Investigating proton tunneling dynamics in the time-dependent Schrödinger equation

Understanding the temporal evolution of the wave function in the proton tunneling reactions allows us to make theoretical predictions on the possible femtosecond spectroscopy patterns. However, the analytical solution of the time-dependent Schrödinger equation of complex molecules is challenging and requires a high computational cost. In this study, we solve the time-dependent Schrödinger equation using the Fourier grid Hamiltonian method, highlighting its simplicity of calculation, even for multidimensional tunneling reactions. The obtained model is applied to studying malonaldehyde's two-dimensional intramolecular proton tunneling, comparing the results with those obtained using other computational methods.

New classifications for quantum bioinformatics: Q-bioinformatics, QCt-bioinformatics, QCg-bioinformatics, and QCr-bioinformatics

Bioinformatics has revolutionized biology and medicine by using computational methods to analyze and interpret biological data. Quantum mechanics has recently emerged as a promising tool for the analysis of biological systems, leading to the development of quantum bioinformatics. This new field employs the principles of quantum mechanics, quantum algorithms, and quantum computing to solve complex problems in molecular biology, drug design, and protein folding. However, the intersection of bioinformatics, biology, and quantum mechanics presents unique challenges. One significant challenge is the possibility of confusion among scientists between quantum bioinformatics and quantum biology, which have similar goals and concepts. Additionally, the diverse calculations in each field make it difficult to establish boundaries and identify purely quantum effects from other factors that may affect biological processes. This review provides an overview of the concepts of quantum biology and quantum mechanics and their intersection in quantum bioinformatics. We examine the challenges and unique features of this field and propose a classification of quantum bioinformatics to promote interdisciplinary collaboration and accelerate progress. By unlocking the full potential of quantum bioinformatics, this review aims to contribute to our understanding of quantum mechanics in biological systems.

Study of entanglement via a multi-agent dynamical quantum game

At both conceptual and applied levels, quantum physics provides new opportunities as well as fundamental limitations. We hypothetically ask whether quantum games inspired by population dynamics can benefit from unique features of quantum mechanics such as entanglement and nonlocality. For doing so, we extend quantum game theory and demonstrate that in certain models inspired by ecological systems where several predators feed on the same prey, the strength of quantum entanglement between the various species has a profound effect on the asymptotic behavior of the system. For example, if there are sufficiently many predator species who are all equally correlated with their prey, they are all driven to extinction. Our results are derived in two ways: by analyzing the asymptotic dynamics of the system, and also by modeling the system as a quantum correlation network. The latter approach enables us to apply various tools from classical network theory in the above quantum scenarios. Several generalizations and applications are discussed.

Dehydrogenation versus deprotonation of disaccharide molecules in vacuum: a thorough theoretical investigation

Dehydrogenation and deprotonation of sucrose and trehalose molecules in vacuum is theoretically studied by using ab initio calculations in the framework of the density functional theory. The differences in the structural, electronic, energetic and vibrational properties of dehydrogenated and deprotonated molecules are discussed, depending on the site from which the hydrogen atom or the proton has been removed. The dehydrogenated molecules are found to be stable, regardless of which hydrogen atom is removed. This contrasts with the instability of the deprotonated molecules, where break-ups or structural reorganizations of the molecule are observed in 20-30% of the cases, but only when the hydrogen atom whose proton is removed was bonded to a carbon atom. Considering the stability and possible rearrangements of the hydrogen network of the deprotonated/dehydrogenated molecule, the formation of additional hydrogen-bridge bonds compared with the nominal molecule appears to be more pronounced for the deprotonated molecules than for the dehydrogenated ones. Moreover, our calculations show that the hydrogen-transfer energy barriers are usually larger for the deprotonated molecules than for the dehydrogenated ones. Finally, compared with the nominal molecule, the vibrational frequency spectrum is shifted to lower frequencies for both the dehydrogenated and the deprotonated molecules.

Petkov P, Milenov TI, Vayssilov GN. Sodium and Magnesium Ion Location at the Backbone and at the Nucleobase of RNA: Ab Initio Molecular Dynamics in Water Solution

The interactions between Na⁺ or Mg²⁺ ions with different parts of single-stranded RNA molecules, namely, the oxygen atoms from the phosphate groups or the guanine base, in water solution have been studied using first-principles molecular dynamics. Sodium ions were found to be much more mobile than Mg²⁺ ions and readily underwent transitions between a state directly bonded to RNA oxygen atoms and a completely solvated state. The inner solvation shell of Na⁺ ions fluctuated stochastically at a femtosecond timescale coordinating on average 5 oxygen atoms for bonded Na⁺ ions and 5.5 oxygen atoms for solvated Na⁺ ions. In contrast, the inner solvation shell of Mg²⁺ ions was stable in both RNA-bonded and completely solvated states. In both cases, Mg²⁺ ions coordinated 6 oxygen atoms from the inner solvation shell. Consistent with their stable solvation shells, Mg²⁺ ions were more effective than Na⁺ ions in stabilizing the RNA backbone conformation. The exclusion zones between the first and second solvation shells, solvation shell widths, and angles for binding to carbonyl oxygen of guanine for solvated Na⁺ or Mg²⁺ ions exhibited a number of quantitative differences when compared with RNA crystallographic data. The presented results support the distinct capacity of Mg²⁺ ions to support the RNA structure not only in the crystal phase but also in the dynamic water environment both on the side of the phosphate moiety and on the side of the nucleobase.

Chronobiology Meets Quantum Biology: A New Paradigm Overlooking the Horizon?

Biological processes and physiological functions in living beings are featured by oscillations with a period of about 24 h (circadian) or cycle at the second and third harmonic (ultradian) of the basic frequency, driven by the biological clock. This molecular mechanism, common to all kingdoms of life, comprising animals, plants, fungi, bacteria, and protists, represents an undoubted adaptive advantage allowing anticipation of predictable changes in the environmental niche or of the interior milieu. Biological rhythms are the field of study of Chronobiology. In the last decade, growing evidence hints that molecular platforms holding up non-trivial quantum phenomena, including entanglement, coherence, superposition and tunnelling, bona fide evolved in biosystems. Quantum effects have been mainly implicated in processes related to electromagnetic radiation in the spectrum of visible light and ultraviolet rays, such as photosynthesis, photoreception, magnetoreception, DNA mutation, and not light related such as mitochondrial respiration and enzymatic activity. Quantum effects in biological systems are the field of study of Quantum Biology. Rhythmic changes at the level of gene expression, as well as protein quantity and subcellular distribution, confer temporal features to the molecular platform hosting electrochemical processes and non-trivial quantum phenomena. Precisely, a huge amount of molecules plying scaffold to quantum effects show rhythmic level fluctuations and this biophysical model implies that timescales of biomolecular dynamics could impinge on quantum mechanics biofunctional role. The study of quantum phenomena in biological cycles proposes a profitable “entanglement” between the areas of interest of these seemingly distant scientific disciplines to enlighten functional roles for quantum effects in rhythmic biosystems.

Emergence of correlated proton tunnelling in water ice

Several experimental and theoretical studies report instances of concerted or correlated multiple proton tunnelling in solid phases of water. Here, we construct a pseudo-spin model for the quantum motion of protons in a hexameric H₂O ring and extend it to open system dynamics that takes environmental effects into account in the form of O-H stretch vibrations. We approach the problem of correlations in tunnelling using quantum information theory in a departure from previous studies. Our formalism enables us to quantify the coherent proton mobility around the hexagonal ring by one of the principal measures of coherence, the l ₁ norm of coherence. The nature of the pairwise pseudo-spin correlations underlying the overall mobility is further investigated within this formalism. We show that the classical correlations of the individual quantum tunnelling events in long-time limit is sufficient to capture the behaviour of coherent proton mobility observed in low-temperature experiments. We conclude that long-range intra-ring interactions do not appear to be a necessary condition for correlated proton tunnelling in water ice.