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Surfaces, Microstructure and Fracture Group

Thu 26 Jan 15:00: Quantum tunnelling effects in the guanine-thymine wobble misincorporation via tautomerism

Seminars - Tue, 24/01/2023 - 15:32
Quantum tunnelling effects in the guanine-thymine wobble misincorporation via tautomerism

DNA polymerase is an enzyme that catalyzes the synthesis of DNA molecules by matching complementary deoxyribonucleoside triphosphates (dNTP) to the template DNA strand using the standard Watson–Crick base pair rules. However, when a noncomplementary dNTP diffuses into the active site during the polymerase dNTP sampling, the polymerase domain will transition from an open to an ajar conformation, thus forming a different nonstandard hydrogen-bonded base-pairing arrangement called wobble mispair [1]. While there are other sources of replication errors, the fidelity of replication primarily depends on the ability of polymerases to select and incorporate the correct complementary base [2].

Consequently, misincorporating a noncomplementary DNA base in the polymerase active site is a critical source of replication errors that can lead to genetic mutations [3]. In this work [4], 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 [5]. 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.

References

[1] Wang, W., Hellinga, H. W., & Beese, L. S. (2011). Proceedings of the National Academy of Sciences, 108(43), 17644-17648.

[2] Kimsey, I. J., Szymanski, E. S., Zahurancik, W. J., Shakya, A., Xue, Y., Chu, C. C., ... & Al-Hashimi, H. M. (2018). Nature, 554(7691), 195-201.

[3] Li, P., Rangadurai, A., Al-Hashimi, H. M., & Hammes-Schiffer, S. (2020). Journal of the American Chemical Society, 142(25), 11183-11191.

[4] Slocombe, L., Winokan, M., Al-Khalili, J., & Sacchi, M. (2022). The Journal of Physical Chemistry Letters, 14, 9-15.

[5] Slocombe, L., Sacchi, M., & Al-Khalili, J. (2022). Communications Physics, 5(1), 1-9.

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Thu 26 Jan 15:00: Quantum rate theory and proton tunnelling in DNA

Seminars - Mon, 23/01/2023 - 13:01
Quantum rate theory and proton tunnelling in DNA

Abstract not available

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Thu 02 Mar 15:00: Keeping up the pressure

Seminars - Thu, 12/01/2023 - 17:49
Keeping up the pressure

An overview of the high-pressure techniques in Moissanite and diamond anvil cells used to study transport and magnetic phase transitions in strongly correlated systems. These cells are used for ac-susceptibility, DC-magnetisation, TDO , and resistivity measurements, including pressure induced superconductivity and metal-insulator transitions.

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Thu 23 Feb 15:00: The formation of contrast in scanning helium microscopy

Seminars - Tue, 10/01/2023 - 20:21
The formation of contrast in scanning helium microscopy

Over the last decade a new microscopy technique has emerged that uses neutral helium atoms as the probe particles. It has been termed scanning helium microscopy (SHeM), also known as neutral atom microscopy (NAM). SHeM produces helium atom micrographs by scanning the sample beneath a focused or collimated helium microprobe. As the technique is maturing, research efforts are moving on from the development of proof of concept instruments to the exploring of applications and optimising designs for the second generation of machine. In particular the mechanisms of contrast formation in SHeM are an active area of investigation.

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Thu 02 Mar 15:00: High pressure physics

Seminars - Fri, 06/01/2023 - 10:57
High pressure physics

Abstract not available

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Thu 23 Feb 15:00: Title to be confirmed

Seminars - Fri, 06/01/2023 - 10:56
Title to be confirmed

Abstract not available

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Thu 02 Mar 15:00: Title to be confirmed

Seminars - Fri, 09/12/2022 - 17:57
Title to be confirmed

Abstract not available

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Thu 09 Mar 15:00: Ultrafast diffusion at the onset of 2D growth: O/Ru(0001) and S/Ni(111)

Seminars - Mon, 14/11/2022 - 16:36
Ultrafast diffusion at the onset of 2D growth: O/Ru(0001) and S/Ni(111)

The mechanisms that underpin growth at surfaces are of increasing interest as 2D materials are explored for applications. Here, I present an experimental study of clustering dynamics observed during ultrafast surface motion, measured using helium-3 spin echo (HeSE) spectroscopy. I will discuss two systems that exhibit islanding phenomena, namely O/Ru(0001) and S/Ni(111); each is measured at high temperatures, corresponding to picosecond-timescale diffusion which has been inaccessible using past techniques

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Thu 09 Feb 15:00: Experimental and numerical study of detonation reaction zones

Seminars - Wed, 09/11/2022 - 10:59
Experimental and numerical study of detonation reaction zones

The chemical reaction zone is the region in a detonating explosive between the initial pressure spike and the sonic locus. Its length is affected by the properties of the explosive, and in some circumstances is difficult to determine experimentally. The reaction zone of one explosive (PETN) was measured using a capacitative sensing technique, and the results were used to develop a reactive hydrocode.

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Thu 17 Nov 15:00: Fundamentals of thermodynamics (and a bit of quantum mechanics)

Seminars - Wed, 26/10/2022 - 17:38
Fundamentals of thermodynamics (and a bit of quantum mechanics)

Five years ago I attempted to talk about a somewhat new approach to thermodynamics at an SMF seminar. This seminar is aimed are presenting ‘round 2’ where hopefully some of the key arguments are clarified. Given thermodynamics is based on the quantum mechanical behaviour of the world, one ends up looking at the fundamental principles of QM for ‘the reason why’, and this seminar proposes a way of approaching the basis of QM that just starts from the notion that there are waves that obey linear superposition and that there is a time development operator.

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