Thinking, holograms, and the quantum brain.

This article continues the development of the idea that all human behavior and thinking are innate. A model of thinking and functioning of the brain has been constructed, which is capable of explaining both the accuracy of molecular processes and the innateness of behaviors. The focus of the model is the phase of the wave function of the particle, which is an additional (free) parameter. It should also be emphasized that the phase of the wave function of a particle is inextricably linked with the quantum action S in the Feynman's formulation of quantum mechanics (path integrals). A hypothesis is proposed: the set of particles that make up neurons and the brain is controlled by changing the phases from the outside (by a higher order system). Such a control system must be outside our world because our measurement methods do not allow us to determine the phase of an elementary particle. In a sense, it can be viewed as an extension of Bohm's ideas about the holographic brain and the holographic universe. Experiments are proposed that could confirm or disprove this model.

Viruses, immunity and evolution.

In this article, the evolution of viruses is analyzed in terms of their complexity. It is shown that the evolution of viruses is a partially directed process. The participation of viruses and mobile genetic elements in the evolution of other organisms by integration into the genome is also an a priori directed process. The high variability of genomes (including the genes of antibodies), which differs by orders of magnitude for various viruses and their hosts, is not a random process but is the result of the action of a molecular genetic control system. Herein, a model of partially directed evolution of viruses is proposed. Throughout the life cycle of viruses, there is an interaction of complex biologically important molecules that cannot be explained on the basis of classic laws. The interaction of a virus with a cell is essentially a quantum event, including selective long-range action. Such an interaction can be interpreted as the "remote key-lock" principle. In this article, a model of the interaction of biologically important viral molecules with cellular molecules based on nontrivial quantum interactions is proposed. Experiments to test the model are also proposed.

Can Quantum Correlations Lead to Violation of the Second Law of Thermodynamics?

Quantum entanglement can cause the efficiency of a heat engine to be greater than the efficiency of the Carnot cycle. However, this does not mean a violation of the second law of thermodynamics, since there is no local equilibrium for pure quantum states, and, in the absence of local equilibrium, thermodynamics cannot be formulated correctly. Von Neumann entropy is not a thermodynamic quantity, although it can characterize the ordering of a system. In the case of the entanglement of the particles of the system with the environment, the concept of an isolated system should be refined. In any case, quantum correlations cannot lead to a violation of the second law of thermodynamics in any of its formulations. This article is devoted to a technical discussion of the expected results on the role of quantum entanglement in thermodynamics.

Intra- and intercellular transport of substances: Models and mechanisms.

Non-equilibrium-statistical models of intracellular transport are built. The most significant features of these models are microscopic reversibility and the explicit considerations of the driving forces of the process - the ATP-ADP chemical potential difference. In this paper, water transport using contractile vacuoles, the transport and assembly of microtubules and microfilaments, the protein distribution within a cell, the transport of neurotransmitters from the synaptic cleft and the transport of substances between cells using plasmodesmata are discussed. Endocytosis and phagocytosis models are considered, and transport tasks and information transfer mechanisms inside the cell are explored. Based on an analysis of chloroplast movement, it was concluded that they have a complicated method of influencing each other in the course of their movements. The role of quantum effects in sorting and control transport mechanisms is also discussed. It is likely that quantum effects play a large role in these processes, otherwise reliable molecular recognition would be impossible, which would lead to very low intracellular transport efficiency.

Protocells and LUCA: Transport of substances from first physicochemical principles.

Models of the transport of substances in protocells are considered from first physicochemical principles. Functional similarities and differences in the transport systems of archaea, cyanobacteria, E. coli, and diatoms have been analyzed. Based on the selection of the most important transport systems, a model of transport of substances through the membrane of the last universal common ancestor, LUCA, was constructed. Models of isotope separation in protocells were considered. Based on the proposed models, the difference in isotope concentrations in rocks can be predicted, which can serve as an indicator of the presence of life in the early stages of evolution. Mechanisms of energy conversion for the simplest forms of directed motion in protocells are considered. A special stage in the evolution of protocells is proposed - the minimal mobile cell.

Thinking as a quantum phenomenon.

In this study, a model is constructed in which the formation of new synaptic contacts and the tuning of synaptic weights are mediated by quantum nonlocal interactions. The interaction between biologically important molecules in the brain can be the basis of the quantum metalanguage, which controls the behavior of humans and animals. The dynamics of biologically important molecules must include their topological properties. Thus the work of the brain can only be consistently described using quantum mechanics.

Mechanisms of directed evolution of morphological structures and the problems of morphogenesis.

Morphogenesis mechanisms are considered from the point of view of complexity. It has been shown that the presence of long-range interactions between biologically important molecules is a necessary condition for the formation and stable operation of morphological structures. A quantum model of morphogenesis based on non-Archimedean analysis and the presence of long-range interactions between biologically important molecules has been constructed. This model shows that the evolution of morphological structures essentially depends on the availability of a priori information on these structures. Critical steps in evolution related to the most important morphological and behavioral findings have been analyzed; the results have shown that the implementation of such steps can only be explained within the framework of a partially directed evolution. Thus, the previously proposed model for a partially directed evolution is established for modeling the evolution of morphological structures.

On a generalized Levinthal's paradox: The role of long- and short range interactions in complex bio-molecular reactions, including protein and DNA folding.

The current protein folding literature is reviewed. Two main approaches to the problem of folding were selected for this review: geometrical and biophysical. The geometrical approach allows the formulation of topological restrictions on folding, that are usually not taken into account in the construction of physical models. In particular, the topological constraints do not allow the known funnel-like energy landscape modeling, although most common methods of resolving the paradox are based on this method. The very paradox is based on the fact that complex molecules must reach their native conformations (complexes that result from reactions) in an exponentially long time, which clearly contradicts the observed experimental data. In this respect we considered the complexity of the reactions between ligands and proteins. On this general basis, the folding-reaction paradox was reformulated and generalized. We conclude that prospects for solving the paradox should be associated with incorporating a topology aspect in biophysical models of protein folding, through the construction of hybrid models. However, such models should explicitly include long-range force fields and local cell biological conditions, such as structured water complexes and photon/phonon/soliton waves, ordered in discrete frequency bands. In this framework, collective and coherent oscillations in, and between, macromolecules are instrumental in inducing intra- and intercellular resonance, serving as an integral guiding network of life communication: the electrome aspect of the cell. Yet, to identify the actual mechanisms underlying the bonds between molecules (atoms), it will be necessary to perform dedicated experiments to more definitely solve the particular time paradox.

Molecular recognition of the environment and mechanisms of the origin of species in quantum-like modeling of evolution.

A review of the mechanisms of speciation is performed. The mechanisms of the evolution of species, taking into account the feedback of the state of the environment and mechanisms of the emergence of complexity, are considered. It is shown that these mechanisms, at the molecular level, cannot work steadily in terms of classical mechanics. Quantum mechanisms of changes in the genome, based on the long-range interaction potential between biologically important molecules, are proposed as one of possible explanation. Different variants of interactions of the organism and environment based on molecular recognition and leading to new species origins are considered. Experiments to verify the model are proposed. This bio-physical study is completed by the general operational model of based on quantum information theory. The latter is applied to model of epigenetic evolution. We briefly present the basics of the quantum-like approach to modeling of bio-informational processes. This approach is illustrated by the quantum-like model of epigenetic evolution.

Quantum-like model of partially directed evolution.

The background of this study is that models of the evolution of living systems are based mainly on the evolution of replicators and cannot explain many of the properties of biological systems such as the existence of the sexes, molecular exaptation and others. The purpose of this study is to build a complete model of the evolution of organisms based on a combination of quantum-like models and models based on partial directivity of evolution. We also used optimal control theory for evolution modeling. We found that partial directivity of evolution is necessary for the explanation of the properties of an evolving system such as the stability of evolutionary strategies, aging and death, the presence of the sexes. The proposed model represents a systems approach to the evolution of species and will facilitate the understanding of the evolution and biology as a whole.

Nontrivial quantum and quantum-like effects in biosystems: Unsolved questions and paradoxes.

Non-trivial quantum effects in biological systems are analyzed. Some unresolved issues and paradoxes related to quantum effects (Levinthal's paradox, the paradox of speed, and mechanisms of evolution) are addressed. It is concluded that the existence of non-trivial quantum effects is necessary for the functioning of living systems. In particular, it is demonstrated that classical mechanics cannot explain the stable work of the cell and any over-cell structures. The need for quantum effects is generated also by combinatorial problems of evolution. Their solution requires a priori information about the states of the evolving system, but within the framework of the classical theory it is not possible to explain mechanisms of its storage consistently. We also present essentials of so called quantum-like paradigm: sufficiently complex bio-systems process information by violating the laws of classical probability and information theory. Therefore the mathematical apparatus of quantum theory may have fruitful applications to describe behavior of bio-systems: from cells to brains, ecosystems and social systems. In quantum-like information biology it is not presumed that quantum information bio-processing is resulted from quantum physical processes in living organisms. Special experiments to test the role of quantum mechanics in living systems are suggested. This requires a detailed study of living systems on the level of individual atoms and molecules. Such monitoring of living systems in vivo can allow the identification of the real potentials of interaction between biologically important molecules.

Paradoxes of early stages of evolution of life and biological complexity.

Two of the most fundamental questions concerning the origin of life, how biologically important molecules (RNA, proteins) find their unique spatial configuration, and how coding sequences can evolve beyond a certain critical length, are discussed. It is shown that both of these problems have not been solved. Experiments that could clarify the mechanisms of interaction between biologically important molecules in the simplest cells are discussed.

Congenital programs of the behavior and nontrivial quantum effects in the neurons work.

The problem of processing and transmitting information within neurons is considered. The fundamental paradox of molecular biology is formulated, namely that interactions between biologically important molecules should lead to an exponentially large number of variants of molecular structures, but only a small number of them are biologically relevant. The problem is that the known interaction potentials between atoms do not allow this. The solution of the paradox, based on the nonlinear quantum model of interaction between biologically important molecules, is proposed. The model includes a nonlinear equation for many-particle nonlocal potential describing this interaction. Under the action of this potential there occurs the formation of synaptic connections between neurons, and transport processes and molecular recognition inside neurons. The information on which programs of innate behavior operate is hypothesized to reside in the quantum degrees of freedom of the proposed potential. Possible experiments to test the model are proposed.

Quantum information and the problem of mechanisms of biological evolution.

One of the most important conditions for replication in early evolution is the de facto elimination of the conformational degrees of freedom of the replicators, the mechanisms of which remain unclear. In addition, realistic evolutionary timescales can be established based only on partially directed evolution, further complicating this issue. A division of the various evolutionary theories into two classes has been proposed based on the presence or absence of a priori information about the evolving system. A priori information plays a key role in solving problems in evolution. Here, a model of partially directed evolution, based on the learning automata theory, which includes a priori information about the fitness space, is proposed. A potential repository of such prior information is the states of biologically important molecules. Thus, the need for extended evolutionary synthesis is discussed. Experiments to test the hypothesis of partially directed evolution are proposed.

The problems of replication in the early stages of evolution: enumeration of variants and spatial configurations of replicators.

Two main problems of replication in the early stages of evolution are discussed: the problem of exponentially large number of conformational degrees of freedom and the problem of enumeration of variants.

Carnot cycle at finite power: attainability of maximal efficiency.

We want to understand whether and to what extent the maximal (Carnot) efficiency for heat engines can be reached at a finite power. To this end we generalize the Carnot cycle so that it is not restricted to slow processes. We show that for realistic (i.e., not purposefully designed) engine-bath interactions, the work-optimal engine performing the generalized cycle close to the maximal efficiency has a long cycle time and hence vanishing power. This aspect is shown to relate to the theory of computational complexity. A physical manifestation of the same effect is Levinthal's paradox in the protein folding problem. The resolution of this paradox for realistic proteins allows to construct engines that can extract at a finite power 40% of the maximally possible work reaching 90% of the maximal efficiency. For purposefully designed engine-bath interactions, the Carnot efficiency is achievable at a large power.

Biological complexity, quantum coherent states and the problem of efficient transmission of information inside a cell.

The intracellular channel of information transmission was analyzed from the point of view of complexity. The most important steps in the transfer of information within a cell are the folding, transport and recognition of proteins. It was shown that the large number of conformational degrees of freedom that proteins possess can paradoxically lead to an information channel with an exponentially small capacity. To resolve this paradox, a model, which assumes a quantum collective behavior of biologically important molecules, was proposed. Experiments to test the quantum nature of the intracellular transfer of information were also proposed.

Origin of the directed movement of protocells in the early stages of the evolution of life.

The origin of the directed motion of protocells during the early stages of evolution was discussed. The expenditures for movement, space orientation, and reception of information about the environment were taken into consideration, and it was shown that directed movement is evolutionarily advantageous in the following cases: when opposite gradients of different resources (for example, matter and energy) are great enough and when there is a rapid change in environmental parameters. It was also shown that the advantage of directed movement strategies depends greatly on how information about the environment is obtained by a protocell.

Mechanisms and models of the active transport of ions and the transformation of energy in intracellular compartments.

Various transport models and mechanisms for ions from different compartments of the cell are considered. Compartments such as mitochondria, synaptic vesicles, sarco- and endoplasmic reticulum and vacuoles are considered. It is shown that an adequate description of the compartment-based substance transport can be developed using thermodynamically correct models. Such models are used to calculate both the concentrations of ions in such compartments and the resting potential on their membranes. The problem of the complexity of transport systems is also discussed.

Analytical model of ion transport and conversion of light energy in chloroplasts.

An analytical model, which describes the stationary transformation of light energy to the energy of pigment electronic excitation, has been constructed. A proton pump of the thylakoid membrane has been considered as a two-level conformon. The difference between the energies of the excited and ground states of both the pigment and the protein complex is assumed to be the energy of an absorbed photon. It has been found how the concentration of ions in a lumen and the potential across the thylakoid membrane depend on the concentration of ions in the stroma and the brightness temperature of absorbed radiation. Conditions for the maximum efficiency of the photosynthesis process have been analyzed. This model has been used to determine the electric potential (phi approximately 6.7mV) at the chloroplast thylakoid membrane. The calculated value of the electric potential is in good agreement with the experimental data. A limitation on the stoichiometric coefficient of the proton transport through ATP-synthase, m>3, has been found theoretically.