Revealing the nuclearity of iron citrate complexes at biologically relevant conditions.

Citric acid plays an ubiquitous role in the complexation of essential metals like iron and thus it has a key function making them biologically available. For this, iron(III) citrate complexes are considered among the most significant coordinated forms of ferric iron that take place in biochemical processes of all living organisms. Although these systems hold great biological relevance, their coordination chemistry has not been fully elucidated yet. The current study aimed to investigate the speciation of iron(III) citrate using Mössbauer and electron paramagnetic resonance spectroscopies. Our aim was to gain insights into the structure and nuclearity of the complexes depending on the pH and iron to citrate ratio. By applying the frozen solution technique, the results obtained directly reflect the iron speciation present in the aqueous solution. At 1:1 iron:citrate molar ratio, polynuclear species prevailed forming most probably a trinuclear structure. In the case of citrate excess, the coexistence of several monoiron species with different coordination environments was confirmed. The stability of the polynuclear complexes was checked in the presence of organic solvents.

A simple method for comparing peripheral and central color vision by means of two smartphones.

Information on peripheral color perception is far from sufficient, since it has predominantly been obtained using small stimuli, limited ranges of eccentricities, and sophisticated experimental conditions. Our goal was to consider the possibility of facilitating technical realization of the classical method of asymmetric color matching (ACM) developed by Moreland and Cruz (1959) for assessing appearance of color stimuli in the peripheral visual field (VF). We adopted the ACM method by employing two smartphones to implement matching procedure at various eccentricities. Although smartphones were successfully employed in vision studies, we are aware that some photometric parameters of smartphone displays are not sufficiently precise to ensure accurate color matching in foveal vision; moreover, certain technical characteristics of commercially available devices are variable. In the present study we provided evidence that, despite these shortages, smartphones can be applied for general and wide investigations of the peripheral vision. In our experiments, the smartphones were mounted on a mechanical perimeter to simultaneously present colored stimuli foveally and peripherally. Trying to reduce essential discomfort and fatigue experienced by most observers in peripheral vision studies, we did not apply bite bars, pupil dilatation, and Maxwellian view. The ACM measurements were performed without prior training of observers and in a wide range of eccentricities, varying between 0 and 95°. The results were presented in the HSV (hue, saturation, value) color space coordinates as a function of eccentricity and stimulus luminance. We demonstrated that our easy-to-conduct method provided a convenient means to investigate color appearance in the peripheral vision and to assess inter-individual differences.

New aspects of the photodegradation of iron(III) citrate: spectroscopic studies and plant-related factors.

Iron (Fe) is an essential cofactor for all livings. Although Fe membrane transport mechanisms often utilize FeII, uncoordinated or deliberated ferrous ions can initiate Fenton reactions. FeIII citrate complexes are among the most important complexed forms of FeIII especially in plants that, indeed, can undergo photoreduction. Since leaves as photosynthetic organs of higher plants are generally exposed to illumination in daytime, photoreaction of ferric species may have biological relevance in iron metabolism, the relevance of which is poorly understood. In present work FeIII citrate transformation during the photodegradation in solution and after foliar application on leaves was studied by Mössbauer analysis directly. To obtain irradiation time dependence of the speciation of iron in solutions, four model solutions of different pH values (1.5, 3.3, 5.5, and 7.0) with Fe to citrate molar ratio 1:1.1 were exposed to light. Highly acidic conditions led to a complete reduction of Fe together with the formation of FeII citrate and hexaaqua complexes in equal concentration. At higher pH, the only product of the photodegradation was FeII citrate, which was later reoxidized and polymerized, resulting in the formation of polynuclear stable ferric compound. To test biological relevance, leaves of cabbage were treated with FeIII citrate solution. X-ray fluorescence imaging indicated the accumulation of Fe in the treated leaf parts. Mössbauer analysis revealed the presence of several ferric species incorporated into the biological structure. The Fe speciation observed should be considered in biological systems where FeIII citrate has a ubiquitous role in Fe acquisition and homeostasis.

Brownian dynamics of cylindrical capsule-like particles in a nanopore in an electrically biased solid-state membrane.

We use Brownian dynamics simulations to study the motion of cylindrical capsule-like particles (capsules) as they translocate through nanopores of various radii in an electrically biased silicon membrane. We find that for all pore sizes the electrostatic interaction between the particle and the pore results in the particle localization towards the pore 's center when the membrane and the particle have charges of the same sign (case 1) while in case of the opposite sign charges, the capsule prefers to stay near and along the nanopore wall (case 2). The preferential localization leads to all capsules rotating less while inside the pore compared to the bulk solution, with a larger net charge and/or particle length resulting in a smaller range of rotational movement. It also strongly affects the whole translocation process: in the first case, the translocation is due to the free diffusion along the pore axis and is weakly dependent on the particle charge and the nanopore radius while in the second case, the translocation time dramatically increases with the particle size and charge as the capsule gets "stuck" to the nanopore surface.

Mössbauer, Nuclear Forward Scattering, and Raman Spectroscopic Approaches in the Investigation of Bioinduced Transformations of Mixed-Valence Antimony Oxide.

Mössbauer spectroscopy, nuclear forward scattering, and Raman spectroscopy were applied to study redox transformations of the synthesized mixed-valence (III/V) antimony oxide. The transformations were induced by a culture of a hyperthermophilic archaeon of the genus Pyrobaculum. The applied methods allowed us to reveal the minor decrease of ca. 11.0 ± 1.2% of the antimony(V) content of the mixed-valence oxide with the concomitant increase of antimony(III). The method sensitivities for the quantitative assessment of the Sb(III/V) ratio have been considered.

Atomistic model of a ceria nanoparticle with Ce3 + and Ce4 + atoms.

We develop an atomistic model of a cerium dioxide CeO2 nanoparticle, which we then extend to our model of a ceria nanoparticle with a varied Ce3 + /Ce4 + composition. For a pure CeO2 particle we compute the radial distribution function for all pairs of atoms in the nanoparticle, which we find is in excellent agreement with the reported experimental data. For a particle with a mixed Ce3 + /Ce4 + we adjust the parameters and modify the crystallization procedure to produce a realistic distribution of Ce3 + atoms on the particle. We improve our initial guess of the Lennard-Jones parameters by melting and recrystallizing the nanoparticle, as well as computing the radial distribution function for the nanoparticle at room temperature.

Brownian dynamics of a neutral protein moving through a nanopore in an electrically biased membrane.

The ability to separate proteins is desirable for many fields of study, and nanoporous membranes may offer a method for rapid protein filtration at high throughput volume, provided there is an understanding of the protein dynamics involved. In this work, we use Brownian dynamics simulations to study the motion of coarse-grained proteins insulin and ubiquitin in an electrically biased membrane. In our model, the protein is subjected to various biases applied to the silicon membrane equipped with a nanopore of different radii. The time each protein takes to find a cylindrical nanopore embedded in a thin silicon membrane, attempt to translocate it (waiting time), and successfully translocate it in a single attempt (translocation time) is calculated. We observe insulin finding the nanopore and translocating it faster than the electrically neutral ubiquitin due to insulin's slightly smaller size and net negative charge. While ubiquitin's dynamics is also affected by the size of the pore, surprisingly, its translocation process is also noticeably changed by the membrane bias. By investigating the protein's multipole moments, we demonstrate that this behavior is largely due to the protein's dipole and quadrupole interactions with the membrane potential.

Finite element modeling to analyze TEER values across silicon nanomembranes.

Silicon nanomembranes are ultrathin, highly permeable, optically transparent and biocompatible substrates for the construction of barrier tissue models. Trans-epithelial/endothelial electrical resistance (TEER) is often used as a non-invasive, sensitive and quantitative technique to assess barrier function. The current study characterizes the electrical behavior of devices featuring silicon nanomembranes to facilitate their application in TEER studies. In conventional practice with commercial systems, raw resistance values are multiplied by the area of the membrane supporting cell growth to normalize TEER measurements. We demonstrate that under most circumstances, this multiplication does not 'normalize' TEER values as is assumed, and that the assumption is worse if applied to nanomembrane chips with a limited active area. To compare the TEER values from nanomembrane devices to those obtained from conventional polymer track-etched (TE) membranes, we develop finite element models (FEM) of the electrical behavior of the two membrane systems. Using FEM and parallel cell-culture experiments on both types of membranes, we successfully model the evolution of resistance values during the growth of endothelial monolayers. Further, by exploring the relationship between the models we develop a 'correction' function, which when applied to nanomembrane TEER, maps to experiments on conventional TE membranes. In summary, our work advances the the utility of silicon nanomembranes as substrates for barrier tissue models by developing an interpretation of TEER values compatible with conventional systems.

Brownian dynamics simulations of the ionic current traces for a neutral nanoparticle translocating through a nanopore.

In this work, the ionic current blockades due to the translocation of a neutral spherical nanoparticle through a nanopore in a solid state membrane are computed. We use a Brownian dynamics approach, in conjunction with a full three-dimensional self-consistent solution of the Poisson-Nernst-Planck and Navier-Stockes system of equations to describe realistic ionic current response arising due to the random motion of a nanoparticle through a nanopore. We find that in addition to the usual geometric blockade, the variations of the current along the axis of the pore are largely caused by a concentration polarization induced by the presence of the translocating nanoparticle in the nanopore while the current changes in the radial (perpendicular to the axis) direction occur because of the local build up of the ionic charge between the particle and the nanopore surface. By performing statistical analysis of the current traces, we also observe that, in general, smaller current blockade values correspond to faster translocation times, while increased dwell times result in a larger current decrease.

Brownian dynamics of a protein-polymer chain complex in a solid-state nanopore.

We study the movement of a polymer attached to a large protein inside a nanopore in a thin silicon dioxide membrane submerged in an electrolyte solution. We use Brownian dynamics to describe the motion of a negatively charged polymer chain of varying lengths attached to a neutral protein modeled as a spherical bead with a radius larger than that of the nanopore, allowing the chain to thread the nanopore but preventing it from translocating. The motion of the protein-polymer complex within the pore is also compared to that of a freely translocating polymer. Our results show that the free polymer's standard deviations in the direction normal to the pore axis is greater than that of the protein-polymer complex. We find that restrictions imposed by the protein, bias, and neighboring chain segments aid in controlling the position of the chain in the pore. Understanding the behavior of the protein-polymer chain complex may lead to methods that improve molecule identification by increasing the resolution of ionic current measurements.

Protein permeation through an electrically tunable membrane.

Protein filtration is important in many fields of science and technology such as medicine, biology, chemistry, and engineering. Recently, protein separation and filtering with nanoporous membranes has attracted interest due to the possibility of fast separation and high throughput volume. This, however, requires understanding of the protein's dynamics inside and in the vicinity of the nanopore. In this work, we utilize a Brownian dynamics approach to study the motion of the model protein insulin in the membrane-electrolyte electrostatic potential. We compare the results of the atomic model of the protein with the results of a coarse-grained and a single-bead model, and find that the coarse-grained representation of protein strikes the best balance between the accuracy of the results and the computational effort required. Contrary to common belief, we find that to adequately describe the protein, a single-bead model cannot be utilized without a significant effort to tabulate the simulation parameters. Similar to results for nanoparticle dynamics, our findings also indicate that the electric field and the electro-osmotic flow due to the applied membrane and electrolyte biases affect the capture and translocation of the biomolecule by either attracting or repelling it to or from the nanopore. Our computational model can also be applied to other types of proteins and separation conditions.

Nanopore gating with an anchored polymer in a switching electrolyte bias.

In this work, we theoretically study the interaction between a solid state membrane equipped with a nanopore and a tethered, negatively charged polymer chain subjected to a time-dependent applied electrolyte bias. In order to describe the movement of the chain in the biomolecule-membrane system immersed in an electrolyte solution, Brownian dynamics is used. We show that we can control the polymer's equilibrium position with various applied electrolyte biases: for a sufficiently positive bias, the chain extends inside the pore, and the removal of the bias causes the polymer to leave the pore. Corresponding to a driven process, we find that the time it takes for a biomolecular chain to enter and extend into a nanopore in a positive bias almost increases linearly with chain length while the amount of time it takes for a polymer chain to escape the nanopore is mainly governed by diffusion.

Charged particle separation by an electrically tunable nanoporous membrane.

We study the applicability of an electrically tunable nanoporous semiconductor membrane for the separation of nanoparticles by charge. We show that this type of membrane can overcome one of the major shortcomings of nanoporous membrane applications for particle separation: the compromise between membrane selectivity and permeability. The computational model that we have developed describes the electrostatic potential distribution within the system and tracks the movement of the filtered particle using Brownian dynamics while taking into consideration effects from dielectrophoresis, fluid flow, and electric potentials. We found that for our specific pore geometry, the dielectrophoresis plays a negligible role in the particle dynamics. By comparing the results for charged and uncharged particles, we show that for the optimal combination of applied electrolyte and membrane biases the same membrane can effectively separate same-sized particles based on charge with a difference of up to 3 times in membrane permeability.

Apoplast utilisation of nanohaematite initiates parallel suppression of RIBA1 and FRO1&3 in Cucumis sativus.

Nanoscale Fe containing particles can penetrate the root apoplast. Nevertheless, cell wall size exclusion questions that for Fe mobilisation, a close contact between the membrane integrating FERRIC REDUCTASE OXIDASE (FRO) enzymes and Fe containing particles is required. Haematite nanoparticle suspension, size of 10-20 nm, characterized by 57Fe Mössbauer spectroscopy, TEM, ICP and SAED was subjected to Fe utilisation by the flavin secreting model plant cucumber (Cucumis sativus). Alterations in the structure and distribution of the particles were revealed by 57Fe Mössbauer spectroscopy, HRTEM and EDS element mapping. Biological utilisation of Fe resulted in a suppression of Fe deficiency responses (expression of CsFRO 1, 2 & 3 and RIBOFLAVIN A1; CsRIBA1 genes and root ferric chelate reductase activity). Haematite nanoparticles were stacked in the middle lamella of the apoplast. Fe mobilisation is evidenced by the reduction in the particle size. Fe release from nanoparticles does not require a contact with the plasma membrane. Parallel suppression in the CsFRO 1&3 and CsRIBA1 transcript amounts support that flavin biosynthesis is an inclusive Fe deficiency response involved in the reduction-based Fe utilisation of Cucumis sativus roots. CsFRO2 is suggested to play a role in the intracellular Fe homeostasis.

Slowing down and stretching DNA with an electrically tunable nanopore in a p-n semiconductor membrane.

We have studied single-stranded DNA translocation through a semiconductor membrane consisting of doped p and n layers of Si forming a p-n-junction. Using Brownian dynamics simulations of the biomolecule in the self-consistent membrane-electrolyte potential obtained from the Poisson-Nernst-Planck model, we show that while polymer length is extended more than when its motion is constricted only by the physical confinement of the nanopore. The biomolecule elongation is particularly dramatic on the n-side of the membrane where the lateral membrane electric field restricts (focuses) the biomolecule motion more than on the p-side. The latter effect makes our membrane a solid-state analog of the α-hemolysin biochannel. The results indicate that the tunable local electric field inside the membrane can effectively control dynamics of a DNA in the channel to either momentarily trap, slow down or allow the biomolecule to translocate at will.

Simulation of ionic current through the nanopore in a double-layered semiconductor membrane.

We study the effects of different nanopore geometries (double-conical, single-conical, cylindrical) on the electrostatic potential distribution and ionic conductivity in a double-layered semiconductor nanopore device as functions of the applied membrane bias. Ionic current-voltage characteristics as well as their rectification ratios are calculated using a simple ion transport model. Based on our calculations, we find that the double-layered semiconductor membrane with a single-conical nanopore with a narrow opening in the n-Si layer exhibits the largest range of available potential variations in the pore and, thus, may be better suited for control of polymer translocation through the nanopore.

A model of fibroblast motility on substrates with different rigidities.

To function efficiently in the body, the biological cells must have the ability to sense the external environment. Mechanosensitivity toward the extracellular matrix was identified as one of the sensing mechanisms affecting cell behavior. It was shown experimentally that a fibroblast cell prefers locomoting over the stiffer substrate when given a choice between a softer and a stiffer substrate. In this article, we develop a discrete model of fibroblast motility with substrate-rigidity sensing. Our model allows us to understand the interplay between the cell-substrate sensing and the cell biomechanics. The model cell exhibits experimentally observed substrate rigidity sensing, which allows us to gain additional insights into the cell mechanosensitivity.

Multiscale simulations of charge and size separation of nanoparticles with a solid-state nanoporous membrane.

Nanoporous membranes provide an attractive approach for rapid filtering of nanoparticles at high-throughput volume, a goal useful to many fields of science and technology. Creating a device to readily separate different particles would require an extensive knowledge of particle-nanopore interactions and particle translocation dynamics. To this end, we use a multiscale model for the separation of nanoparticles by combining microscopic Brownian dynamics simulations to simulate the motion of spherical nanoparticles of various sizes and charges in a system with nanopores in an electrically biased membrane with a macroscopic filtration model accounting for bulk diffusion of nanoparticles and membrane surface pore density. We find that, in general, the separation of differently sized particles is easier to accomplish than of differently charged particles. The separation by charge can be better performed in systems with low pore density and/or smaller filtration chambers when electric nanopore-particle interactions are significant. The results from these simple cases can be used to gain insight in the more complex dynamics of separating, for example, globular proteins.

Reversible control of magnetism in FeRh thin films.

The multilayer of approximate structure MgO(100)/[nFe51Rh49(63 Å)/57Fe51Rh49(46 Å)]10 deposited at 200 °C is primarily of paramagnetic A1 phase and is fully converted to the magnetic B2 phase by annealing at 300 °C for 60 min. Subsequent irradiation by 120 keV Ne+ ions turns the thin film completely to the paramagnetic A1 phase. Repeated annealing at 300 °C for 60 min results in 100% magnetic B2 phase, i.e. a process that appears to be reversible at least twice. The A1 → B2 transformation takes place without any plane-perpendicular diffusion while Ne+ irradiation results in significant interlayer mixing.