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Brain/Mind Activity and Molecular Dynamics in Biological Systems

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Neurobiology".

Deadline for manuscript submissions: closed (31 March 2023) | Viewed by 17092

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Special Issue Editors

Prof. Dr. Giuseppe Vitiello

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Guest Editor

Dipartimento di Fisica ‘‘E.R.Caianiello’’, Università di Salerno, I-84100 Fisciano, Salerno, Italy
Interests: elementary particle physics; condensed matter; quantum field theory; fractals; coherent states; mathematical models of brain; biological systems

Dr. Carlo Dal Lin

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Co-Guest Editor

Department of Cardiac, Thoracic and Vascular Sciences, Padua University School of Medicine, Via Giustiniani 2, 35100 Padua, Italy
Interests: Integrative cardiology; Relaxation response; Psycho-neuro-endocrine immunology

Special Issue Information

Dear Colleagues,

There is much knowledge about the individual components that make up the human biological system but still very little is known about the dialogue between them. From the mutual interaction of different molecules and physical forces, properties extraneous to the single components of the system emerge. This is similar to what happens in physics where, for example, a crystal cannot be described solely by its constituent atoms. The crystal properties are described also in terms of the collective dynamical modes of the atoms, i.e., the phonons, plasmons, etc. These modes disappear when the crystal is split into its component atoms. However, crystal properties cannot emerge from the study of individual atoms considered one by one.

In brain studies, such a need of merging the atomist and dynamical views has been stressed since the forties by Karl Lashley who, based on observations in his laboratory, recognized that “nerve impulses are transmitted [...] from cell to cell through definite intercellular connections. Yet, all behavior seems to be determined by masses of excitation [...] within general fields of activity, without regard to particular nerve cells”.

This IJMS Special Issue is devoted to works, articles, or reviews aimed at merging the properties of individual molecules in biological systems with their dynamical interplay in the “living and thinking human being”. The aim is to provide a vision of the already known and possible interactions that link the functioning of the brain with other organs and the continuum of cells immersed in their aqueous environment that is rich in polar molecules in constant reciprocal interaction and as dissipative systems open to the environment.

Prof. Dr. Giuseppe Vitiello
Guest Editor
Dr. Carlo Dal Lin
Co-Guest Editor

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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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.

Keywords

molecular biology
system biology
cell
nervous cell
brain
neurobiology
brain modeling
psycho-neuroendocrine immunology
molecular dynamics
quantum field theory

Published Papers (5 papers)

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Research

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32 pages, 5442 KiB

Open AccessArticle

Learning in Transcriptional Network Models: Computational Discovery of Pathway-Level Memory and Effective Interventions

by Surama Biswas, Wesley Clawson and Michael Levin

Int. J. Mol. Sci. 2023, 24(1), 285; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms24010285 - 23 Dec 2022

Cited by 11 | Viewed by 4203

Abstract

Trainability, in any substrate, refers to the ability to change future behavior based on past experiences. An understanding of such capacity within biological cells and tissues would enable a particularly powerful set of methods for prediction and control of their behavior through specific patterns of stimuli. This top-down mode of control (as an alternative to bottom-up modification of hardware) has been extensively exploited by computer science and the behavioral sciences; in biology however, it is usually reserved for organism-level behavior in animals with brains, such as training animals towards a desired response. Exciting work in the field of basal cognition has begun to reveal degrees and forms of unconventional memory in non-neural tissues and even in subcellular biochemical dynamics. Here, we characterize biological gene regulatory circuit models and protein pathways and find them capable of several different kinds of memory. We extend prior results on learning in binary transcriptional networks to continuous models and identify specific interventions (regimes of stimulation, as opposed to network rewiring) that abolish undesirable network behavior such as drug pharmacoresistance and drug sensitization. We also explore the stability of created memories by assessing their long-term behavior and find that most memories do not decay over long time periods. Additionally, we find that the memory properties are quite robust to noise; surprisingly, in many cases noise actually increases memory potential. We examine various network properties associated with these behaviors and find that no one network property is indicative of memory. Random networks do not show similar memory behavior as models of biological processes, indicating that generic network dynamics are not solely responsible for trainability. Rational control of dynamic pathway function using stimuli derived from computational models opens the door to empirical studies of proto-cognitive capacities in unconventional embodiments and suggests numerous possible applications in biomedicine, where behavior shaping of pathway responses stand as a potential alternative to gene therapy. Full article

(This article belongs to the Special Issue Brain/Mind Activity and Molecular Dynamics in Biological Systems)

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14 pages, 1532 KiB

Open AccessArticle

Generation of Electromagnetic Field by Microtubules

by Jan Pokorný, Jiří Pokorný and Jan Vrba

Int. J. Mol. Sci. 2021, 22(15), 8215; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22158215 - 30 Jul 2021

Cited by 6 | Viewed by 2854

Abstract

The general mechanism of controlling, information and organization in biological systems is based on the internal coherent electromagnetic field. The electromagnetic field is supposed to be generated by microtubules composed of identical tubulin heterodimers with periodic organization and containing electric dipoles. We used a classical dipole theory of generation of the electromagnetic field to analyze the space–time coherence. The structure of microtubules with the helical and axial periodicity enables the interaction of the field in time shifted by one or more periods of oscillation and generation of coherent signals. Inner cavity excitation should provide equal energy distribution in a microtubule. The supplied energy coherently excites oscillators with a high electrical quality, microtubule inner cavity, and electrons at molecular orbitals and in ‘semiconduction’ and ‘conduction’ bands. The suggested mechanism is supposed to be a general phenomenon for a large group of helical systems. Full article

(This article belongs to the Special Issue Brain/Mind Activity and Molecular Dynamics in Biological Systems)

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16 pages, 2413 KiB

Open AccessArticle

Transition between Random and Periodic Electron Currents on a DNA Chain

by Elham Faraji, Roberto Franzosi, Stefano Mancini and Marco Pettini

Int. J. Mol. Sci. 2021, 22(14), 7361; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22147361 - 08 Jul 2021

Viewed by 1751

Abstract

By resorting to a model inspired to the standard Davydov and Holstein-Fröhlich models, in the present paper we study the motion of an electron along a chain of heavy particles modeling a sequence of nucleotides proper to a DNA fragment. Starting with a model Hamiltonian written in second quantization, we use the Time Dependent Variational Principle to work out the dynamical equations of the system. It can be found that, under the action of an external source of energy transferred to the electron, and according to the excitation site, the electron current can display either a broad frequency spectrum or a sharply peaked frequency spectrum. This sequence-dependent charge transfer phenomenology is suggestive of a potentially rich variety of electrodynamic interactions of DNA molecules under the action of electron excitation. This could imply the activation of interactions between DNA and transcription factors, or between DNA and external electromagnetic fields. Full article

(This article belongs to the Special Issue Brain/Mind Activity and Molecular Dynamics in Biological Systems)

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Review

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14 pages, 1052 KiB

Open AccessReview

On Collective Molecular Dynamics in Biological Systems: A Review of Our Experimental Observations and Theoretical Modeling

by Carlo Dal Lin, Paola Romano, Sabino Iliceto, Francesco Tona and Giuseppe Vitiello

Int. J. Mol. Sci. 2022, 23(9), 5145; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23095145 - 05 May 2022

Cited by 4 | Viewed by 1506

Abstract

We review processes by which different sounds, such as meditation music, mantra, kindness, or hatred expressions, and noises induce responses from cells and their components. We define ‘good’ or ‘bad’ sounds as those enhancing or inhibiting the cell’s biological activity, respectively. It is highlighted that the cellular dynamics results in a coherent organization with the formation of ordered patterns due to long-range correlations among the system constituents. Due to coherence, in the framework of quantum field theory, extended domains become independent of quantum fluctuations. Non-dissipative energy transfer on macromolecule chains is briefly discussed. Observed fractal features are analyzed by the fast Fourier transform and a linear relationship between logarithms of conjugate variables is observed. The fractal relation to the generation of forms (morphogenesis) and to the transition from form to form (metamorphosis) is commented. The review is also motivated by the suggestions coming from the cells’ responses, which show their ability to move from the syntactic level of the sound component frequencies to the semantic level of their collective envelope. The process by which sounds are selected to be good or bad sounds sheds some light on the problem of the construction of languages. Full article

(This article belongs to the Special Issue Brain/Mind Activity and Molecular Dynamics in Biological Systems)

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25 pages, 1591 KiB

Open AccessReview

Psychic Life-Biological Molecule Bidirectional Relationship: Pathways, Mechanisms, and Consequences for Medical and Psychological Sciences—A Narrative Review

by Anna Giulia Bottaccioli, Mauro Bologna and Francesco Bottaccioli

Int. J. Mol. Sci. 2022, 23(7), 3932; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23073932 - 01 Apr 2022

Cited by 10 | Viewed by 5650

Abstract

Today, it is possible to investigate the biological paths and mechanisms that link mental life to biological life. Emotions, feelings, desires, and cognitions influence biological systems. In recent decades, psychoneuroendocrinoimmunology research has highlighted the routes linking the psyche–brain–immune systems. Recently, epigenetics research has shown the molecular mechanisms by which stress and mental states modulate the information contained in the genome. This research shapes a new paradigm considering the human being as a whole, integrating biology and psychology. This will allow us to progress towards personalized precision medicine, deeply changing medical and psychological sciences and clinical practice. In this paper, we recognize leading research on both bidirectional relations between the psyche–brain–immunity and molecular consequences of psychological and mental states. Full article

(This article belongs to the Special Issue Brain/Mind Activity and Molecular Dynamics in Biological Systems)

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