and Newton. The paper is not intended to be a comprehensive survey of the subject such as one might find in history of science journals; instead, it is aimed at the curious physicist who has probably been taught that nothing much of note was understood about the behaviour of light, beyond outdated philosophical musings, prior to the seventeenth century. The paper will focus on advances during the medieval period between the ninth and fourteenth centuries, in both the east and the west, when the theories of the Ancient Greeks were tested, advanced, corrected and mathematised. In particular, it concentrates on a multivolume treatise on optics written one thousand years ago by the Arab scholar, Ibn al-Haytham, and examines how it influenced our understanding of the nature of reflection and refraction of light. Even...

Quantum physicist and broadcaster Jim Al-Khalili on oil painting, the nature of space-time and why he once wanted to play football for Leeds United

Jim Al-Khalili describes the new experiments and theories exploring whether quantum tunnelling of hydrogen causes mutations in our DNA.

There are more than a billion Muslims in the world today – over a fifth of the world's total population – spread over many more than the 57 member states of the Organisation of the Islamic Conference (OIC) in which Islam is the official religion. These include some of the world's wealthiest nations, such as Saudi Arabia and Kuwait, as well as some of the poorest, like Somalia and Sudan. The economies of some of these countries – such as the Gulf States, Iran, Turkey, Egypt, Morocco, Malaysia and Pakistan – have been growing steadily for a number of years, and yet, in comparison with the West, the Islamic world still appears somewhat disengaged from modern science.

The 18 C spectrum has been studied in a three body n + n + 16 C model that includes deformation and the 2 + excitation of the 16 C core as well as Pauli projection of forbidden states. The 16 C − n interaction employed in this study has been fitted to reproduce the experimental spectrum of 17 C. The calculations show that two neutron separation energy in 18 C in consistent with three-body structure of this nucleus and predict more states bound with respect to three-body decay. The comparison of their position to known excited states in 18 C is discussed. These calculations suggest also that a few states may exist in astrophysically relevant region between the 17 C + n and 16 C + 2n decay thresholds. The most important of them is 1 − as it can give a large E1 resonant contribution to 17 C(n ,γ) 18 C neutron capture. The calculations also suggest that a virtual s-wave state may exist above the 17 C+n threshold that can give rise to non-negligible M1 contributions to the 17 C(n ,γ) 18 C reaction rate. The presence of these states in the 18 C spectrum can lead to an increased 17 C(n ,γ) 18 C reaction rate, which can significantly influence the abundances of uranium and thorium synthesized in the r -process in the supernovae explosions.

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.

WOS: 000240847400007, The observation of the new nuclide Re-159(75)84 provides important insights into the evolution of single-particle structure and the mass surface in heavy nuclei beyond the proton drip line. This nuclide, 26 neutrons away from the nearest stable rhenium isotope, was synthesised in the reaction Cd-106(Ni-58, p4n) and identified via its proton radioactivity using the RITU gas-filled separator and the GREAT focal-plane spectrometer. Comparisons of the measured proton energy (E-p = 1805 +/- 20 keV) and decay half-life (t(1/2) = 21 +/- 4 mu s) with values calculated using the WKB method indicate that the proton is emitted from an h(11/2) state. The implications of these results for future experimental investigations into even more proton unbound nuclei using in-flight separation techniques are considered. (c) 2006 Elsevier B.V. All rights reserved., Science and Technology Facilities Council [EP/C543157/1, EP/C015371/1, EP/C015266/1, ST/G008671/1]

To many people outside our field, both scientists and the general public, nuclear physics is no longer regarded as being at the forefront of scientific endeavour. Indeed it is often met with outright hostility. Other physicists will point out that the last time a Nobel Prize was awarded in the field was in 1975 1 . This paper, based on a lecture delivered during an Open Plenary Session of the recent International Nuclear Physics Conference INPC2004, which was aimed at a non-specialist audience, will seek to dispel this myth. Nuclear physics is currently enjoying a period of rapid advances. Many new discoveries have been made in the past few years, from neutron halos and nuclear molecules to a new form of radioactive decay via two protons; from hints of a new particle consisting of five quarks to new 'superheavy' elements. This talk will give a personal perspective on why, far from looking with envy at our neighbours in areas of physics that currently enjoy a higher media profile, we have more than enough to keep us busy and excited in the 21st century.

A quark-model framework for studying nuclear medium effects on nucleon resonances is described and applied here to pion photoproduction on the deuteron, which is the simplest composite nucleon system and serves as a first test case. Pion photoproduction on nuclei is discussed within a chiral constituent quark model in which the quark degrees of freedom are explicitly introduced through an effective chiral Lagrangian for the quark-pseudoscalar-meson coupling. The advantage of this model is that a complete set of nucleon resonances can be systematically included with a limited number of parameters. Also, the systematic description of the nucleon and its resonances at quark level allows us to self-consistently relate the nuclear medium's influence on the baryon properties to the intrinsic dynamic aspects of the baryons. As the simplest composite nucleus, the deuteron represents the first application of this effective theory for meson photoproduction on light nuclei. The influence of the medium on the transition operators for a free nucleon is investigated in the Delta resonance region. No evidence is found for a change of the Delta properties in the pion photoproduction reaction on the deuteron since the nuclear medium here involves just one other nucleon and the low binding energy implies low nuclear density. However, we show that the reaction mechanism is in principle sensitive to changes of Delta properties that would be produced by the denser nuclear medium of heavier nuclei through the modification of the quark model parameters., Revtex, 8 pages, 4 figures

The Wallace Fourier-Bessel expansion of the scattering amplitude is generalised to the case of the scattering of a spin-one particle from a potential with a single tensor coupling as well as central and spin-orbit terms. A generating function for the eikonal-phase (quantum) corrections is evaluated in closed form. For medium-energy deuteron-nucleus scattering, the first-order correction is dominant and is shown to be significant in the interpretation of analysing power measurements. This conclusion is supported by a numerical comparison of the eikonal observables, evaluated with and without corrections, with those obtained from a numerical resolution of the Schrodinger equation for d-58 Ni scattering at incident deuteron energies of 400 and 700 MeV.

While many physicists regard the subject of time travel as having no place in serious scientific discussion and teaching, I will show that, on the contrary, this is just the topic to fire the imagination, and it provides an ideal opportunity to introduce some of the ideas behind our most beautiful and fundamental theories about the nature of space and time. The mathematics, if and when required, can be made simple to follow, and the logical steps in the explanations are, while counter-intuitive, perfectly straightforward.

Halo nuclei are characterised by their weak binding, large spatial extent and hence a quite pronounced, yet highly correlated, few-body structure. This is typically in terms of a well-defined core plus one or more valence nucleons. Over the past decade the properties of halo nuclei have been studied theoretically using a range of reaction models, many of which having served us well for half a century or more in the study of less exotic, “mean-field”, nuclei. However, it is now clear that for many reactions with halo nuclei, it is not appropriate to disentangle (factorise out) the structure information from the reaction information. That is, the few-body nature of these systems requires few-body reaction models in which the nuclear structure and reaction mechanisms are necessarily entangled. This talk will briefly review the physical assumptions made by various reaction models, and point to areas where progress is being made to extend their range of applicability in order to provide further insights into halo structure.