Flexible Triboelectric Nanogenerator for Promoting the Proliferation and Migration of Human Fibroblast Cells

Chronic wound healing is often a prolonged process with the migration and proliferation of fibroblast cells playing crucial roles. Electrical stimulation (ES) has emerged as a promising physical therapy modality to promote these key events. In this study, we address this issue by employing a triboelectric nanogenerator (TENG) as an electrical stimulator for both drug release and the stimulation of fibroblast cells. The flexible TENG with a sandwich structure was fabricated using a PCL nanofibrous layer, Kapton, and silicon rubber. The TENG could be folded to any degree and twisted, and it could return to its original shape when the force was removed. Cultured cells received ES twice and three times daily for 8 days, with a 30 min interval between sessions. By applying current in a safe range and appropriate time (twice daily), fibroblasts demonstrate an accelerated proliferation and migration rate. These observations were confirmed through cell staining. Additionally, in vitro tests demonstrated the TENG's ability to simultaneously provide ES and release vitamin C from the patch. After 2 h, the amount of released drug increased 2 times in comparison to the control group. These findings provide support for the development of a TENG for the treatment of wounds, which underlines the promise of this new technique for developing portable electric stimulation devices.

Application of Nanoscopic Quantum Systems in Retinal Restoration

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Computational modeling of the variation of the transmembrane potential of the endothelial cells of the blood-brain-barrier subject to an external electric field

The electromechanical properties of the membrane of endothelial cells forming the blood-brain barrier play a vital role in the function of this barrier. The mechanical effect exerted by external electric fields on the membrane could change its electrical properties. In this study the effect of extremely low frequency (ELF) external electric fields on the electrical activity of these cells has been studied by considering the mechanical effect of these fields on the capacitance of the membrane. The effect of time-dependent capacitance of the membrane is incorporated in the current components of the parallel conductance model for the electrical activity of the cells. The results show that the application of ELF electric fields induces hyperpolarization, having an indirect effect on the release of nitric oxide from the endothelial cell and the polymerization of actin filaments. Accordingly, this could play an important role in the permeability of the barrier. Our finding can have possible consequences in the field of drug delivery into the central nervous system.

Shortening the sulfur cell cycle by a green approach for bio-production of extracellular metalloid-sulfide nanoparticles

In the present study, a new approach was introduced regarding the extracellular synthesis of selenium sulfide micro/nano-particles using Saccharomyces cerevisiae in different ammonium sulfate supplementation and in the presence of sodium selenosulfate precursors (S₁) and a blend of selenous acid and sodium sulfite (S₂). In S₁, only cell supernatant exposed to ammonium sulfate was able to reduce sodium selenosulfate. Whereas, in S₂, cell supernatant in both pre-conditions of with or without ammonium sulfate (S₂ + or S₂-) were able to reduce selenous acid and sodium sulfite. Electron microscopy, also indicated that selenium sulfide NPs were successfully synthesized with average size of 288 and 332 nm for S₂ + and S₂- in SEM and 268 and 305 nm in TEM. Additionally, elemental mapping by energy-dispersive x-ray analysis confirmed the presence of sulfur/selenium elements in the particles in a proportion of 24.50 and 23.31 for S₂- and S₂ + , respectively. The mass spectrometry indicated the probability of Se₂S₂, SeS_1.1, Se₂, Se, SeS₅, SeS₃, Se₃S₅/Se₅, Se₃/SeS₅, Se₆, Se₄/SeS₇, Se_2.57S_5.43/Se₂S₂ and Se₄S/Se₂S₆ molecules for S₂ + and of Se, Se₂, Se₃S₅/Se₅, Se₆ and Se₄ species for S₂-. In FTIR spectra, primary (i.e. 1090-1020 and 1650-1580 cm^-1) and secondary (1580-1490 cm^-1) amine bands duly confirmed the protein corona around the NPs.

Enhanced proliferation and migration of fibroblast cells by skin-attachable and self-cleaning triboelectric nanogenerator

Skin wounds are common in accidental injuries, surgical operations, and chronic diseases. The migration and proliferation of fibroblast cells are fundamental to wound healing, which can be promoted by electrical stimulation as a physical therapy modality. Therefore, the development of portable electrical stimulation devices that can be used by patients on-site is an essential need. In the present study, a self-cleaning triboelectric nanogenerator (TENG) has been fabricated for enhancing cell proliferation and migration. The polycaprolactone‑titanium dioxide (PCL/TiO₂₎ and polydimethylsiloxane (PDMS) layers were fabricated via a facile method and used as the electropositive and electronegative pair, respectively. The effect of stimulation time on proliferation and migration of fibroblast cells was investigated. The results demonstrated that when the cells were stimulated once-a-day for 40 min, the cell viability was increased, while a long daily stimulation time has an inhibitory effect. Under electrical stimulation, the cells move toward the middle of the scratch, making the scratch almost invisible. During repeated movements, the prepared TENG connected to a rat skin generated an open-circuit voltage and a short-circuit current around 4 V and 0.2 μA, respectively. The proposed self-powered device can pave the way for a promising therapeutic strategy for patients with chronic wounds.

Density functional theory computation of the intermolecular interactions of Al2@C24 and Al2@Mg12O12 semiconducting quantum dots conjugated with the glycine tripeptide

The nature of intermolecular forces within semiconductor quantum dot systems can determine various physicochemical properties, as well as their functions, in nanomedical applications. The purpose of this study has been to investigate the nature of the intermolecular forces operating between Al₂@C₂₄ and A_l2@Mg₁₂O₁₂ semiconducting quantum dots and the glycine tripeptide (GlyGlyGly), and also consider whether permanent electric dipole–dipole interactions play a significant role vis-à-vis these molecular systems. The energy computations, including the Keesom and the total electronic interactions and the energy decomposition, together with the quantum topology analyses were performed. Our results demonstrate that no significant correlation is found between the magnitude and orientation of the electrical dipole moments, and the interaction energy of the Al₂@C₂₄ and A_l2@Mg₁₂O₁₂ with GlyGlyGly tripeptide. The Pearson correlation coefficient test revealed a very weak correlation between the quantum and the Keesom interaction energies. Apart from the quantum topology analyses, the energy decomposition consideration confirmed that the dominant share of the interaction energies was associated with the electrostatic interactions, yet both the steric and the quantum effects also made appreciable contributions. We conclude that, beside the electrical dipole–dipole interactions, other prominent intermolecular forces, such as the polarization attraction, the hydrogen bond, and the van der Waals interactions can also influence the interaction energy of the system. The findings of this study can be utilized in several areas in the field of nanobiomedicine, including the rational design of cell-penetrating and intracellular drug delivery systems using semiconducting quantum dots functionalized with a peptide.

The nature of intermolecular forces within semiconducting quantum dot systems can determine various physicochemical properties, as well as their functions, in nanomedical applications.

The investigation into the effect of the length of RGD peptides and temperature on the interaction with the αIIbβ3 integrin: a molecular dynamic study

The tripeptide Arg-Gly-Asp acid (RGD) is a protein sequence in the binding of proteins to cell surfaces, and is involved in various biological processes such as cell adhesion to the extracellular matrix, platelet activation, hemostasis, etc. The C2 domain of the Von Willebrand Factor (VWF), containing the RGD motif, plays an important role in the initial homeostasis process. It binds to the αIIbβ3 integrin and stimulates platelet aggregation. We have investigated, using the molecular Dynamic (MD) simulation method, the effect of the RGD-peptide length, and temperature variation, on the binding to the αIIbβ3 integrin receptor. We examined 10 different structural modes of the αIIbβ3 at three different temperatures; 237 K, 310 K and 318 K. Our findings show that the amino acids that form a binding pocket include Asp₂₂₄, Tyr₂₃₄, Ser₂₂₆, Tyr₁₉₀, Tyr₁₈₉, Trp₂₆₀, Trp₂₆₂, Asp_259, Lys₂₅₃, Arg₂₁₄, Asp₂₁₇, Ser₁₆₁ and Ala₂₁₈ and that the ligand-receptor interaction was increased at higher temperatures. It was also found that the increase in the number of ligands' amino acids and their types (% glycine) plays an important role in the stability, conformation, and ligand-receptor interaction.Communicated by Ramaswamy H. Sarma.

Deflection-based laser sensing platform for selective and sensitive detection of H2S using plasmonic nanostructures

Considering the severe hazards of abnormal concentration level of H₂S as an extremely toxic gas to the human body and due to the disability of olfactory system in sensing toxic level of H₂S concentration, a reliable, sensitive, selective and rapid method for the detection of H₂S is proposed and its efficacy is analyzed through simulation. The proposed system is based on the deflection of a laser beam in response to the temperature variations in its path. In order to provide selectivity and improve sensitivity, gold nanostructures were employed in the system. The selectivity was introduced based on the thiol-gold interactions and the sensitivity of the system was enhanced due to the modification of plasmon resonance behavior of gold nanostructures in response to gas adsorption. Results from our analysis demonstrate that compared with Au and SiO₂-Au, the Au nanomatryoshka structures (Au-SiO₂-Au) showed the highest sensitivity due to promoting higher deflections of the laser beam.

A computational modelling study of excitation of neuronal cells with triboelectric nanogenerators

Neurological disorders and nerve injuries, such as spinal cord injury, stroke, and multiple sclerosis can result in the loss of muscle function. Electrical stimulation of the neuronal cells is the currently available clinical treatment in this regard. As an effective energy harvester, the triboelectric nanogenerators (TENG) can be used for self-powered neural/muscle stimulations because the output of the TENG provides stimulation pulses for nerves. In the present study, using a computational modelling approach, the effect of surface micropatterns on the electric field distribution, induced voltage and capacitance of the TENG structures have been investigated. By incorporating the effect of the TENG inside the mathematical model of neuron’s electrical behavior (cable equation with Hodgkin-Huxley model), its impact on the electrical behavior of the neurons has been studied. The results show that the TENG operates differently with various surface modifications. The performance of the TENG in excitation of neurons depends on the contact and release speed of its electrodes accordingly.

A modeling study of the effect of an alternating magnetic field on magnetite nanoparticles in proximity of the neuronal microtubules: A proposed mechanism for detachment of tau proteins

BACKGROUND AND OBJECTIVE

It is known that the disintegration of microtubules in neurons occurs in response to the phosphorylation of the tau proteins that promotes the structural instability of the microtubules, as one of the factors underlying the onset of Alzheimer's disease (AD).

METHODS

In this study, the mechanical variations undergone by the tau protein's and microtubule's structures due to the action of intrinsic magnetite nanoparticles inside the brain tissue have been computationally modeled using the finite element (FEM) method.

RESULTS

The von Mises stress induced by magnetite nanoparticles, subject to an applied alternating magnetic field, leads to local heating and mechanical forces, prompting a corresponding deformation in, and displacement of, the microtubule and the tau protein.

CONCLUSIONS

The induction of these deformations would increase the probability of the microtubules' depolymerization, and hence their eventual structural disintegration.

A proposed implantable voltammetric carbon fiber-based microsensor for corticosteroid monitoring by cochlear implants

A novel carbon fiber microsensor (CFMS) with the capability of being inserted in the cochlear implant structure is introduced for in situ measurement of corticosteroid concentration. The microsensor structure is composed of a carbon microfiber, an Ag wire, and a Pt wire acting respectively as a working electrode, a reference electrode, and a counter electrode. In addition, a silicone septum is used for isolation purposes in place of the epoxy resin. The septum-insulated microsensor is capable of monitoring the concentration of the corticosteroids in the perilymph fluid without a need for sampling from the inner ear fluid and the consequent ex vivo analysis. The electrochemical determination of the corticosteroids was investigated on the carbon fiber electrode surface by differential pulse voltammetry. During the reduction of dexamethasone (DEX), a cathodic peak with a peak potential of -1.3 V appeared at the CFMS. Using the CFMS under optimized conditions, a calibration plot of the dexamethasone (DEX) in the artificial perilymph solution exhibited two linear ranges from 10 nM to 2 μM and 2 to 40 μM (sensitivity equal to 16.55 μA μM^-1 cm^-2; LOD = 4 nM) conforming with the DEX concentration range inside the inner ear after the insertion of a drug-eluting cochlear implant electrode (CIE). Furthermore, the interferences occurring in the hearing functions of the CIE after the presence and function of the CFMS were simulated numerically using the finite element method. According to our results, decreasing the size of the microsensor introduces lower interferences with the auditory function of the cochlear implant electrode.

Determination of the optimal location of samples on quartz tuning fork-based biosensors: a computational study

In view of efficiency, simple operation, and affordable cost and disposability, quartz tuning fork systems form good candidates for mechanical-based biosensors in point of care applications. Based on the geometrical structure, the frequency response of the tuning fork- based sensors is dependent on the location of absorbed samples. In order to have the maximum efficiency and sensitivity, the optimized condition of sample loading on the fork structures should be considered. In this regard, here, we have determined the optimized sample location to be on the prongs of the quartz tuning fork by calculating the frequency response of the quartz tuning fork using the finite element method. From an application point of view, we have obtained an agreement between the calculational method and the experimental excitation technique of the structure. The results from our study show that by using an appropriate location for the sample, the quartz tuning fork could be exploited with high sensitivity.

Computational modeling to determine key regulators of hypoxia effects on the lactate production in the glycolysis pathway

In solid tumors, hypoxia can trigger aberrant expression of transcription factors and genes, resulting in abnormal biological functions such as altered energetic pathways in cancer cells. Glucose metabolism is an important part of this phenomenon, which is associated with changes in the functional expression of transporters and enzymes involved in the glycolysis pathway. The latter phenomenon can finally lead to the lactate accumulation and pH dysregulation in the tumor microenvironment and subsequently further invasion and metastasis of cancer cells. Having capitalized on the computational modeling, in this study, for the first time, we aimed to investigate the effects of hypoxia-induced factor-1 (HIF-1) mediated hypoxia on the magnitude of functional expression of all the enzymes and transporters involved in the glycolysis process. The main objective was to establish a quantitative relationship between the hypoxia intensity and the intracellular lactate levels and determine the key regulators of the glycolysis pathway. This model clearly showed an increase in the lactate concentration during the oxygen depletion. The proposed model also predicted that the phosphofructokinase-1 and phosphoglucomutase enzymes might play the most important roles in the regulation of the lactate production.

Population Kinetics and Mechanistic Aspects of Saccharomyces cerevisiae Growth in Relation to Selenium Sulfide Nanoparticle Synthesis

Biosynthesis of nanoparticles (NPs) by microorganisms is a cost- and energy-effective approach. However, how the production of NPs affects the population of producing organism remains as an unresolved question. The present study aimed to evaluate the kinetics of Saccharomyces cerevisiae growth in relation to synthesis of selenium sulfide nanoparticles by using a population model. To this end, the population of S. cerevisiae cells was investigated in terms of colony forming units (CFU) in the presence of the substrate in different time points. Fluctuation of sulfite reductase (SiR) activity, expression of MET5 and MET10 genes, and concentrations of sulfite and selenium were evaluated to support the population findings. CFU values in the test groups were lower than those in the control counterparts. The rise and fall of the SiR activity and MET5 and MET10 gene expression conformed to the variations of CFU values. The rate of reduction in the selenium and sulfite concentrations tended to decrease over the time. In conclusion, the cells population was negatively and positively affected by selenium and sulfite concentrations, respectively. The indirect relationship of the selenium ions concentration in the path analysis revealed that the product, selenium sulfide nanoparticles, caused this drop in S. cerevisiae cells population.

Phototherapy alters the oncogenic metabolic activity of breast cancer cells

BACKGROUND

Metabolic reprogramming in cancer cells is a strategy to attain a high proliferation rate, invasion, and metastasis. In this study, the effects of phototherapy at different wavelengths were investigated on the metabolic activity of breast cancer cells.

METHODS

The states of the MCF7 cells proliferation and viability were measured by the MTT assay. Glucose consumption and the lactate formation in the LED-irradiated cells culture were analyzed by biochemical assay kits. The Amino acid concentration in the culture media of the MCF7 cells was analyzed using HPLC. Moreover, the gene expression of some glycolytic, TCA cycle and pentose phosphate cycleenzymes were assessed by real time PCR.

RESULTS

Phototherapy at wavelength of 435 nm decreased the cell viability by 23 % when the energy dose was 17.5 J/cm² compared to the control group. The expression of the LDHA and GLS was up-regulated in 629 nm-treated cells while the expression of these genes was down-regulated in the MCF7 cells irradiated at 435 nm in comparison with the control group. Consequently, the glucose consumption and the lactate formation were diminished respectively by 22 % and 15 % in the 435 nm-irradiated cells while the glucose consumption and the lactate formation were increased in the 629 nm-irradiated cells by 112 % and 107 % in comparison with the control group. In addition, the analysis of the glutamine concentration by the HPLC indicated that the blue light irradiation decreased the glutamine consumption while the red light increased it in comparison with the control group.

Enhancement of the biological autoluminescence by mito-liposomal gold nanoparticle nanocarriers

One of the most important barriers to the detection of the biological autoluminescence (BAL) from biosystems using a non-invasive monitoring approach, in both the in vivo and the in vitro applications, is its very low signal intensity (< 1000 photons/s/cm²). Experimental studies have revealed that the formation of electron excited species, as a result of reactions of biomolecules with reactive oxygen species (ROS), is the principal biochemical source of the BAL which occurs during the cell metabolism. Mitochondria, as the most important organelles involved in oxidative metabolism, are considered to be the main intracellular BAL source. Hence, in order to achieve the BAL enhancement via affecting the mitochondria, we prepared a novel mitochondrial-liposomal nanocarrier with two attractive features including the intra-liposomal gold nanoparticle synthesizing ability and the mitochondria penetration capability. The results indicate that these nanocarriers (with the average size of 131.1 ± 20.1 nm) are not only able to synthesize the gold nanoparticles within them (with the average size of 15 nm) and penetrate into the U2OS cell mitochondria, but they are also able to amplify the BAL signals. Our results open new possibilities for the use of biological autoluminescence as a non-invasive and label-free monitoring method in nanomedicine and biotechnology.

Electrochemical Determination of Dexamethasone by Graphene Modified Electrode: Experimental and Theoretical Investigations

We report on a combined experimental and theoretical study concerning the electrochemical behavior of the dexamethasone (DEX) on a graphene modified glassy carbon electrode (GCE). A good agreement between experiments and density functional theory (DFT)-based calculations is observed for the DEX reduction. The electrochemical behavior of the DEX was investigated on the surface of a glassy carbon electrode (GCE) modified with different type of graphenes, including graphene quantum dot (GQD), graphene oxide (GO), electrochemically synthesized graphene (EG), graphene synthesized by the Hummer method (HG) and graphene nanoplate (GNP) using voltammetric techniques (CV, DPV and SWV). The results exhibited a significant increase in the reduction of the peak current of the DEX in  the GNP modified GCE (GNP/GCE) in comparison to other modified electrodes and bare GCE. The unique morphology, size and electro catalytic properties of the GNP cause a sensitive response of the DEX in a novel sensor. Under the optimized experimental condition, the GNP/ GCE showed two linear dynamic ranges of 0.1-50 μM and 50-5000 μM with a low detection limit of 15 nM for determination of the DEX. The novel sensor is successfully applied to the sensitive determination of the DEX in human plasma samples with satisfactory recoveries. Energy of the LUMO and HUMO orbitals and energy calculations for the DEX molecule interacting with graphene were performed using the density functional B3LYP/6-31G. The theoretical results allied to significant charge transfer took place due to the interaction of the DEX with the applied graphene.

Physicochemical properties, antifungal activity and cytotoxicity of selenium sulfide nanoparticles green synthesized by Saccharomyces cerevisiae

Selenium sulfide is a well-known bioactive chemical whose biosynthesis as a nanoparticle (NP) is a controversial issue. In the present study, we employed Saccharomyces cerevisiae to generate a novel synthetic process of selenium sulfide NPs. The addition of selenium/sulfur precursors to S. cerevisiae culture produced NPs, which we isolated and characterized the physicochemical properties, toxicity, and antifungal activity. Transmission electron microscopy indicated the presence of the NPs inside the cells. Selenium sulfide NPs were successfully synthesized with average size of 6.0 and 153 nm with scanning electron micrographs and 360 and 289 nm in Zeta sizer using different precursors. The presence of sulfur/selenium in the particles was confirmed by energy-dispersive X-ray spectroscopy and elemental mapping. Fourier-transform infrared spectroscopy supported the production of selenium sulfide NPs. X-ray diffractograms showed the presence of characteristic peaks of selenium sulfide NPs which were further confirmed by mass spectrometry. The obtained NPs strongly inhibited the growth of pathogenic fungi that belonged to the genera Aspergillus, Candida, Alternaria and the dermatophytes, while no cytotoxicity was observed in MTT assay. In conclusion, efficient green synthesis of selenium sulfide NPs with appropriate physicochemical properties is possible in bio-systems like S. cerevisiae.

An investigation into non-covalent functionalization of a single-walled carbon nanotube and a graphene sheet with protein G:A combined experimental and molecular dynamics study

Investigation of non-covalent interaction of hydrophobic surfaces with the protein G (PrG) is necessary due to their frequent utilization in immunosensors and ELISA. It has been confirmed that surfaces, including carbonous-nanostructures (CNS) could orient proteins for a better activation. Herein, PrG interaction with single-walled carbon nanotube (SWCNT) and graphene (Gra) nanostructures was studied by employing experimental and MD simulation techniques. It is confirmed that the PrG could adequately interact with both SWCNT and Gra and therefore fine dispersion for them was achieved in the media. Results indicated that even though SWCNT was loaded with more content of PrG in comparison with the Gra, the adsorption of the PrG on Gra did not induce significant changes in the IgG tendency. Several orientations of the PrG were adopted in the presence of SWCNT or Gra; however, SWCNT could block the PrG-FcR. Moreover, it was confirmed that SWCNT reduced the α-helical structure content in the PrG. Reduction of α-helical structure of the PrG and improper orientation of the PrG-SWCNT could remarkably decrease the PrG tendency to the Fc of the IgG. Importantly, the Gra could appropriately orient the PrG by both exposing the PrG-FcR and also by blocking the fragment of the PrG that had tendency to interact with Fab in IgG.

Protein G selects two binding sites for carbon nanotube with dissimilar behavior; a molecular dynamics study

BACKGROUND

Study of nanostructure-protein interaction for development of various types of nano-devices is very essential. Among carbon nanostructures, carbon nanotube (CNT) provides a suitable platform for functionalization by proteins. Previous studies have confirmed that the CNT induces changes in the protein structure.

METHODS

Molecular dynamics (MD) simulation study was employed to illustrate the changes occurring in the protein G (PGB) in the presence of a CNT. In order to predict the PGB surface patches for the CNT, Autodock tools were utilized.

RESULTS

Docking results indicate the presence of two different surface patches with diverse amino acids: the dominant polar residues in the first (PGB-CNT1) and the aromatic residues in the second (PGB-CNT2) surface patch. Displacement of amino acids in the PGB-CNT2 complex occurred during the simulation and it caused an increase in its stability at the end of simulation. The amino acids' displacements diminished the PGB α-helix structure by breakage of hydrogen bonds and generated more transient structures. Principal component analysis determined that the interaction of the CNT with the second surface patch of the PGB raised the extent and modes of the PGB motions. In contrast, insignificant structural changes induced in the PGB while the CNT bonded through the first surface patch.

CONCLUSION

Even though neither of the PGB-CNT complexes could prevent structural changes in the PGB, development of the PGB-CNT1 complex induce slight structural changes in its fragment of crystallizable receptor (FCR). Dissimilar structural changes induced in the PGB-CNT complexes are possibly related to various characteristics of the PGB binding sites.

Detection and Discrimination of Bacterial Colonies with Mueller Matrix Imaging

The polarization imaging technique is a powerful approach to probe microstructural and optical information of biological structures (e.g., tissue samples). Here, we have studied the polarization properties of different bacterial colonies in order to evaluate the possibility of bacterial detection and discrimination. In this regard, we have taken the backscattering Mueller matrix images of four different bacteria colonies (i.e., Escherichia coli, Lactobacillus rhamnosus, Rhodococcus erythropolis, and Staphylococcus aureus). Although the images have the potential to distinguish qualitatively different bacterial colonies, we explored more accurate and quantitative parameters criteria for discrimination of bacterial samples; more specifically, we have exploited the Mueller matrix polar decomposition (MMPD),frequency distribution histogram (FDH), and central moment analysis method. The outcomes demonstrated a superior capacity of Mueller matrix imaging, MMPD, and FDH in bacterial colonies identification and discrimination. This approach might pave the way for a reliable, efficient, and cheap way of identification of infectious diseases.

Investigation of the role of ion channels in human pancreatic β-cell hubs: A mathematical modeling study

In many cellular networks, the structure of the network follows a scale-free organization, where a limited number of cells are strongly coupled to other cells. These cells are called hub cells and their critical roles are well accepted. Despite their importance, there have been only a few studies investigating the characteristic features of these cells. In this paper, a computational approach is proposed to study the possible role of different ion channels in distinguishing between the hub and non-hub cells. The results show that the P/Q-type and T-type calcium channels may have an especial role in the β-cell hubs because the high-level expressions of these channels make a pancreatic β-cell more potent to force other coupled cells to follow it. In addition, in order to consider the variation of the coupling strength with voltage, a novel mathematical model is proposed for the gap junction coupling between the pancreatic β-cells. The proposed approach is validated based on the data from the literature.

Deconstruction of the human connexin 26 hemichannel due to an applied electric field; A molecular dynamics simulation study

Connexins are a 21-member membrane protein family constituting channels evolved in direct communication between adjacent cells by passaging cytoplasmic molecules and ions. Hexametrical assembly of connexin proteins in plasma membrane forms a wide aqueous pore known as connexin hemichannel. These hemichannels mediate cytoplasm and extracellular milieu communication both in many external tissues and in the central nervous system. In this study, a series of molecular dynamics simulations has been performed to investigate the effect of applied static and alternating electric fields on the stability and conformation of human connexin26 hemichannel. The root mean square deviations of C-alpha atoms, the dipole moment distribution, the number of inter-protein hydrogen bonds and the number of water-protein hydrogen bonds were used to assess connexin26 hemichannel stability. In the static field case, our results show that although the lowest field used in this study (0.1V/nm) does not lead to the hemichannel deconstruction, stronger fields (>0.1V/nm), however, disrupt the protein structure during the simulations time period. Furthermore, in the alternating case, compared to static field case, field effects on the connexin26 hemichannel conformation are reduced and consequently the protein maintains its native structure for longer times. Specifically, for the highest frequency used in this study (50GHz), the hemichannel keeps its structure even under the effect of the strongest field (0.4V/nm). According to our results, the protein secondary structure is preserved in the characteristic times determined for the protein deconstruction. Consequently, we suggest that the protein deconstruction is due to the tertiary and quaternary structure loss.

Modeling ion permeation through a bacterial voltage-gated calcium channel CaVAb using molecular dynamics simulations

Ca²⁺ion binds tightly to the center of the selectivity filter of voltage-gated calcium channels.

Structural and Functional Effect of an Oscillating Electric Field on the Dopamine-D3 Receptor: A Molecular Dynamics Simulation Study

Dopamine as a neurotransmitter plays a critical role in the functioning of the central nervous system. The structure of D3 receptor as a member of class A G-protein coupled receptors (GPCRs) has been reported. We used MD simulation to investigate the effect of an oscillating electric field, with frequencies in the range 0.6–800 GHz applied along the z-direction, on the dopamine-D3R complex. The simulations showed that at some frequencies, the application of an external oscillating electric field along the z-direction has a considerable effect on the dopamine-D3R. However, there is no enough evidence for prediction of changes in specific frequency, implying that there is no order in changes. Computing the correlation coefficient parameter showed that increasing the field frequency can weaken the interaction between dopamine and D3R and may decrease the Arg128{3.50}-Glu324{6.30} distance. Because of high stability of α helices along the z-direction, applying an oscillating electric field in this direction with an amplitude 10-time higher did not have a considerable effect. However, applying the oscillating field at the frequency of 0.6 GHz along other directions, such as X-Y and Y-Z planes, could change the energy between the dopamine and the D3R, and the number of internal hydrogen bonds of the protein. This can be due to the effect of the direction of the electric field vis-à-vis the ligands orientation and the interaction of the oscillating electric field with the dipole moment of the protein.

Effects of electromagnetic field exposure on conduction and concentration of voltage gated calcium channels: A Brownian dynamics study

A three-dimensional Brownian Dynamics (BD) in combination with electrostatic calculations is employed to specifically study the effects of radiation of high frequency electromagnetic fields on the conduction and concentration profile of calcium ions inside the voltage-gated calcium channels. The electrostatic calculations are performed using COMSOL Multiphysics by considering dielectric interfaces effectively. The simulations are performed for different frequencies and intensities. The simulation results show the variations of conductance, average number of ions and the concentration profiles of ions inside the channels in response to high frequency radiation. The ionic current inside the channel increases in response to high frequency electromagnetic field radiation, and the concentration profiles show that the residency of ions in the channel decreases accordingly.

Photocount statistics of ultra-weak photon emission from germinating mung bean

Ultra-weak photon emission (UPE) is an endogenous bioluminescence phenomenon present in all biological samples with an active oxidative metabolism, even without an external pre-illumination. To verify the potential of UPE for non-invasive monitoring of metabolism and growth in germinating plants, the aim of this study was to investigate the UPE from a model system - germinating mung bean seedlings (Vigna radiata) - and analyze the statistical properties of UPE during the growth in two different conditions of imbibition (pure water and 1% sucrose). We found that in all days and in both conditions, photocount distributions of UPE time series follow the negative binomial distribution whose parameters changed during the growth due to the increasing ratio of signal-to-detector dark count. Correspondingly for both groups, the mean values of UPE increased during the seedlings growth, while the values of Fano factor show a decreasing trend towards 1 during the 6day period. While our results do not show any significant difference in hypocotyl length and weight gain between the two groups of mung seedlings, there is an indication of a tiny suppressing effect of sucrose on UPE intensity. We believe that UPE can be exploited for a sensitive non-invasive analysis of oxidative metabolism during the plant development and growth with potential applications in agricultural research.

Water molecules response to an external GHz electric field in KcsA potassium channel: A molecular modeling approach

KcsA potassium channel is a membrane protein that allows the passage of potassium ions and water molecules across the cellular membrane. Using molecular dynamics (MD) simulation method, the effect of an applied GHz oscillating electric field of strength 0.004 V/nm on the dynamics of K + and water molecules in a KcsA channel was modeled. It was found that the application of GHz range electric field caused a change in the potential energy profile of the water molecules in the filter sites, causing an increase in the delay time of the water molecules in these sites. Therefore, exposing the channel to the GHz fields can perturb the dynamics of the water molecules in the filter, and consequently, the channel operation may be disturbed. Furthermore, the results show that the applied field has no major effects on the dipole orientation of water molecules in the channel.

Effect of peptide length on the conjugation to the gold nanoparticle surface: a molecular dynamic study

BACKGROUND

Gold nanoparticles now command a great deal of attention for medical applications. Despite the importance of nano-bio interfaces, interaction between peptides and proteins with gold surfaces is not still fully understood, especially in a molecular level.

METHODS

In the present study computational simulation of adsorption of 20 amino acids, in three forms of mono-amino acid, homo di-peptide and homo tri-peptide, on the gold nanoparticles was performed by Gromacs using OPLSAA force field. The flexibility, stability, and size effect of the peptides on the gold nanoparticles were studied as well as the molecular structure of them.

RESULTS

According to our results, adsorbed homo tri-peptides on the gold surface had more flexibility, more gyration, and the farthest distance from the GNP in comparison with homo di-peptides and mono-amino acids.

CONCLUSION

Our findings provide new insights into the precise control of interactions between amino acids anchored on the GNPs.

An in-depth view of human serum albumin corona on gold nanoparticles

Upon entering biological systems, such as the blood stream, nanoparticles form molecular complexes with the proteins encountered called protein coronas, which shield the surface of the exogenous nanoparticle. The most abundant blood proteins, such as albumin, initially occupy the surface of the nanoparticle. Owing to the widespread applications of gold nanoparticles in medicine, in this study, the docking of human serum albumin to gold nanoparticles was examined and the changes in protein structure were investigated by a molecular dynamic simulation and GOLP force field. The results showed that after the adsorption of albumin on the gold nanoparticle, human serum albumin was denatured and the amount of alpha-helix significantly decreased. Domain III, which has a large cavity of fatty acids binding sites, plays an important role in the adsorption on the gold nanoparticles. Lys464, Thr504, Phe505, and Leu581 are critical amino acids in HSA adsorption on the GNPs. After the adsorption of albumin on the surface of gold nanoparticles, the fluctuations in some of the domains of the protein increased. Variations in the helix properties, such as helix length, dipole, radius, average phi and psi angles, and the length of hydrogen bonds, were calculated in detail.

Study of orotidine 5'-monophosphate decarboxylase in complex with the top three OMP, BMP, and PMP ligands by molecular dynamics simulation

Catalytic mechanism of orotidine 5'-monophosphate decarboxylase (OMPDC), one of the nature most proficient enzymes which provides large rate enhancement, has not been fully understood yet. A series of 30 ns molecular dynamics (MD) simulations were run on X-ray structure of the OMPDC from Saccharomyces cerevisiae in its free form as well as in complex with different ligands, namely 1-(5'-phospho-D-ribofuranosyl) barbituric acid (BMP), orotidine 5'-monophosphate (OMP), and 6-phosphonouridine 5'-monophosphate (PMP). The importance of this biological system is justified both by its high rate enhancement and its potential use as a target in chemotherapy. This work focuses on comparing two physicochemical states of the enzyme (protonated and deprotonated Asp91) and three ligands (substrate OMP, inhibitor, and transition state analog BMP and substrate analog PMP). Detailed analysis of the active site geometry and its interactions is properly put in context by extensive comparison with relevant experimental works. Our overall results show that in terms of hydrogen bond occupancy, electrostatic interactions, dihedral angles, active site configuration, and movement of loops, notable differences among different complexes are observed. Comparison of the results obtained from these simulations provides some detailed structural data for the complexes, the enzyme, and the ligands, as well as useful insights into the inhibition mechanism of the OMPDC enzyme. Furthermore, these simulations are applied to clarify the ambiguous mechanism of the OMPDC enzyme, and imply that the substrate destabilization and transition state stabilization contribute to the mechanism of action of the most proficient enzyme, OMPDC.

Modelling the influence of thermal effects induced by radio frequency electric field on the dynamics of the ATPase nano-biomolecular motors

We model the dynamics of the F(0) component of the F(0)F(1)-ATPase mitochondrion-based nano-motor operating in a stochastically-fluctuating medium that represents the intracellular environment. The stochastic dynamics are modeled via Langevin equation of motion wherein fluctuations are treated as white noise. We have investigated the influence of an applied alternating electric field on the rotary motion of the F(0) rotor in such an environment. The exposure to the field induces a temperature rise in the mitochondrion's membrane, within which the F(0) is embedded. The external field also induces an electric potential that promotes a change in the mitochondrion's transmembrane potential (TMP). Both the induced temperature and the change in TMP contribute to a change in the dynamics of the F(0). We have found that for external fields in the radio frequency (RF) range, normally present in the environment and encountered by biological systems, the contribution of the induced thermal effects, relative to that of the induced TMP, to the dynamics of the F(0) is more significant. The changes in the dynamics of the F(0) part affect the frequency of the rotary motion of the F(0)F(1)-ATPase protein motor which, in turn, affects the production rate of the ATP molecules.

Influence of Adsorbate Monolayer on the Nano-Mechanics of TIP-Substrate Interactions

We employ constant temperature molecular dynamics simulations to study, at the atomistic level, the interactions of an Ir tip with a Pb substrate. We have considered the complete cycle of approach.contact, indentation and retraction of the tip from the substrate. We have observed the wetting of the tip by the substrate atoms, and the formation of atomic necking between the tip and the substrate.

We have carried out further simulations to study the interactions of an Ir tip with an Ir substrate covered with an adsorbate monolayer of Pb film. We show that the introduction of the adsorbate considerably reduces the work of adhesion and the extent of plastic flow, in agreement with experimental results.

Three-dimensional geometries have been generated on computer and used for the animation of the simulation runs.

Stability of the Fullerenes Thin Film Deposited on the SI(100) Surface

We have performed a constant temperature classical molecular dynamics simulation of the epitaxial growth of a C60 monolayer film deposited on the dimerized Si(100) surface. Our simulation, based on non-central many-body inter-atomic potentials, is capable of predicting the structural stability of the C60 film and the Si substrate and provides a theoretical basis for the results of a recently-performed STM- based experiment for this system.

Three-dimensional geometries have been generated on computer and used for the animation of the simulation runs.

Computational modeling of a carbon nanotube-based DNA nanosensor

During the last decade the design of biosensors, based on quantum transport in one-dimensional nanostructures, has developed as an active area of research. Here we investigate the sensing capabilities of a DNA nanosensor, designed as a semiconductor single walled carbon nanotube (SWCNT) connected to two gold electrodes and functionalized with a DNA strand acting as a bio-receptor probe. In particular, we have considered both covalent and non-covalent bonding between the DNA probe and the SWCNT. The optimized atomic structure of the sensor is computed both before and after the receptor attaches itself to the target, which consists of another DNA strand. The sensor's electrical conductance and transmission coefficients are calculated at the equilibrium geometries via the non-equilibrium Green's function scheme combined with the density functional theory in the linear response limit. We demonstrate a sensing efficiency of 70% for the covalently bonded bio-receptor probe, which drops to about 19% for the non-covalently bonded one. These results suggest that a SWCNT may be a promising candidate for a bio-molecular FET sensor.

Computational modelling of a non-viscous fluid flow in a multi-walled carbon nanotube modelled as a Timoshenko beam

In the design of nanotube-based fluidic devices, a critical issue is the effect of the induced vibrations in the nanotube arising from the fluid flow, since these vibrations can promote structural instabilities, such as buckling transitions. It is known that the induced resonant frequencies depend on the fluid flow velocity in a significant manner. We have studied, for the first time, the flow of a non-viscous fluid in stubby multi-walled carbon nanotubes, using the Timoshenko classical beam theory to model the nanotubes as a continuum structure. We have obtained the variations of the resonant frequencies with the fluid flow velocity under several experimentally interesting boundary conditions and aspect ratios of the nanotube. The main finding from our work is that, compared to an Euler-Bernoulli classical beam model of a nanotube, the Timoshenko beam predicts the loss of stability at lower fluid flow velocities.

Computational modeling of an ion-driven nanomotor

The dynamics of an ion-driven rotary nanomotor, mimicking the F(0) part of the ATPase biomolecular motor, in the presence, and absence, of an external electric field have been simulated via the application of the stochastic molecular dynamics (MD) method. The rotary motion of the proposed motor arises as a result of an ion gradient established between the outer and inner parts of the environment within which the motor is embedded. We show that the operation of this motor can be controlled by such parameters as the amount of the positive ions placed in the stator part of the motor, the density of the positive ions, and the strength and frequency of the applied electric field.