Short-chain polyphosphates: Extraction effects on migration and size estimation of Saccharomyces cerevisiae extracts with polyacrylamide gel electrophoresis

Polyacrylamide gel electrophoresis is commonly used to characterize the chain length of polyphosphates (polyP), more generally called condensed phosphates. After separation, nonradioactive, optical polyP staining is limited to chain lengths greater than 15 ${\mathrm{PO}}_3^{-}$monomers with toluidine blue or 4′,6-diamidino-2-phenylindole. PolyP chain lengths longer than 62${\mathrm{PO}}_3^{-}$monomers were correlated to the shortest DNA ladders. In this study, synthetic linear polyPs (Sigma-Aldrich “Type 45”, estimated mean length of 45 ${\mathrm{PO}}_3^{-}$ monomers), trimetaphosphate (trimetaP: 3 ${\mathrm{PO}}_3^{-}$ ring), tripolyphosphate (tripolyP), pyrophosphate (PP_i), and inorganic orthophosphate (o-P_i) were visualized after separation by an in situ hydrolytic degradation process to o-P_i that was subsequently stained with methyl green. Statistically insignificant migration reduction of synthetic short-chain polyP after perchloric acid or phenol–chloroform extraction was confirmed with the Friedman test. ³¹P diffusion–ordered NMR spectroscopy confirmed that extraction also reduced PP_i diffusivity by <10%. Linear regression between the R_f peak migration value and the logarithm of synthetic polyP molecular weights enabled estimation of extracted polyP chain lengths from 2 to 45 ${\mathrm{PO}}_3^{-}$monomers. Linear polyP extracts from Saccharomyces cerevisiae grown in aerobic conditions were generally shorter than extracts cultured in anaerobic conditions. Extractions from both aerobic and anaerobic S. cerevisiae included tripolyP and o-P_i, but no PP_i.     

High-throughput dielectrophoretic separator based on printed circuit boards

The separation of particles with respect to their intrinsic properties is an ongoing task in various fields such as biotechnology and recycling of electronic waste. Especially for small particles in the lower micrometer or nanometer range, separation techniques are a field of current research since many existing approaches lack either throughput or selectivity. Dielectrophoresis (DEP) is a technique that can address multiple particle properties, making it a potential candidate to solve challenging separation tasks. Currently, DEP is mostly used in microfluidic separators and thus limited in throughput. Additionally, DEP setups often require expensive components, such as electrode arrays fabricated in the clean room. Here, we present and characterize a separator based on two inexpensive custom-designed printed circuit boards (80 × 120 mm board size). The boards consist of interdigitated electrode arrays with $250\mu$m electrode width and spacing. We demonstrate the separation capabilities using polystyrene particles ranging from 500 nm to $6\mu$m in monodisperse experiments. Further, we demonstrate selective trapping at flow rates up to 240 ml/h in the presented device for a binary mixture. Our experiments demonstrate an affordable way to increase throughput in electrode-based DEP separators.     

Quantitative model for predicting the electroosmotic flow in dual-pole nanochannels

Developing and assessing nanofluidic systems is time-consuming and costly owing to the method's novelty; hence, modeling is essential to determine the optimal areas for implementation and to grasp its workings. In this work, we examined the influence of dual-pole surface and nanopore configuration on ion transfer simultaneously. To achieve this, the two trumpet and cigarette configuration were coated with a dual-pole soft surface so that the negative charge could be positioned in the nanopore's small aperture. Subsequently, the Poisson–Nernst–Planck and Navier–Stokes equations were simultaneously solved under steady-state circumstances using varied values physicochemical properties for the soft surface and electrolyte. The pore's selectivity was $S_{\mathrm{Trumpet}}>S_{\mathrm{Cigarette}}$, and the rectification factor, on the other hand, was , when the overall concentration was very low. When the ion partitioning effect is taken into account, we clearly show that the rectifying variables for the cigarette configuration and the trumpet configuration can reach values of 45 and 49.2, when the charge density and mass concentration were 100 mol/m³ and 1 mM, respectively. By using dual-pole surfaces, the controllability of nanopores’ rectifying behavior may be modified to produce superior separation performance.     

Numerical study supplemented with simplified model on electrophoresis of a hydrophobic colloid incorporating finite ion size effects and ion-solvent interactions

We consider a modified electrokinetic model to study the electrophoresis of a hydrophobic particle by considering the finite sized ions. The mathematical model adopted in this study incorporates the ion steric repulsion, ion-solvent interactions as well as Maxwell stress on the electrolyte. The dielectric permittivity and viscosity of the electrolyte is considered to vary with the local ionic volume fraction. Based on this modified model for the electrokinetics we have analyzed the electrophoresis in a single as well as mixture of electrolytes of monovalent and non-$z:z$ electrolytes. The dependence of viscosity on local ionic volume fraction modifies the hydrodynamic drag as well as diffusivity of ions, which are ignored in existing studies on electrophoresis. A simplified model for electrophoresis of a hydrophobic particle incorporating the ion steric repulsion and ion-solvent interactions is developed based on the first-order perturbation on applied electric field. This simplified model is established to be efficient for a Debye layer thinner than the particle size and a smaller range of slip length. This model can be implemented for any number of ionic species as well as non-$z:z$ electrolytes. It is established that the ion steric interactions and dielectric decrement creates a counterion saturation in the Debye layer leading to an enhanced mobility compared to the standard model. However, experimental data for non-dilute cases often under predicts the theoretically determined mobility. The present modified model fills this lacuna and demonstrate that the consideration of finite ion size modifies the medium viscosity and hence, ionic mobility, which in combination lowers the mobility value.     

Rapid prototyping of polydimethylsiloxane (PDMS) microchips using electrohydrodynamic jet printing: Application to electrokinetic assays

Polydimethylsiloxane (PDMS) based microfluidic devices have found increasing utility for electrophoretic and electrokinetic assays because of their ease of fabrication using replica molding. However, the fabrication of high-resolution molds for replica molding still requires the resource-intensive and time-consuming photolithography process, which precludes quick design iterations and device optimization. We here demonstrate a low-cost, rapid microfabrication process, based on electrohydrodynamic jet printing (EJP), for fabricating non-sacrificial master molds for replica molding of PDMS microfluidic devices. The method is based on the precise deposition of an electrically stretched polymeric solution of polycaprolactone in acetic acid on a silicon wafer placed on a computer-controlled motion stage. This process offers the high-resolution (order 10 $\mu$m) capability of photolithography and rapid prototyping capability of inkjet printing to print high-resolution templates for elastomeric microfluidic devices within a few minutes. Through proper selection of the operating parameters such as solution flow rate, applied electric field, and stage speed, we demonstrate microfabrication of intricate master molds and corresponding PDMS microfluidic devices for electrokinetic applications. We demonstrate the utility of the fabricated PDMS microchips for nonlinear electrokinetic processes such as electrokinetic instability and controlled sample splitting in ITP. The ability to rapid prototype customized reusable master molds with order 10 $\mu$m resolution within a few minutes can help in designing and optimizing microfluidic devices for various electrokinetic applications.     

A dielectrophoresis-based platform of cancerous cell capture using aptamer-functionalized gold nanoparticles in a microfluidic channel

In this paper, a microfluidic chip for the manipulation and capture of cancer cells was introduced, in which the combination of dielectrophoresis (DEP) and a binding method based on chemical interactions by using cell-specific aptamers was performed to enhance the capture strength and specificity. The device has been simply constructed from a straight-channel PDMS placed on a glass substrate that has patterned electrode structures and a self-assembled monolayer of gold nanoparticles (AuNPs). The target cells were transported to the manipulation area by flow and attracted down to the region between the electrodes under the influence of positive DEP force. This approach facilitated subsequent selective capture by the modified aptamers on the AuNPs. The distribution of the electric field in the channel has also been simulated to clarify the DEP operation. As a result, the device has been shown to effectively capture target lung cancer cells with a concentration as low as $2\times {10}^4$cells/mL. The capture specificity in a sample of mixed cells is up to 80.4%. This technique has the potential to be applied to detection methods for many types of cancer.     

The confined helium atom: An information–theoretic approach

In this article, we study the helium atom confined in a spherical impenetrable cavity by using informational measures. We use the Ritz variational method to obtain the energies and wave functions of the confined helium atom as a function of the cavity radius $r_0$. As trial wave functions we use one uncorrelated function and five explicitly correlated basis sets in Hylleraas coordinates with different degrees of electronic correlation. We computed the Shannon entropy, Fisher information, Kullback–Leibler entropy, Tsallis entropy, disequilibrium and Fisher–Shannon complexity, as a function of $r_0$. We found that these entropic measures are sensitive to electronic correlation and can be used to measure it. As expected these entropic measures are less sensitive to electron correlation in the strong confinement regime ( a.u.).     

Minor amounts of glycerol improve the properties of polyisobutylene‐based polyurethane and its nanocomposites

The synthesis of primary hydroxyl‐telechelic polyisobutylene, HOCH₂‐PIB‐CH₂OH, often yields product the number average terminal functionality ( $f_{n,{\mathrm{CH}}_2\mathrm{OH}}$) of which is less than theoretical 2.0, typically $f_{n,{\mathrm{CH}}_2\mathrm{OH}}$ = 1.75–1.95. Polyurethane (PU) prepared with such low‐cost imperfect PIB‐diols, unsurprisingly, exhibit poor overall properties. Herein we report that mechanical, rheological, and thermal properties of polyisobutylene‐based polyurethane (PIB‐PU) and PIB‐PU reinforced with organically modified montmorillonite (OmMMT) prepared with PIB‐diol of $f_{n,{\mathrm{CH}}_2\mathrm{OH}}$ = 1.85 are significantly enhanced by glycerol. Specifically, we document that calculated minor amounts of glycerol substantially improves tensile strength, ultimate elongation, elastic modulus, toughness, rubbery plateau, flow temperature, creep, permanent set, rate of recovery after loading, and thermal properties of PIB‐PU and OmMMT‐reinforced PIB‐PU prepared with PIB‐diol of $f_{n,{\mathrm{CH}}_2\mathrm{OH}}$ = 1.85. The observations are summarized and discussed in terms of chemistry, micromorphology, and viscoelasticity. © 2019 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2019 , 57, 929–935     

The lift force on a charged sphere that translates and rotates in an electrolyte

The distortion of the charge cloud around a uniformly charged, dielectric, rigid sphere that translates and rotates in an unbounded binary, symmetric electrolyte at zero Reynolds number is examined. The zeta potential of the particle ζ is assumed small relative to the thermal voltage scale. It is assumed that the equilibrium structure of the cloud is slightly distorted, which requires that the Péclet numbers characterizing distortion due to particle translation, , and rotation, , are small compared to unity. Here, a is radius of the particle; D is the ionic diffusion coefficient; and , where U and Ω are the rectilinear and angular velocities of the particle, respectively. Perturbation expansions for small and are employed to calculate the nonequilibrium structure of the cloud, whence the force and torque on the particle are determined. In particular, we predict that the sphere experiences a force orthogonal to its directions of translation and rotation. This “lift” force arises from the nonlinear distortion of the cloud under the combined actions of particle translation and rotation. The lift force is given by . Here, ε is the permittivity of the electrolyte; is the Debye length; and is a negative function that decreases in magnitude with increasing . The lift force implies that an unconstrained particle would follow a curved path; an electrokinetic analog of the inertial Magnus effect. Finally, the implication of the lift force on cross‐streamline migration of an electrophoretic particle in shear flow is discussed.     

Modeling of a linear ion trap with driving rectangular waveforms

We consider the operation of a digital linear ion trap with resonant radial ejection. A sequence of rectangular voltage pulses with a dipole resonance signal is applied to the trap electrodes. The periodic waveform is piecewise constant, has zero mean, and is determined by an asymmetry parameter $d$: one value is taken on interval $\left(0,\mathit{dT}\right)$ and another on $\left(\mathit{dT},T\right)$, where $T$ is the RF period. Ion mass scanning is performed by varying the asymmetry parameter $d$ and amplitude of the negative pulse part with time. The ion oscillation frequencies and acceptance of the linear trap are calculated. The dependence of the ion mass to charge ratio $m/z$ on the parameter $d$ is $m/z~d^2$. The maximum value is about $m/z=30$ kDa for typical parameters of the linear trap: frequency 0.5 MHz, rod radius 4 mm, and negative pulse amplitude 1 kV. The dipolar excitation frequency is 0.125 MHz at which the LIT acceptance is maximal.     

Transient electrophoresis of a charged porous particle

The starting electrophoretic motion of a porous, uniformly charged, spherical particle, which models a solvent-permeable and ion-penetrable polyelectrolyte coil or floc of nanoparticles, in an arbitrary electrolyte solution due to the sudden application of an electric field is studied for the first time. The unsteady Stokes/Brinkman equations with the electric force term governing the fluid velocity fields are solved by means of the Laplace transform. An analytical formula for the electrophoretic mobility of the porous sphere is obtained as a function of the dimensionless parameters , , , and , where a is the radius of the particle, κ is the Debye screening parameter, λ is the reciprocal of the square root of the fluid permeability in the particle, ρ_p and ρ are the mass densities of the particle and fluid, respectively, ν is the kinematic viscosity of the fluid, and t is the time. The electrophoretic mobility normalized by its steady-state value increases monotonically with increases in and , but decreases monotonically with an increase in , keeping the other parameters unchanged. In general, a porous particle with a high fluid permeability trails behind an identical porous particle with a lower permeability and a corresponding hard particle in the growth of the normalized electrophoretic mobility The normalized electrophoretic acceleration of the porous sphere decreases monotonically with an increase in the time and increases with an increase in from zero at .     

Effect of magnetic field on electroosmotic flow of viscoelastic fluids in a microchannel

Electroosmotic flow is an efficient transportation technology driven by applying an external electric field across the microchannel, which has a great potential for future application. This work is presented to study the unsteady electroosmotic flow of viscoelastic fluids combined with a constant pressure gradient and a vertical magnetic field through a parallel plate microchannel. For the reason that the upper and bottom walls of the parallel plate microchannel in microfluidic devices can be made of different materials, this leads to different hydrophobic properties, asymmetric zeta wall potentials, and different slip boundary conditions. The Navier slip model with different slip coefficients at walls is considered. The generalized Maxwell fluid with fractional derivative is adopted for the constitutive equation of the fluid. The analytical and numerical solutions of velocity are derived by employing the integral transform method and finite difference method, respectively. Excellent agreement is found between the numerical solutions and analytical solutions. Finally, the effects of fractional parameter , relaxation time , slip coefficients and , the ratio of wall zeta potentials , Hartmann number , and electrical field strength parameter on velocity profiles are interpreted graphically in detail.     

Thermodynamic features of perfectly crystalline poly(3‐hexylthiophene) based on Flory's relation

Poly(3‐hexylthiophene) (P3HT) as a conjugated polymer has many electrical and photovoltaic applications. However, reliable values for the equilibrium melting temperature ( ${T°}_m$) and for the enthalpy of fusion of a perfect P3HT crystal ( ${\Delta H°}_m$) are still in doubt. In the published works, ${\Delta H°}_m$ ranges from 33 to 99 J/g. Here, the melting point of P3HT in P3HT‐diluent mixtures is measured with changing the diluent concentration. By satisfying the requirements of Flory relation, “working with the same polymer crystals” and “working in the equilibrium state,” usually neglected in the literature, a reliable value of ${\Delta H°}_m$ = 83 ± 2 J/g is obtained. The reported values for ${T°}_m$ of P3HT are also in a wide range, 260?300 °C. In this work, accurate applying of the Hoffman‐Weeks relation, against the effects of lamellar thickening, yields ${T°}_m$ = 272 ± 2 °C rather than 300 ± 2°C reported in the literature. © 2019 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2019 , 57, 431–437     

Simulations of a weakly conducting droplet under the influence of an alternating electric field

We investigate the electrohydrodynamics of an initially spherical droplet under the influence of an external alternating electric field by conducting axisymmetric numerical simulations using a charge-conservative volume-of-fluid based finite volume flow solver. The mean amplitude of shape oscillations of a droplet subjected to an alternating electric field for leaky dielectric fluids is similar to the steady-state deformation under an equivalent root mean squared direct electric field for all possible electrical conductivity ratio and permittivity ratio of the droplet to the surrounding fluid. In contrast, our simulations for weakly conducting media show that this equivalence between alternating and direct electric fields does not hold for . Moreover, for a range of parameters, the deformation obtained using the alternating and direct electric fields is qualitatively different, that is, for low and high , the droplet becomes prolate under alternating electric field but deforms to an oblate shape in the case of the equivalent direct electric field. A parametric study is conducted by varying the time period of the applied alternating electric field, the permittivity and the electrical conductivity ratios. It is observed that while increasing has a negligible effect on the deformation dynamics of the droplet for , it enhances the deformation of the droplet when for both alternating and direct electric fields. We believe that our results may be of immense consequence in explaining the morphological evolution of droplets in a plethora of scenarios ranging from nature to biology.     

Photodynamic Therapy Minimally Affects HEMA-DMAEMA Hydrogel Viscoelasticity

Soft matter implants are a rapidly growing field in medicine for reconstructive surgery, aesthetic treatments, and regenerative medicine. Though these procedures are efficacious, all implants carry risks associated with microbial infection which are often aggressive. Preventative and responsive measures exist but are limited in applicability to soft materials. Photodynamic therapy (PDT) presents a means to perform safe and effective antimicrobial treatments in proximity to soft implants. HEMA-DMAEMA hydrogels are prepared with the photosensitizer methylene blue included at 10 and 100 µM in solution used for swelling over 2 or 4 days. Thirty minutes or 5 h of LED illumination at $9.20\frac{mW}{c{m}^2}$ is then used for PDT-induced generation of reactive oxygen species in direct contact with hydrogels to test viable limits of treatment. Frequency sweep rheological measurements reveal minimal overall changes in terms of loss modulus and loss factor but a statistically significant drop in storage modulus for some PDT doses, though within the range of controls and biological variation. These mild impacts suggest the feasibility of PDT application for infection clearing in proximity to soft implants. Future investigation with additional hydrogel varieties and current implant models will further detail the safety of PDT in implant applications.     

A DFT calculation of electronic structures,magnetic, and thermoelectric properties of the new equiatomic quaternary Heusler alloy RuTiCrSi

The stabilities, mechanical, electronic, and magnetic properties of the new equiatomic quaternary Heusler alloy (EQHA) RuTiCrSi were investigated using the Kohn-Sham DFT (KS-DFT) calculations within the generalized gradient approach (GGA), the modified version of the exchange potential introduced by Becke and Johnson in addition to the GGA (mBJ-GGA), and Heyd-Scuseria-Ernzerhof (HSE06) hybrid functional. The ground-state equilibrium energy reveals that the ferromagnetic with type 2 structure is the more stable. The RuTiCrSi is energetically, mechanically, and dynamically stable. The calculated self-consistent total magnetic moment is 2 μB and agrees well with the Slater-Pauling rule of $M_{\mathrm{t}}=\left|Z_{\mathrm{t}}-24\right|$. The electronic structure results from mBJ-GGA and HSE06 functionals show a half-metallic behavior. A high Curie temperature is obtained using the mean-field approximation. The thermoelectric response was calculated using the semi-classical Boltzmann transport equation under constant relaxation time. The maximum value of Seebeck coefficient is observed at the ambient temperature of $741\mathrm{\mu V}{\mathrm{K}}^{-1}$. It was also observed that the power factor increases significantly as temperature rises. Therefore, the new EQHA RuTiCrSi seems to be a potential candidate for spintronic thermoelectric applications.     

Analysis of the Binding of Cytokines to Highly Charged Polymer Networks

A model describing the binding of biological signaling proteins to highly charged polymer networks is presented. The networks are formed by polyelectrolyte chains for which the distance between two charges at the chain is smaller than the Bjerrum length. Counterion condensation on such highly charged chains immobilizes a part of the counterions. The Donnan-equilibrium between the polymer network and the aqueous solution with salt concentration $c_s^b$ is used to calculate the salt concentration of the co- and counterions $c_s^g$ entering the network. Two factors are decisive: i) The electrostatic interaction between the network and the protein is given by the Donnan-potential of the network and the net charge of the protein. In addition to this leading term, a second term describes the change in the Born-energy of the proteins when entering the network. ii) The interaction of the protein with the highly charged chains within the network is governed by counterion release: Patches of positive charge at the protein become multivalent counterions of the polyelectrolyte chains thus releasing a concomitant number of condensed counterions. The model compares favorably to experimental data obtained on a set of biohybrid polymer networks composed of crosslinked glycosaminoglycan chains that interact with a mixture of key signaling proteins.     

Inherent Adaptivity of Alzheimer Peptides to Crowded Environments

Amyloid β (Aβ) is the major constituent in senile plaques of Alzheimer's disease in which peptides initially undergo structural conversions to form elongated fibrils. The impact of crowding on the fibrillation pathways of Aβ₄₀ and Aβ₄₂, the most common peptide isoforms are studied. PEG and Ficoll are used as model crowders to mimic a macromolecular enriched surrounding. The fibrillar growth is monitored with the help of ThT-fluorescence assays in order to extract two rates describing primary and secondary processes of nucleation and growth. Techniques as fluorescence correlation spectroscopy and analytical ultracentrifugation are used to discuss oligomeric states; fibril morphologies are investigated using negative-staining transmission electron microscopy. While excluded volume effects imposed by macromolecular crowding are expected to always increase rates of intermolecular interactions and structural conversion, a vast variety of effects are found depending on the peptide, the crowder, or ionic strength of the solution. While investigations of the obtained rates with respect to a reactant-occluded model are capable to display specific surface interactions with the crowder, the employment of crystallization-like models reveal the crowder-induced entropic gain with $\mathrm{\Delta }\mathrm{\Delta }{G}_{\text{fib}}^{\text{crow}}=-116\pm 21k$J mol⁻¹ per volume fraction of the crowder.     

Continuous organelle separation in an insulator-based dielectrophoretic device

Heterogeneity in organelle size has been associated with devastating human maladies such as neurodegenerative diseases or cancer. Therefore, assessing the size-based subpopulation of organelles is imperative to understand the biomolecular foundations of these diseases. Here, we demonstrated a ratchet migration mechanism using insulator-based dielectrophoresis in conjunction with a continuous flow component that allows the size-based separation of submicrometer particles. The ratchet mechanism was realized in a microfluidic device exhibiting an array of insulating posts, tailoring electrokinetic and dielectrophoretic transport. A numerical model was developed to elucidate the particle migration and the size-based separation in various conditions. Experimentally, the size-based separation of a mixture of polystyrene beads (0.28 and 0.87 $\mu$m) was accomplished demonstrating good agreement with the numerical model. Furthermore, the size-based separation of mitochondria was investigated using a mitochondria mixture isolated from HepG2 cells and HepG2 cells carrying the gene Mfn-1 knocked out, indicating distinct size-related migration behavior. With the presented continuous flow separation device, larger amounts of fractionated organelles can be collected in the future allowing access to the biomolecular signature of mitochondria subpopulations differing in size.