Eleonora Alfinito

Eleonora Alfinito
Università del Salento | Unisalento · Department of Mathematics and Physics "Ennio De Giorgi"

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About

144
Publications
9,014
Reads
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1,173
Citations
Additional affiliations
January 2006 - present
Position
  • Researcher
January 2004 - December 2008
Position
  • Researcher
January 2002 - December 2004
Università del Salento
Position
  • Research Assistant

Publications

Publications (144)
Preprint
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 comp...
Article
Biological matter is attracting increasing attention because it shows innovative features that have found several applications in technology, from highly sensitive sensors for medical treatments to devices for energy harvesting. Furthermore, most of its phenomenology remains unclear, thus giving hints for speculative investigations. In this Letter,...
Preprint
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
Preprint
Full-text available
The Stefan-Boltzmann (SB) law relates the emissivity q,to the fourth power of the absolute temperature T, the proportionaly factor, $\sigma$ firstly estimated by Stefan to within 11 per cent of the actual value. The law is a pillar of modern physics since its microscopic derivation implies the quantization of the energy related to the electromagnet...
Preprint
Full-text available
New science and new technology need new materials and new concepts. In this respect, biological matter can play a primary role because it is a material with interesting and innovative features which has found several applications in technology, from highly sensitive sensors for medical treatments to devices for energy harvesting. Furthermore, most...
Article
Full-text available
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...
Preprint
Full-text available
Cytokines are a family of proteins which play a major role in the regulation of immune system, and enter the development of several diseases from rheumatoid arthritis to cancer and, more recently, COVID-19. Therefore, many efforts are currently being spent in therapy and diagnosis, producing inhibitory drugs, as well as biosensors for a rapid, poor...
Article
Full-text available
The quantum formula of the fluctuation dissipation theorem (FDT) was given by Callen and Welton in 1951 [1] for the case of conductors, and then expanded by Kubo in 1966 [2, 3]. The drawback of these quantum relations concerns with the appearance of a zero-point contribution, hω/2 with h the reduced Planck constant and ω the angular frequency of th...
Article
Full-text available
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 i...
Preprint
Full-text available
Bio-devices are designed to allow biological matter to perform in vitro almost the same functions it performs in vivo. Therefore, they can benefit from the specificities of such materials and are expected to perform better than traditional devices. On the other hand, the integration of biological material with electronic/electrochemical instrumenta...
Article
Aptamers represent a challenging field of research, relevant for diagnosis in macular degeneration, cancer, thrombosis and many inflammatory diseases, and promising in drug discovery and development. Their selection is currently performed by a stable in vitro technology, namely, SELEX. Furthermore, computationalstatistical tools have been developed...
Research
Full-text available
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 softwar...
Article
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 softwar...
Article
Full-text available
The use of aptamers (short single strands of DNA or RNA) in therapy, diagnosis and early detection of illness is a challenging field of research. Aptamers are artificially produced, tailored to best fit a specific target, and are a competitive alternative to antibodies. The in vivo procedures to synthetize aptamers are in continuous development, en...
Article
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 w...
Article
The selection of high-affinity aptamers is of paramount interest for clinical and technological applications. A novel strategy is proposed to validate the reliability of the 3D structures of a group of anti- Angiopoietin-2 aptamers, produced in silico by using free software. In a previous literature these aptamers were processed both in vitro and i...
Preprint
Full-text available
Computational procedures to foresee the 3D structure of aptamers are in continuous progress. They constitute a crucial input to research, mainly when the crystallographic counterpart of the structures in silico produced is not present. At now, many codes are able to perform structure and binding prediction, although their ability in scoring the res...
Preprint
Full-text available
Computational procedures to foresee the 3D structure of aptamers are in continuous progress. They constitute a crucial input to research, mainly when the crystallographic counterpart of the structures in silico produced is not present. At now, many codes are able to perform structure and binding prediction, although their ability in scoring the res...
Article
Full-text available
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 d...
Preprint
Selected by in vitro techniques (SELEX, cell-SELEX), aptamers are strands of DNA or RNA molecules 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, aptamers are extensively used in different fields of applications. For example, th...
Conference Paper
Aptamers are target specific single stranded DNA, RNA or peptide sequences having the ability to bind a variety of proteins, molecules and also ions. Aptasensors, sensors based on aptamers, are at the frontier of sensing technology, mainly in diagnosis and therapy. They appear to be competitive with traditional sensors due to the possibility of det...
Article
Full-text available
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 {\em indifference} w.r.t. the game at all: their dynamics is designed to account for risk-aversion as an innovative b...
Article
Full-text available
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) behaviours. Similarly, excess noise measurements at a given frequency and increasing voltages evi...
Article
Full-text available
Motivation: The selection of high-affinity aptamers is of paramount interest for clinical and technological applications. A computational investigation to evaluate the relative binding ability of a group of anti- Angiopoietin-2 aptamers is proposed and tested against data already available in the literature. Results: The procedure consists of three...
Article
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 c...
Article
We study the large $N$ expansion of winding Wilson loops in the off-critical regime of the Gross-Witten-Wadia (GWW) unitary matrix model. These have been recently considered in arXiv:1705.06542 and computed by numerical methods. We present various analytical algorithms for the precise computation of both the perturbative and instanton corrections t...
Article
Full-text available
Aptamers are single stranded DNA, RNA or peptide sequences having the ability to bind a variety of specific targets (proteins, molecules as well as ions). Therefore, aptamer production and selection for therapeutic and diagnostic applications is very challenging. Usually they are in vitro generated, but, recently, computational approaches have been...
Article
Epidemic spreading on complex networks depends on the topological structure as well as on the dynamical properties of the infection itself. On general grounds, highly connected individuals and sites exposed to the infection have similar roles in the epidemic propagation. Motivated by this feature, we propose a novel vaccination scheme that exploits...
Article
Full-text available
The role played by zero-point contribution, also called quantum noise or vacuum fluctuations, in the quantum expression of the fluctuation-dissipation theorem (FDT) is a long-standing open problem widely discussed by the physicist community since its announcement by Callen and Welton pioneer paper of 1951 [1]. From one hand, it has the drawbacks of...
Article
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...
Article
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, with significant applications in diagnostics and drug delivery. In particular, the anti-thrombin aptamers are...
Article
Full-text available
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 sourc...
Article
Full-text available
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 res...
Conference Paper
Full-text available
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 rec...
Article
Full-text available
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 implie...
Book
importance in the design of protein‐based electronics and in attaining an adequate level of understanding of protein functioning. This is particularly true in the case of transmembrane proteins, such as those pertaining to the G protein¬–coupled receptors (GPCRs) that are involved in a broad range of biological processes, and a large number of clin...
Article
Full-text available
The system of two damped/amplified oscillator equations is of widespread interest in the study of many physical problems and phenomena, from inflationary models of the Universe to thermal field 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 para...
Article
Full-text available
The electrical properties of a set of seven-helix transmembrane proteins, whose space arrangement (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 t...
Conference Paper
Different scientific disciplines from biochemistry to electronics are recently converging their interests toward the investigation of nanodevices useful for biological, medical and electronic *everyday * applications. The strategies to attempt this aim are therefore more and more interconnected and innovative so that it is legitimate to announce th...
Conference Paper
Full-text available
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...
Article
Full-text available
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....
Article
Full-text available
Recently, a growing interest has been addressed to the electrical properties of bacteriorhodopsin (bR), a protein belonging to the transmembrane protein family. 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 neighbouring amino acids. As a matter...
Article
Full-text available
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 actio...
Article
Full-text available
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 b...
Article
Full-text available
The continuous research of new diagnostical methods, early, low invasive and much efficient is orienting the technological research toward the use of bio-integrated devices and in particular sensors, able to use the excellent ability of proteins to selectively react to a specific stimulus, in a fast, reproducible and reversible way. To explore thes...
Article
Full-text available
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 seq...
Article
Full-text available
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) t...
Conference Paper
Full-text available
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...
Article
Full-text available
We investigate conductance and conductance fluctuations of two transmembrane proteins, bacteriorhodopsin and proteorhodopsin, belonging to the family of protein light receptors. These proteins are widely diffused in aqueous environments, are sensitive to visible light and are promising biomaterials for the realization of novel photodevices. The con...
Article
We present here the results of the investigation of the electrical properties of two olfactory receptors (ORs): rat, OR I7, and human, OR 17-40, which are of interest in the creation of smell nanobiosensors. Described here is our investigation comparing the results from experiments using electrochemical impedance spectroscopy with the theoretical p...
Article
Full-text available
We investigate the nature of a class of probability density functions, say G(a), with a the shape parameter, which generalizes the Gumbel distribution. These functions appear in a model of charge transport, when applied to a metal-insulator-metal structure, where the insulator is constituted by a monolayer of bacteriorhodopsin. Current shows a shar...
Article
Full-text available
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...
Article
Full-text available
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 molecu...
Article
Full-text available
Current-voltage (I-V) characteristics in proteins are sensitive to conformational changes induced by an external stimulus (photons, chemical, etc.). This sensitivity can be used in medical and industrial applications as well as shedding new light on the microscopic structure of biological materials. Here, we show that a sequential tunneling model o...
Article
Full-text available
In this paper we explore 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 obta...
Article
Full-text available
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 abru...