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Quantum Processes in Living Systems
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Quantum Processes in Living Systems

A special issue of Entropy (ISSN 1099-4300). This special issue belongs to the section "Quantum Information".

Deadline for manuscript submissions: closed (31 March 2024) | Viewed by 12217

Special Issue Editors

Dr. Alessandro Sergi

E-Mail Website
Guest Editor
Dipartimento di Scienze Matematiche e Informatiche, Scienze Fisiche e Scienze della Terra, Università degli Studi di Messina, Viale Stagno d’Alcontres 31, 98166 Messina, Italy
Interests: quantum-classical hybrid systems; non-Hermitian quantum mechanics; non-Hamiltonian systems; open quantum systems; quantum-biology
Special Issues, Collections and Topics in MDPI journals
Prof. Antonino Messina

E-Mail Website
Guest Editor
Department of Mathematics and Computer Science, University of Palermo, 90133 Palermo, PA, Italy
Interests: quantum electrodynamics; open systems; time dependent spin Hamiltonians; quantum and semiclassical Rabi models
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

In recent years, experiments on energy transport in photosynthetic systems have revived the idea that quantum mechanics plays a fundamental role in living systems. This idea is almost as old as quantum mechanics—none other than Pascual Jordan and Erwin Schrödinger were the first to propose it. Phenomena such as quantum tunneling, exciton coherent propagation, resonances of molecular vibrations, entanglement as a tool for weak signals perception, quantum stability and modification of DNA, and even the ambitious project of unveiling the mysteries of the mind’s working are all applications of quantum mechanics that appear nowadays in scientific literature. Are these quantum phenomena really necessary for life? What are the other ingredients that are missing for a true understanding of life?

This Special Issue’s goal is to be a milestone for our current understanding of what life is from the point of view of quantum mechanics. Not only we are looking for contributions that review or give different interpretations of the already known quantum effects, but we welcome proposals of novel statistical mechanisms. Moreover, we will appreciate both experimental and theoretical papers as long as they contribute to discussing their results within the wider perspective of assessing the quantum nature of life processes.

Prof. Dr. Alessandro Sergi
Prof. Dr. Antonino Messina
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Entropy is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Published Papers (6 papers)

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Research

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14 pages, 1803 KiB  
Article
Engineering Transport via Collisional Noise: A Toolbox for Biology Systems
by Alessandro Civolani, Vittoria Stanzione, Maria Luisa Chiofalo and Jorge Yago Malo
Entropy 2024, 26(1), 20; https://doi.org/10.3390/e26010020 - 24 Dec 2023
Viewed by 840
Abstract
The study of noise assisted-transport in quantum systems is essential in a wide range of applications, from near-term NISQ devices to models for quantum biology. Here, we study a generalized XXZ model in the presence of stochastic collision noise, which allows describing environments [...] Read more.
The study of noise assisted-transport in quantum systems is essential in a wide range of applications, from near-term NISQ devices to models for quantum biology. Here, we study a generalized XXZ model in the presence of stochastic collision noise, which allows describing environments beyond the standard Markovian formulation. Our analysis through the study of the local magnetization, the inverse participation ratio (IPR) or its generalization, and the inverse ergodicity ratio (IER) showed clear regimes, where the transport rate and coherence time could be controlled by the dissipation in a consistent manner. In addition, when considering various excitations, we characterized the interplay between collisions and system interactions, identifying regimes in which transport was counterintuitively enhanced when increasing the collision rate, even in the case of initially separated excitations. These results constitute an example of an essential building block for the understanding of quantum transport in structured noisy and warm-disordered environments. Full article
(This article belongs to the Special Issue Quantum Processes in Living Systems)
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9 pages, 746 KiB  
Article
Novel Entropy-Based Phylogenetic Algorithm: A New Approach for Classifying SARS-CoV-2 Variants
by Vladimir Perovic, Sanja Glisic, Milena Veljkovic, Slobodan Paessler and Veljko Veljkovic
Entropy 2023, 25(10), 1463; https://doi.org/10.3390/e25101463 - 19 Oct 2023
Viewed by 921
Abstract
The SARS-CoV-2 virus, the causative agent of COVID-19, is known for its genetic diversity. Virus variants of concern (VOCs) as well as variants of interest (VOIs) are classified by the World Health Organization (WHO) according to their potential risk to global health. This [...] Read more.
The SARS-CoV-2 virus, the causative agent of COVID-19, is known for its genetic diversity. Virus variants of concern (VOCs) as well as variants of interest (VOIs) are classified by the World Health Organization (WHO) according to their potential risk to global health. This study seeks to enhance the identification and classification of such variants by developing a novel bioinformatics criterion centered on the virus’s spike protein (SP1), a key player in host cell entry, immune response, and a mutational hotspot. To achieve this, we pioneered a unique phylogenetic algorithm which calculates EIIP-entropy as a distance measure based on the distribution of the electron–ion interaction potential (EIIP) of amino acids in SP1. This method offers a comprehensive, scalable, and rapid approach to analyze large genomic data sets and predict the impact of specific mutations. This innovative approach provides a robust tool for classifying emergent SARS-CoV-2 variants into potential VOCs or VOIs. It could significantly augment surveillance efforts and understanding of variant characteristics, while also offering potential applicability to the analysis and classification of other emerging viral pathogens and enhancing global readiness against emerging and re-emerging viral pathogens. Full article
(This article belongs to the Special Issue Quantum Processes in Living Systems)
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14 pages, 4545 KiB  
Article
Biophotons: New Experimental Data and Analysis
by Maurizio Benfatto, Elisabetta Pace, Ivan Davoli, Roberto Francini, Fabio De Matteis, Alessandro Scordo, Alberto Clozza, Luca De Paolis, Catalina Curceanu and Paolo Grigolini
Entropy 2023, 25(10), 1431; https://doi.org/10.3390/e25101431 - 10 Oct 2023
Viewed by 2400
Abstract
Biophotons are an ultra-weak emission of photons in the visible energy range from living matter. In this work, we study the emission from germinating seeds using an experimental technique designed to detect light of extremely small intensity. The emission from lentil seeds and [...] Read more.
Biophotons are an ultra-weak emission of photons in the visible energy range from living matter. In this work, we study the emission from germinating seeds using an experimental technique designed to detect light of extremely small intensity. The emission from lentil seeds and single bean was analyzed during the whole germination process in terms of the different spectral components through low pass filters and the different count distributions in the various stages of the germination process. Although the shape of the emission spectrum appears to be very similar in the two samples used in our experiment, our analysis can highlight the differences present in the two cases. In this way, it was possible to correlate the various types of emissions to the degree of development of the seed during germination. Full article
(This article belongs to the Special Issue Quantum Processes in Living Systems)
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24 pages, 462 KiB  
Article
A Quantum–Classical Model of Brain Dynamics
by Alessandro Sergi, Antonino Messina, Carmelo M. Vicario and Gabriella Martino
Entropy 2023, 25(4), 592; https://doi.org/10.3390/e25040592 - 30 Mar 2023
Cited by 2 | Viewed by 2991
Abstract
The study of the human psyche has elucidated a bipartite structure of logic reflecting the quantum–classical nature of the world. Accordingly, we posited an approach toward studying the brain by means of the quantum–classical dynamics of a mixed Weyl symbol. The mixed Weyl [...] Read more.
The study of the human psyche has elucidated a bipartite structure of logic reflecting the quantum–classical nature of the world. Accordingly, we posited an approach toward studying the brain by means of the quantum–classical dynamics of a mixed Weyl symbol. The mixed Weyl symbol can be used to describe brain processes at the microscopic level and, when averaged over an appropriate ensemble, can provide a link to the results of measurements made at the meso and macro scale. Within this approach, quantum variables (such as, for example, nuclear and electron spins, dipole momenta of particles or molecules, tunneling degrees of freedom, and so on) can be represented by spinors, whereas the electromagnetic fields and phonon modes can be treated either classically or semi-classically in phase space by also considering quantum zero-point fluctuations. Quantum zero-point effects can be incorporated into numerical simulations by controlling the temperature of each field mode via coupling to a dedicated Nosé–Hoover chain thermostat. The temperature of each thermostat was chosen in order to reproduce quantum statistics in the canonical ensemble. In this first paper, we introduce a general quantum–classical Hamiltonian model that can be tailored to study physical processes at the interface between the quantum and the classical world in the brain. While the approach is discussed in detail, numerical calculations are not reported in the present paper, but they are planned for future work. Our theory of brain dynamics subsumes some compatible aspects of three well-known quantum approaches to brain dynamics, namely the electromagnetic field theory approach, the orchestrated objective reduction theory, and the dissipative quantum model of the brain. All three models are reviewed. Full article
(This article belongs to the Special Issue Quantum Processes in Living Systems)

Review

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20 pages, 863 KiB  
Review
A Computational Quantum-Based Perspective on the Molecular Origins of Life’s Building Blocks
by Gabriele Amante, Judit E. Sponer, Jiri Sponer, Franz Saija and Giuseppe Cassone
Entropy 2022, 24(8), 1012; https://doi.org/10.3390/e24081012 - 22 Jul 2022
Cited by 1 | Viewed by 1960
Abstract
The search for the chemical origins of life represents a long-standing and continuously debated enigma. Despite its exceptional complexity, in the last decades the field has experienced a revival, also owing to the exponential growth of the computing power allowing for efficiently simulating [...] Read more.
The search for the chemical origins of life represents a long-standing and continuously debated enigma. Despite its exceptional complexity, in the last decades the field has experienced a revival, also owing to the exponential growth of the computing power allowing for efficiently simulating the behavior of matter—including its quantum nature—under disparate conditions found, e.g., on the primordial Earth and on Earth-like planetary systems (i.e., exoplanets). In this minireview, we focus on some advanced computational methods capable of efficiently solving the Schrödinger equation at different levels of approximation (i.e., density functional theory)—such as ab initio molecular dynamics—and which are capable to realistically simulate the behavior of matter under the action of energy sources available in prebiotic contexts. In addition, recently developed metadynamics methods coupled with first-principles simulations are here reviewed and exploited to answer to old enigmas and to propose novel scenarios in the exponentially growing research field embedding the study of the chemical origins of life. Full article
(This article belongs to the Special Issue Quantum Processes in Living Systems)
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Other

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12 pages, 2793 KiB  
Hypothesis
Docosahexaenoic Acid Explains the Unexplained in Visual Transduction
by Michael A. Crawford, Andrew J. Sinclair, Yiqun Wang, Walter F. Schmidt, C. Leigh Broadhurst, Simon C. Dyall, Larry Horn, J. Thomas Brenna and Mark R. Johnson
Entropy 2023, 25(11), 1520; https://doi.org/10.3390/e25111520 - 06 Nov 2023
Viewed by 1577
Abstract
In George Wald’s Nobel Prize acceptance speech for “discoveries concerning the primary physiological and chemical visual processes in the eye”, he noted that events after the activation of rhodopsin are too slow to explain visual reception. Photoreceptor membrane phosphoglycerides contain near-saturation amounts of [...] Read more.
In George Wald’s Nobel Prize acceptance speech for “discoveries concerning the primary physiological and chemical visual processes in the eye”, he noted that events after the activation of rhodopsin are too slow to explain visual reception. Photoreceptor membrane phosphoglycerides contain near-saturation amounts of the omega-3 fatty acid docosahexaenoic acid (DHA). The visual response to a photon is a retinal cis–trans isomerization. The trans-state is lower in energy; hence, a quantum of energy is released equivalent to the sum of the photon and cis–trans difference. We hypothesize that DHA traps this energy, and the resulting hyperpolarization extracts the energized electron, which depolarizes the membrane and carries a function of the photon’s energy (wavelength) to the brain. There, it contributes to the creation of the vivid images of our world that we see in our consciousness. This proposed revision to the visual process provides an explanation for these previously unresolved issues around the speed of information transfer and the purity of conservation of a photon’s wavelength and supports observations of the unique and indispensable role of DHA in the visual process. Full article
(This article belongs to the Special Issue Quantum Processes in Living Systems)
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