The Decoherent Arrow of Time and the Entanglement Past Hypothesis.

If an asymmetry in time does not arise from the fundamental dynamical laws of physics, it may be found in special boundary conditions. The argument normally goes that since thermodynamic entropy in the past is lower than in the future according to the Second Law of Thermodynamics, then tracing this back to the time around the Big Bang means the universe must have started off in a state of very low thermodynamic entropy: the Thermodynamic Past Hypothesis. In this paper, we consider another boundary condition that plays a similar role, but for the decoherent arrow of time, i.e. the subsystems of the universe are more mixed in the future than in the past. According to what we call the Entanglement Past Hypothesis, the initial quantum state of the universe had very low entanglement entropy. We clarify the content of the Entanglement Past Hypothesis, compare it with the Thermodynamic Past Hypothesis, and identify some challenges and open questions for future research.

Multiscale simulations reveal the role of PcrA helicase in protecting against spontaneous point mutations in DNA.

Proton transfer across hydrogen bonds in DNA can produce non-canonical nucleobase dimers and is a possible source of single-point mutations when these forms mismatch under replication. Previous computational studies have revealed this process to be energetically feasible for the guanine-cytosine (GC) base pair, but the tautomeric product (G[Formula: see text]C[Formula: see text]) is short-lived. In this work we reveal, for the first time, the direct effect of the replisome enzymes on proton transfer, rectifying the shortcomings of existing models. Multi-scale quantum mechanical/molecular dynamics (QM/MM) simulations reveal the effect of the bacterial PcrA Helicase on the double proton transfer in the GC base pair. It is shown that the local protein environment drastically increases the activation and reaction energies for the double proton transfer, modifying the tautomeric equilibrium. We propose a regime in which the proton transfer is dominated by tunnelling, taking place instantaneously and without atomic rearrangement of the local environment. In this paradigm, we can reconcile the metastable nature of the tautomer and show that ensemble averaging methods obscure detail in the reaction profile. Our results highlight the importance of explicit environmental models and suggest that asparagine N624 serves a secondary function of reducing spontaneous mutations in PcrA Helicase.

Tautomerisation Mechanisms in the Adenine-Thymine Nucleobase Pair during DNA Strand Separation.

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 time scales and dynamics of DNA strand separation and the 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 tautomerization reaction. We propose that DNA strand separation allows the stable tautomerization of adenine-thymine, providing a feasible pathway for genetic point mutations via proton transfer between the A-T bases.

Quantum Tunnelling Effects in the Guanine-Thymine Wobble Misincorporation via Tautomerism.

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.

Proton transfer during DNA strand separation as a source of mutagenic guanine-cytosine tautomers.

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.

Reaching out.

In the midst of the COVID-19 pandemic, science is crucial to inform public policy. At the same time, mistrust of scientists and misinformation about scientific facts are rampant. Six scientists, actively involved in outreach, reflect on how to build a better understanding and trust of science.

The origins of quantum biology.

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.

The birth of the electric machines: a commentary on Faraday (1832) 'Experimental researches in electricity'.

The history of science is filled with examples of key discoveries and breakthroughs that have been published as landmark texts or journal papers, and to which one can trace the origins of whole disciplines. Such paradigm-shifting publications include Copernicus' De revolutionibus orbium coelestium (1543), Isaac Newton's Philosophiæ Naturalis Principia Mathematica (1687) and Albert Einstein's papers on relativity (1905 and 1915). Michael Faraday's 1832 paper on electromagnetic induction sits proudly among these works and in a sense can be regarded as having an almost immediate effect in transforming our world in a very real sense more than any of the others listed. Here we review the status of the subject-the relationship between magnetism and electricity both before and after Faraday's paper and delve into the details of the key experiments he carried out at the Royal Institution outlining clearly how he discovered the process of electromagnetic induction, whereby an electric current could be induced to flow through a conductor that experiences a changing magnetic field. His ideas would not only enable Maxwell's later development of his theory of classical electromagnetism, but would directly lead to the development of the electric dynamo and electric motor, two technological advances that are the very foundations of the modern world. This commentary was written to celebrate the 350th anniversary of the journal Philosophical Transactions of the Royal Society.