Photonic Potential of Haloarchaeal Pigment Bacteriorhodopsin for Future Electronics: A Review

Bacteriorhodopsin of purple membrane reverses anisotropy outside the pH range of proton pumping based on logic gate realization

The bacteriorhodopsin of purple membrane is the first discovered light-sensing protein among ion transporting microbial rhodopsins, some of which (e.g. Archaerhodopsin 3) could be broadly used as tools in optogenetics having wide potential of medical applications. Since its discovery as early as in 1971, bacteriorhodopsin has attracted wide interests in nano-biotechnology, particularly in optoelectronics devices. Therefore, the present work has been motivated due to two topics; firstly, anisotropy demand became indispensible in bioelectronics; secondly, the stationary level of electric response in bacteriorhodopsin within the pH range of proton pumping (pH 3 - pH 10) implies, in turn, raising here a question about whether the electric anisotropy is implicated for reducing (or switching off) such level beyond such pH range. Noteworthy is that the purple membrane converts to blue form upon acidification, while to reddish purple form upon alkalization. In the present study, the acidic and alkaline forms of bacteriorhodopsin have exhibited most probable state of reversal for the dielectric anisotropy around pH 2.5 and pH 10.5, respectively. This is underscored by proposing a correlation seemingly found between disassembly of the crystalline structure of bacteriorhodopsin and the reversal of dielectric anisotropy, at such acidic and alkaline reversal pH's, in terms of the essence of the crystalline lattice. Most importantly, the results have substantiated dual frequency characteristics and logic gate-based dielectric anisotropy reversal to bacteriorhodopsin, which may implicate it for potential applications in bioelectronics.

Impact of doping with organic dopants and mixed doping with alkali metals and organic dopants on the absorption, electronic, optoelectronic, thermodynamic and nonlinear optical properties of dibenzo[b,def]chrysene in gaseous media: DFT and TD-DFT studies

CONTEXT

In this study, we evaluate the geometrical, absorption, optoelectronic, electronic, nonlinear optical (NLO) and thermodynamic properties of dibenzo[b,def]chrysene molecule derivatives by means of DFT and TD-DFT simulations. In view of the aim of producing new high-performance materials for non-linear optics (NLO) by doping test, two types of doping were used. We obtained six derivatives by doping with organic dopants (Nitro, amide and ticyanoethenyl) and mixed alkali metal (potassium) and organic dopants. Doping with organic dopants produced molecules A, B and C, respectively when substituting one hydrogen with nitro (NO2), amide (CONH2) and tricyanoethenyl (C5N3) groups, while mixed doping involved considering A, B and C and then substituting two hydrogens with two potassiums to obtain compounds D, E and F respectively. The negative values of the various interaction energies calculated for all the doped molecules show that they are all stable, but also that molecules C and F are the most stable in the case of both dopings. The gap energies calculated at the B3LYP level of theory are all below 3 eV, which means that all the molecules obtained are semiconductors. Better still, compounds C and F, with gap energies of 1.852 eV and 1.204 eV, respectively, corresponding to decreases of 35.67% and 58.18% in gap energy compared with the pristine molecule, are more reactive than the other doped molecules. Mixed doping is therefore a highly effective way of narrowing the energy gap and boosting the semiconducting character and reactivity of organic materials. Optoelectronic properties have also been improved, with refractive index values higher than those of the reference material, glass. This shows that our compounds could be used under very high electric field conditions of the order of 4.164 × 109 V.m-1 for C and 7.410 × 109 V.m-1 for F the highest values at the B3LYP level of theory. The maximum first-order hyperpolarizability values for both types of doping are obtained at the CAM-B3LYP level of theory by C:β mol = 92.088 × 10-30esu and by F:β mol = 129.449 × 10-30esu, and second-order values are also given by these same compounds. These values are higher than the reference value, which is urea, making our compounds potential candidates for high-performance NLO applications. In dynamic mode and at a frequency of 1064 nm, at the CAM-B3LYP level of theory, the highest dynamic hyperpolarizability coefficients were obtained by C and F. Hyper-Rayleigh scattering β HRS , coefficients of the electro-optical Pockel effect (EOPE), EFISHG, third-order NLO-response degree four-wave mixingγ DFWM , quadratic nonlinear refractive index n2 were also calculated. The maximum values of n2 are obtained by C (6.13 × 10-20 m2/W) and F (6.60 × 10-20 m2/W), these values are 2.24 times higher than that of fused silica which is the reference for degenerate four-wave mixing so our molecules could also have applications in optoelectronics as wavelength converters, optical pulse modulators and optical switches.

METHODS

Using the DFT method, we were able to determine the optimized and stable electronic structures of doped dibenzo[b,def]chrysene derivatives in the gas phase. We limited ourselves to using the proven B3LYP and CAMB3LYP levels of theory for calculating electronic properties, and non-linear optics with the 6-311G +  + (d,p) basis set, which is a large basis set frequently used for these types of compound. Gaussian 09 software was used to run our calculations, and Gauss View 6.0.16 was used to visualize the output files. TD-DFT was also used to determine absorption properties at the B3LYP level of theory, using the same basis set.

Photosynthetic Protein-Based Retinal Ganglion Cell Receptive Fields for Detecting Edges and Brightness Illusions

Bacteriorhodopsin, isolated from a halophilic bacterium, is a photosynthetic protein with a structure and function similar to those of the visual pigment rhodopsin. A voltaic cell with bacteriorhodopsin sandwiched between two transparent electrodes exhibits a time-differential response akin to that observed in retinal ganglion cells. It is intriguing as a means to emulate excitation and inhibition in the neural response. Here, we present a neuromorphic device emulating the retinal ganglion cell receptive field fabricated by patterning bacteriorhodopsin onto two transparent electrodes and encapsulating them with an electrolyte solution. This protein-based artificial ganglion cell receptive field is characterized as a bandpass filter that simultaneously replicates excitatory and inhibitory responses within a single element, successfully detecting image edges and phenomena of brightness illusions. The device naturally emulates the highly interacting ganglion cell receptive fields by exploiting the inherent properties of proteins without the need for electronic components, bias power supply, or an external operating circuit.

Archaea: current and potential biotechnological applications

Archaea are microorganisms with great ability to colonize some of the most inhospitable environments in nature, managing to survive in places with extreme characteristics for most microorganisms. Its proteins and enzymes are stable and can act under extreme conditions in which other proteins and enzymes would degrade. These attributes make them ideal candidates for use in a wide range of biotechnological applications. This review describes the most important applications, both current and potential, that archaea present in Biotechnology, classifying them according to the sector to which the application is directed. It also analyzes the advantages and disadvantages of its use.

Giant NLO response and deep ultraviolet transparency of dual (alkali/alkaline earth) metals doped C6O6Li6 electrides

The designing of new materials having outstanding nonlinear optical (NLO) response is much needed for use in latest optics. Herein, the geometric, electronic and NLO properties of alkali and alkaline earth metals doped C6O6Li6 (alk-C6O6Li6-alkearth, alkearth = Ca, Mg, Be and alk = K, Na, Li) electrides is studied via quantum chemical approach. The interaction energies (Eint) are examined to illustrate their thermodynamic stability. The strong interaction energy of -39.99 kcal mol-1 is observed for Ca-C6O6Li6-Li electride in comparison to others. Frontier molecular orbitals (FMOs) energy gap of considered complexes is changed due to the electronic density shifting between metals and C6O6Li6 surface, which notifies the semi conducting properties of these electrides. The FMOs isodensities and natural bond orbital (NBO) charge analysis are performed to justify charge transfer between dopants and complexant. UV-Visible study also confirmed the application of these electrides as deep ultra-violet laser devices. NLO response is studied through calculation of first hyperpolarizability (βo). The highest βo value of 1.68 × 105 au is calculated for Mg-C6O6Li6-K electride. NLO response is further rationalized by three- and two-level models approach.

Medical hypothesis: Neurodegenerative diseases arise from oxidative damage to electron tunneling proteins in mitochondria

Mitochondria likely arose from serial endosymbiosis by early eukaryotic cells and control electron flow to molecular oxygen to facilitate energy transformation. Mitochondria translate between the quantum and macroscopic worlds and utilize quantum tunneling of electrons to reduce activation energy barriers to electron flow. Electron tunneling has been extensively characterized in Complex I of the electron transport chain. Age-related increases in oxidative damage to these electron tunneling systems may account for decreased energy storage found in aged and neurodegenerative disease tissues, such as those from sufferers of amyotrophic lateral sclerosis (ALS), Alzheimer's disease (AD) and Parkinson's disease (PD). This hypothesis is testable. If correct, this hypothesis supports pre-symptomatic, mitochondrially-directed oxygen free radical scavenging therapies.

Macroalgal biomass subcritical hydrolysates for the production of polyhydroxyalkanoate (PHA) by Haloferax mediterranei

Non-conventional carbon sources, such as macroalgae, are sustainable alternatives for large-scale production of biopolymers. The present study examined macroalgae-derived carbohydrates, as carbon sources for the production of polyhydroxyalkanoates (PHAs) by Haloferax mediterranei. Simulants of the hydrolysates of seven different macroalgal biomasses were prepared and the PHA production was studied. A maximum biomass concentration with maximum PHA content was detected in medium prepared from green macroalgae. The highest cell dry weight and PHA concentrations were 3.8 ± 0.2 g·L^-1 and 2.2 ± 0.12 g·L^-1 respectively when Haloferax mediterranei was grown in 25% (w/w) of Ulva sp. hydrolysate, at 42 °C temperature and initial pH of 7.2. Poly(3-hydroxy-butyrate-co-3-hydroxyvalerate was the major PHA constituent. The present study demonstrated that Ulva sp. is a promising feedstock for PHA production.

S-Layer Protein for Resistive Switching and Flexible Nonvolatile Memory Device

In this work, a flexible resistive switching memory device consisting of S-layer protein (Slp) is demonstrated for the first time. This novel device (Al/Slp/indium tin oxide/polyethylene terephthalte) based on a simple and easy fabrication method is capable of bistable switching to low resistive state (LRS) and high resistive state (HRS). This device exhibits bistable memory behavior with stability and a long retention time (>4 × 10³ s), being stable up to a 500 cycle endurance test and with significant HRS/LRS ratio. The device possesses consistent switching performance for more than 100 times bending, corresponding to desired applicability for biocompatible wearable electronics. The memory mechanism is attributed to a trapping/de-trapping process in S-layer protein. These promising results of the flexible memory device could find a way in the wearable storage applications like smart bands and sports equipments' sensors.

Efficient non-cytotoxic fluorescent staining of halophiles

Research on halophilic microorganisms is important due to their relation to fundamental questions of survival of living organisms in a hostile environment. Here we introduce a novel method to stain halophiles with MitoTracker fluorescent dyes in their growth medium. The method is based on membrane-potential sensitive dyes, which were originally used to label mitochondria in eukaryotic cells. We demonstrate that these fluorescent dyes provide high staining efficiency and are beneficial for multi-staining purposes due to the spectral range covered (from orange to deep red). In contrast with other fluorescent dyes used so far, MitoTracker does not affect growth rate, and remains in cells after several washing steps and several generations in cell culture. The suggested dyes were tested on three archaeal (Hbt. salinarum, Haloferax sp., Halorubrum sp.) and two bacterial (Salicola sp., Halomonas sp.) strains of halophilic microorganisms. The new staining approach provides new insights into biology of Hbt. salinarum. We demonstrated the interconversion of rod-shaped cells of Hbt. salinarium to spheroplasts and submicron-sized spheres, as well as the cytoplasmic integrity of giant rod Hbt. salinarum species. By expanding the variety of tools available for halophile detection, MitoTracker dyes overcome long-standing limitations in fluorescence microscopy studies of halophiles.