Flow Behavior of Entangled Polymer Nanoparticle Composites in a Nanotube: Insights into Jamming State.

Using molecular dynamics simulations, this study investigates the equilibrium properties and flow behaviors of entangled polymer nanoparticle composites (PNCs) within a nanotube. The results show that the density distribution of nanoparticles (NPs), displacement of polymer chains and NPs, and the moduli of PNCs remain relatively unaffected when NP volume fractions (ΦN) ≤0.10. However, the flow behavior of entangled PNCs deviates from the ideal parabolic profile seen in unentangled PNCs, displaying plug-like flow characteristics with a significant platform region, indicating the presence of shear bands. Interestingly, entangled PNCs at intermediate ΦN values undergo a significant alteration in NP distribution under steady flow, resulting in notable NP aggregation. At ΦN = 0.30, a distinct change in the static structure of PNCs occurs, reducing the equilibrium distance between neighboring NPs. Consequently, the motion of both polymer chains and NPs becomes restricted, leading to an increase in the moduli of PNCs resembling solid-like behavior. Additionally, the entangled PNCs experience a complete absence of flow, indicating the entry into a jamming state. This study contributes to the understanding of PNCs flow behavior and provides insights into fundamental aspects and practical implications of PNCs.

Integration of DSF and Temperature Signals for RpfC/RpfG Two-Component System Modulating Protease Production in Stenotrophomonas maltophilia FF11.

Two-component signal system (TCS) is the predominant bacterial sense-and-response machinery. RpfC/RpfG TCS involved in quorum sensing molecule Diffuse Signal Factor (DSF) signal perception and transduction was well studied in many bacteria. However, whether other environmental factors participating in the signal perception and transduction of RpfC/RpfG was still unclear. Here, we showed that RpfC/RpfG could integrate temperature and DSF signal partially controlling the production of the temperature-dependent protease (SmtP) in S. maltophilia FF11, a strain isolated from frozen Antarctic krill, exhibited spoilage potential due to secret more protease at low temperatures involving in protein degradation. qRT-PCR analysis revealed rpf system mediating approximately 60% transcription activity of Clp, a critical transcription factor linking with LotS/LotR, consisting a signal network controlling completely the SmtP production in previous study. Protease production was partially reduced in rpfF (coding DSF synthetase) mutant strains at 15 °C or 25 °C, not be increased through addition DSF or overexpression RpfF in WT at 37 °C, indicating that DSF was effective for protease production only at low temperatures in S. maltophilia. Additionally, biochemical analysis revealed the enzymatic activity of RpfG from strain FF11 cultured at 37 °C or DSF-deficient strains grown at 25 °C was significantly reduced compared to that of RpfG from strain FF11 cultured at 25 °C. These findings outline an interplay mechanism that allows S. maltophilia to integrate quorum sensing and temperature cues controlling protease production, and imply a potential relationship between two distinct systems of RpfC/RpfG and LotS/LotR.

Salt-Induced Liquid-Liquid Phase Separation: Combined Experimental and Theoretical Investigation of Water-Acetonitrile-Salt Mixtures.

Salt-induced liquid-liquid phase separation in liquid mixtures is a common phenomenon in nature and in various applications, such as in separation and extraction of chemicals. Here, we present results of a systematic investigation of the phase behaviors in water-acetonitrile-salt mixtures using a combination of experiment and theory. We obtain complete ternary phase diagrams for nine representative salts in water-acetonitrile mixtures by cloud point and component analysis. We construct a thermodynamic free energy model by accounting for the nonideal mixing of the liquids, ion hydration, electrostatic interactions, and Born energy. Our theory yields phase diagrams in good agreement with the experimental data. By comparing the contributions due to the electrostatic interaction, Born energy, and hydration, we find that hydration is the main driving force for the liquid-liquid separation and is a major contributor to the specific ion effects. Our theory highlights the important role of entropy in the hydration driving force. We discuss the implications of our findings in the context of salting-out assisted liquid-liquid extraction and make suggestions for selecting salt ions to optimize the separation performance.

Potassium channels and their role in glioma: A mini review.

K+ channels regulate a multitude of biological processes and play important roles in a variety of diseases by controlling potassium flow across cell membranes. They are widely expressed in the central and peripheral nervous system. As a malignant tumor derived from nerve epithelium, glioma has the characteristics of high incidence, high recurrence rate, high mortality rate, and low cure rate. Since glioma cells show invasive growth, current surgical methods cannot completely remove tumors. Adjuvant chemotherapy is still needed after surgery. Because the blood-brain barrier and other factors lead to a lower effective concentration of chemotherapeutic drugs in the tumor, the recurrence rate of residual lesions is extremely high. Therefore, new therapeutic methods are needed. Numerous studies have shown that different K+ channel subtypes are differentially expressed in glioma cells and are involved in the regulation of the cell cycle of glioma cells to arrest them at different stages of the cell cycle. Increasing evidence suggests that K+ channels express in glioma cells and regulate glioma cell behaviors such as cell cycle, proliferation and apoptosis. This review article aims to summarize the current knowledge on the function of K+ channels in glioma, suggests K+ channels participating in the development of glioma.

Individual circular polyelectrolytes under shear flow.

Individual circular polyelectrolytes in simple shear flow are studied by means of mesoscale hydrodynamic simulations, revealing the complex coupling effects of shear rate, electrostatic interaction, and circular architecture on their conformational and dynamical properties. Shear flow deforms the polyelectrolyte and strips condensed counterions from its backbone. A decrease in condensed counterions alters electrostatic interactions among charged particles, affecting shear-induced polymer deformation and orientation. Circular architecture determines the features of deformation and orientation. At weak electrostatic interaction strengths, the polyelectrolyte changes its shape from an oblate ring at small shear rates to a prolate ring at large shear rates, whereas strong electrostatic interaction strengths are associated with a transition from a prolate coil to a prolate ring. Circular polyelectrolytes exhibit tumbling and tank-treading motions in the range of large shear rates. Further study reveals a similarity between the roles of intramolecular electrostatic repulsion and chain rigidity in shear-induced dynamics.

The influence of polymer architectures on the dewetting behavior of thin polymer films: from linear chains to ring chains.

The dewetting behavior of ring polystyrene (RPS) film and linear polystyrene (LPS) film on silanized Si substrates with different grafting densities and PDMS substrate was investigated. Results showed that polymer architectures greatly influenced the dewetting behavior of the thin polymer film. On the silanized Si substrate with 69% grafting density, RPS chains exhibited stronger adsorption compared with LPS chains, and as a result the wetting layer formed more easily. For LPS films, with a decreased annealing temperature, the stability of the polymer film changed from non-slip dewetting via apparent slip dewetting to apparently stable. However, for RPS films, the polymer film stability switched from apparent slip dewetting to apparently stable. On the silanized Si substrate with 94% grafting density, the chain adsorption became weaker and the dewetting processes were faster than that on the substrate with 69% grafting density at the same experimental temperature for both the LPS and RPS films. Moreover, on the PDMS substrate, LPS films always showed non-slip dewetting, while the dewetting kinetics of RPS films switched from non-slip dewetting to slip dewetting behaviour. Forming the wetting layer strongly influenced the stability and dewetting behavior of the thin polymer films.

Point-to-set dynamic length scale in binary Lennard-Jones glass-formers.

Our recent molecular dynamics simulation results of binary particle glass-former systems demonstrated that the non-monotonic temperature T-dependence of the point-to-set dynamic length scale ξcdyn in harmonic (HM) systems is not an intrinsic property of bulk liquids but originates from wall effects. We would expect our results to apply equally to other simple models, such as Lennard-Jones (LJ) systems. However, Hocky et al. presented a monotonic T-dependent ξcdyn in a LJ system. Therefore, the present work employs molecular dynamics simulations to investigate the T-dependent behavior of ξcdyn in the LJ system employed by Hocky et al. to clarify our expectation. Results employing a geometry size d that is somewhat smaller than that employed by Hocky et al. reveal that a non-monotonic behavior exists in the LJ system. By varying the value of d, we demonstrate that the formation of a peak in ξcdyn with respect to T in the LJ system is the natural result of wall effects. More importantly, a new non-monotonic behavior is observed, where the temperature at which the ratio of the characteristic time required for the overlap profile of the system to decay to a given value for a point near the wall to the corresponding characteristic time at a point in the center attains a maximum is in good agreement with the temperature Tmax-c at which ξcdyn attains a maximum value, indicating that the non-monotonic behavior of ξcdyn with respect to T is a natural property of liquids in a sandwiched geometry. Furthermore, we find that, contrary to HM systems, where the values of Tmax-c obtained for all values of d considered were greater than the mode-coupling temperature Tc, the value of Tmax-c obtained for LJ systems can be either greater than, equal to, or less than Tc because an HM system has a stronger finite-size effect than that in a LJ system, indirectly implying that the conclusion derived from random first-order transition theory that a dramatic change occurs near Tc bears no necessary relationship with the non-monotonic evolution of ξcdyn with respect to T.

Expression of KCNA5 Protein in Human Mammary Epithelial Cell Line Associated with Caveolin-1.

Voltage-gated potassium (Kv) channels are involved in the proliferation and transformation of mammary epithelial cells. They are thought to be related to the development of breast carcinoma, although the exact role they play in this event remains unclear. In this study, we investigated whether the expression and function of Kv channels is associated with Caveolin-1 (Cav-1, a principal component of caveolae) in different cell lines. We found that expression of Cav-1 correlated with the expression of Kv channels in mammary epithelial cells (MCF10A, MCF10A-ST1, and MCF7), and silencing of Cav-1 inhibited the expression of KCNA5 (voltage-gated shaker-related subfamily A, member 5). Immunofluorescence analysis indicated the colocalization of KCNA5 with Cav-1, whereas immunoprecipitation suggested a possible interaction between the two proteins. Overall, our finding indicated that KCNA5 protein may interact with Cav-1, thereby contributing to the proliferation and early transformation of mammary cells.

NMD mechanism and the functions of Upf proteins in plant.

Nonsense-mediated decay (NMD) mechanism, also called mRNA surveillance, is a universal mRNA degradation pathway in eukaryotes. Hundreds of genes can be regulated by NMD whether in single-celled or higher organisms. There have been many studies on NMD and NMD factors (Upf proteins) with regard to their crucial roles in mRNA decay, especially in mammals and yeast. However, research focusing on NMD in plant is still lacking compared to the research that has been dedicated to NMD in mammals and yeast. Even so, recent study has shown that NMD factors in Arabidopsis can provide resistance against biotic and abiotic stresses. This discovery and its associated developments have given plant NMD mechanism a new outlook and since then, more and more research has focused on this area. In this review, we focused mainly on the distinctive NMD micromechanism and functions of Upf proteins in plant with references to the role of mRNA surveillance in mammals and yeast. We also highlighted recent insights into the roles of premature termination codon location, trans-elements and functions of other NMD factors to emphasize the particularity of plant NMD. Furthermore, we also discussed conventional approaches and neoteric methods used in plant NMD researches.

Characterization of a salt-activated protease with temperature-dependent secretion in Stenotrophomonas maltophilia FF11 isolated from frozen Antarctic krill.

Seafood is sometimes wasted due to the growth of psychrotolerant microbes which secrete proteases and break down proteins. Stenotrophomonas maltophilia FF11, isolated from frozen Antarctic krill, grows at a wide range of temperatures and secretes more proteases at low temperatures. According to zymogram analysis, two kinds of proteases were produced from this strain. A major protease was produced largely at 15 °C, but not at 37 °C. The temperature-dependent secreted protease was purified to homogeneity. Its molecular mass was determined at 37.4 kDa and its amino acid sequence was also obtained. This protease is a member of the subtilase group according to the NCBI blast analysis. The enzyme was highly stable at high salt concentration (4 M). Interestingly, its activity increased about 1.6-fold under high salt condition. The enzyme remains active and stable in different organic solvents (50 %, v/v) such as dimethylsulfoxide, dimethyl formamide, dioxane and acetone. These properties may provide potential applications in quality control for sea foods, in protein degradation at high salt concentration, in biocatalysis and biotransformation within non-aqueous media, such as detergent and transesterification.

Relaxation dynamics in a binary hard-ellipse liquid.

Structural relaxation in binary hard spherical particles has been shown recently to exhibit a wealth of remarkable features when size disparity or mixture composition is varied. In this paper, we test whether or not similar dynamical phenomena occur in glassy systems composed of binary hard ellipses. We demonstrate via event-driven molecular dynamics simulation that a binary hard-ellipse mixture with an aspect ratio of two and moderate size disparity displays characteristic glassy dynamics upon increasing density in both the translational and the rotational degrees of freedom. The rotational glass transition density is found to be close to the translational one for the binary mixtures investigated. More importantly, we assess the influence of size disparity and mixture composition on the relaxation dynamics. We find that an increase of size disparity leads, both translationally and rotationally, to a speed up of the long-time dynamics in the supercooled regime so that both the translational and the rotational glass transition shift to higher densities. By increasing the number concentration of the small particles, the time evolution of both translational and rotational relaxation dynamics at high densities displays two qualitatively different scenarios, i.e., both the initial and the final part of the structural relaxation slow down for small size disparity, while the short-time dynamics still slows down but the final decay speeds up in the binary mixture with large size disparity. These findings are reminiscent of those observed in binary hard spherical particles. Therefore, our results suggest a universal mechanism for the influence of size disparity and mixture composition on the structural relaxation in both isotropic and anisotropic particle systems.

Effects of excluded volume and hydrodynamic interaction on the deformation, orientation and motion of ring polymers in shear flow.

A ring polymer is a classical model to explore the behaviors of biomacromolecules. Compared with its linear counterpart in shear flow, the ring polymer should be more sensitive to excluded volume and hydrodynamic interaction attributed to the absence of chain ends. We carried out multiparticle collision dynamics combined with molecular dynamics simulation to study the effects of excluded volume and hydrodynamic interaction on the behaviors of ring polymers in shear flow. The results show that in the absence of the strong excluded volume interaction, the ring polymer prefers a two-strand linear conformation with high deformation and orientation in the flow-gradient plane, and the tank-treading motion is nearly negligible. Ring polymers without excluded volume show no significant difference from linear polymers in the scaling exponents for the deformation, orientation and tumbling motion. We also observed that the hydrodynamic interaction could efficiently slow down the relaxation of ring polymers while the scaling exponents against the Weissenberg number have rarely been affected.

Simulation studies on architecture dependence of unentangled polymer melts.

The dependences of the properties of linear, ring, star, and H-shaped polymer melts on architecture are investigated by nonequilibrium molecular dynamics simulations. We find that zero-shear viscosities η0 for various architectures follow a universal relation, η0=Cη〈Rg0 (2)〉, where Cη is a constant and 〈Rg0 (2)〉 the equilibrium mean-square radius of gyration, in the unentangled regime. This law is also found valid for asymmetrical polymers but invalid for polymers with a hard core, such as stars with many arms and short arm lengths. In the unentangled regime, from the point of view of polymer size, the relaxation times show weak dependences on architecture, but the architecture dependence of the diffusion coefficient is still apparent. Then, we examine unentangled melts of various architectures having the same size over a wide range of shear rates covering linear and nonlinear viscoelastic regimes and find that the rheological quantities, namely, viscosity, first and second normal stress differences, are independent of architecture. In contrast, the polymer deformation shows an apparent dependence on architecture in the nonlinear regime. These findings shall shed significant light on the nature of rheological behaviors of unentangled melts.

Effects of topology on the adsorption of singly tethered ring polymers to attractive surfaces.

We investigate the effect of topology on the equilibrium behavior of singly tethered ring polymers adsorbed on an attractive surface. We focus on the change of square radius of gyration Rg(2), the perpendicular component Rg⊥(2) and the parallel component Rg‖(2) to the adsorbing surface, the mean contacting number of monomers with the surface , and the monomer distribution along z-direction during transition from desorption to adsorption. We find that both of the critical point of adsorption εc and the crossover exponent ϕ depend on the knot type when the chain length of ring ranges from 48 to 400. The behaviors of Rg(2), Rg⊥(2), and Rg‖(2) are found to be dependent on the topology and the monomer-surface attractive strength. At weak adsorption, the polymer chains with more complex topology are more adsorbable than those with simple topology. However, at strong adsorption, the polymer chains with complex topology are less adsorbable. By analyzing the distribution of monomer along z-direction, we give a possible mechanism for the effect of topology on the adsorption behavior.

Glass formation in a mixture of hard disks and hard ellipses.

We present an event-driven molecular dynamics study of glass formation in two-dimensional binary mixtures composed of hard disks and hard ellipses, where both types of particles have the same area. We demonstrate that characteristic glass-formation behavior appears upon compression under appropriate conditions in such systems. In particular, while a rotational glass transition occurs only for the ellipses, both types of particles undergo a kinetic arrest in the translational degrees of freedom at a single density. The translational dynamics for the ellipses is found to be faster than that for the disks within the same system, indicating that shape anisotropy promotes the translational motion of particles. We further examine the influence of mixture's composition and aspect ratio on the glass formation. For the mixtures with an ellipse aspect ratio of k = 2, both translational and rotational glass transition densities decrease with increasing the disk concentration at a similar rate, and hence, the two glass transitions remain close to each other at all concentrations investigated. By elevating k, however, the rotational glass transition density diminishes at a faster rate than the translational one, leading to the formation of an orientational glass for the ellipses between the two transitions. Our simulations imply that mixtures of particles with different shapes emerge as a promising model for probing the role of particle shape in determining the properties of glass-forming liquids. Furthermore, our work illustrates the potential of using knowledge concerning the dependence of glass-formation properties on mixture's composition and particle shape to assist in the rational design of amorphous materials.

Effect of polyelectrolyte adsorption on lateral distribution and dynamics of anionic lipids: a Monte Carlo study of a coarse-grain model.

We employ Monte Carlo simulations to investigate the interaction between an adsorbing linear flexible cationic polyelectrolyte and a ternary mixed fluid membrane containing neutral (phosphatidylcholine, PC), monovalent (phosphatidylserine, PS), and multivalent (phosphatidylinositol, PIP2) anionic lipids. We systematically explore the influences of polyelectrolyte chain length, polyelectrolyte charge density, polyelectrolyte total charge amount, and salt solution ionic strength on the static and dynamic properties of different anionic lipid species. Our results show that the multivalent PIP2 lipids dominate the polyelectrolyte-membrane interaction and competitively inhibit polyelectrolyte-PS binding. When the total charge amount of the polyelectrolyte is less than that of the local oppositely charged PIP2 lipids, the polyelectrolyte can drag the bound multivalent lipids to diffuse on the membrane, but cannot interact with the PS lipids. Under this condition, the diffusion behaviors of the polyelectrolyte closely follow the prediction of the Rouse model, and the polyelectrolyte chain properties determine the adsorption amount, concentration gradients, and hierarchical mobility of the bound PIP2 lipids. However, when the total charge amount of the polyelectrolyte is larger than that of the local PIP2 lipids, the polyelectrolyte further binds the PS lipids around the polyelectrolyte-PIP2 complex to achieve local electrical neutrality. In this condition, parts of the polyelectrolyte desorb from the membrane and show faster mobility, and the bound PS presents much faster mobility than the segregated PIP2. This work provides an explanation for heterogeneity formation in different anionic lipids induced by polyelectrolyte adsorption.

Compositional redistribution and dynamic heterogeneity in mixed lipid membrane induced by polyelectrolyte adsorption: effects of chain rigidity.

Monte Carlo simulation is employed to investigate the interaction between a polyelectrolyte and a fluid mixed membrane containing neutral (phosphatidyl-choline, PC), monovalent anionic (phosphatidylserine, PS), and multivalent anionic (phosphatidylinositol, PIP2) lipids. The effects of the intrinsic polyelectrolyte rigidity and solution ionic strength on the lateral rearrangement and dynamics of different anionic lipid species are systematically studied. Our results show that, the increase of polyelectrolyte chain rigidity reduces the loss of polyelectrolyte conformational entropy and the energy gains in electrostatic interaction, but raises the demixing entropy loss of the segregated anionic lipids. Therefore, the polyelectrolyte/membrane adsorption strength exhibits a non-monotonic dependence on the polyelectrolyte rigid parameter k ang, and there exists a certain optimal k ang for which the adsorption strength is maximal. Because the less loss of chain conformational entropy dominates the increase of the demixing entropy loss of the segregated anionic lipids and the decreases of the electrostatic energy gains, the semiflexible polyelectrolyte adsorbs onto the membrane more firmly than the flexible one. Whereas, for the adsorption of rigid polyelectrolyte, larger anionic lipid demixing entropy loss and less energy gain in the electrostatic interaction dominate over the decrease of the polyelectrolyte conformation entropy loss, leading to the desorption of the chain from the membrane. By decreasing the ionic concentration of the salt solution, the certain optimal k ang shifts to larger values. The cooperative effects of the adsorbing polyelectrolyte beads determine the concentration gradients and hierarchical mobility of the bound anionic lipids, as well as the polyelectrolyte dynamics.

Shear thinning behavior of linear polymer melts under shear flow via nonequilibrium molecular dynamics.

The properties of both untangled and entangled linear polymer melts under shear flow are studied by nonequilibrium molecular dynamics simulations. The results reveal that the dependence of shear viscosity η on shear rate γ, expressed by n ~ γ(-n), exhibits three distinct regimes. The first is the well-known Newtonian regime, namely, η independent of shear rate at small shear rates γ < τ0(-1) (where τ0 is the longest polymer relaxation time at equilibrium). In the non-Newtonian regime (γ > τ0(-1)) the shear dependence of viscosity exhibits a crossover at a critical shear rate γc dividing this regime into two different regimes, shear thinning regime I (ST-I) and II (ST-II), respectively. In the ST-I regime (τ0(-1) < γ < γc), the exponent n increases with increasing chain length N, while in the ST-II regime (γ > γc) a universal power law n ~ γ(-0.37) is found for considered chain lengths. Furthermore, the longer the polymer chain is, the smaller the shear viscosity for a given shear rate in the ST-II regime. The simulation also shows that a characteristic chain length, below which γc will be equal to τ0(-1), lies in the interval 30 < N < 50. For all considered chain lengths in the ST-II regime, we also find that the first and second normal stress differences N1 and N2 follow power laws of N1 ~ γ(2/3) and N2 ~ γ(0.82), respectively; the orientation resistance parameter mG follows the relation mG ~ γ(0.75) and the tumbling frequency ftb follows ftb ~ γ(0.75). These results imply that the effects of entanglement on the shear dependences of these properties may be negligible in the ST-II regime. These findings may shed some light on the nature of shear thinning in flexible linear polymer melts.

Orientation and surface activity of Janus particles at fluid-fluid interfaces.

We study the influence of shape of Janus particles on their orientation and surface activity at fluid-fluid interfaces via molecular dynamics simulations. The Janus particles are characterized by two regions with different wettability divided along their major axes. Three types of Janus particles are considered: Janus spheres, Janus rods, and Janus disks. We find that Janus spheres and Janus rods prefer one orientation at the interface, regardless of the surface property. In contrast, Janus disks can adopt one of two orientations when adhered to a fluid-fluid interface: one orientation corresponds to the equilibrium state and the other is a kinetically trapped metastable state. The orientation of Janus disks strongly depends on the disk characteristics, such as their size, aspect ratio, and surface property. Furthermore, we find that changes in the shape of Janus particles strongly influence the interfacial tension at the fluid-fluid interface. According to the time evolution of the interfacial tension, the adsorption of Janus particles is characterized by three adsorption stages based on different surface activities and adsorption kinetics depending on the particle shape.

The CBL-CIPK network mediates different signaling pathways in plants.

The calcineurin B-like protein-CBL-interacting protein kinase (CBL-CIPK) signaling pathway in plants is a Ca²âº-related pathway that responds strongly to both abiotic and biotic environmental stimuli. The CBL-CIPK system shows variety, specificity, and complexity in response to different stresses, and the CBL-CIPK signaling pathway is regulated by complex mechanisms in plant cells. As a plant-specific Ca²âº sensor relaying pathway, the CBL-CIPK pathway has some crosstalk with other signaling pathways. In addition, research has shown that there is crosstalk between the CBL-CIPK pathway and the low-K⁺ response pathway, the ABA signaling pathway, the nitrate sensing and signaling pathway, and others. In this paper, we summarize and review research discoveries on the CBL-CIPK network. We focus on the different modification and regulation mechanisms (phosphorylation and dephosphorylation, dual lipid modification) of the CBL-CIPK network, the expression patterns and functions of CBL-CIPK network genes, the responses of this network to abiotic stresses, and its crosstalk with other signaling pathways. We also discuss the technical research methods used to analyze the CBL-CIPK network and some of its newly discovered functions in plants.