We present a procedure of investigation of the sensing protein behaviour when captures a molecule (ligand). In particular the procedure is applied to a couple of olfactory receptors (ORs), the human OR17-40 and the rat OR-I7. The interest in these proteins resides in the possible selection of olfactory receptors as sensing components of nanobiosensors. Accordingly, within a simple network model, we produce the impedance spectra of the ORs under consideration, in the native and activated state and analyze their differences. Furthermore, we get insights on the protein structure by means of the so-called contact maps. The impedance spectra connect the protein morphological transformation, caused by the sensing action, with its change of electrical impedance; the contact maps give complementary information on the structural protein transformations. Our investigations indicate that a change in morphology goes with a change in impedance spectrum and that the size of the variation is in qualitative agreement with existing experiments on these proteins. 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.

The increasing interest in the production and selection of aptamers for therapeutic and diagnostic applications yields many studies in recent years. Most of them investigated the production techniques, usually performed in vitro, but also the possibility of an in silico selection. Due to their specific ability of target-inhibition, some aptamers are under clinical trials, and some other were just patented by several pharmaceutical companies. However, the mechanism of aptamer-ligand formation is not completely understood. In this paper we explore the possibility to describe some topological and electrical features of the aptamer TBA alone and complexed with thrombin, its specific ligand, by using a network consisting of two different networks. The results are quite intriguing, confirming some conjectures about the different role of two cations, i.e. Na+ and K+, in stabilizing the compound. Furthermore, this study suggests the use of resistance measurements to discriminate among different affinities.

We propose a nanosensor with a biological active part able to identify specific odorants. The biological part should be constituted by olfactory receptors pertaining to the G protein-coupled receptors, the most efficient natural sensors for odorant discrimination. Modeling, design, and experiments performed for proving the concept are reported and discussed.

We study the phase diagram of a minority game where three classes of agents are present. Two types of agents play a risk-loving game that we model by the standard Snowdrift Game. The behaviour of the third type of agents is coded by indifference with respect to the game at all: their dynamics is designed to account for risk-aversion as an innovative behavioral gambit. From this point of view, the choice of this solitary strategy is enhanced when innovation starts, while is depressed when it becomes the majority option. This implies that the payoff matrix of the game becomes dependent on the global awareness of the agents measured by the relevance of the population of the indifferent players. The resulting dynamics is nontrivial with different kinds of phase transition depending on a few model parameters. The phase diagram is studied on regular as well as complex networks.

We report on charge transport and current fluctuations in a single bacteriorhodpsin protein in a wide range of applied voltages covering direct and injection tunnelling regimes. The satisfactory agreement between theory and available experiments validates the physical plausibility of the model developed here. In particular, we predict a rather abrupt increase of the variance of current fluctuations in concomitance with that of the I-V characteristic. The sharp increase, for about five orders of magnitude of current variance is associated with the opening of low resistance paths responsible for the sharp increase of the I-V characteristics. A strong non-Gaussian behavior of the associated probability distribution function is further detected by numerical calculations.

Current voltage (I-V) characteristics in proteins can be sensitive to conformational change induced by an external stimulus (photon, odour, etc.). This sensitivity can be used in medical and industrial applications besides shedding new light in the microscopic structure of biological materials. Here, we show that a sequential tunneling model of carrier transfer between neighbouring amino-acids in a single protein can be the basic mechanism responsible of the electrical properties measured in a wide range of applied potentials. We also show that such a strict correlation between the protein structure and the electrical response can lead to a new generation of nanobiosensors that mimic the sensorial activity of living species. To demonstrate the potential usefulness of protein electrical properties, we provide a microscopic interpretation of recent I-V experiments carried out in bacteriorhodopsin at a nanoscale length.

The extreme vulnerability of humans to new and old pathogens is constantly highlighted by unbound outbreaks of epidemics. This vulnerability is both direct, producing illness in humans (dengue, malaria), and also indirect, affecting its supplies (bird and swine flu, Pierce disease, and olive quick decline syndrome). In most cases, the pathogens responsible for an illness spread through vectors. In general, disease evolution may be an uncontrollable propagation or a transient outbreak with limited diffusion. This depends on the physiological parameters of hosts and vectors (susceptibility to the illness, virulence, chronicity of the disease, lifetime of the vectors, etc.). In this perspective and with these motivations, we analyzed a stochastic lattice model able to capture the critical behavior of such epidemics over a limited time horizon and with a finite amount of resources. The model exhibits a critical line of transition that separates spreading and non-spreading phases. The critical line is studied with new analytical methods and direct simulations. Critical exponents are found to be the same as those of dynamical percolation.

The electrical properties of a set of seven-helix transmembrane proteins, whose space arrangement [threedimensional (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 showa good agreement between the predicted current-voltage characteristics obtained from a cubic array and those obtained from a detailed 3Dstructure. 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.

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 ¯eld-assisted trapping-detrapping processes of injected carriers. To this purpose, the fraction of ¯lled traps determined by the I–V characteristics is used to evaluate the excess noise in the trap-¯lled transition (TFT) regime. We have found an excellent agreement between the predictions of our model and existing experimental results in tetracene and pentacene thin ¯lms of di®erent length in the range 0:65 35 m.

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.

By considering a set of experiments carried out on bacteriorhodopsin in vitro by Casuso et al (2007 Phys. Rev. E 76 041919), we extract the conductance as function of the applied voltage. The microscopic interpretation of experiments shows that charge transfer is ruled by a direct tunneling (DT) mechanism at low bias and by a Fowler–Nordheim (FN) tunneling mechanism at high bias. A nucleation region at the cross-over between the DT and FN regimes can be identified. A theoretical analysis of conductance fluctuations is performed by calculating the corresponding variance and the probability density functions (PDFs): these constitute a powerful indicator in order to understand the internal dynamics of the system. Conductance fluctuations are non-Gaussian and follow well the standard generalized Gumbel distributions G.a/. In particular, at low bias, the PDFs are bimodal and can be resolved in at least a couple of G.a/ functions with different values of the shape parameter a. The nucleation region is characterized by a single Gumbel distribution, G.1/. At increasing bias, the G.1/ distribution turns in a bimodal distribution. We discuss possible correlations between the voltage dependence of the G.a/ and the microscopic mechanisms that determine the electrical response of the system.

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 behaviour 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.

Aptamers are single stranded DNA, RNA or peptide sequences having the ability to bind several specific targets (proteins, molecules as well as ions). Therefore, aptamer production and selection for therapeutic and diagnostic applications is very challenging. Usually, they are generated in vitro, although computational approaches have been recently developed for the in silico production. Despite these efforts, the mechanism of aptamer-ligand formation is not completely clear, and producing high affinity aptamers is still quite difficult. This paper aims to develop a computational model able to describe aptamer-ligand affinity. Topological tools, such as the conventional degree distribution, the rank-degree distribution (hierarchy), and the node assortativity are employed. In doing so, the macromolecules tertiary-structures are mapped into appropriate graphs. These graphs reproduce the main topological features of the macromolecules, by preserving the distances between amino acids (nucleotides). Calculations are applied to the thrombin binding aptamer (TBA), and the TBA-thrombin complex, produced in the presence of Na+ or K+. The topological analysis is able to detect several differences between complexes obtained in the presence of the two cations, as expected by previous investigations. These results support graph analysis as a novel computational tool for testing affinity. Otherwise, starting from the graphs, an electrical network can be obtained by using the specific electrical properties of amino acids and nucleobases. Therefore, a further analysis concerns with the electrical response, revealing that the resistance is sensitively affected by the presence of sodium or potassium, thus suggesting resistance as a useful physical parameter for testing binding affinity

Increasing attention has been recently devoted to protein-based nanobiosensors. The main reason is the huge number of possible technological applications, going from drug detection to cancer early diagnosis. Their operating model is based on the protein activation and the corresponding conformational change, due to the capture of an external molecule, the so-called ligand. Recent measurements, performed with different techniques on human 17-40 olfactory receptor, evidenced a very narrow window of response in respect of the odour concentration. This is a crucial point for understanding whether the use of this olfactory receptor as sensitive part of a nanobiosensor is a good choice. In this paper we investigate the topological and electrical properties of the human olfactory receptor 17-40 with the objective of providing a microscopic interpretation of available experiments. To this purpose, we model the protein by means of a graph able to capture the mean features of the 3D backbone structure. The graph is then associated with an equivalent impedance network, able to evaluate the impedance spectra of the olfactory receptor, in its native and activated state. We assume a topological origin of the different protein electrical responses to different ligand concentrations: In this perspective all the experimental data are collected and interpreted satisfactorily within a unified scheme, also useful for application to other proteins.

We report a theoretical/computational approach for modeling the current-voltage characteristics of sensing proteins. The modeling is applied to a couple of transmembrane proteins, bacteriorhodopsin and proteorhodopsin, sensitive to visible light and promising biomaterials for the development of a new generation of photo-transducers. The agreement between theory and experiments sheds new light on the microscopic interpretation of charge transfer in proteins and biological materials in general.

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.

Aptamers are chemically produced oligonucleotides, able to bind a variety of targets such as drugs, proteins and pathogens with high sensitivity and selectivity. Therefore, aptamers are largely employed for producing label-free biosensors (aptasensors), with significant applications in diagnostics and drug delivery. In particular, the anti-thrombin aptamers are biomolecules of high interest for clinical use, because of their ability to recognize and bind the thrombin enzyme. Among them, the DNA 15-mer aptamer (TBA), has been widely explored around the possibility of using it in aptasensors. This paper proposes a microscopic model of the electrical properties of TBA and of the aptamer-thrombin complex, combining information from both structure and function, following the issues addressed in an emerging branch of electronics known as proteotronics. The theoretical results are compared and validated with measurements reported in the literature. Finally, the model suggests resistance measurements as a novel tool for testing aptamer-target affinity.

Different scientific disciplines, from biochemistry to electronics, are converging toward the investigation of nanodevices useful for biological, medical and electronic applications. The strategies to attempt this aim are therefore more and more interconnected and innovative so that it is legitimate to announce the born of a new discipline, the proteotronics . Proteotronics has the main objective to propose and develop innovative electronic devices, based on the selective action of specific proteins.

We investigate conductance fluctuations of two transmembrane proteins, bacteriorhodopsin and proteorhodopsin, belonging to the family of opsins. These proteins are sensitive to visible light and are promising biomaterials for the realization of novel photodevices. The conductance exhibits, over a threshold bias value, a rapid increase which is well described by a power-law behaviour. In the same way, over the threshold value the variance fast decreases following a power-law. Furthermore, the conductance fluctuations evidence a non-Gaussian behaviour with a probability density function (PDF) which follows a generalized Gumbel distribution, typical of extreme-value statistics. The theoretical model is validated on existing current-voltage measurements and the interpretation of the PDF of conductance fluctuations is proven to be in line with the microscopic mechanisms responsible of charge transport.

Il trasferimento e l’integrazione di informazione fra discipline scientifiche molto diverse è sempre foriero di progresso. Questo seminario si propone di illustrare le caratteristiche della materia vivente, coniugando gli strumenti della fisica tradizionale con quelli della biologia e della chimica. Il fine è quello di aprire nuove strade, inventare nuove strategie e, nel far questo, da una parte si progredisce nella ricerca specifica, dall’altro si approda a visioni nuove, prospettive inesplorate che allargano gli orizzonti della scienza in generale.

Mammalian olfactory system is the archetype of smell sensor devices. Its complexity resides both in the odorant mechanism of capture by the single olfactory receptor (OR) and in the space organization and codification of the information. The result is a unique profile for each odorant. Our aim is to partially mimick this system, in order to produce a biosensor on nanometric scale. In this paper we present a possible theoretical framework in which the experimental results should be embedded. It consists of the description of the protein in terms of an impedance network able to simulate the electrical characteristics associated with the protein topology.

In this paper we explore relevant electrical properties of two olfactory receptors (ORs), the rat OR I7 and the human, OR 17-40, which are of interest for the realization of smell nanobiosensors. We compare existing experiments, carried out by electrochemical impedance spectroscopy, with theoretical expectations obtained from an impedance network protein analogue, recently developed. The changes in the electrical response due to the sensing action of the proteins are correlated with the conformational change undergone by the single protein. The satisfactory agreement between theory and experiments points to a promising development of a new class of nanobiosensors based on the electrical properties of sensing proteins.

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 devi- ces, 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 proteo- tronics . 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.

The increasing interest in photoactivated proteins as natural replacements for standard inorganic materials in photocells leads to the comparison analysis of bacteriorhodopsin and proteorhodopsin, two widely diffused proteins belonging to the family of type-1 opsins. These proteins share similar behaviors but exhibit relevant differences in the sequential chain of the amino acids constituting their tertiary structure. The use of an impedance network analog to model the protein main features provides a microscopic interpretation of a set of experiments on their photo-conductance properties. In particular, this model links the protein electrical responses to the tertiary structure and to the interactions between neighboring amino acids. The same model is also used to predict the small-signal response in terms of the Nyquist plot. Interestingly, these rhodopsins are found to behave like a wide-gap semiconductor with intrinsic conductivities of the order of 107 S cm1.

Epidemic evolution on complex networks strongly depends on their topology and the infection dynamical properties, as highly connected nodes and individuals exposed to the contagion have competing roles in the disease spreading. In this spirit, we propose a new immunization strategy exploiting the knowledge of network geometry and dynamical information about the spreading infection. The flexibility and effectiveness of the proposed scheme are successfully tested with numerical simulations on a wide set of complex networks.

Human olfactory 17-40 and Bacteriorhodopsin are two protein receptors that received particular attention in electronics, due to the possibility of implementing nano-biodevices able to detect odours and light and thus useful for medical and green energy harvesting applications. Some recent experiments concerning the electrical responses of these receptors are reviewed. Data are interpreted in the framework of a new science exploiting the complexity in biology and biomedical engineering called proteotronics. In particular, the single protein is modelled as an impedance network whose topological properties affect the electrical response as measured by experiments.

Protein-mediated charge transport is of relevant importance in the design of protein-based electronics and in attaining an adequate level of understanding of protein functioning. This book reviews a variety of experiments devoted to the investigation of charge transport in proteins and presents a unified theoretical model to interpret macroscopic results in terms of the amino acids backbone-structure of the single protein. It aims to serve a broad audience of researchers involved in the field of electrical characterization of biological materials and in the development of new molecular devices based on proteins and also as a reference platform that surveys existing data and presents the basis for future development of a new branch of nano-electronics, which by mixing proteomics, that is, the large-scale study of proteins, particularly their structures and functions, and electronics is introduced here as proteotronics.

Protein-mediated charge transport is of relevant importance in the design of protein based electronics and in attaining an adequate level of understanding of protein functioning. This is particularly true for the case of transmembrane proteins, like those pertaining to the G protein coupled receptors (GPCRs). These proteins are involved in a broad range of biological processes like catalysis, substance transport, etc., thus being the target of a large number of clinically used drugs. This paper briefly reviews a variety of experiments devoted to investigate charge transport in proteins and present a unified theoretical model able to relate macroscopic experimental results with the conformations of the amino acids backbone of the single protein.

The convergent interests of different scientific disciplines, from biochemistry to electronics, toward the investigation of protein electrical properties, has promoted the development of a novel bailiwick, the so called proteotronics. The main aim of proteotronics is to propose and achieve innovative electronic devices, based on the selective action of specific proteins. This paper gives a sketch of the fields of applications of proteotronics, by using as significant example the detection of a specific odorant molecule carried out by an olfactory receptor. The experiment is briefly reviewed and its theoretical interpretation given. Further experiments are envisioned and expected results discussed in the perspective of an experimental validation.

Epidemic spreading on complex networks depends on the topological structure as well as on the dynamical properties of the infection itself. Generally speaking, highly connected individuals play the role of hubs and are crucial to channel information across the network. On the other hand, static topological quantities measuring the connectivity structure are independent of the dynamical mechanisms of the infection. A natural question is therefore how to improve the topological analysis by some kind of dynamical information that may be extracted from the ongoing infection itself. In this spirit, we propose a novel vaccination scheme that exploits information from the details of the infection pattern at the moment when the vaccination strategy is applied. Numerical simulations of the infection process show that the proposed immunization strategy is effective and robust on a wide class of complex networks.

Fluctuation-dissipation relations are complemented by relating the macrovariables conductance and resistance, that describe dissipation, to the microvariables variance of carrier number and drift velocity fluctuations, that are the noise sources for constant voltage and constant current operation conditions, respectively. Thermal equilibrium implies a relationship between these two noise sources which follows from the reciprocity property of conductance and resistance. The boundary conditions of the measurement select the proper microscopic source of fluctuations to be related to the dissipation. An important consequence is that the source of shot noise, being associated with fluctuations of the carrier number inside the sample, is already present under equilibrium conditions, while the time scale of the source changes from an effective transport time to a current transit time when going from equilibrium to nonequilibrium conditions.

Fluctuation-dissipation relations are complemented by relating the macrovariables conductance and resistance, that describe dissipation, to the microvariables variance of carrier number and drift velocity fluctuations, that are the noise sources for constant voltage and constant current operation conditions, respectively. Thermal equilibrium implies a relationship between these two noise sources which follows from the reciprocity property of conductance and resistance. The boundary conditions of the measurement select the proper microscopic source of fluctuations to be related to the dissipation. An important consequence is that the source of shot noise, being associated with fluctuations of the carrier number inside the sample, is already present under equilibrium conditions, while the time scale of the source changes from an effective transport time to acurrent transit time when going from equilibrium to nonequilibrium conditions.

We investigate relevant electrical properties of two olfactory receptors (ORs), one from rat, OR I7, and the other from human, OR 17-40, which are of interest for the realization of smell nanobiosensors. The investigation compares existing experiments, coming from electrochemical impedance spectroscopy, with the theoretical expectations obtained from an impedance network protein analogue, recently developed. The changes in the response due to the sensing action of the ORs are correlated with the conformational change undergone by the single protein. The satisfactory agreement between theory and experiments points to a promising development of a new class of nanobiosensors based on the electrical properties of sensing proteins.

The role played by zero-point contribution in black-body radiation spectrum is investigated in connection with the presence of Casimir force. We assert that once mechanical stability for the physical system is established, there is no further role for zero-point contribution to the spectrum in full agreement with experimental evidence. As a direct consequence, Johnson–Nyquist noise in dissipative conductors, should be interpreted just in terms of thermal fluctuations only, thus neglecting quantum fluctuations predicted by [H. Callen and T. Welton, Irreversibility and generalized noise, Phys. Rev. 83 (1951) 34]. Casimir force between opposite metallic plates can be independently measured by its equilibration through application of a mechanical force and measuring it at a mechanical equilibrium.

We report on electrical properties of the two sensing proteins: bacteriorhodopsin and rat olfactory receptor OR-I7. As relevant transport parameters we consider the small-signal impedance spectrum and the static current-voltage characteristics. Calculations are compared with available experimental results and the model predictability is tested for future perspectives.

The system of two damped/amplied oscillator equations is of widespread interest in the study of many physical problems and phenomena, from in ationary models of the Universe to thermal eld theories, in condensed matter physics as well in high energy physics, and also in neuroscience. In this report we review the equivalence, in a suitable parametrization, between such a system of equations and the Bessel equations. In this connection, we discuss the breakdown of loop-antiloop symmetry, its relation with time-reversal symmetry and the mechanism of group contraction. Euclidean algebras such as e(2) and e(3) are also discussed in relation with Virasoro-like algebra.