Quantum effects in biology: golden rule in enzymes, olfaction, photosynthesis and magnetodetection

Persistence of Correlations in Neurotransmitter Transport through the Synaptic Cleft

The "quantum brain" proposal can revolutionize our understanding of cognition if proven valid. The core of the most common "quantum brain" mechanism is the appearance of correlated neuron triggering induced by quantum correlations between ions. In this work, we examine the preservation of the correlations created in the pre-synaptic neurons through the transfer of neurotransmitters across the synaptic cleft, a critical ingredient for the validity of the "quantum brain" hypothesis. We simulated the transport of two neurotransmitters at two different clefts, with the only assumption that they start simultaneously, and determined the difference in their first passage times. We show that in physiological conditions, the correlations are persistent even if the parameters of the two neurons are different.

The complexities of ligand/receptor interactions: Exploring the role of molecular vibrations and quantum tunnelling

Molecular vibrations and quantum tunneling may link ligand binding to the function of pharmacological receptors. The well-established lock-and-key model explains a ligand's binding and recognition by a receptor; however, a general mechanism by which receptors translate binding into activation, inactivation, or modulation remains elusive. The Vibration Theory of Olfaction was proposed in the 1930s to explain this subset of receptor-mediated phenomena by correlating odorant molecular vibrations to smell, but a mechanism was lacking. In the 1990s, inelastic electron tunneling was proposed as a plausible mechanism for translating molecular vibration to odorant physiology. More recently, studies of ligands' vibrational spectra and the use of deuterated ligand analogs have provided helpful information to study this admittedly controversial hypothesis in metabotropic receptors other than olfactory receptors. In the present work, based in part on published experiments from our laboratory using planarians as an experimental organism, I will present a rationale and possible experimental approach for extending this idea to ligand-gated ion channels.

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.

Accelerating an integrative view of quantum biology

Quantum biology studies span multiple disciplines including physics, engineering, and biology with the goal of understanding the quantum underpinnings of living systems. Recent findings have brought wide attention to the role of quantum mechanisms in the function and regulation of biological processes. Moreover, a number of activities have been integral in building a vibrant quantum biology community. Due to the inherent interdisciplinary nature of the field, it is a challenge for quantum biology researchers to integrate and advance findings across the physical and biological disciplines. Here we outline achievable approaches to developing a shared platform-including the establishment of standardized manipulation tools and sensors, and a common scientific lexicon. Building a shared community framework is also crucial for fostering robust interdisciplinary collaborations, enhancing knowledge sharing, and diversifying participation in quantum biology. A unified approach promises not only to deepen our understanding of biological systems at a quantum level but also to accelerate the frontiers of medical and technological innovations.

Isotope effects on radical pair performance in cryptochrome: A new hypothesis for the evolution of animal migration: The quantum biology of migration

Mechanisms occurring at the atomic level are now known to drive processes essential for life, as revealed by quantum effects on biochemical reactions. Some macroscopic characteristics of organisms may thus show an atomic imprint, which may be transferred across organisms and affect their evolution. This possibility is considered here for the first time, with the aim of elucidating the appearance of an animal innovation with an unclear evolutionary origin: migratory behaviour. This trait may be mediated by a radical pair (RP) mechanism in the retinal flavoprotein cryptochrome, providing essential magnetic orientation for migration. Isotopes may affect the performance of quantum processes through their nuclear spin. Here, we consider a simple model and then apply the standard open quantum system approach to the spin dynamics of cryptochrome RP. We changed the spin quantum number (I) and g-factor of hydrogen and nitrogen isotopes to investigate their effect on RP's yield and magnetic sensitivity. Strong differences arose between isotopes with I = 1 and I = 1/2 in their contribution to cryptochrome magnetic sensitivity, particularly regarding Earth's magnetic field strengths (25-65 µT). In most cases, isotopic substitution improved RP's magnetic sensitivity. Migratory behaviour may thus have been favoured in animals with certain isotopic compositions of cryptochrome.

Converting genetic information to non-equilibrium cellular thermodynamics in enzyme-catalyzed reactions

Living systems use genomic information to maintain a stable highly ordered state far from thermodynamic equilibrium but the specific mechanisms and general principles governing the interface of genetics and thermodynamics has not been extensively investigated. Genetic information is quantified in unitless bits termed "Shannon entropy", which does not directly relate to thermodynamic entropy or energy. Thus, it is unclear how the Shannon entropy of genetic information is converted into thermodynamic work necessary to maintain the non-equilibrium state of living systems. Here we investigate the interface of genetic information and cellular thermodynamics in enzymatic acceleration of a chemical reaction S + E → E S → E + P , where S and E are substrate and enzyme, E S is the enzyme substrate complex and P product. The rate of any intracellular chemical reaction is determined by probability functions at macroscopic (Boltzmann distribution of the reactant kinetic energies governed by temperature) or microscopic (overlap of reactant quantum wave functions) scales - described, respectively, by the Arrhenius and Knudsen equations. That is, the reaction rate, in the absence of a catalyst, is governed by temperature which determines the kinetic energy of the interacting molecules. Genetic information can act upon a when the encoded string of amino acids folds into a 3-deminsional structure that permits a lock/key spatial matching with the reactants. By optimally superposing the reactants' wave functions, the information in the enzyme increases the reaction rate by up to15 orders of magnitude under isothermal conditions. In turn, the accelerated reaction rate alters the intracellular thermodynamics environment as the products are at lower Gibbs free energy which permits thermodynamic work W m a x = - Δ G . Mathematically and biologically, the critical event that allows genetic information to produce thermodynamic work is the folding of the amino acid string specified by the gene into a 3-dimensional shape determined by its lowest energy state. Biologically, this allows the amino acid string to bind substrate and place them in an optimal spatial orientation. These key-lock are mathematically characterized by Kullback-Leibler Divergence and the interactions with the reaction channel now represent Fisher Information (the second derivative Kullback-Leibler divergence), which can take on the units of the process to which it is applied. Interestingly, Shannon is typically derived by "coarse graining" Shannon information. Thus, living system, by acting at a quantum level, "fine grain" Shannon information.

The isothermal Boltzmann-Gibbs entropy reduction affects survival of the fruit fly Drosophila melanogaster

To the best of our knowledge, this is the first experimental evidence of the effect of isothermal changes in entropy on a living organism. In greater detail, the effect of the reduction of the total Boltzmann-Gibbs entropy (S) of the aquatic environment on the survival rate and body mass of the fruit fly Drosophila melanogaster was investigated. The tests were carried out in standard thermodynamic states at room temperature of 296.15 K and ambient atmospheric pressure of 1 bar. Two variants of entropy reduction (ΔS) were tested for ΔS = 28.49 and 51.14 J K-1 mol-1 compared to the blind and control samples. The entropy level was experimentally changed, using the quantum system for isothermal entropy reduction. This system is based on quantum bound entanglement of phonons and the phenomenon of phonon resonance (interference of phonon modes) in condensed matter (Silicon dioxide (SiO2) and single crystals of Silicon (Si0), Aluminum (Al0) plates ("chips"), glass, and water). All studied organisms were of the same age (1 day). Mortality was observed daily until the natural death of the organisms. The investigations showed that changes in the Boltzmann-Gibbs entropy affected the survival and body mass of the fruit flies. On the one hand, the reduction in entropy under isothermal conditions in the aquatic environment for ΔS = 28.49 J K-1 mol-1 resulted in an extension of the lifespan and an increase in the body mass of female fruit flies. On the other hand, the almost twofold reduction in this entropy for ΔS = 51.14 J K-1 mol-1 shortened the lives of the males. Thus, the lifespan and body mass of flies turned out to be a specific reaction of metabolism related to changes in the entropy of the aquatic environment.

Nanotherapy based on magneto-mechanochemical modulation of tumor redox state

Magnetic nanoparticles (MNs) are typically used as contrast agents for magnetic resonance imaging or as drug carriers with a remotely controlled delivery to the tumor. However, they can also potentiate the action of anticancer drugs under the influence of applied constant magnetic (CMFs) and electromagnetic fields (EMFs). This review demonstrates the role of magneto-mechanochemical effects produced by MNs alone and loaded with anticancer agents (MNCs) in response to CMFs and EMFs for modulation of tumor redox state. The combined treatment is suggested to act by two mechanisms: spin-dependent electron transport propagates free radical chain reactions, while magnetomechanical interactions cause conformational changes in drug molecules loaded onto MNs and generate reactive oxygen species (ROS). By adjusting the parameters of CMFs and EMFs during the magneto-mechanochemical synthesis and subsequent treatment, it is possible to modulate ROS production and switch redox signaling involved in ERK1/2 and NF-κB pathways from initiation of tumor growth to inhibition. Observations of tumor volume in different animal models and treatment combinations reported a 6%-70% reduction as compared with conventional drugs. Despite these results, there is a general lack of research in magnetic nanotheranostics that link redox changes across multiple levels of organization in the tumor-bearing host. Further multidisciplinary studies with more focus on the relationship between the electron transport processes in biomolecules and their effects on the tumor-host interaction should accelerate the clinical translation of magnetic nanotheranostics. This article is categorized under: Therapeutic Approaches and Drug Discovery > Nanomedicine for Oncologic Disease Therapeutic Approaches and Drug Discovery > Emerging Technologies Nanotechnology Approaches to Biology > Nanoscale Systems in Biology.

When morphology does not fit the genomes: the case of rodent olfaction

Linking genes to phenotypes has been a major question in evolutionary biology for the last decades. In the genomic era, few studies attempted to link olfactory-related genes to different anatomical proxies. However, they found very inconsistent results. This study is the first to investigate a potential relation between olfactory turbinals and olfactory receptor (OR) genes. We demonstrated that despite the use of similar methodology in the acquisition of data, OR genes do not correlate with the relative and the absolute surface area of olfactory turbinals. These results challenged the interpretations of several studies based on different proxies related to olfaction and their potential relation to olfactory capabilities.

MiMiCPy: An Efficient Toolkit for MiMiC-Based QM/MM Simulations

MiMiC is a highly flexible, extremely scalable multiscale modeling framework. It couples the CPMD (quantum mechanics, QM) and GROMACS (molecular mechanics, MM) codes. The code requires preparing separate input files for the two programs with a selection of the QM region. This can be a tedious procedure prone to human error, especially when dealing with large QM regions. Here, we present MiMiCPy, a user-friendly tool that automatizes the preparation of MiMiC input files. It is written in Python 3 with an object-oriented approach. The main subcommand PrepQM can be used to generate MiMiC inputs directly from the command line or through a PyMOL/VMD plugin for visually selecting the QM region. Many other subcommands are also provided for debugging and fixing MiMiC input files. MiMiCPy is designed with a modular structure that allows seamless extensions to new program formats depending on the requirements of MiMiC.

Microtubules as a potential platform for energy transfer in biological systems: a target for implementing individualized, dynamic variability patterns to improve organ function

Variability characterizes the complexity of biological systems and is essential for their function. Microtubules (MTs) play a role in structural integrity, cell motility, material transport, and force generation during mitosis, and dynamic instability exemplifies the variability in the proper function of MTs. MTs are a platform for energy transfer in cells. The dynamic instability of MTs manifests itself by the coexistence of growth and shortening, or polymerization and depolymerization. It results from a balance between attractive and repulsive forces between tubulin dimers. The paper reviews the current data on MTs and their potential roles as energy-transfer cellular structures and presents how variability can improve the function of biological systems in an individualized manner. The paper presents the option for targeting MTs to trigger dynamic improvement in cell plasticity, regulate energy transfer, and possibly control quantum effects in biological systems. The described system quantifies MT-dependent variability patterns combined with additional personalized signatures to improve organ function in a subject-tailored manner. The platform can regulate the use of MT-targeting drugs to improve the response to chronic therapies. Ongoing trials test the effects of this platform on various disorders.

From the origins to the stream of consciousness and its neural correlates

There are now dozens of very different theories of consciousness, each somehow contributing to our understanding of its nature. The science of consciousness needs therefore not new theories but a general framework integrating insights from those, yet not making it a still-born "Frankenstein" theory. First, the framework must operate explicitly on the stream of consciousness, not on its static description. Second, this dynamical account must also be put on the evolutionary timeline to explain the origins of consciousness. The Cognitive Evolution Theory (CET), outlined here, proposes such a framework. This starts with the assumption that brains have primarily evolved as volitional subsystems of organisms, inherited from primitive (fast and random) reflexes of simplest neural networks, only then resembling error-minimizing prediction machines. CET adopts the tools of critical dynamics to account for metastability, scale-free avalanches, and self-organization which are all intrinsic to brain dynamics. This formalizes the stream of consciousness as a discrete (transitive, irreflexive) chain of momentary states derived from critical brain dynamics at points of phase transitions and mapped then onto a state space as neural correlates of a particular conscious state. The continuous/discrete dichotomy appears naturally between the brain dynamics at the causal level and conscious states at the phenomenal level, each volitionally triggered from arousal centers of the brainstem and cognitively modulated by thalamocortical systems. Their objective observables can be entropy-based complexity measures, reflecting the transient level or quantity of consciousness at that moment.

Excited-state dynamics of all-trans protonated retinal Schiff base in CRABPII-based rhodopsin mimics

The rhodopsin mimic is a chemically synthetized complex with retinyl Schiff base (RSB) formed between protein and the retinal chromophore that can mimic the natural rhodopsin-like protein. The artificial rhodopsin mimic is more stable and designable than the natural protein and hence has wider uses in photon detection devices. The mimic structure RSB, like the case in the actual rhodopsin-like protein, undergoes isomerization and protonation throughout the photoreaction process. As a result, understanding the dynamics of the RSB in the photoreaction process is critical. In this study, the ultrafast transient absorption spectra of three mutants of the cellular retinoic acid-binding protein II-based rhodopsin mimic at acidic environment were recorded, from which the related excited-state dynamics of the all-trans protonated RSB (AT-PRSB) were investigated. The transient fluorescence spectra measurements are used to validate some of the dynamic features. We find that the excited-state dynamics of AT-PRSB in three mutants share a similar pattern that differs significantly from the dynamics of 15-cis PRSB of the rhodopsin mimic in neutral solution. By comparing the dynamics across the three mutants, we discovered that the aromatic residues near the β-ionone ring structure of the retinal may help stabilize the AT-PRSB and hence slow down its isomerization rate. The experimental results provide implications on designing a rhodopsin-like protein with significant infrared fluorescence, which can be particularly useful in the applications in biosensing or bioimaging in deeper tissues.

UVC radiation intensity dependence of pathogen decontamination rate: semiclassical theory and experiment

A semiclassical (light classical and molecule quantum) model describing the dependence of DNA/RNA dimerization rate as function of the ultraviolet C (UVC) radiation's intensity is proposed. Particularly, a nonlinear model is developed based on the Raman-like processes in quantum optics. The main result of the theory shows that the process of dimerization in the DNA/RNA depends strongly on the UVC light's intensity, thus proving a possible quantum microscopical mechanism of the interaction of UV light with the DNA. To corroborate the theoretical findings, we realize some experiments, by which want to investigate how the inactivation rate of the yeast colonies depends on the intensity of the UVC irradiation. The experimental results evidence a nonlinear decreasing of the residual yeast colonies as a function of the intensity in the irradiation process. The possibilities to optimize the intensity of UVC radiation in the considered decontamination equipment by using metamaterials are studied. The application of such equipment in disinfection of fluids (air, water, droplets, etc.), as well for the SARS-CoV-2-infected aerosols, is discussed.

Challenges and opportunities in quantum machine learning

At the intersection of machine learning and quantum computing, quantum machine learning has the potential of accelerating data analysis, especially for quantum data, with applications for quantum materials, biochemistry and high-energy physics. Nevertheless, challenges remain regarding the trainability of quantum machine learning models. Here we review current methods and applications for quantum machine learning. We highlight differences between quantum and classical machine learning, with a focus on quantum neural networks and quantum deep learning. Finally, we discuss opportunities for quantum advantage with quantum machine learning.

What is consciousness? Artificial intelligence, real intelligence, quantum mind and qualia

We approach the question ‘What is consciousness?’ in a new way, not as Descartes’ ‘systematic doubt’, but as how organisms find their way in their world. Finding one’s way involves finding possible uses of features of the world that might be beneficial or avoiding those that might be harmful. ‘Possible uses of X to accomplish Y’ are ‘affordances’. The number of uses of X is indefinite (or unknown), the different uses are unordered, are not listable, and are not deducible from one another. All biological adaptations are either affordances seized by heritable variation and selection or, far faster, by the organism acting in its world finding uses of X to accomplish Y. Based on this, we reach rather astonishing conclusions:

1. Artificial general intelligence based on universal Turing machines (UTMs) is not possible, since UTMs cannot ‘find’ novel affordances.

2. Brain-mind is not purely classical physics for no classical physics system can be an analogue computer whose dynamical behaviour can be isomorphic to ‘possible uses’.

3. Brain-mind must be partly quantum—supported by increasing evidence at 6.0 to 7.3 sigma.

4. Based on Heisenberg’s interpretation of the quantum state as ‘potentia’ converted to ‘actuals’ by measurement, where this interpretation is not a substance dualism, a natural hypothesis is that mind actualizes potentia. This is supported at 5.2 sigma. Then mind’s actualizations of entangled brain-mind-world states are experienced as qualia and allow ‘seeing’ or ‘perceiving’ of uses of X to accomplish Y. We can and do jury-rig. Computers cannot.

5. Beyond familiar quantum computers, we discuss the potentialities of trans-Turing systems.

Thermodynamic basis for comparative photobiomodulation dosing with multiple wavelengths to direct odontoblast differentiation

Multiple wavelength devices are now available for photobiomodulation (PBM) treatments, but their dosimetry for individual or combinatorial use remains unclear. The present work investigated the effects of 447, 532, 658, 810, 980 and 1064 nm wavelengths on odontoblast differentiation at 10 mW/cm² using either equal treatment time for conventional fluence (300 seconds for 3 J/cm² ) or varying times to adjust for individual wavelength photon fluence (4.6 p.J/cm² ). Both 447 and 810 nm significantly increased alkaline phosphatase (ALP) activity, while 1064 nm showed reduced ALP activity at 3 J/cm² . However, ALP induction was significantly improved when equivalent photon fluence dosing was used. Other wavelengths did not show significant changes compared to untreated controls. The data suggest that accounting for wavelength-specific photon energy transfer during PBM dosing could improve clinical safety and efficacy.

A free energy principle for generic quantum systems

The Free Energy Principle (FEP) states that under suitable conditions of weak coupling, random dynamical systems with sufficient degrees of freedom will behave so as to minimize an upper bound, formalized as a variational free energy, on surprisal (a.k.a., self-information). This upper bound can be read as a Bayesian prediction error. Equivalently, its negative is a lower bound on Bayesian model evidence (a.k.a., marginal likelihood). In short, certain random dynamical systems evince a kind of self-evidencing. Here, we reformulate the FEP in the formal setting of spacetime-background free, scale-free quantum information theory. We show how generic quantum systems can be regarded as observers, which with the standard freedom of choice assumption become agents capable of assigning semantics to observational outcomes. We show how such agents minimize Bayesian prediction error in environments characterized by uncertainty, insufficient learning, and quantum contextuality. We show that in its quantum-theoretic formulation, the FEP is asymptotically equivalent to the Principle of Unitarity. Based on these results, we suggest that biological systems employ quantum coherence as a computational resource and - implicitly - as a communication resource. We summarize a number of problems for future research, particularly involving the resources required for classical communication and for detecting and responding to quantum context switches.

Multiphonon processes of the inelastic electron transfer in olfaction

Inelastic electron transfer, regarded as one of the potential mechanisms to explain odorant recognition in atomic-scale processes, is still a matter of intense debate. Here, we study multiphonon processes of electron transfer using the Markvart model and calculate their lifetimes with the values of key parameters widely adopted in olfactory systems. We find that these multiphonon processes are as quick as the single phonon process, which suggests that contributions from different phonon modes of an odorant molecule should be included for electron transfer in olfaction. Meanwhile, the temperature dependence of electron transfer could be analyzed effectively based on the reorganization energy which is expanded into the linewidth of multiphonon processes. Our theoretical results not only enrich the knowledge of the mechanism of olfaction recognition, but also provide insights into quantum processes in biological systems.

Alzheimer's and Consciousness: How Much Subjectivity Is Objective?

Does Alzheimer Disease show a decline in cognitive functions that relate to the awareness of external reality? In this paper, we will propose a perspective that patients with increasing symptoms of AD show a change in the awareness of subjective versus objective representative axis of reality thus consequently move to a more internal like perception of reality. This paradigm shift suggests that new insights into the dynamicity of the conscious representation of reality in the AD brain may give us new clues to the very early signs of memory and self-awareness impairment that originates from, in our view the microtubules. Dialog between Adso and William, in Umberto Eco's The Name of the Rose, Third Day: Vespers. "But how does it happen," I said with admiration, "that you were able to solve the mystery of the library looking at it from the outside, and you were unable to solve it when you were inside?" "Thus, God knows the world, because He conceived it in His mind, as if it was from the outside, before it was created, and we do not know its rule, because we live inside it, having found it already made."

Photochemistry of phthalocyanine based on spin angular momenta: a kinetic study of fluorescent probes for ascorbic acid

Ascorbic acid, i.e., vitamin C, is a well-known essential nutrient, and has attracted considerable attention as a new candidate for cancer therapy. Previously, R2c consisting of silicon tetra-tert-butylphthalocyanine (SiPc) and two 2,2,6,6-tetramethyl-1-piperidinyloxy (TEMPO) radicals has been encapsulated into the hydrophobic cavity of dimeric bovine serum albumin (BSA), i.e., R2c@(BSA)2, and the system was found to behave as a highly sensitive and selective fluorescent probe for detecting ascorbic acid not only in aqueous solutions but also in vivo. In this study, kinetics of the reaction of R2c@(BSA)2 with ascorbic acid have been studied based on the temporal evolution of fluorescence. Global fitting of the concentration dependence using the Runge-Kutta method revealed the existence of stepwise two proton-coupled electron transfer processes. The rate constants for the reactions with ascorbic acid (k AA ) and ascorbate radical (k AR ) were 3 × 10 and 1 × 105 min−1 M−1, respectively, suggesting that the reaction with ascorbate radical was much faster than that with ascorbic acid. These results were further corroborated by theoretical calculations of the Gibbs free energy differences and by spin statistical factors. The analysis presented herein will aid in understanding the two proton-coupled electron transfer processes in the reaction with ascorbic acid.

Quantum energy levels of glutamate modulate neural biophotonic signals

Glutamate is the most abundant excitatory neurotransmitter in the brain, and it plays an essential and important role in neural functions. Current studies have shown that glutamate can induce neural biophotonic activity and transmission, which may involve the mechanism of photon quantum brain; however, it is unclear whether such a mechanism follows the principle of quantum mechanics. Here we show that the action of glutamate on its receptors leads to a decrease in its quantum energy levels, and glutamate then partially or completely loses its function to further induce the biophotonic activity in mouse brain slices. The reduced quantum energy levels of glutamate can be restored by direct-current electrical discharges and the use of energy transfer of chloroplast photosynthesis; hence, the quantum energy recovered glutamate can again induce significant biophotonic activity. Furthermore, the changes in quantum energy levels of glutamate are related to the exchange and transfer of electron energy on its active hydrogen atom. These findings suggest that the glutamate-induced neural biophotonic signals may be involved in the transfer of the quantum energy levels of glutamate, which implies a quantum mechanism of neurotransmitter action.

Influence of Water Polarization Caused by Phonon Resonance on Catalytic Activity of Enolase

Enolase is a conservative protein. Its cellular enzymatic activity catalyzes the conversion of 2-phospho-d-glycerate (2-PGA) to a phosphoenolpyruvate (PEP) product in the glycolysis pathway. This enzyme also has a multifunctional nature participating in several biological processes. This work aims to determine the effect of water polarization on the catalytic activity of enolase. The experiments have been set based on the concept that water, a polar dielectric, may undergo the phenomenon of electric polarization, decreasing its configurational and vibrational entropy. Prior to the reaction, the 2-PGA substrate was incubated for 5 h in the glass cuvette with an attached chip-inductor. The latter device was designed to transfer quantum information about a given quantum state from the quantum state generator to water by a phonon resonance. Then, such substrate samples preincubated with the chip-inductor were removed every hour in a separate quartz cuvette with the enzyme to determine its catalytic activity. The influence of the chip-inductor on the preincubated substrate resulted in an increase in the catalytic activity of enolase by 30% compared to the control substrate, not preincubated with the chip-inductor. This suggests that the catalytic activity of the enzyme is augmented when the substrate was primed by chip-inductors. In another kind of experiment, wherein enolase was exposed to methylglyoxal modification, the catalytic activity of the enzyme dropped to 71.7%, while the same enzyme glycated with methylglyoxal primed by chip-inductors restored its activity by 8.4%. This shows the protective effect of chip-inductors on enolase activity despite the harmful effect of methylglyoxal on the protein.

Quantum aspects of evolution: a contribution towards evolutionary explorations of genotype networks via quantum walks

Quantum biology seeks to explain biological phenomena via quantum mechanisms, such as enzyme reaction rates via tunnelling and photosynthesis energy efficiency via coherent superposition of states. However, less effort has been devoted to study the role of quantum mechanisms in biological evolution. In this paper, we used transcription factor networks with two and four different phenotypes, and used classical random walks (CRW) and quantum walks (QW) to compare network search behaviour and efficiency at finding novel phenotypes between CRW and QW. In the network with two phenotypes, at temporal scales comparable to decoherence time TD, QW are as efficient as CRW at finding new phenotypes. In the case of the network with four phenotypes, the QW had a higher probability of mutating to a novel phenotype than the CRW, regardless of the number of mutational steps (i.e. 1, 2 or 3) away from the new phenotype. Before quantum decoherence, the QW probabilities become higher turning the QW effectively more efficient than CRW at finding novel phenotypes under different starting conditions. Thus, our results warrant further exploration of the QW under more realistic network scenarios (i.e. larger genotype networks) in both closed and open systems (e.g. by considering Lindblad terms).

Intra- and intermolecular atomic-scale interactions in the receptor binding domain of SARS-CoV-2 spike protein: implication for ACE2 receptor binding

The COVID-19 pandemic poses a severe threat to human health with unprecedented social and economic disruption. Spike (S) glycoprotein in the SARS-CoV-2 virus is pivotal in understanding the virus anatomy, since it initiates the early contact with the ACE2 receptor in the human cell. The subunit S1 in chain A of S-protein has four structural domains: the receptor binding domain (RBD), the n-terminal domain (NTD) and two subdomains (SD1, SD2). We report details of the intra- and inter-molecular binding mechanism of RBD using density functional theory, including electronic structure, interatomic bonding and partial charge distribution. We identify five strong hydrogen bonds and analyze their roles in binding. This provides a pathway to a quantum-chemical understanding of the interaction between the S-protein and the ACE2 receptor with insights into the function of conserved features in the ACE2 receptor binding domain that could inform vaccine and drug development.

Consciousness as an Emergent Phenomenon: A Tale of Different Levels of Description

One of the biggest queries in cognitive sciences is the emergence of consciousness from matter. Modern neurobiological theories of consciousness propose that conscious experience is the result of interactions between large-scale neuronal networks in the brain, traditionally described within the realm of classical physics. Here, we propose a generalized connectionist framework in which the emergence of "conscious networks" is not exclusive of large brain areas, but can be identified in subcellular networks exhibiting nontrivial quantum phenomena. The essential feature of such networks is the existence of strong correlations in the system (classical or quantum coherence) and the presence of an optimal point at which the system's complexity and energy dissipation are maximized, whereas free-energy is minimized. This is expressed either by maximization of the information content in large scale functional networks or by achieving optimal efficiency through the quantum Goldilock effect.

Chemical Exchange at the Trinuclear Copper Center of Small Laccase from Streptomyces coelicolor

The trinuclear copper center (TNC) of laccase reduces oxygen to water with very little overpotential. The arrangement of the coppers and ligands in the TNC is known to be from many crystal structures, yet information about possible dynamics of the ligands is absent. Here, we report dynamics at the TNC of small laccase from Streptomyces coelicolor using paramagnetic NMR and electron paramagnetic resonance spectroscopy. Fermi contact-shifted resonances tentatively assigned to histidine Hδ1 display a two-state chemical exchange with exchange rates in the order of 100 s⁻¹. In the electron paramagnetic resonance spectra, at least two forms are observed with different g_z-values. It is proposed that the exchange processes reflect the rotational motion of histidine imidazole rings that coordinate the coppers in the TNC.

In light-sensitive drug delivery system nanoparticles mediate oxidative stress

In light-sensitive drug delivery systems, more and more nanoparticles were applied to load various drug molecules. However, few studies focused on their biomedical effects such as the regulation of heme oxygenase-1 (HO-1) expression and reactive oxygen species (ROS) generation which could influence cellular redox reaction. In the present article, through review of literature, analysis of high-throughput sequencing database, the mechanisms of drug delivery based on organic (poly-lactic-co-glycolic acid (PLGA) and polyethylene glycol (PEG)) and inorganic (Au, ZnO, SiO₂ and TiO₂) nanoparticles were introduced briefly. Besides, it was also expounded that nuclear factor-erythroid 2 (NF-E2)-related factor 2/BTB domain and CNC homolog 1 (Nrf2/Bach1) might be involved in the regulation of HO-1 and the quantum effect of photon altered ROS generation. The exogenous nanoparticles certainly have various biomedical effects that even affect the pathogenesis of some diseases like atopic dermatitis. Thus, biomedical effect of nanoparticles depends on HO-1/ROS needs further research.

The QBIT Theory of Consciousness

The QBIT theory is an attempt toward solving the problem of consciousness based on empirical evidence provided by various scientific disciplines including quantum mechanics, biology, information theory, and thermodynamics. This theory formulates the problem of consciousness in the following four questions, and provides preliminary answers for each question: Question 1: What is the nature of qualia?

ANSWER

A quale is a superdense pack of quantum information encoded in maximally entangled pure states. Question 2: How are qualia generated?

ANSWER

When a pack of quantum information is compressed beyond a certain threshold, a quale is generated. Question 3: Why are qualia subjective?

ANSWER

A quale is subjective because a pack of information encoded in maximally entangled pure states are essentially private and unshareable. Question 4: Why does a quale have a particular meaning?

ANSWER

A pack of information within a cognitive system gradually obtains a particular meaning as it undergoes a progressive process of interpretation performed by an internal model installed in the system. This paper introduces the QBIT theory of consciousness, and explains its basic assumptions and conjectures.

Quantum biology revisited

Photosynthesis is a highly optimized process from which valuable lessons can be learned about the operating principles in nature. Its primary steps involve energy transport operating near theoretical quantum limits in efficiency. Recently, extensive research was motivated by the hypothesis that nature used quantum coherences to direct energy transfer. This body of work, a cornerstone for the field of quantum biology, rests on the interpretation of small-amplitude oscillations in two-dimensional electronic spectra of photosynthetic complexes. This Review discusses recent work reexamining these claims and demonstrates that interexciton coherences are too short lived to have any functional significance in photosynthetic energy transfer. Instead, the observed long-lived coherences originate from impulsively excited vibrations, generally observed in femtosecond spectroscopy. These efforts, collectively, lead to a more detailed understanding of the quantum aspects of dissipation. Nature, rather than trying to avoid dissipation, exploits it via engineering of exciton-bath interaction to create efficient energy flow.

Exploring the mechanism of olfactory recognition in the initial stage by modeling the emission spectrum of electron transfer

Olfactory sense remains elusive regarding the primary reception mechanism. Some studies suggest that olfaction is a spectral sense, the olfactory event is triggered by electron transfer (ET) across the odorants at the active sites of odorant receptors (ORs). Herein we present a Donor-Bridge-Acceptor model, proposing that the ET process can be viewed as an electron hopping from the donor molecule to the odorant molecule (Bridge), then hopping off to the acceptor molecule, making the electronic state of the odorant molecule change along with vibrations (vibronic transition). The odorant specific parameter, Huang–Rhys factor can be derived from ab initio calculations, which make the simulation of ET spectra achievable. In this study, we revealed that the emission spectra (after Gaussian convolution) can be acted as odor characteristic spectra. Using the emission spectrum of ET, we were able to reasonably interpret the similar bitter-almond odors among hydrogen cyanide, benzaldehyde and nitrobenzene. In terms of isotope effects, we succeeded in explaining why subjects can easily distinguish cyclopentadecanone from its fully deuterated analogue cyclopentadecanone-d28 but not distinguishing acetophenone from acetophenone-d8.

The transformation of medical genetics by clinical genomics: hubris meets humility

There is no question that the advent of massively parallel ("next-generation") DNA sequencing has thrust Medical Genetics and Molecular Diagnostics into a new era, availing practitioners and patients of a form of genetic testing unprecedented in its scope and comprehensiveness. It has produced impressive diagnostic yield, ended the "diagnostic odyssey" for many patients and families, expanded the known phenotypes of countless disorders, and led to almost weekly new disease gene discoveries. Nevertheless, it still fails to identify the molecular cause of many patients who clearly exhibit genetic/syndromic conditions, while at the same time unmasking other sequence changes of uncertain significance or unexpected consequences. With over six years' experience in the clinical application of NGS, this seems an opportune time to take stock and face up honestly to how much we still do not know about genome action and, indeed, the DNA molecule itself. This review and assessment examines a number of residual deficiencies and misconceptions in clinical genomics, while daring to predict its future incorporation of other "-omics" approaches and even quantum phenomena in our unending quest to understand the heredity of Homo sapiens.

Molecular Basis of Mammalian Odor Discrimination: A Status Report

Humans have 396 unique, intact olfactory receptors (ORs), G-protein coupled receptors (GPCRs) containing receptor-specific binding sites; other mammals have more. Activation of these transmembrane proteins by an odorant initiates a signaling cascade, evoking an action potential leading to perception of a smell. Because the number of distinguishable odorants vastly exceeds the number of ORs, research has focused on mechanisms of recognition and signaling processes for classes of odorants. In this review, selected recent examples will be presented of "deorphaned" mammalian receptors, where the OR ligands (odorants) as well as key aspects of receptor-odorant interactions were identified using odorant-mediated receptor activation data together with site-directed mutagenesis and molecular modeling. Based on cumulative evidence from OR deorphaning and olfactory receptor neuron activation studies, a receptor-ligand docking model rather than an alternative bond vibration model is suggested to best explain the molecular basis of the exquisitely sensitive odor discrimination in mammals.

The future of quantum biology

Biological systems are dynamical, constantly exchanging energy and matter with the environment in order to maintain the non-equilibrium state synonymous with living. Developments in observational techniques have allowed us to study biological dynamics on increasingly small scales. Such studies have revealed evidence of quantum mechanical effects, which cannot be accounted for by classical physics, in a range of biological processes. Quantum biology is the study of such processes, and here we provide an outline of the current state of the field, as well as insights into future directions.

Proton tunnelling in hydrogen bonds and its implications in an induced-fit model of enzyme catalysis

The role of proton tunnelling in biological catalysis is investigated here within the frameworks of quantum information theory and thermodynamics. We consider the quantum correlations generated through two hydrogen bonds between a substrate and a prototypical enzyme that first catalyses the tautomerization of the substrate to move on to a subsequent catalysis, and discuss how the enzyme can derive its catalytic potency from these correlations. In particular, we show that classical changes induced in the binding site of the enzyme spreads the quantum correlations among all of the four hydrogen-bonded atoms thanks to the directionality of hydrogen bonds. If the enzyme rapidly returns to its initial state after the binding stage, the substrate ends in a new transition state corresponding to a quantum superposition. Open quantum system dynamics can then naturally drive the reaction in the forward direction from the major tautomeric form to the minor tautomeric form without needing any additional catalytic activity. We find that in this scenario the enzyme lowers the activation energy so much that there is no energy barrier left in the tautomerization, even if the quantum correlations quickly decay.

Ferritin and neuromelanin "quantum dot" array structures in dopamine neurons of the substantia nigra pars compacta and norepinephrine neurons of the locus coeruleus

In this review, the author shows that ferritin has documented quantum dot material properties that have been reported in numerous independent studies, and can enable quantum mechanical electron transport over substantial distances. In addition, neuromelanin is a pi-conjugated polymer, and quantum dot/pi-conjugated polymer combinations have been reported in numerous independent studies to facilitate electron transport for solar photovoltaic and other applications. Both ferritin and neuromelanin are present in large quantities in the dopamine neurons of the substantia nigra pars compactaand the norepinephrine neurons of the locus coeruleus. The unique structure of subgroups of these neurons that have a large number of axon branches and synapses may have evolved to take advantage of this electron transport mechanism, if it is present, such as to coordinate conscious action, or for other purposes. Independent clinical and laboratory studies are also reviewed that corroborate this theory of coordinated action in these neuron groups. Research to validate the theory using charge transport measurements, materials characterization, existing fluorescent probe material and reaction time testing is proposed.

Can the Electron-Accepting Properties of Odorants Be Involved in Their Recognition by the Olfactory System?

The present study examines the possible importance of the electron-accepting properties of odorant molecules and, in particular, the formation and decay of temporary negative ions via low-energy electron attachment as a possible contribution toward understanding odorant recognition by olfactory receptors (ORs). Fragments formed by dissociative electron attachment (DEA) of mustard oil odorants represented by a series of isothiocyanates are studied experimentally using DEA spectroscopy and DFT calculations. Relative intensities for the most abundant fragment species, S^- and SCN^-, are found to be characteristic of structurally similar odorants under investigation. This novel approach for the investigation of odorants may contribute to understanding the initial stages of the olfactory process and may provide a means to distinguish between odorants and their interactions with the olfactory receptor system.

Biological Entanglement-Like Effect After Communication of Fish Prior to X-Ray Exposure

The phenomenon by which irradiated organisms including cells in vitro communicate with unirradiated neighbors is well established in biology as the radiation-induced bystander effect (RIBE). Generally, the purpose of this communication is thought to be protective and adaptive, reflecting a highly conserved evolutionary mechanism enabling rapid adjustment to stressors in the environment. Stressors known to induce the effect were recently shown to include chemicals and even pathological agents. The mechanism is unknown but our group has evidence that physical signals such as biophotons acting on cellular photoreceptors may be implicated. This raises the question of whether quantum biological processes may occur as have been demonstrated in plant photosynthesis. To test this hypothesis, we decided to see whether any form of entanglement was operational in the system. Fish from 2 completely separate locations were allowed to meet for 2 hours either before or after which fish from 1 location only (group A fish) were irradiated. The results confirm RIBE signal production in both skin and gill of fish, meeting both before and after irradiation of group A fish. The proteomic analysis revealed that direct irradiation resulted in pro-tumorigenic proteomic responses in rainbow trout. However, communication from these irradiated fish, both before and after they had been exposed to a 0.5 Gy X-ray dose, resulted in largely beneficial proteomic responses in completely nonirradiated trout. The results suggest that some form of anticipation of a stressor may occur leading to a preconditioning effect or temporally displaced awareness after the fish become entangled.

Revisiting the Quantum Brain Hypothesis: Toward Quantum (Neuro)biology?

The nervous system is a non-linear dynamical complex system with many feedback loops. A conventional wisdom is that in the brain the quantum fluctuations are self-averaging and thus functionally negligible. However, this intuition might be misleading in the case of non-linear complex systems. Because of an extreme sensitivity to initial conditions, in complex systems the microscopic fluctuations may be amplified and thereby affect the system's behavior. In this way quantum dynamics might influence neuronal computations. Accumulating evidence in non-neuronal systems indicates that biological evolution is able to exploit quantum stochasticity. The recent rise of quantum biology as an emerging field at the border between quantum physics and the life sciences suggests that quantum events could play a non-trivial role also in neuronal cells. Direct experimental evidence for this is still missing but future research should address the possibility that quantum events contribute to an extremely high complexity, variability and computational power of neuronal dynamics.