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The production of public goods is a necessary condition for the survival of the species, but it comes at the expense of individual growth. In a prototype bacterial colony, we model the role of quorum sensing as a resource redistribution mechanism. Two types of bacterial colonies are analyzed, one made up of a single strain and one made up of two different strains. Based on a recent series of experimental data present in the literature, we analyze two types of strains with different extinction times: strains that consume available resources very quickly, therefore becoming extinct quickly, and strains that consume resources slowly and die due to aging. We show that the proposed quorum sensing model describes the main experimental result that coexistence may favor the survival of both strains. Furthermore, the production of public goods is maximized when both types of individuals have the maximum proliferation output. Finally, we highlight the role played by so-called dormant cells in the duration of survival time. These cells are of particular interest because their ability to counteract different types of stress (e.g., the use of antibiotics) still constitutes a challenge. [ABSTRACT FROM AUTHOR]

Stefan–Boltzmann law, stating the fourth power temperature dependence of the radiation emission by a black-body, was empirically formulated by Stefan in 1874 by fitting existing experiments and theoretically validated by Boltzmann in 1884 on the basis of a classical physical model involving thermodynamics principles and the radiation pressure predicted by Maxwell equations. At first sight the electromagnetic (EM) gas assumed by Boltzmann and following Rayleigh (1900) identifiable as an ensemble of N classical normal-modes, looks like an extension of the classical model of the massive ideal-gas. Accordingly, for this EM gas the internal total energy, U, was assumed to be function of volume V and temperature T as U = U (V , T) , and the equation of state was given by U = 3 P V , with P the radiation pressure. In addition, Boltzmann implicitly assumed that, for given values of V and T, U and the number of modes N would take finite values. However, from one hand these assumptions are not justified by Maxwell equations and classical statistics since, in vacuum (i.e., far from the EM sources), the values of N and U diverge, the so-called ultraviolet catastrophe introduced by Ehrenfest in 1911. From another hand, Boltzmann derivation of Stefan law is found to be macroscopically compatible with its derivation from quantum statistics announced by Planck in 1901. In this paper, we present a justification of this puzzling classical/quantum compatibility by noticing that the implicit assumptions made by Boltzmann is fully justified by Planck quantum statistics. Furthermore, we shed new light on the interpretation of recent classical simulations of a black body carried out by Wang, Casati, and Benenti in 2022 who found an analogous puzzling consistency between Stefan–Boltzmann law and their simulations to induce speculations on classical physics and black body radiation that are claimed to require a critical reconsideration of the role of classical physics for the understanding of quantum mechanics. [ABSTRACT FROM AUTHOR]

Food and drinks can be contaminated with pollutants such as lead and strontium, which poses a serious danger to human health. For this reason, a number of effective sensors have been developed for the rapid and highly selective detection of such contaminants. TBA, a well-known aptamer developed to selectively target and thereby inhibit the protein of clinical interest α-thrombin, is receiving increasing attention for sensing applications, particularly for the sensing of different cations. Indeed, TBA, in the presence of these cations, folds into the stable G-quadruplex structure. Furthermore, different cations produce small but significant changes in this structure that result in changes in the electrical responses that TBA can produce. In this article, we give an overview of the expected data regarding the use of TBA in the detection of lead and strontium, calculating the expected electrical response using different measurement techniques. Finally, we conclude that TBA should be able to detect strontium with a sensitivity approximately double that achievable for lead. [ABSTRACT FROM AUTHOR]

The growing interest in bio-inspired materials is driven by the need for increasingly targeted and efficient devices that also have a low ecological impact. These devices often use specially developed materials (e.g., polymers, aptamers, monoclonal antibodies) capable of carrying out the process of recognizing and capturing a specific target in a similar way to biomaterials of natural origin. In this article, we present two case studies, in which the target is a biomolecule of medical interest, in particular, α-thrombin and cytokine IL-6. In these examples, different biomaterials are compared to establish, with a theoretical-computational procedure known as proteotronics, which of them has the greatest potential for use in a biodevice. [ABSTRACT FROM AUTHOR]

The Stefan–Boltzmann (SB) law relates the radiant emittance of an ideal black-body cavity at thermal equilibrium to the fourth power of the absolute temperature T as q = σ T 4 , with σ = 5. 6 7 × 1 0 − 8 W m − 2 K − 4 the SB constant, first estimated by Stefan to within 1 1 % of the present theoretical value. The law is an important achievement of modern physics since, following Planck [Ueber das Gesetz der Energieverteilung im Normalspectrum [On the law of distribution of energy in the normal spectrum], Ann. Phys. 4 (1901) 553–563], its microscopic derivation implies the quantization of the energy related to the electromagnetic field spectrum. Somewhat astonishing, Boltzmann presented his derivation in 1878 making use only of electrodynamic and thermodynamic classical concepts, apparently without introducing any quantum hypothesis (here called first Boltzmann paradox). By contrast, the Boltzmann derivation implies two assumptions not justified within a classical approach, namely: (i) the zero value of the chemical potential and (ii) the internal energy of the black body with a finite value and dependent from both temperature and volume. By using Planck [Ueber das Gesetz der Energieverteilung im Normalspectrum [On the law of distribution of energy in the normal spectrum], Ann. Phys. 4 (1901) 553–563] quantization of the radiation field in terms of a gas of photons, the SB law received a microscopic interpretation free from the above assumptions that also provides the value of the SB constant on the basis of a set of universal constants including the quantum action constant h. However, the successive consideration by Planck [Uber die Begründung des Gesetzes der schwarzen Strahlung [On the grounds of the law of black body radiation], Ann. Phys. 6 (1912) 642–656] concerning the zero-point energy contribution was found to be responsible of another divergence of the internal energy for the single photon mode at high frequencies. This divergence is of pure quantum origin and is responsible for a vacuum-catastrophe, to keep the analogy with the well-known ultraviolet catastrophe of the classical black-body radiation spectrum, given by the Rayleigh–Jeans law in 1900. As a consequence, from a rigorous quantum-mechanical derivation we would expect the divergence of the SB law (here called second Boltzmann paradox). Here, both the Boltzmann paradoxes are revised by accounting for both the quantum-relativistic photon gas properties, and the Casimir force. [ABSTRACT FROM AUTHOR]

We propose a model for bacterial Quorum Sensing based on an auxiliary electrostatic-like interaction originating from a fictitious electrical charge that represents bacteria activity. A cooperative mechanism for charge/activity exchange is introduced to implement chemotaxis and replication. The bacteria system is thus represented by means of a complex resistor network where link resistances take into account the allowed activity-flow among individuals. By explicit spatial stochastic simulations, we show that the model exhibits different quasi-realistic behaviors from colony formation to biofilm aggregation. The electrical signal associated with Quorum Sensing is analyzed in space and time and provides useful information about the colony dynamics. In particular, we analyze the transition between the planktonic and colony phases as the intensity of Quorum Sensing is varied. [ABSTRACT FROM AUTHOR]

Featured Application: Bio-electronic devices take advantages of some specific duties of biological matter. The specific ability of some proteins to use sunlight is considered for the realization of photo-electronic devices. Here the focus is on the role of the pH, whose variations seem to affect the protein conductance. In the perspective of an increasing attention to ecological aspects of science and technology, it is of interest to design devices based on architectures of modular, low cost, and low-pollutant elements, each of them able to perform simple duties. Elemental devices may be themselves green as, for example, proteins able to make simple actions, like sensing. To this aim, photosensitive proteins are often considered because of the possibility of transferring their specific reaction to visible light into electronic signals. Here, we investigate the expected electrical response of the photoactive protein Reaction Center (bRC) of Rhodobacter Sphaeroides within the proteotronics, a recent branch of molecular electronics that evaluates the electrical properties of a protein by using an impedance network protein analog based on the protein tertiary structure and the degree of electrical connectivity between neighboring amino acids. To this purpose, the linear and nonlinear regimes of the electrical response to an applied bias are studied when the protein is in its native state or in an active state. In the linear response regime, results evidence a significant difference in the electrical properties of bRC when the pH value of the solution in which the protein is embedded changes from acid to basic. In the non-linear response regime, the current-voltage characteristics experimentally reported in the recent literature are interpreted in terms of a sequential tunneling mechanism of charge transfer. The qualitative agreement of present findings with available experiments strongly suggests the use of this protein as a bio-rheostat or a pH sensor. [ABSTRACT FROM AUTHOR]

The need of new diagnostic methods satisfying, as an early detection, a low invasive procedure and a cost-efficient value, is orienting the technological research toward the use of bio-integrated devices, in particular, bio-sensors. The set of know-why necessary to achieve this goal is wide, from biochemistry to electronics and is summarized in an emerging branch of electronics, called proteotronics. Proteotronics is here applied to state a comparative analysis of the electrical responses coming from type-1 and type-2 opsins. In particular, the procedure is used as an early investigation of a recently discovered family of opsins, the proteorhodopsins activated by blue light, BPRs. The results reveal some interesting and unexpected similarities between proteins of the two families, suggesting the global electrical response are not strictly linked to the class identity. [ABSTRACT FROM AUTHOR]

We present a theoretical investigation on possible selection of olfactory receptors (ORs) as sensing components of nanobiosensors. Accordingly, we generate the impedance spectra of the rat OR I7 in the native and activated states and analyze their differences. In this way, we connect the protein morphological transformation, caused by the sensing action, with its change in electrical impedance. The results are compared with those obtained by studying the best known protein of the G protein coupled receptor (GPCR) family: bovine rhodopsin. Our investigations indicate that a change in morphology goes with a change in impedance spectrum mostly associated with a decrease in the static impedance up to about 60% of the initial value, in qualitative agreement with existing experiments on rat OR I7. The predictiveness of the model is tested successfully for the case of recent experiments on bacteriorhodopsin. The present results point to a promising development of a new class of nanobiosensors based on the electrical properties of GPCR and other sensing proteins. [ABSTRACT FROM AUTHOR]

In electrochemical experiments much of information is enclosed in the impedance response. It is usually represented by means of an equivalent electrical circuit, whose elements are able to describe the most general physico-chemical phenomena which characterize the system. To this aim, some standard circuits have been designed and commercial software is available to perform the best fit of the experimental data. However, the search of the most appropriate equivalent circuit is sometimes not a simple task due to experimental constraints and also due to a limited knowledge of the phenomenon. Therefore, a blind fitting procedure could give unsatisfactory results. Graphical representations of impedance, in particular the phase plot, offer useful tips in guessing the most appropriate equivalent circuit and estimating the values of the circuit parameters. Here we present a procedure in three steps: a. the analysis of some graphical representations of impedance for the selection of a suitable equivalent circuit, b. the formulation of a minimal set of equations useful for guessing the circuit parameters; c. a numerical test. An application to a set of data referring to quite different experimental conditions complete the study. [ABSTRACT FROM AUTHOR]

The fluctuation dissipation theorem (FDT) is the basis for a microscopic description of the interaction between electromagnetic radiation and matter. By assuming the electromagnetic radiation in thermal equilibrium and the interaction in the linear-response regime, the theorem interrelates the macroscopic spontaneous fluctuations of an observable with the kinetic coefficients that are responsible for energy dissipation in the linear response to an applied perturbation. In the quantum form provided by Callen and Welton in their pioneering paper of 1951 for the case of conductors [H. B. Callen and T. A. Welton, Irreversibility and generalized noise, Phys. Rev.83 (1951) 34], electrical noise in terms of the spectral density of voltage fluctuations, S V (ω) , detected at the terminals of a conductor was related to the real part of its impedance, Re [ Z (ω) ] , by the simple relation S V (ω) = 2 ℏ ω coth ℏ ω 2 K B T Re [ Z (ω) ] , where K B is the Boltzmann constant, T is the absolute temperature, ℏ is the reduced Planck constant and ω = 2 π f is the angular frequency. The drawbacks of this relation concern with: (i) the appearance of a zero-point contribution which implies a divergence of the spectrum at increasing frequencies; (ii) the lack of detailing the appropriate equivalent-circuit of the impedance, (iii) the neglect of the Casimir effect associated with the quantum interaction between zero-point energy and boundaries of the considered physical system; (iv) the lack of identification of the microscopic noise sources beyond the temperature model. These drawbacks do not allow to validate the relation with experiments, apart from the limiting conditions when ℏ ω ≪ K B T. By revisiting the FDT within a brief historical survey of its formulation, since the announcement of Stefan–Boltzmann law dated in the period 1879–1884, we shed new light on the existing drawbacks by providing further properties of the theorem with particular attention to problems related with the electrical noise of a two-terminals sample under equilibrium conditions. Accordingly, among others, we will discuss the duality and reciprocity properties of the theorem, the role played by different statistical ensembles, its applications to the ballistic transport-regime, to the case of vacuum and to the case of a photon gas. [ABSTRACT FROM AUTHOR]

Experiments in organic semiconductors (polyacenes) evidence a strong super quadratic increase of the current-voltage (I-V) characteristic at voltages in the transition region between linear (Ohmic) and quadratic (trap-free space-charge-limited current) behaviors. Similarly, excess noise measurements at a given frequency and increasing voltages evidence a sharp peak of the relative spectral density of the current noise in concomitance with the strong superquadratic I-V characteristics. Here, we discuss the physical interpretation of these experiments in terms of an essential contribution from field-assisted trapping-detrapping processes of injected carriers. To this purpose, the fraction of filled traps determined by the I-V characteristics is used to evaluate the excess noise in the trap-filled transition (TFT) regime. We have found an excellent agreement between the predictions of our model and existing experimental results in tetracene and pentacene thin films of different length in the range . [ABSTRACT FROM AUTHOR]

Current-voltage characteristics of metal-protein-metal structures made of proteorhodopsin and bacteriorhodopsin are modeled by using a percolation-like approach. Starting from the tertiary structure pertaining to the single protein, an analogous resistance network is created. Charge transfer inside the network is described as a sequential tunneling mechanism and the current is calculated for each value of the given voltage. The theory is validated with available experiments, in dark and light. The role of the tertiary structure of the single protein and of the mechanisms responsible for the photo-activity is discussed. [ABSTRACT FROM PUBLISHER]

Recently, there has been growing interest in the electrical properties of bacteriorhodopsin (bR), a protein belonging to the transmembrane protein family. Several experiments pointed out the role of green light in enhancing the current flow in nanolayers of bR, thus confirming potential applications of this protein in the field of optoelectronics. By contrast, the mechanisms underlying the charge transfer and the associated photocurrent are still far from being understood at a microscopic level. To take into account the structure-dependent nature of the current, in a previous set of papers we suggested a mechanism of sequential tunneling among neighboring amino acids. As a matter of fact, when irradiated with green light, bR undergoes a conformational change at a molecular level. Thus, the role played by the protein tertiary-structure in modeling the charge transfer cannot be neglected. The aim of this paper is to go beyond previous models, in the framework of a new branch of electronics we call proteotronics, which exploits the ability of using proteins as reliable, well-understood materials for the development of novel bioelectronic devices. In particular, the present approach assumes that the conformational change is not the unique transformation the protein undergoes when irradiated by light. Instead, the light can also promote an increase of the protein state free energy that, in turn, should modify its internal degree of connectivity. This phenomenon is here described by the change of the value of an interaction radius associated with the physical interactions among amino acids. The implemented model enables us to achieve a better agreement between theory and experiments in the region of a low applied bias by preserving the level of agreement at high values of applied bias. Furthermore, results provide new insights on the mechanisms responsible for bR photoresponse. [ABSTRACT FROM AUTHOR]

We investigate a particular phase transition between two different tunneling regimes, direct and injection (Fowler-Nordheim), experimentally observed in the current-voltage characteristics of the light receptor bacteriorhodopsin (bR). Here, the sharp increase of the current above about 3 V is theoretically interpreted as the cross-over between the direct and injection sequential-tunneling regimes. Theory also predicts a very special behavior for the associated current fluctuations around steady state. We find the remarkable result that in a large range of bias around the transition between the two tunneling regimes, the probability density functions can be traced back to the generalization of the Gumbel distribution. This non-Gaussian distribution is the universal standard to describe fluctuations under extreme conditions. [ABSTRACT FROM AUTHOR]

The Bessel equation is shown to be equivalent, under suitable transformations, to a system of two damped/amplified parametric oscillator equations, which have been used in the study of inflationary models of the Universe, thermal field theories and Chern–Simons gauge theories. The breakdown of loop-antiloop symmetry due to group contraction manifests itself as breaking of time-reversal symmetry. The relation between some infinite dimensional loop-algebras, such as the Virasoro-like algebra, and the Euclidean algebras e(2) and e(3) is also analyzed. [ABSTRACT FROM AUTHOR]

By resorting to some results in quantum field theories with spontaneous breakdown of symmetry, we show that an explanation based on microscopic dynamics can be given for the fact that topological defect formation is observed during the process of nonequilibrium phase transitions characterized by a non-zero order parameter. We show that the Nambu-Goldstone particle acquires an effective non-zero mass due to boundary (finite volume) effects and this is related to the size of the defect. We also relate such volume effects with temperature effects. [ABSTRACT FROM AUTHOR]

The decoherence mechanism signals the limits beyond which the system dynamics approaches the classical behavior. We show that in some cases decoherence may also signal the limits beyond which the system dynamics has to be described by quantum field theory, rather than by quantum mechanics. [ABSTRACT FROM AUTHOR]

We show that in the dissipative quantum model of brain the time-dependence of the frequencies of the electrical dipole wave quanta leads to the dynamical organization of the memories in space (i.e., to their localization in more or less diffused regions of the brain) and in time (i.e., to their longer or shorter life-time). The life-time and the localization in domains of the memory states also depend on internal parameters and on the number of links that the brain establishes with the external world. These results agree with the physiological observations of the dynamic formation of neural circuitry which grows as brain develops and relates to external world. [ABSTRACT FROM AUTHOR]

Cytokines are a family of proteins which play a major role in the regulation of the immune system and the development of several diseases, from rheumatoid arthritis to cancer and, more recently, COVID-19. Therefore, many efforts are currently being developed to improve therapy and diagnosis, as well as to produce inhibitory drugs and biosensors for a rapid, minimally invasive, and effective detection. In this regard, even more efficient cytokine receptors are under investigation. In this paper we analyze a set of IL-6 cytokine receptors, investigating their topological features by means of a theoretical approach. Our results suggest a topological indicator that may help in the identification of those receptors having the highest complementarity with the protein, a feature expected to ensure a stable binding. Furthermore, we propose and discuss the use of these receptors in an idealized experimental setup. [ABSTRACT FROM AUTHOR]

The impedance response of an electrochemical cell able to convert sunlight into electrical power is analyzed and discussed. Light conversion is due to a photosynthetic system known as reaction center, which is the core of photosynthesis in several living beings. Under illumination, an abrupt transformation drives the cell electrical response from insulator to conductor and a photocurrent is observed. The impedance spectrum shows a peculiar shape which significantly modifies after the protein activation. It has been analyzed by means of a graphical/analytical/numerical procedure. Some impedance graphical representations are indicated as the most appropriate to suggest the design of an equivalent electrical circuit. Then, the analytical expression of this circuit is formulated and used to set-up a custom Phyton code useful for fitting experimental data. Finally, an appropriate normalization procedure is proposed, which validates data in dark and light and can be useful as a fast screening of measurements. [ABSTRACT FROM AUTHOR]

Aptamers are strands of DNA or RNA molecules, chemically synthetized and able to bind a wide range of targets, from small molecules to live cells, and even tissues, with high affinity and specificity. Due to their efficient targeting ability, they have many different kinds of applications. Particularly attractive is their use in biotechnology and disease therapy, in substitution of antibodies. They represent a promising way for early diagnosis (aptasensors), but also for delivering imaging agents and drugs and for inhibiting specific proteins (therapeutic aptamers). Starting by briefly reviewing the most recent literature concerning advances in biomedical applications of aptamers and aptasensors, the focus is on the issues of a theoretical/computational framework (proteotronics) for modelling the electrical properties of biomolecules. Some recent results of proteotronics concerning the electrical, topological and affinity properties of aptamers are reviewed. [ABSTRACT FROM AUTHOR]

By analogy with linear response, we formulate the duality and reciprocity properties of current and voltage fluctuations expressed by Nyquist relations, including the intrinsic bandwidths of the respective fluctuations. For this purpose, we individuate total-number and drift-velocity fluctuations of carriers inside a conductor as the microscopic sources of noise. The spectral densities at low frequency of the current and voltage fluctuations and the respective conductance and resistance are related in a mutually exclusive way to the corresponding noise source. The macroscopic variances of current and voltage fluctuations are found to display a dual property via a plasma conductance that admits a reciprocal plasma resistance. Analogously, the microscopic noise sources are found to obey a dual property and a reciprocity relation. The formulation is carried out in the frame of the grand canonical (for current noise) and canonical (for voltage noise) ensembles, and results are derived that are valid for classical as well as degenerate statistics, including fractional exclusion statistics. The unifying theory so developed sheds new light on the microscopic interpretation of dissipation and fluctuation phenomena in conductors. In particular, it is proven that for fermions, as a consequence of the Pauli principle, nonvanishing single-carrier velocity fluctuations at zero temperature are responsible for diffusion but not for current noise, which vanishes in this limit. [ABSTRACT FROM AUTHOR]

The electrical properties of a set of seven-helix transmembrane proteins, whose space arrangement [three-dimensional (3D) structure] is known, are investigated by using regular arrays of the amino acids. These structures, specifically cubes, have topological features similar to those shown by the chosen proteins. The theoretical results show a good agreement between the predicted current-voltage characteristics obtained from a cubic array and those obtained from a detailed 3D structure. The agreement is confirmed by available experiments on bacteriorhodopsin. Furthermore, all the analyzed proteins are found to share the same critical behavior of the voltage-dependent conductance and of its variance. In particular, the cubic arrangement evidences a short plateau of the excess conductance and its variance at high voltages. The results of the present investigation show the possibility to predict the I-V characteristics of a multiple-protein sample even in the absence of detailed knowledge of the proteins' 3D structure. [ABSTRACT FROM AUTHOR]

Abstract: In this study, we report a dose-dependent detection of odorant molecules in solution by rat olfactory receptor I7 (OR I7) in its membrane fraction. The OR I7 is immobilized on a gold electrode by multilayer bioengineering based on a mixed self-assembled monolayer and biotin/avidin system, which allows for a well-controlled immobilization of the bioreceptor within its lipid environment. The odorant detection is electronically performed in a quantitative manner by electrochemical impedance spectroscopy (EIS) measurements on samples and controls. [Copyright &y& Elsevier]