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Protein–protein interaction in solution strongly depends on dissolved ions and solution pH. Interaction among globular protein (bovine serum albumin, BSA), above and below of its isoelectric point (pI ≈ 4.8), is studied in the presence of anions (Cl(–), Br(–), I(–), F(–), SO(4)(2–)) using small-angle neutron scattering (SANS) technique. The SANS study reveals that the short-range attraction among BSA molecules remains nearly unchanged in the presence of anions, whereas the intermediate-range repulsive interaction increases following the Hofmeister series of anions. Although the interaction strength modifies below and above the pI of BSA, it nearly follows the series.

The paper delves into the plausibility of applying fractal, spectral, and nonlinear time series analyses for lung auscultation. The thirty-five sound signals of bronchial (BB) and pulmonary crackle (PC) analysed by fast Fourier transform and wavelet not only give the details of number, nature, and time of occurrence of the frequency components but also throw light onto the embedded air flow during breathing. Fractal dimension, phase portrait, and sample entropy help in divulging the greater randomness, antipersistent nature, and complexity of airflow dynamics in BB than PC. The potential of principal component analysis through the spectral feature extraction categorises BB, fine crackles, and coarse crackles. The phase portrait feature-based supervised classification proves to be better compared to the unsupervised machine learning technique. The present work elucidates phase portrait features as a better choice of classification, as it takes into consideration the temporal correlation between the data points of the time series signal, and thereby suggesting a novel surrogate method for the diagnosis in pulmonology. The study suggests the possible application of the techniques in the auscultation of coronavirus disease 2019 seriously affecting the respiratory system.

One fundamental problem of protein biochemistry is to predict protein structure from amino acid sequence. The inverse problem, predicting either entire sequences or individual mutations that are consistent with a given protein structure, has received much less attention even though it has important applications in both protein engineering and evolutionary biology. Here, we ask whether 3D convolutional neural networks (3D CNNs) can learn the local fitness landscape of protein structure to reliably predict either the wild-type amino acid or the consensus in a multiple sequence alignment from the local structural context surrounding site of interest. We find that the network can predict wild type with good accuracy, and that network confidence is a reliable measure of whether a given prediction is likely going to be correct or not. Predictions of consensus are less accurate and are primarily driven by whether or not the consensus matches the wild type. Our work suggests that high-confidence mis-predictions of the wild type may identify sites that are primed for mutation and likely targets for protein engineering. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10867-021-09593-6.

SAM-I riboswitches regulate gene expression through transcription termination upon binding a S-adenosyl-L-methionine (SAM) ligand. In previous work, we characterized the conformational energy landscape of the full-length Bacillus subtilis yitJ SAM-I riboswitch as a function of Mg2+ and SAM ligand concentrations. Here, we have extended this work with measurements on a structurally similar ligand, S-adenosyl-l-homocysteine (SAH), which has, however, a much lower binding affinity. Using single-molecule Förster resonance energy transfer (smFRET) microscopy and hidden Markov modeling (HMM) analysis, we identified major conformations and determined their fractional populations and dynamics. At high Mg2+ concentration, FRET analysis yielded four distinct conformations, which we assigned to two terminator and two antiterminator states. In the same solvent, but with SAM added at saturating concentrations, four states persisted, although their populations, lifetimes and interconversion dynamics changed. In the presence of SAH instead of SAM, HMM revealed again four well-populated states and, in addition, a weakly populated ‘hub’ state that appears to mediate conformational transitions between three of the other states. Our data show pronounced and specific effects of the SAM and SAH ligands on the RNA conformational energy landscape. Interestingly, both SAM and SAH shifted the fractional populations toward terminator folds, but only gradually, so the effect cannot explain the switching action. Instead, we propose that the noticeably accelerated dynamics of interconversion between terminator and antiterminator states upon SAM binding may be essential for control of transcription.

As part of the growing evolution in nanotechnology and thermal sciences, nanoparticles are considered as an alternative solution for the energy depletion due to their ultra-high thermal effectives. Nanofluids reflect inclusive and broad-spectrum significances in engineering, industrial and bio-engineering like power plants, energy source, air conditioning systems, surface coatings, evaporators, power consumptions, nano-medicine, cancer treatment, etc. The present study describes the bio-convective peristaltic flow of a third-grade nanofluid in a tapered asymmetric channel. Basic conservation laws of mass, momentum, energy, and concentration as well as the microorganism diffusion equation are utilized to model the problem. The simplified form of the modeled expressions is accounted with long wavelength assumptions. For solving the resulting coupled and nonlinear equations, a well-known numerical method implicit finite difference scheme has been utilized. The graphical results describe the velocity, temperature and concentration profiles, and the density of motile microorganisms at the nanoscale. Furthermore, microorganism concentration lines are analyzed.

We explore the physical influence of magnetic field on double-diffusive convection in complex biomimetic (peristaltic) propulsion of nanofluid through a two-dimensional divergent channel. Additionally, porosity effects along with rheological properties of the fluid are also retained in the analysis. The mathematical model is developed by equations of continuity, momentum, energy, and mass concentration. First, scaling analysis is introduced to simplify the rheological equations in the wave frame of reference and then get the final form of equations after applying the low Reynolds number and lubrication approach. The obtained equations are solved analytically by using integration method. Physical interpretation of velocity, pressure gradient, pumping phenomena, trapping phenomena, heat, and mass transfer mechanisms are discussed in detail under magnetic and porous environment. The magnitude of velocity profile is reduced by increasing Grashof parameter. The bolus circulations disappeared from trapping phenomena for larger strength of magnetic and porosity medium. The magnitude of temperature profile and mass concentration are increasing by enhancing the Brownian motion parameter. This study can be productive in manufacturing non-uniform and divergent shapes of micro-lab-chip devices for thermal engineering, industrial, and medical technologies.

Vertebrate hearts have undergone marked morphological and structural changes to adapt to different environments and lifestyles as part of the evolutionary process. Amphibians were the first vertebrates to migrate to land. Transition from aquatic to terrestrial environments required the ability to circulate blood against the force of gravity. In this study, we investigated the passive mechanical properties and histology of the ventricles of three species of Anura (frogs and toads) from different habitats, Xenopus laevis (aquatic), Pelophylax nigromaculatus (semiaquatic), and Bufo japonicus formosus (terrestrial). Pressure-loading tests demonstrated stiffer ventricles of P. nigromaculatus and B. j. formosus compared X. laevis ventricles. Histological analysis revealed a remarkable difference in the structure of cardiac tissue: thickening of the compact myocardium layer of P. nigromaculatus and B. j. formosus and enrichment of the collagen fibers of B. j. formosus. The amount of collagen fibers differed among the species, as quantitatively confirmed by second-harmonic generation light microscopy. No significant difference was observed in cardiomyocytes isolated from each animal, and the sarcomere length was almost the same. The results indicate that the ventricles of Anura stiffen during adaptation to life on land. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10867-021-09579-4.

The treatment outcome of a given fractionated radiotherapy scheme is affected by oxygen tension and cell cycle kinetics of the tumor population. Numerous experimental studies have supported the variability of radiosensitivity with cell cycle phase. Oxygen modulates the radiosensitivity through hypoxia-inducible factor (HIF) stabilization and oxygen fixation hypothesis (OFH) mechanism. In this study, an existing mathematical model describing cell cycle kinetics was modified to include the oxygen-dependent G1/S transition rate and radiation inactivation rate. The radiation inactivation rate used was derived from the linear-quadratic (LQ) model with dependence on oxygen enhancement ratio (OER), while the oxygen-dependent correction for the G1/S phase transition was obtained from numerically solving the ODE system of cyclin D-HIF dynamics at different oxygen tensions. The corresponding cell cycle phase fractions of aerated MCF-7 tumor population, and the resulting growth curve obtained from numerically solving the developed mathematical model were found to be comparable to experimental data. Two breast radiotherapy fractionation schemes were investigated using the mathematical model. Results show that hypoxia causes the tumor to be more predominated by the tumor subpopulation in the G1 phase and decrease the fractional contribution of the more radioresistant tumor cells in the S phase. However, the advantage provided by hypoxia in terms of cell cycle phase distribution is largely offset by the radioresistance developed through OFH. The delayed proliferation caused by severe hypoxia slightly improves the radiotherapy efficacy compared to that with mild hypoxia for a high overall treatment duration as demonstrated in the 40-Gy fractionation scheme.

This paper examines the effect of electromagnetic waves, with maxima in the green or red regions of the spectrum, on the morphofunctional state of multipotent mesenchymal stromal cells. The illumination regimes used in our experiments did not lead to any substantial heating of the samples; the physical parameters of the lighting were carefully monitored. When the samples were illuminated with a green light, no significant photostimulatory effect was observed. Red light, on the other hand, had an evident photostimulatory effect. It is shown that photostimulation with a red light decreases the enzymatic activities of mitochondrial dehydrogenases and enhances the viability of cells, their proliferative activity, and their ability to form bone tissue. It is also established that red light stimulates cell proliferation, while not activating the genes that increase the risk of the subsequent malignant transformation of cells or their death. This paper discusses the possible role of hydrogen peroxide in the processes examined.

In any ecosystem, chaotic situations may arise from equilibrium state for different reasons. To overcome these chaotic situations, sometimes the system itself exhibits some mechanisms of self-adaptability. In this paper, we explore an eco-epidemiological model consisting of three aquatic groups: phytoplankton, zooplankton, and marine free viruses. We assume that the phytoplankton population is infected by external free viruses and zooplankton get affected on consumption of infected phytoplankton; also, the infected phytoplankton do not compete for resources with the susceptible one. In addition, we model a mechanism by which zooplankton recognize and avoid infected phytoplankton, at least when susceptible phytoplankton are present. The zooplankton extinction chance increases on increasing the force of infection or decreasing the intensity of avoidance. Further, when the viral infection triggers chaotic dynamics, high zooplankton avoidance intensity can stabilize again the system. Interestingly, for high avoidance intensity, nutrient enrichment has a destabilizing effect on the system dynamics, which is in line with the paradox of enrichment. Global sensitivity analysis helps to identify the most significant parameters that reduce the infected phytoplankton in the system. Finally, we compare the dynamics of the system by allowing the infected phytoplankton also to share resources with the susceptible phytoplankton. A gradual increase of the virus replication factor turns the system dynamics from chaos to doubling state to limit cycle to stable state and the system finally settles down to the zooplankton-free equilibrium point. Moreover, on increasing the intensity of avoidance, the system shows a transcritical bifurcation from the zooplankton-free equilibrium to the coexistence steady state and remains stable thereafter.

Titin is a giant elastic protein which is responsible for passive muscle stiffness when muscle sarcomeres are stretched. Chloramphenicol, besides being a broad-spectrum antibiotic, also acts as a muscle relaxant. Therefore, it is important to study the interaction between titin I27 and chloramphenicol. We investigated the interaction of chloramphenicol with octamer of titin I27 using single-molecule force spectroscopy and fluorescence spectroscopy. The fluorescence data indicated that binding of chloramphenicol with I27 results in fluorescence quenching. Furthermore, it is observed that chloramphenicol binds to I27 at a particular concentration ([Formula: see text] 40 μM). Single-molecule force spectroscopy shows that, in the presence of 40 μM chloramphenicol concentration, the I27 monomers become mechanically stable, resulting in an increment of the unfolding force. The stability was further confirmed by chemical denaturation experiments on monomers of I27, which corroborate the evidence for enhanced mechanical stability at 40 μM drug concentration. The free energy of stabilization for I27 (wild type) was found to be 1.95 ± 0.93 kcal/mole and I27 with 40 μM drug was 3.25 ± 0.63 kcal/mole. The results show a direct effect of the broad-spectrum antibiotic chloramphenicol on the passive elasticity of muscle protein titin. The I27 is stabilized both mechanically and chemically by chloramphenicol.

Non-invasive estimation of the pressure gradient in cardiovascular stenosis has much clinical importance in assisting the diagnosis and treatment of stenotic diseases. In this research, a systematic comparison is conducted to investigate the accuracy of a group of stenosis models against the MRI- and catheter-measured patient data under the aortic coarctation condition. Eight analytical stenosis models, including six from the literature and two proposed in this study, are investigated to examine their prediction accuracy against the clinical data. The two improved models proposed in this study consider comprehensively the Poiseuille loss, the Bernoulli loss in its exact form, and the entrance effect, of the blood flow. Comparison of the results shows that one of the proposed models demonstrates a cycle-averaged mean prediction error of −0.15 ± 3.03 mmHg, a peak-to-peak prediction error of −1.8 ± 6.89 mmHg, which is the best among the models studied., This research was funded by the European Community’s Seventh Framework Programme (FP7/2007–2013) under the grant agreement number 224495 (euHeart project).

The characteristics of cultured cell attachment onto poly-l-lysine (PLL), collagen, and the thermoresponsive polymer poly(N-isopropylacrylamide) (PNIPAM) were studied using a quartz crystal microbalance (QCM). A QCM with microscope cameras enclosed in a Peltier chamber was developed to enable QCM measurements and microphotographic imaging to be conducted in a temperature-controlled CO(2) incubator. Human hepatoma cell line HepG2 cells were cultured on the quartz crystals coated with PLL, collagen, and PNIPAM. Response curves of the resonant frequency of the quartz crystals during the cell attachment process were analyzed on the basis of the parameters of modeling curves fit to the experimentally obtained curves. Analysis of the fitting curves showed that the time constants of the first-lag response were 11 h for PLL, 16 h for collagen, and 38 h for PNIPAM and that the frequency change for the PNIPAM films was six times smaller than those for the PLL and collagen films. These findings were supported by photographic images showing wider cell spread on PLL and collagen than on PNIPAM. The response of cells on PNIPAM was measured during a thermal cycle from 37 to 20 °C to 37 °C. In the resonance frequency–resonance resistance (F–R) diagram, the slopes of ΔR/ΔF corresponding to the cell attachment process and those corresponding to the thermal cycling process differed; the positions in the F–R diagram also shifted to higher resonant frequencies after the thermal cycle. These results suggested that the mass effect decreased as a result of the weakening of the cell attachment strength by the thermal cycle because the molecular brushes of PNIPAM were disarranged. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10867-021-09568-7.

Voltage-gated sodium channels (NavChs) are pore-forming membrane proteins that regulate the transport of sodium ions through the cell membrane. Understanding the structure and function of NavChs is of major biophysical, as well as clinical, importance given their key role in cellular pathophysiology. In this work, we provide a computational framework for modeling system-size-dependent, i.e., cumulative, atomic properties around a NavCh’s pore. We illustrate our methodologies on the bacterial NavAb channel captured in a closed-pore state where we demonstrate that the atomic environment around its pore exhibits a bi-phasic spatial organization dictated by the structural separation of the pore domains (PDs) from the voltage-sensing domains (VSDs). Accordingly, a mathematical model describing packing of atoms around NavAb’s pore is constructed that allows—under certain conservation conditions—for a power-law approximation of the cumulative hydropathic dipole field effect acting along NavAb’s pore. This verified the non-extensitivity hypothesis for the closed-pore NavAb channel and revealed a long-range hydropathic interactions law regulating atom-packing around the NavAb’s selectivity filter. Our model predicts a PDs-VSDs coupling energy of \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$\sim \!282.1$\end{document}∼282.1 kcal/mol corresponding to a global maximum of the atom-packing energy profile. Crucially, we demonstrate for the first time how critical phenomena can emerge in a single-channel structure as a consequence of the non-extensive character of its atomic porous environment. Supplementary Information The online version contains supplementary material available at 10.1007/s10867-021-09565-w.

Reliability engineering concerned with failure of technical inanimate systems usually uses the vocabulary and notions of human mortality, e.g., infant mortality vs. senescence mortality. Yet, few data are available to support such a parallel description. Here, we focus on early-stage (infant) mortality for two inanimate systems, incandescent light bulbs and soap films, and show the parallel description is clearly valid. Theoretical considerations of the thermo-electrical properties of electrical conductors allow us to link bulb failure to inherent mechanical defects. We then demonstrate the converse, that is, knowing the failure rate for an ensemble of light bulbs, it is possible to deduce the distribution of defects in wire thickness in the ensemble. Using measurements of lifetimes for soap films, we show how this methodology links failure rate to geometry of the system; in the case presented, this is the length of the tube containing the films. In a similar manner, for a third example, the time-dependent death rate due to congenital aortic valve stenosis is related to the distribution of degrees of severity of this condition, as a function of time. The results not only validate clearly the parallel description noted above, but also point firmly to application of the methodology to humans, with the consequent ability to gain more insight into the role of abnormalities in infant mortality.

In the terrestrial dipolar magnetic field, magnetic circular dichroism (MCD) of UV sunlight by paramagnetic O(2) in an Archean atmosphere (mostly CO(2) and N(2)) results in circular polarization anisotropy (~ 10(−10)). This is used to calculate enantiomeric excess (EE~10(−13)) of glyceraldehyde (3-carbon sugar) with a model that includes racemic production and asymmetric photolysis of its enantiomers. The sign and magnitude of enantiomeric excess (EE) vary with the Earth’s latitude. Unlike random noise fluctuation in spontaneous mirror symmetry breaking (SMSB) models, the sign of EE is deterministic and constant over large areas of prebiotic Earth. The magnitude is several orders greater than the mean amplitude of stochastically fluctuating EE. MCD could provide the initial EE for growth of homochirality by asymmetric autocatalysis.

In this report, we propose a modification on the Asano-Ohya-Khrennikov quantum-like decision-making process model of a two-player game by adding additional nonlinear terms to the related comparison step dynamical equation. The additions are in the form of a self-interaction and cross-interaction of the brain's amygdala and prefrontal cortex. We show that the cross-interaction significantly determines the final decision of a player, whether it becomes a rational or an irrational choice. In contrast, the nonlinear self-interaction term provides a feedback mechanism that speeds up the corresponding decision-making process. We also suggest the form of expectation values of the overall reaction rate coefficients of those nonlinear terms by making an analogy with the original model formulation.

Autophagy is an important cell activity which is the process of formation of autophagosomes, docking with lysosomes and degradation. The intrinsic pathway of apoptosis involves mitochondrial outer membrane permeabilization (MOMP) and cytochrome c release followed by caspase activation. Many molecules, e.g., Ca(2+) and mTOR, and different stresses such as endoplasmic reticulum (ER) stress and nutritional stress take part in these two processes. However, the mechanism of how they work together so as to determine cell fate decisions remains to be clarified. Here, we present a computational model for cell fate decisions based on intertwined dynamics with autophagy and apoptosis involving Ca(2+), mTOR, and both ER stress and nutritional stress. In agreement with experimental observations, the model predicts that both Ca(2+) and the stresses play critical roles in regulating the choice between autophagy and apoptosis in a combinatorial way. The model presented here might be a good candidate for providing the qualitative mechanism of cell fate decisions mediated by Ca(2+), mTOR, and two kinds of stress.

Continuous exposure of 395 nm light increases the fluorescence emission intensity of photosynthetic purple non-sulphur bacteria, Rhodobacter capsulatus (SB1003). We show that such an increase in fluorescence emission of extracellular pigment complexes (PC) from these photosynthetic bacteria depends on the concentration of the pigment and temperature and can also be modulated by the static magnetic field. The time-dependent enhanced emission disappears either at or below 300 K or below a threshold sample concentration (0.1 mg/ml). The enhanced emission reappears at this condition (T 0). At PC concentration higher than a threshold, k becomes negative if the temperature is lowered. But, surprisingly, at low temperature, a static magnetic field reverts the k value to positive. We explain the logical nature of k-switching and photo-dynamics of the aforesaid microbial fluorescence emission by aggregation of protoporphyrin rings present in the PC. While the simultaneous presence of decay in fluorescence and susceptibility to static magnetic field suggests the dominance of triplet states at low temperatures, the process is reversed by SMF-induced removal of spin degeneracy. At higher temperatures, the optical excitability and lack of magnetic response suggest the dominance of singlet states. We propose that the restructuring of the singlet-triplet distribution by intersystem crossing may be the basis of this logical behaviour. In context with microbial function, time-dependent enhancement of fluorescence also implies relay of red photons to the neighbouring microbes not directly exposed to the incident radiation, thus serving as an indirect photosynthetic regulator. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s10867-020-09545-6) contains supplementary material, which is available to authorized users.

In this study, we model avascular tumour growth in epithelial tissue. This can help us to understand that how an avascular tumour interacts with its microenvironment and what type of physical changes can be observed within the tumour spheroid before angiogenesis. This understanding is likely to assist in the development of better diagnostics, improved therapies, and prognostics. In biological systems, most of the diffusive processes are through cellular membranes which are porous in nature. Due to its porous nature, diffusion in biological systems are heterogeneous. The fractional diffusion equation is well suited to model heterogeneous biological systems, though most of the early studies did not use this fact. They described tumour growth with simple diffusion-based model. We have developed a spherical model based on simple diffusion initially, and then the model is upgraded with fractional diffusion equations to express the anomalous nature of biological system. In this study, two types of fractional models are developed: one of fixed order and the other of variable order. The memory formalism technique is also included in these anomalous diffusion models. These three models are investigated from phenomenological point view by measuring some parameters for characterizing avascular tumour growth over time. Tumour microenvironment is very complex in nature due to several concurrent molecular mechanisms. Diffusion with memory (fixed as well as variable) formation may be an oversimplified technique, and does not reflect the detailed view of the tumour microenvironment. However, it is found that all the models offer realistic and insightful information of the tumour microenvironment at the macroscopic level, and approximate well the physical phenomena. Also, it is observed that the anomalous diffusion based models offer a closer description to clinical facts than the simple model. As the simulation parameters get modified due to different biochemical and biophysical processes, the robustness of the model is determined. It is found that the anomalous diffusion models are moderately sensitive to the parameters.

During cell migration, forces applied to a cell from its environment influence the motion. When the cell is placed on a substrate, such a force is provided by the cell-substrate adhesion. Modulation of adhesivity, often performed by the modulation of the substrate stiffness, tends to cause common responses for cell spreading, cell speed, persistence, and random motility coefficient. Although the reasons for the response of cell spreading and cell speed have been suggested, other responses are not well understood. In this study, we develop a simple toy model for cell migration driven by the relation of two forces: the adhesive force and the plasma membrane tension. The simplicity of the model allows us to perform the calculation not only numerically but also analytically, and the analysis provides formulas directly relating the adhesivity to cell spreading, persistence, and the random motility coefficient. Accordingly, the results offer a unified picture on the causal relations between those multiple cellular responses. In addition, cellular properties that would influence the migratory behavior are suggested.

The decrease in apparent relative viscosity that occurs when blood is made to flow through a tube whose diameter is less than about 0.3 mm is a well-known and documented phenomenon in physiology, known as the Fåhræus-Lindqvist effect. However, since the historical work of Fåhræus and Lindqvist (Amer. J. Physiol. 96(3): pp. 562–568, 1931), the underlying physical mechanism has remained enigmatic. A widely accepted qualitative explanation was provided by Haynes (Amer. J. Physiol. 198, pp. 1193–1200, 1960) according to which blood flows in microvessels with a core-annulus structure, where the erythrocytes concentrate within a central core surrounded by a plasma layer. Although sustained by observations, this conjecture lacks a rigorous deduction from the basic principles of continuum dynamics. Moreover, relations aimed to reproduce the blood apparent relative viscosity, extensively used in micro-circulation, are all empirical and not derived from the analysis of the fluid mechanical phenomena involved. In this paper, we apply the recent results illustrated in Guadagni and Farina (Int. J. Nonlinear Mech. 126, p. 103587, 2020), with the purpose of showing that Haynes’ conjecture, slightly corrected to make it more realistic, can be proved and can be used to reach a sound explanation of the Fåhræus-Lindqvist effect based on continuum mechanics. We propose a theoretical model for the blood apparent relative viscosity which is validated by matching not only the original experimental data reported by Fåhræus and Lindqvist (Amer. J. Physiol. 96(3), pp. 562–568, 1931), but also those provided by several subsequent authors.

Transmembrane acid–base fluxes affect the intracellular pH and unstirred layer pH around a superfused biological preparation. In this paper the factors influencing the unstirred layer pH and its gradient are studied. An analytical expression of the unstirred layer pH gradient in steady state is derived as a function of simultaneous transmembrane fluxes of (weak) acids and bases with the dehydration reaction of carbonic acid in equilibrium. Also a multicompartment computer model is described consisting of the extracellular bulk compartment, different unstirred layer compartments and the intracellular compartment. With this model also transient changes and the influence of carbonic anhydrase (CA) can be studied. The analytical expression and simulations with the multicompartment model demonstrate that in steady state the unstirred layer pH and its gradient are influenced by the size and type of transmembrane flux of acids and bases, their dissociation constant and diffusion coefficient, the concentration, diffusion coefficient and type of mobile buffers and the activity and location of CA. Similar principles contribute to the amplitude of the unstirred layer pH transients. According to these models an immobile buffer does not influence the steady-state pH, but reduces the amplitude of pH transients especially when these are fast. The unstirred layer pH provides useful information about transmembrane acid–base fluxes. This paper gives more insight how the unstirred layer pH and its transients can be interpreted. Methodological issues are discussed.

In this paper, we perform flexible and reliable dynamics simulations on different sizes of two or more particles’ interactive motions, where they encounter positive or negative dielectrophoresis (DEP) forces. The particles with identical or non-identical size are in close proximity suspended freely in a solution under a homogeneous electric field. According to the description of classic dipole moment, DEP forces make the particles form a straight chain. Therefore, dynamics simulation based on Newton’s laws is utilized to understand AC DEP phenomena among multiple particles. To solve the relevant governing equations, Stokes drag and repulsive forces (including wall and particles) are combined with DEP forces to obtain the trajectories of particles. Results show that particles with the same sign of the Clausius–Mossotti (CM) factor revolve clockwise or counterclockwise to attract each other parallel to the electric field direction. Conversely, the particle chain is perpendicular to the field. This programmable advantage is of great benefit to the study of three or four particle motions. Meanwhile, the pearl chain consisting of three or four particles is related not only to an individual CM factor but also to initial spatial configuration. Both the cluster and short chain are dependent on symmetry between the geometric distribution and electric field, while it implies different size particles easily cause the chain structure with less time. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s10867-018-9514-7) contains supplementary material, which is available to authorized users.

The dynamics of ion translocation through membrane transporters is visualized from a comprehensive point of view by a Gibbs energy landscape approach. The ΔG calculations have been performed with the Kirkwood–Tanford–Warshel (KTW) electrostatic theory that properly takes into account the self-energies of the ions. The Gibbs energy landscapes for translocation of a single charge and an ion pair are calculated, compared, and contrasted as a function of the order parameter, and the characteristics of the frustrated system with bistability for the ion pair are described and quantified in considerable detail. These calculations have been compared with experimental data on the ΔG of ion pairs in proteins. It is shown that, under suitable conditions, the adverse Gibbs energy barrier can be almost completely compensated by the sum of the electrostatic energy of the charge–charge interactions and the solvation energy of the ion pair. The maxima in ΔG(KTW) with interionic distance in the bound H(+) – A(−) charge pair on the enzyme is interpreted in thermodynamic and molecular mechanistic terms, and biological implications for molecular mechanisms of ATP synthesis are discussed. The timescale at which the order parameter moves between two stable states has been estimated by solving the dynamical equations of motion, and a wealth of novel insights into energy transduction during ATP synthesis by the membrane-bound F(O)F(1)-ATP synthase transporter is offered. In summary, a unifying analytical framework that integrates physics, chemistry, and biology has been developed for ion translocation by membrane transporters for the first time by means of a Gibbs energy landscape approach. [Image: see text]

The quality and strength of drug and albumin interaction affecting the drug-free concentration and physiological activity are important issues in pharmacokinetic research. In the present study, not only did we evaluate the binding strength of ceftriaxone and ceftizoxime to bovine serum albumin (BSA), but we also investigated the kinetic and thermodynamic parameters including KD, KA, ΔS, and ΔH. We applied in vitro optical fluorescence spectroscopy and surface plasmon resonance (SPR) sensing approaches as well as molecular docking analyses. The kinetic and thermodynamic investigations were done using different concentrations of drugs at three temperatures. Thermodynamic parameters visibly demonstrated that the binding was an exothermic and spontaneous process. The obtained negative values of both enthalpy change (ΔH) and entropy change (ΔS) in fluorescence and SPR and also molecular docking investigations showed that the major binding force involved in the complexation of drugs to BSA was hydrogen bonding. Static quenching was the foremost fluorescence quenching mechanism between them. Furthermore, the results of ΔG and K(D) values proved that the interaction of ceftriaxone-BSA was stronger than ceftizoxime-BSA. Finally, molecular docking confirmed that the preferable binding sites of ceftizoxime and ceftriaxone were site IIA and site IB of albumin, respectively. GRAPHIC ABSTRACT: [Image: see text] SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10867-021-09599-0.

This paper describes the application of the photoacoustic spectroscopic (PAS) for detection of bioactive compounds in Agaricus brasiliensis mycelium. The mycelium was cultivated by solid-state fermentation and by submerged fermentation. Vegetal residues from food industry were used as substrates for fermentation: apple pomace (Malus domestica), wheat (Triticum aestivum), peel and pomace of pineapple (Ananas comosus), malt (Hordeum vulgare) and grape pomace (Vitis vinifera). Dry and ground samples of biomass were directly put into the PA cell. The optical absorption spectra indicated the existence of three main absorption bands: one around 280 nm related to phytosterols (ergosterol), phenolic acids, flavonoids and aromatic amino acids, another at 340 nm, due to phenolic and flavonoid compounds, and the third one at around 550 nm associated with anthocyanins and anthocyanidins. A correlation between the PA signal and the total phenolic content was satisfactory, as well as for the analyzed spectrum region (270 nm up to 1000 nm), using multivariate methods. Our results indicated that PA technique may be considered as an analytical tool to quickly detect bioactive compounds in mushrooms without the need of sample pretreatment.

We employ some of the machinery developed in previous work to investigate the inferential and memory functions of quantum-like neural networks. We set up a logical apparatus to implement this in the form of a Gentzen sequent calculus which codifies some of the combinatory rules for the state spaces of the neuronal networks introduced earlier. We discuss memory storage in this context and along the way find formal proof that synchronicity promotes binding and storage. These results lead to an algorithmic fragment in calculus that simulates the memory function known as pattern completion. This claim is tested by noting that the failure of certain steps in the algorithm leads to memory deficits essentially identical to those found in such pathologies as Alzheimer's dementia, schizophrenia, and certain forms of autism. Moreover, a specific "power-of-two" wiring architecture and computational logic, which have been postulated and observed across many brain circuits, emerge spontaneously from our model. We draw conclusions concerning the possible nature of such mental processes qua computations.

Pertussis (or whooping cough) is a contagious disease mainly affecting infants and children and predominantly caused by Bordetella pertussis followed by Bordetella parapertussis. B. parapertussis causes a milder cough but usually symptomatically appears like B. pertussis infection. Thus the epidemiology of illness caused by B. parapertussis is not well understood. In this study, a sensitive and specific method for the rapid diagnosis of B. parapertussis is presented. The covalent immobilization of thiol-terminated DNA oligonucleotides (ss DNA SAM) on a silicon surface by disulfide bond formation is investigated with atomic force microscopy (AFM) and ellipsometry. The measurements indicated an average layer thickness of 5 ± 0.84 nm for 2 μg/μl concentration and 24 h incubation time. This thickness changed to 8.4 ± 0.92 nm for the same concentration (2 μg/μl) by altering the incubation time to 48 h. Ellipsometric data recorded before and after hybridization of B. parapertussis revealed an increase in mean grain area from 91 nm(2) to 227 nm(2) and a change in the refractive index from 1.489 to 1.648 for 2 μg/μl B. parapertussis, respectively. This change in the refractive index was used to evaluate the amount of adsorbed molecules and their density. The results showed that the density of adsorbed molecules increased from 0.2 to 0.97 g/cm(3) after B. parapertussis attachment, respectively. To confirm the hybridization of B. parapertussis to ss DNA SAM, the ds DNA SAM was denatured and the ss DNA SAM surface was reproduced with an average height variation of 6.42 ± 0.75 nm. This showed the stability of the DNA film that can be tuned by varying the concentration and incubation time, thus providing a robust method for the label-free detection of B. parapertussis other than routinely used PCR detection.

The stiffness of adherent mammalian cells is regulated by the elasticity of substrates due to mechanotransduction via integrin-based focal adhesions. Dictyostelium discoideum is an ameboid protozoan model organism that does not carry genes for classical integrin and can adhere to substrates without forming focal adhesions. It also has a life cycle that naturally includes both single-cellular and multicellular life forms. In this article, we report the measurements of the elastic modulus of single cells on varied substrate stiffnesses and the elastic modulus of the multicellular “slug” using atomic force microscopy (AFM) as a microindenter/force transducer. The results show that the elastic modulus of the Dictyostelium cell is regulated by the stiffness of the substrate and its surrounding cells, which is similar to the mechanotransduction behavior of mammalian cells. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s10867-019-09529-1) contains supplementary material, which is available to authorized users.

Predator-prey systems are used to model time-dependent virus and lymphocyte population during a liver infection and to discuss the influence of chemotactic behavior on the chronification tendency of such infections. Therefore, a model family of reaction-diffusion equations is presented, and the long-term behavior of the solutions is estimated by a critical value containing the reaction strength, the diffusion rate, and the extension of the liver domain. Fourier techniques are applied to evaluate the influence of chemotactic behavior of the immune response to the long-term behavior of locally linearized models. It turns out that the chemotaxis is a subordinated influence with respect to the chronification of liver infections.

Diatoms are microalgae encased in highly structured and regular frustules of porous silica. A long-standing biological question has been the function of these frustules, with hypotheses ranging from them acting as photonic light absorbers to being particle filters. While it has been observed that the girdle band pores of the frustule of Coscinodiscus sp. resemble those of a hydrodynamic drift ratchet, we show using scaling arguments and numerical simulations that they cannot act as effective drift ratchets. Instead, we present evidence that frustules are semi-active filters. We propose that frustule pores simultaneously repel viruses while promoting uptake of ionic nutrients via a recirculating, electroosmotic dead-end pore flow, a new mechanism of “hydrodynamic immunity”.

The objective of this study is to observe the echo feature curves, vibrational dephasing, and heat capacity of a protein-hormone system taking thyroid hormone receptor-beta (THR-β) as an example. Constrained and unconstrained molecular dynamics simulations are performed by implementing the theory of velocity reassignments to probe the phase coherent state in terms of echo pulses. The constrained vibrations are incorporated by adjusting rigid bonds to all hydrogen atoms with an integrator parameter of 2 fs/step in order to reduce the degrees of freedom whereas 1 fs/step is used in the free vibrations of the atomic cluster. The nature of temperature auto-correlation functions changes so that echo feature curves also show a distinct nature in the cases of constrained and unconstrained vibrations. There is a large variation in kinetic temperature and internal potential energy in the echo time zone. The temperature rate of change of internal potential energy is the main contributor to the heat capacity of the native state protein-hormone system. The heat capacity of proteins estimated from this technique is in good agreement with the values from experiments. This study shows that triiodothyronine (T3) hormone makes some differences in heat capacity upon binding to the THR-β ligand binding domain (LBD). The physical properties of unliganded THR-β and T3-bound THR-β LBD in the cases of constrained and unconstrained dynamics are observed distinctly under the effect of anharmonicity on the phase coherent state of normal modes and the dephasing time lies in a range of 0.6-0.8 ps when the systems are perturbed suddenly.

The objective of this research is to study the combined influences of applied electric and magnetic fields on the two-phase peristaltic motion of nanofluid through a curved channel. A two-phase model of a nanofluid, Maxwell’s model of thermal conductivity [1], and no-slip velocity and thermal boundary conditions have been used in this study. Hall effects, Joule heating (due to magnetic and electric fields), and viscous heating aspects are under consideration. Governing equations for the present flow configuration have been modeled and simplified by enforcing the lubrication scheme. Debye-Huckel approximation is used to obtain the analytical solution of the electric potential function (Poisson-Boltzmann equation). Resulting expressions are solved numerically through the NDSolve command in Mathematica and plotted in order to understand the effects of different dimensionless parameters on the temperature, stress, heat transmission rate, and fluid’s velocity. Graphical results demonstrated that the thermal transmission rate is augmented by increasing the Hartmann number, Brinkman number, and Debye-Huckel parameter while decreases for zeta potential ratio, Joule dissipation parameter, and electro-osmotic velocity. A decrease in axial velocity is noted near the lower wall for higher values of $${m}^{\ast}$$ .

The morphology and proliferation of eukaryotic cells depend on their microenvironment. When electrospun mats are used as tissue engineering scaffolds, the local alignment of the fibers has a pronounced influence on cells. Here we analyzed the morphology of the patterned mats produced by electrospinning of PLA-gelatin blend onto a conductive grid. We investigated the cellular morphology and proliferation of two cell lines (keratinocytes HaCaT and fibroblasts NIH 3T3) on the patterned mats. The non-patterned mats of the same chemical composition were used as control ones. The HaCaT cells predominantly grew on convex areas of the patterned mats along with increasing their nucleus area and decreasing cell area. The 3T3 cells had a lower proliferative rate when grown on the patterned mats. The results can be valuable for further development of the procedures, which allow the patterned electrospun mats development as well as for the investigation of cell-substrate interactions. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10867-021-09574-9.

This paper presents a Fourier analysis of the Ortega equation that examines the growth dynamics of plants, specifically the pollen tubes or non-meristematic zones of elongating coleoptiles. A frequency-induced transition from highly nonlinear (periodical) growth-like the one observed in pollen tubes-to monotonically ascending and asymptotically saturated (sigmoid-like) growth, which is anticipated within the framework of a 'two-fluid model', is shown. A dynamic phase diagram is calculated and presented in the form of a live video clip.

Recently there has been much interest in the possible quantum-like behavior of the human brain in such functions as cognition, the mental lexicon, memory, etc., producing a vast literature. These studies are both empirical and theoretical, the tenets of the theory in question being mainly, and apparently inevitably, those of quantum physics itself, for lack of other arenas in which quantum-like properties are presumed to obtain. However, attempts to explain this behavior on the basis of actual quantum physics going on at the atomic or molecular level within some element of brain or neuronal anatomy (other than the ordinary quantum physics that underlies everything), do not seem to survive much scrutiny. Moreover, it has been found empirically that the usual physics-like Hilbert space model seems not to apply in detail to human cognition in the large. In this paper we lay the groundwork for a theory that might explain the provenance of quantum-like behavior in complex systems whose internal structure is essentially hidden or inaccessible. The approach is via the logic obeyed by these systems which is similar to, but not identical with, the logic obeyed by actual quantum systems. The results reveal certain effects in such systems which, though quantum-like, are not identical to the kinds of quantum effects found in physics. These effects increase with the size of the system.

Donnan theory and Goldman-Hodgkin-Katz equation (GHK eq.) state that the nonzero membrane potential is generated by the asymmetric ion distribution between two solutions separated by a semipermeable membrane and/or by the continuous ion transport across the semipermeable membrane. However, there have been a number of reports of the membrane potential generation behaviors in conflict with those theories. The authors of this paper performed the experimental and theoretical investigation of membrane potential and found that (1) Donnan theory is valid only when the macroscopic electroneutrality is sufficed and (2) Potential behavior across a certain type of membrane appears to be inexplicable on the concept of GHK eq. Consequently, the authors derived a conclusion that the existing theories have some limitations for predicting the membrane potential behavior and we need to find a theory to overcome those limitations. The authors suggest that the ion adsorption theory named Ling’s adsorption theory, which attributes the membrane potential generation to the mobile ion adsorption onto the adsorption sites, could overcome those problems.

In this paper, a long-term in vitro dynamic calcification of three porcine aortic heart valves was investigated using a combined approach that involved accelerated wear testing of the valves in the rapid calcification solution, hydrodynamic assessment of the progressive change of effective orifice area (EOA) along with the transaortic pressure gradient, and quantitative visualization of the flow. The motivation for this study was developing a standardized, economical, and feasible in vitro testing methodology for bioprosthetic heart valve calcification, which would address both the hydrodynamic performance of the valves as well as the subsequent changes in the flow field. The results revealed the failure of the test valves at 40 million cycles mark, associated with the critical decrease in the EOA, followed by the increase in the maximum value of viscous shear stress of up to 52%, compared to the values measured at the beginning of the study. The decrease in the EOA was subsequently followed by the rapid increase in the maximum streamwise velocity of the central orifice jet up to the value of about 2.8 m/s, compared to the initial value of 2 m/s, and to the value of 2.2 m/s in the case of a control valve along with progressive narrowing of the velocity profile for two test valves. The significance of the current work is in demonstrating a correlation between calcification of the aortic valve and spatial as well as the temporal development of abnormal flow features.

Triosephosphate isomerase (TIM) is often described as a fully evolved housekeeping enzyme with near-maximal possible reaction rate. The assumption that an enzyme is perfectly evolved has not been easy to confirm or refute. In this paper, we use maximization of entropy production within known constraints to examine this assumption by calculating steady-state cyclic flux, corresponding entropy production, and catalytic activity in a reversible four-state scheme of TIM functional states. The maximal entropy production (MaxEP) requirement for any of the first three transitions between TIM functional states leads to decreased total entropy production. Only the MaxEP requirement for the product (R-glyceraldehyde-3-phosphate) release step led to a 30% increase in enzyme activity, specificity constant kcat/KM, and overall entropy production. The product release step, due to the TIM molecular machine working in the physiological direction of glycolysis, has not been identified before as the rate-limiting step by using irreversible thermodynamics. Together with structural studies, our results open the possibility for finding amino acid substitutions leading to an increased frequency of loop six opening and product release.

Like any other kind of cell, muscle cells produce energy by oxidizing the fuel substrate that they absorb together with the needed oxygen from the surroundings. Oxidation occurs entirely within the cell. It means that the reactants and products of reaction must at some time be dissolved in the cell's cytosol. If a cell operates at steady state, its cytosol composition remains constant. Therefore, the cytosol in a muscle that produces work at steady state must contain a constant amount of fuel, oxygen, and product of reaction dissolved in it. The greater the power produced, the higher the concentration of these solutes. There is a limit, however, to the maximum amount of solutes that the cytosol can contain without damaging the cell. General thermodynamic arguments, which are reviewed in this paper, help relate this limit to the dehydration and overhydration limits of the cell. The present analysis shows that the same limits entail a limit to the maximum power that a muscle can produce at steady state. This limit depends on the composition of the fuel mixture used by the muscle. The analysis also determines the number of fuel carbon atoms that must be oxidized in parallel within a cell to produce a given power. It may well happen that a muscle cannot reach the maximum attainable power because it cannot activate all the parallel oxidation paths that are needed to produce it. This may be due to a series of reasons ranging from health issues to a lack of training. The paper shows how the methods of indirect calorimetry can provide all the experimental data needed to determine the actual number of parallel oxidation paths that at steady state must be active in a muscle in a given exercise. A diagram relating muscle power to the number of parallel oxidation paths and fuel composition is finally presented. It provides a means to assess the power capacity of animal muscles and can be applied to evaluate their fitness, stamina, margins for improvement, and athletic potential.

For investigations of ongoing processes in plants, such as photosynthesis in conifer leaves, nondestructive and noninvasive measuring techniques are needed. In this paper, a novel approach has been developed for the measurement of chloroplasts' numbers and pigment contents in conifer leaves based on the measurements of leaf absorption spectra using optical fibers and an array spectrophotometer. To eliminate the effect of scattering on the measured absorption spectra, a strategy has been applied taking advantage of the combined use of thin optical fibers normal to the needle's longitudinal axis and the phenomenon that scattering is largest in the forward direction. The optical path in the leaf is nearly the distance between the fiber tips; thus, we were able to obtain the absorption spectrum of the pigments in situ. A effect of the measured absorption spectra, occurring due to the organization of pigments in the leaf and interaction between light and leaf interior, can be accounted for by using the so-called Duysens transformation. Using this transformation, pigment contents and the relative number of chloroplasts can be obtained from the measured absorption spectra. We applied the method to observe pigment concentrations in different stages of the greening process in the leaves of two conifer species, Taxus baccata and Picea abies. The presented method may be used to estimate changes in chloroplast number and pigment content during various phases of greening of a species and to observe differences among various species.

The Fahraeus-Lindqvist effect is usually explained from a physical point of view with the so-called Haynes’ marginal zone theory, i.e., migration of red blood cells (RBCs) to a core layer surrounded by an annular RBCs-free plasma layer. In this paper we show that the marginal layer, though causing a substantial reduction in flow resistance and increasing discharge, does not reduce the rate of energy dissipation. This fact is not surprising if one considers the electric analog of the flow in a vessel: a resistance reduction increases both the current intensity (i.e., the discharge) and the energy dissipation. This result is obtained by considering six rheological models that relate the blood viscosity to hematocrit (volume fraction occupied by erythrocytes). Some physiological implications are discussed.

Thymus (T) and natural killer (NK) lymphocytes are important barriers against diseases. Therefore, it is necessary to understand regulatory mechanisms related to the cell fate decisions involved in the production of these cells. Although some individual information related to T and NK lymphocyte cell fate decisions have been revealed, the related network and its dynamical characteristics still have not been well understood. By integrating individual information and comparing with experimental data, we construct a comprehensive regulatory network and a logical model related to T and NK lymphocyte differentiation. We aim to explore possible mechanisms of how each lineage differentiation is realized by systematically screening individual perturbations. When determining the perturbation strategies, the state transition can be used to identify the roles of specific genes in cell type selection and reprogramming. In agreement with experimental observations, the dynamics of the model correctly restates the cell differentiation processes from common lymphoid progenitors to CD4+ T cells, CD8+ T cells, and NK cells. Our analysis reveals that some specific perturbations can give rise to directional cell differentiation or reprogramming. We test our in silico results by using known experimental observations. The integrated network and the logical model presented here might be a good candidate for providing qualitative mechanisms of cell fate specification involved in T and NK lymphocyte cell fate decisions. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10867-021-09563-y.

In this work, we consider a ternary system formed by a surfactant with a lamellar phase (lecithin) that was doped with a solution of Laponite at 1% by volume. The inclusion of nanoparticles in the lamellar phase was investigated by the small-angle X-ray scattering (SAXS) technique, which revealed three types of structures according to the observed scattering pattern. The lamellar period increased linearly with hydration up to a certain limit; this type of behavior is not the same as that found for a similar system using AOT as a surfactant. In the region that corresponds to an isotropic phase, it was observed that the period corresponds to 60 A, and in the lamellar system of pure lecithin, with the same volumetric fraction (1/φ = 0.66), the corresponding periodicity is 62 A, indicating that the presence of Laponite nanoparticles increases the attractive interaction, reducing the lamellar period, causing the bilayer to become more rigid, that is, with less fluctuations. In the more diluted region, the periodicity reached a limit value of 64 A, which is slightly higher than the lamellar system in the absence of Laponite particles, so there was an expansion of the lamellar phase due to the lack of consistency of Laponite nanoparticles. In the more concentrated lamellar phase (under strong confinement), it was observed that the distance between the bilayers decreased, establishing a long-range order.

We investigate through simulations the phenomena of magnetoreception to enable an understanding of the minimum requirements of a fail-safe mechanism, operational at the cellular level, to sense a weak magnetic field at ambient temperature in a biologically active environment. To do this, we use magnetotactic bacteria (MTB) as our model system. The magnetic field sensing ability of these bacteria is due to the presence of magnetosomes, which are internal membrane-bound organelles that contain an iron-based magnetic mineral crystal. These magnetosomes are usually found arranged in a chain aligned with the long axis of the bacterial body. This arrangement yields an overall magnetic dipole moment to the bacterial cell. To simulate this orientation process, we set up a rotational Langevin stochastic differential equation and solve it repeatedly over appropriate time steps for isolated spherical shaped MTB as well as for a more realistic model of spheroidal MTB with flagella. The orientation process appears to depend on shape parameters with spheroidal MTB showing a slower response time compared to spherical MTB. Further, our simulation also reveals that the alignment to the external magnetic field is more robust for an MTB when compared to single magnetosome. For the simulation involving magnetosomes, we include an extra torque that arises from the twisting of an attachment tether and enhance the viscosity of the surrounding medium to mimic intracellular conditions in the governing Langevin equation. The response time of alignment is found to be substantially reduced when one includes a dipole interaction term with a neighboring magnetosome and the alignment becomes less robust with increase in inter dipole distance. The alignment process can thereby be said to be very sensitively dependent on the distance between magnetosomes. Simulating the process of alignment between two neighboring magnetosomes, both in the absence and presence of an ambient magnetic field, we conclude that alignment between these dipoles at the distances typical in an MTB is highly probable and it would be the locked unit that responds to changes in the external magnetic field.

The Goldman–Hodgkin–Katz equation (GHK equation), one of the most successful achievements of membrane theory in electrophysiology, can precisely predict the membrane potential. Its conceptual foundation lies in the idea that the transmembrane ion transport across the plasma membrane is responsible for the membrane potential generation. However, the potential virtually equivalent to the membrane potential is generated even across the impermeable membrane. In this work, I discus the membrane potential generation mechanism and find that the potential formula based on the long-dismissed Ling’s adsorption theory, which attributes the membrane potential generation to the mobile ion adsorption rather than the transmembrane ion transport, is the same as the GHK equation. Based on this finding, I derive a conclusion that the membrane potential is generated by the ion adsorption against the existing electrophysiological concept.

The control of nonlinear dynamical systems is always a notable problem in science. According to control theory, suitable inputs for a controllable dynamical system are critical. Previous studies have shown some principles to determine control nodes and design control function. In this work, we propose a new control strategy of nonlinear systems by constructing impulsive control functions, i.e., we can realize the transition from an undesired state to a desired one by controlling appropriately chosen nodes in a discrete manner. In order to demonstrate the effectiveness of the strategy, we apply it to two biological networks: the epithelial–mesenchymal transition (EMT) network and the Notch1–Dll1–Jag1 signaling pathway. The strategy can not only be used to guide pharmacological design in a more feasible form but can also be applied into the fields of biological, medical and other multistable dynamical systems.

The impact of gamma irradiation on growth and physiology of Euryale ferox was described in the present investigation. E. ferox is an underutilized aquatic food crop that grows in shallow-water bodies in lower Assam regions and north Bihar of India. The seeds of E. ferox were irradiated with different doses of gamma irradiation ranging from 0 to 500 Gy. It was observed that the germination and survival percentage was inhibited by increasing the irradiation dose. However, plants developed from seed exposed to an irradiation dose beyond 100 Gy did not survive more than 1 month. Further growth parameters (leaf size and number, number of thorns, root number and length, and number of flower and seeds) were also compared with respect to non-irradiated plants. Physiological parameters, viz. chlorophyll a, chlorophyll b, total chlorophyll, photosynthetic rate, transpiration rate, stomatal conductance, and intracellular CO(2) content was higher in the irradiation population of E. ferox. Superoxide dismutase (SOD) and ascorbate peroxidase (APX) activities were observed low in irradiated population of E. ferox. The proline and glycine betaine content was enhanced with increasing the irradiation dose. The present investigation explores the potential use of gamma rays in genetic improvement of E. ferox and improves understanding of the physiological responses inflicted by gamma irradiation.

Blood flow in micro capillaries of diameter approximately 15–500 μm is accompanied with a lower tube hematocrit level and lower apparent viscosity as the diameter decreases. These effects are termed the Fåhraeus and Fåhraeus–Lindqvist effects, respectively. Both effects are linked to axial accumulation of red blood cells. In the present investigation, we extend previous works using a shear-induced model for the migration of red blood cells and adopt a model for blood viscosity that accounts for the suspending medium viscosity and local hematocrit level. For fully developed hematocrit profiles (i.e., independent of axial location), the diffusion fluxes due to particle collision frequency and viscosity gradients are of equal magnitude and opposite directions. The ratio of the diffusion coefficients for the two fluxes affects both the Fåhraeus and Fåhraeus–Lindqvist effects and is found related to the capillary diameter and discharge hematocrit using a well-known data-fit correlation for apparent blood viscosity. The velocity and hematocrit profiles were determined numerically as functions of radial coordinate, tube diameter, and discharge hematocrit. The velocity profile determined numerically is consistent with the derived analytical expression and the results are in good agreement with published numerical results and experimental data for hematocrit ratio and hematocrit and velocity profiles.