arXiv subjects

E. Alfinito

Publications and source records attributed to E. Alfinito.

At least 19 recordsLinked to original sources

arXiv2026

Dielectric response in proteins: The proteotronics approach

The dielectric properties of proteins, particularly in their hydrated state, have been extensively studied. Numerous theoretical and experimental investigations have reported values of both the permittivity and the intrinsic dipole moments of specific proteins under well-defined hydration conditions. Since even approximate estimates of these properties are relevant from both fundamental and applied perspectives, we propose a easy-to-use method to calculate the relative permittivity that can be readily integrated into proteotronics workflows. To validate the proposed approach, we compare the results with those obtained using a classical macroscopic method. The outcomes are consistent and contribute further insight into this long-debated issue.

physics.app-ph↗

arXiv2023

Quorum Sensing as a long-range interaction for bacteria growth and bioluminescence

We study the role of Quorum Sensing (QS) in the growth of bacterial colonies and in the bioluminescence produced. These two phenomena are both regulated by QS and the experimental data show a non-trivial correlation between them. It is also known that the specific bacterial substrate potentially modifies the behavior of the colony. In the specific case of the bioluminescent gram-negative bacterium, Vibrio harveyi, we propose a three-autoinducer model in which QS is described in terms of long-range interaction between charged objects placed on a regular network and playing the role of bacteria. The charges spread in the network through fictitious non-linear electrostatic interactions. QS is monitored by analyzing the current flowing within the network. The model parameters are determined by comparing the simulations with the data present in the literature and related to liquid cultures. New colony growth measurements are then performed on Vibrio campbelli (a member of the clade Harveyi) grown on hydroxyapatite (HA) substrates relevant for biomedical applications. Growth on the substrate differs from growth in liquid culture, although the observed bioluminescence is similar. We exploit our model to understand the differences between colonies in liquid culture and on substrate in terms of the relative role and cooperation of the three autoinducers.

physics.bio-ph↗

arXiv2021

A pH-based bio-rheostat: a proof-of-concept

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 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 new hints for speculative investigations. In this letter, we explore the possibility to use a well-known photosensitive protein, the Reaction Center of Rhodobacter Sphaeroides, to build up an electrical pH sensor, i.e., a device able to change its resistance depending on the pH of the solution in which it crystalizes. By using a microscopic model successfully tested on analogue proteins, we investigate the electrical response of the Reaction Center single protein under different conditions of applied bias, showing the feasibility of the bio-rheostat hypothesis. As a matter of facts, the calculated resistance of this protein grows of about 100% when going from a pH = 10 to a pH = 6.5. Moreover, calculations of the current voltage characteristics well agree with available experiments performed with a current atomic force microscopy under neutral conditions. All findings are in qualitative agreement with the known role of pH in biochemical activities of Reaction Center and similar proteins, therefore supporting a proof-of-concept for the development of new electron devices based on biomaterials.

physics.app-ph↗

arXiv2018

A validation strategy for in silico generated aptamers

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 aptamers, produced in silico by using free software. The procedure consists of three steps: a. the production of a large set of conformations for each candidate aptamer, b. the rigid docking upon the receptor, c. the topological and electrical characterization of the products. Steps a. and b. allow a global binding score of the ligand-receptor complexes based on the distribution of the "effective affinity", i.e. the sum of the conformational and the docking energy. Step c. employs a complex network approach (Proteotronics) to characterize the electrical properties of the aptamers and the ligand-receptor complexes. The test-bed is represented by a group of anti- Angiopoietin-2 aptamers. In a previous literature these aptamers were processed both in vitro and in silico, by using an approach different from that here presented, and finally tested with a SPS experiment. Computational expectations and experimental outcomes did not agree, while our results show a good agreement with the known measurements. The devised procedure is not aptamer-specific and, integrating structure production with structure selection, candidates itself as a quite complete theoretical approach for aptamer selection.

q-bio.QM↗

arXiv2018

Current voltage characteristics and excess noise at the trap filling transition in polyacenes

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 evidence a sharp peak of the relative spectral density of the current noise in concomitance with the strong super-quadratic 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 $0.65 ÷35 \ μm$.

cond-mat.mtrl-sci↗

arXiv2017

Hierarchy and assortativity as new tools for affinity investigation: the case of the TBA aptamer-ligand complex

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 developed for the in silico selection, with a higher affinity for the specific target. Anyway, the mechanism of aptamer-ligand formation is not completely clear, and not obvious to predict. This paper aims to develop a computational model able to describe aptamer-ligand affinity performance by using the topological structure of the corresponding graphs, assessed by means of numerical tools such as the conventional degree distribution, but also the rank-degree distribution (hierarchy) and the node assortativity. 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 reveals different affinity performances between the macromolecules in the presence of the two cations, as expected by previous investigations in literature. These results nominate the graph topological analysis as a novel theoretical 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, which reveals that the resistance sensitively depends on the presence of sodium or potassium thus posing resistance as a crucial physical parameter for testing affinity.

q-bio.BM↗

arXiv2015

On the mechanisms responsible of photocurrent in bacteriorhodopsin (Bacteriorhodopsin's sense of light)

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 of fact, it is well accepted that, 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 called proteotronics, which exploits the ability to use 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 that the protein undergoes when irradiated by light. Instead, the light can also promote a free-energy increase of the protein state that, in turn, should modify its internal degree of connectivity, here described by the change in 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.

cond-mat.soft↗

arXiv2014

Opsin vs opsin: new materials for biotechnological applications

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 \textit{proteotronics}. Proteotronics is here 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.

q-bio.BM↗

arXiv2014

Proteotronics: Electronic devices based on proteins

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.

cond-mat.soft↗

arXiv2013

Current-Voltage Characteristics and non-Gaussian fluctuations in two different protein light receptors

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 conductance exhibits a rapid increase at increasing applied voltages, over a threshold value. Around the threshold value the variance of conductance fluctuations shows a dramatic jump of about 5 orders of magnitude: conductance and variance behaviours trace a second order phase transition. 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.

cond-mat.soft↗

arXiv2012

Gumbel distribution and current fluctuations in critical systems

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.

cond-mat.stat-mech↗

arXiv2011

Olfactory receptors for a smell sensor: A comparative study of the electrical responses of rat I7 and human 17-40

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 obtained from an impedance network protein analogue, recently developed. The changes in the 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.

cond-mat.soft↗

arXiv2011

Charge transport and current fluctuations in bacteriorhodopsin based nanodevices

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.

cond-mat.mes-hall↗

arXiv2011

The role of topology in electrical properties of bacteriorhodopsin and rat olfactory receptor I7

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.

cond-mat.mes-hall↗

arXiv2009

Tuning the Correlation Decay in the Resistance Fluctuations of Multi-Species Networks

A new network model is proposed to describe the $1/f^α$ resistance noise in disordered materials for a wide range of $α$ values ($0< α< 2$). More precisely, we have considered the resistance fluctuations of a thin resistor with granular structure in different stationary states: from nearly equilibrium up to far from equilibrium conditions. This system has been modelled as a network made by different species of resistors, distinguished by their resistances, temperature coefficients and by the energies associated with thermally activated processes of breaking and recovery. The correlation behavior of the resistance fluctuations is analyzed as a function of the temperature and applied current, in both the frequency and time domains. For the noise frequency exponent, the model provides $0< α< 1$ at low currents, in the Ohmic regime, with $α$ decreasing inversely with the temperature, and $1< α<2$ at high currents, in the non-Ohmic regime. Since the threshold current associated with the onset of nonlinearity also depends on the temperature, the proposed model qualitatively accounts for the complicate behavior of $α$ versus temperature and current observed in many experiments. Correspondingly, in the time domain, the auto-correlation function of the resistance fluctuations displays a variety of behaviors which are tuned by the external conditions.

cond-mat.mtrl-sci↗

arXiv2007

A network model to investigate structural and electrical properties of proteins

One of the main trend in to date research and development is the miniaturization of electronic devices. In this perspective, integrated nanodevices based on proteins or biomolecules are attracting a major interest. In fact, it has been shown that proteins like bacteriorhodopsin and azurin, manifest electrical properties which are promising for the development of active components in the field of molecular electronics. Here we focus on two relevant kinds of proteins: The bovine rhodopsin, prototype of GPCR protein, and the enzyme acetylcholinesterase (AChE), whose inhibition is one of the most qualified treatments of Alzheimer disease. Both these proteins exert their functioning starting with a conformational change of their native structure. Our guess is that such a change should be accompanied with a detectable variation of their electrical properties. To investigate this conjecture, we present an impedance network model of proteins, able to estimate the different electrical response associated with the different configurations. The model resolution of the electrical response is found able to monitor the structure and the conformational change of the given protein. In this respect, rhodopsin exhibits a better differential response than AChE. This result gives room to different interpretations of the degree of conformational change and in particular supports a recent hypothesis on the existence of a mixed state already in the native configuration of the protein.

q-bio.QM↗

arXiv2007

Long-term Correlations and 1/f^alpha Noise in the Steady States of Multi-Species Resistor Networks

We introduce a multi-species network model which describes the resistance fluctuations of a resistor in a non-equilibrium stationary state. More precisely, a thin resistor characterized by a 1/f^alpha resistance noise is described as a two-dimensional network made by different species of elementary resistors. The resistor species are distinguished by their resistances and by their energies associated with thermally activated processes of breaking and recovery. Depending on the external conditions, stationary states of the network can arise as a result of the competition between these processes. The properties of the network are studied as a function of the temperature by Monte Carlo simulations carried out in the temperature range 300 ÷800 K. At low temperatures, the resistance fluctuations display long-term correlations expressed by a power-law behavior of the auto-correlation function and by a value approx 1 of the alpha-exponent of the spectral density. On the contrary, at high temperatures the resistance fluctuations exhibit a finite and progressively smaller correlation time associated with a non-exponential decay of correlations and with a value of the alpha-exponent smaller than one. This temperature dependence of the alpha coefficient reproduces qualitatively well the experimental findings.

cond-mat.mtrl-sci↗

arXiv2005

Modelization of Thermal Fluctuations in G Protein-Coupled Receptors

We simulate the electrical properties of a device realized by a G protein coupled receptor (GPCR), embedded in its membrane and in contact with two metallic electrodes through which an external voltage is applied. To this purpose, recently, we have proposed a model based on a coarse graining description, which describes the protein as a network of elementary impedances. The network is built from the knowledge of the positions of the C-alpha atoms of the amino acids, which represent the nodes of the network. Since the elementary impedances are taken depending of the inter-nodes distance, the conformational change of the receptor induced by the capture of the ligand results in a variation of the network impedance. On the other hand, the fluctuations of the atomic positions due to thermal motion imply an impedance noise, whose level is crucial to the purpose of an electrical detection of the ligand capture by the GPCR. Here, in particular, we address this issue by presenting a computational study of the impedance noise due to thermal fluctuations of the atomic positions within a rhodopsin molecule. In our model, the C-alpha atoms are treated as independent, isotropic, harmonic oscillators, with amplitude depending on the temperature and on the position within the protein (alpha-helix or loop). The relative fluctuation of the impedance is then calculated for different temperatures.

q-bio.QM↗