1,721,093 research outputs found
Current-voltage characteristics of seven-helix proteins from a cubic array of amino acids
No full textThe 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
The role of topology in electrical properties of bR and rat-olfactory receptor
No full textWe 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
Proteotronics: a toolkit for bioelectronics
No full textThe talk gives a bird’s eye view on a procedure named Proteotronics [1], used to analyze some physical properties of biomolecules, in particular proteins and aptamers. The name refers to the principal aim of this method, i.e. to investigate the electronic features of this special kind of matter, starting from its peculiar topology, which is not regular but ordered. In doing so, a complex network approach is used to reproduce the space (3D) structure of the biomolecule, while its electronic features are mimicked by using lumped elements. Particular attention is paid to proteins when used as the active part of electrical biosensors. In that case, the biochemical sequence of actions due to the capture of the specific target is converted into an electrical signal. This signal is the result of the protein-target interaction and is finely captured by an impedance network. Linear and super-linear electrical responses are analyzed in facts and figures, comparing experimental data and theoretical expectations.
Affinity is a quite complex concept used to define the quality of binding of two (macro)molecules, and is connected with both topological (structure complementarity) and functional (stability of bonds) features of the partners. As a very recent result, the affinity of different aptamers for their specific targets has been interpreted in terms of some standard topological properties of the analogue complex networks, as well as of the associated resistance. Affinity is also the key concept adopted by several in silico structure prediction procedures and docking methods. Some new tools developed inside the proteotronics framework were applied to the analysis of a set of 5 aptamers whose structure with and without the target protein was obtained by using a computational procedure based on free software, SimRNA and Autodock Vina [2]. The configuration produced for each aptamer belong to two different families one, called hair, in which the aptamer is on the top of the protein, in the natural binding domain; the other, called belt, in which the aptamer hangs the protein often far from the binding domain. The scoring of the structures given by the computational procedure is in line with the closeness of the partner biomolecules, as verified by using the proteotronics approach, but it is not able to select between hair and belt configurations [2]. To better refine this scoring, we build a novel structure-based indicator. The selection based on both the indicators, produces a prevalence of the hair configurations for the highest affinity aptamer, and a prevalence of the belt configurations for lowest affinity aptamer. However, the final say about the role of belt configurations is expected by crystallographic data. In conclusion, we have analyzed several facets of the affinity concept, in different frameworks and by using the proteotronics approach. Present and future results will help us get a deep comprehension of chemical affinity
Fluctuation Dissipation Theorem and Electrical Noise Revisited
No full textThe 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, SV(), detected at the terminals of a conductor was related to the real part of its impedance, Re[Z()], by the simple relation SV()= [Z()], where KB is the Boltzmann constant, T is the absolute temperature, is the reduced Planck constant and =2f 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 KBT. 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
Mechanisms responsible for the photocurrent in bacteriorhodopsin
Full text linkRecently, 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
Time reversal, Loop-antiloop symmetry and Bessel equation
No full textThe 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 analyze
Evidence of Gumbel distributions of conductance fluctuations in bacteriorhodopsin thin films
Full text linkBy 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
Modeling current-voltage charateristics of proteorhodopsin and bacteriorhodopsin: towards an optoelectronics based on proteins
No full textCurrent-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
DISSIPATION AND MEMORY DOMAINS IN THE QUANTUM MODEL OF BRAIN, IN ``QUANTUM BRAIN DYNAMICS"
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