Description Of Equilibrium Research Articles

Exploring the Dynamics and Mutational Landscape of Riboregulation with a Minimal Synthetic Circuit in Living Cells

The regulation of gene expression, triggered by conformational changes in RNA molecules, is widely observed in cellular systems. Here, we examine this mode of control by means of a model-based design and construction of a fully synthetic riboregulatory device. We present a theoretical framework that rests on a simple energy model to predict the dynamic response of such a system. Following an equilibrium description, our framework integrates thermodynamic properties—anticipated with an RNA physicochemical model—with a detailed description of the intermolecular interaction. The theoretical calculations are confirmed with an experimental characterization of the action of the riboregulatory device within living cells. This illustrates, more broadly, the predictability of genetic robustness on synthetic systems, and the faculty to engineer gene expression programs from a minimal set of first principles.

Facility location design under continuous traffic equilibrium

This paper presents two modeling approaches for median-type facility location design under elastic customer demand and traffic equilibrium in a continuous space. The first approach, following the continuum approximation scheme, builds upon the special case of an infinite homogeneous plane where traffic equilibrium can be described by an ordinary differential equation. The solution to this homogeneous case, sometimes in a closed form, is then used to develop approximate solutions to more general cases (e.g., those in a heterogeneous space). This model provides a computationally efficient way to obtain managerial insights and near-optimal solutions, especially for large problem instances. We also develop a more traditional discrete location model in the form of a mixed-integer program, which builds directly upon a nonlinear partial differential equation description of customer traffic equilibrium. We develop a Lagrangian relaxation based solution approach with an embedded finite-element method subroutine, to separate and solve the location decisions as well as the traffic equilibrium. Numerical experiments are conducted to illustrate applicability of the proposed models and to compare performance of the two complementing modeling approaches.

Adsorption of Cu(II) on natural and treated clays

We have studied the pH and the temperature effects on copper ions' adsorption on natural and treated clays from Algeria. The clay was also treated to improve the adsorption capacity. X-ray diffraction identified montmorillonite and kaolinite as major clay minerals. The Langmuir adsorption model was used for the mathematical description of the adsorption equilibrium and the equilibrium data adhered very well to this model. The treated and natural clay had a monolayer adsorption capacity equal to 15.40 and 12.22 mg/g, respectively, at pH value of 6.5 and temperature 20 °C, the adsorption isotherms could be fitted with Langmuir isotherms, and the coefficients indicated favorable adsorption of Cu(II) on the clays. Determination of the thermodynamic parameters, H, S, and G showed that the adsorption process was spontaneous and exothermic accompanied by a decrease in entropy and Gibbs energy. Results of this study will be useful for future scale-up for using this material as a low-cost adsorbent for the removal of Cu(II) from wastewater.

Preparation of graphene oxide/chitosan/FeOOH nanocomposite for the removal of Pb(II) from aqueous solution

In the present study, a graphene oxide/chitosan/FeOOH (GO/Ch/FeOOH) nanostructured composite was prepared and used as an adsorbent for the removal of Pb(II) ions from aqueous solution. The nanocomposite was characterized by FT-IR, XRD, and SEM techniques. Several important parameters influencing the adsorption of Pb(II) ions such as pH (3–7), temperature (25–80°C), shaking speed (150–800rpm), contact time (10–70min), and sorbent mass (10–100mg) were studied. The results showed that, benefiting from the surface property of graphene oxide, the abundant amino and hydroxyl functional groups of chitosan, the adsorbent provides adequate and versatile adsorption for the Pb(II) ions under investigation. The batch adsorption experiments showed that the adsorption of the Pb(II) is considerably dependent on pH of milieu, amount of adsorbent, and contact time. The Freundlich and Langmuir adsorption models were used for the mathematical description of adsorption equilibrium and isotherm constants. Both models were applicable for the description of Pb(II) adsorption isotherm in the concentration range studied. However, Langmuir model showed higher correlation coefficient (R2) than Freundlich model. The study suggests that the GO/Ch/FeOOH is a promising nano adsorbent for the removal of Pb(II) ions from aqueous solution.

New regime of low ion collisionality in the neoclassical equilibrium of tokamak plasmas

The neoclassical description of an axisymmetric toroidal plasma equilibrium is formulated for an unconventionally low ordering of the collisionality that suits realistic thermonuclear fusion conditions. This requires a drift-kinetic analysis to the second order of the ion Larmor radius, which yields a new contribution to the leading solution for the non-Maxwellian part of the ion distribution function if the equilibrium geometry is not up-down symmetric. An explicit geometrical factor weighs this second Larmor-radius order, low-collisionality effect that modifies the neoclassical ion parallel flow, and the ion contribution to the bootstrap current.

Conformational Transitions in the Glycine-Bound GluN1 NMDA Receptor LBD via Single-Molecule FRET

The N-methyl-D-aspartate receptor (NMDAR) is a member of the glutamate receptor family of proteins and is responsible for excitatory transmission. Activation of the receptor is thought to be controlled by conformational changes in the ligand binding domain (LBD); however, glutamate receptor LBDs can occupy multiple conformations even in the activated form. This work probes equilibrium transitions among NMDAR LBD conformations by monitoring the distance across the glycine-bound LBD cleft using single-molecule Förster resonance energy transfer (smFRET). Recent improvements in photoprotection solutions allowed us to monitor transitions among the multiple conformations. Also, we applied a recently developed model-free algorithm called “step transition and state identification” to identify the number of states, their smFRET efficiencies, and their interstate kinetics. Reversible interstate conversions, corresponding to transitions among a wide range of cleft widths, were identified in the glycine-bound LBD, on much longer timescales compared to channel opening. These transitions were confirmed to be equilibrium in nature by shifting the distribution reversibly via denaturant. We found that the NMDAR LBD proceeds primarily from one adjacent smFRET state to the next under equilibrium conditions, consistent with a cleft-opening/closing mechanism. Overall, by analyzing the state-to-state transition dynamics and distributions, we achieve insight into specifics of long-lived LBD equilibrium structural dynamics, as well as obtain a more general description of equilibrium folding/unfolding in a conformationally dynamic protein. The relationship between such long-lived LBD dynamics and channel function in the full receptor remains an open and interesting question.

Removal of Rhodamine B from aqueous solution using magnetic NiFe nanoparticles.

Surface-modified magnetic nano alloy particles Ni2.33Fe were prepared using a hydrothermal method and they were utilized for removing Rhodamine B (RhB) from aqueous solution. The magnetic nanoparticles were characterized by X-ray diffraction, scanning electron microscopy, thermogravimetric analysis and Fourier transform infrared spectroscopy, which confirmed that the surface of the magnetic product with a face-centered cubic-type structure was successfully modified by sodium citrate. Kinetics studies were conducted. The pseudo-second-order kinetic model was used for fitting the kinetic data successfully. The Freundlich and Langmuir adsorption models were employed for the mathematical description of adsorption equilibrium. It was found that the adsorption isotherm can be very satisfactorily fitted by the Freundlich model.

A statistical mechanics framework for the large-scale structure of turbulent von Kármán flows

In the present paper, recent experimental results on large-scale coherent steady states observed in experimental von Kármán flows are revisited from a statistical mechanics perspective. The latter is rooted on two levels of description. We first argue that the coherent steady states may be described as the equilibrium states of well-chosen lattice models, which can be used to define global properties of von Kármán flows, such as their temperatures. The equilibrium description is then enlarged, in order to reinterpret a series of results about the stability of those steady states and their susceptibility to symmetry breaking, in the light of a deep analogy with the statistical theory of ferro-magnetism.

Synthesis of surfactant-modified ZSM-5 nanozeolite for the removal of nickel(II) from aqueous solution

Removal of nickel ions from aqueous solutions using modified ZSM-5 nanozeolites was investigated. Experiments were conducted in terms of different solute concentrations, temperatures, and pH. Mesoporous Na-ZSM-5 zeolite was modified with tetrapropylammonium bromide (TPABr) and sodium dodecylsulfate (SDS) by using the impregnation method. The modified zeolites were characterized by X-ray diffraction, Fourier transform infrared spectroscopy, Brunauer–Emmett–Teller, and scanning electron microscope techniques. According to the results, SDS-ZSM-5 revealed a higher adsorption capacity than Na-ZSM-5 and TPA-ZSM-5. Langmuir and Freundlich adsorption models were used for the mathematical description of the adsorption equilibrium. The analyses revealed that the sorption of Ni(II) could be considered an endothermic and spontaneous process.

Biosorption of Pb(II) ions from aqueous solutions by waste biomass of Streptomyces fradiae pretreated with NaOH

Biosorption of Pb(II) ions from a model solution was investigated using Streptomyces fradiae biomass as biosorbent pretreated with sodium hydroxide. The mycelium is a waste product from the biotechnological production of the macrolide antibiotic tylosin in the pharmaceutical industry. The biosorption study was conducted in a batch system with respect to initial pH, initial metal concentration and contact time. For a description of the biosorption equilibrium, Langmuir and Freundlich adsorption models were used. Equilibrium data fitted better to the Langmuir model and the calculated maximum biosorption capacity was 138.88 mg·g−1 at initial pH 5.0, contact time of 120 min, biosorbent dose of 1 g·dm−3 and concentration range for the Pb(II) ions from 10 to 200 mg·dm−3. Pseudo-first and pseudo-second order kinetic models were applied to the experimental data. The results indicated that the Pb(II) uptake process followed the Ho equation. The interference of co-present ions Cu(II) and Zn(II) on the Pb(II) biosorption was also studied. It was determined that at the highest Pb(II) concentration (200 mg·dm−3) Cu(II) and Zn(II) caused 27.22% and 24.88% decreasing in Pb(II) uptake, respectively. The obtained results could be useful in prospective applications of chemically modified waste mycelium of S. fradiae as an alternative biosorbent for Pb(II) removal from aqueous solutions.

NMR studies of the equilibria and reaction rates in aqueous solutions of formaldehyde.

Formaldehyde has an important role in the chemical industry and in biological sciences. In dilute aqueous solutions of formaldehyde only traces of the molecular formaldehyde are present and the predominant species are methylene glycol and in lower concentrations, dimethylene glycol. The chemical equilibria and reaction rates of the hydration of formaldehyde in H2O and D2O solutions at low concentrations were studied by (1)H and (13)C NMR at various conditions of pH (1.8-7.8) and temperature (278-333 K). These measurements became possible by direct detection of formaldehyde (13)C and (1)H peaks. The equilibrium and rate constants of the dimerization reaction of methylene glycol were also measured. The rate constants for both the hydration and the dimerization reactions were measured by a new version of the conventional selective inversion transfer method. This study, together with previous published work, completes the description of dynamics and equilibria of all the processes occurring in dilute aqueous formaldehyde solutions.

Fluorescence of isatin N‐phenylsemicarbazones: aggregation and hydrazide–hydrazonol tautomerism

The solution behavior of isatin N‐phenylsemicarbazones and their interaction with anions was investigated using fluorescence technique. Existence of associate/hydrazide (keto)/hydrazonol (enol) tautomeric equilibrium explains the solvent, concentration and excitation/emission effect on fluorescence of studied compounds. Both static and dynamic fluorescence measurements, together with quenching experiments, confirm the dynamic equilibrium between individual tautomeric forms with different emissive character in solution. Because of the nonfluorescent character of hydrazonol tautomer, the quantitative description of tautomeric equilibrium and dimerization was performed using UV–Vis spectroscopy. Determined apparent association constants Kass for interaction with F− anion using Stern–Volmer plots correlate well with the previously determined sensor sensitivity. Their high values indicate again the most acidic urea NH group deprotonation and not the hydrogen bonded sensor : hydrazonol 1:1 complex formation. Copyright © 2015 John Wiley & Sons, Ltd.

Catenoid Stability with a Free Contact Line

We analytically study the stability of catenoids pinned at one contact line, with the other free to move on a substrate subject to axisymmetric and nonaxisymmetric perturbations. A variational formulation is applied to derive the corresponding stability criteria. The maximal stability region and the stability region are represented in the favorable and canonical phase diagrams, providing a complete description of catenoid equilibrium and stability. All catenoids are stable with respect to nonaxisymmetric perturbations. For a fixed contact angle, there exists a critical volume below which catenoids are unstable to axisymmetric perturbations. Equilibrium solution multiplicity is discussed in detail, and we elucidate how geometrical symmetry is reflected in the maximal stability and stability regions.

Use of Activated Carbon Derived from Maize Cob and Mahogany Seed Shell for the Removal of Colour from Textile Effluent

In the present study natural adsorbents Maize Cob (MC) and Mahogany Shells (MS) were carbonized and activated with steam/zinc chloride and sieved into 600μm particle sizes. The adsorbents were treated for the removal of colour from textile effluent at different time. These adsorbents were also evaluated at different adsorbent doses and effluent concentrations. It was found that Maize cob has the highest colour removal efficiency of 86% and also at shorter time of 25minutes compared to Mahogany shells which record 73% and at 30, respectively. Freundlich and Langmuir isotherm models were used for the mathematical description of colour adsorption equilibrium onto the adsorbents and the result obtained showed that the adsorption equilibrium data onto MC was closely fitted to the Langmuir model whereas the adsorption equilibrium data onto MS was closely fitted to the Freundlich model. Hence, adsorption of the colour onto the adsorbents is monolayer adsorption process. Keywords : Adsorption Isotherm, Mahogany Shells, Maize Cob, % Removal, Textile Effluent

Thermodynamic modelling of hydrogen migration in argillite for a deep geological radioactive waste repository: IRSN contribution to FORGE

Abstract The aim of this work is to provide an improved mathematical and physical description of two-phase flow in tight porous media in order to model hydrogen migration within a geological repository for radioactive waste as required to further assess the behaviour in time and space of such facilities. First, we introduce a general physical framework describing multicomponent and two-phase (liquid and gas) flow in porous media with capillary pressure curve and mass exchange between phases. Assuming thermodynamic equilibrium, mass exchange between phases is governed by thermodynamic principles which we briefly describe. This physical modelling is able to describe single-phase flow (only gas mixture or liquid solution) as well as two-phase flow (both liquid and gas phases are present). On the basis of this treatment we obtain a generalized formulation of Henry and Raoult–Kelvin laws. We show that, for a hydrogen–water mixture in repository conditions of pressure and suction, these relationships constitute an adequate mass equilibrium description. Second, we consider the mathematical formulation of the problem, which is mainly determined by the choice of primary variables. Contrary to existing approaches, we are interested in avoiding the need to switch primary variables during calculations. Indeed, such a switch is often proposed as a solution to treat phase appearance or disappearance. We will show that, in our physical framework, taking into account the capillary pressure and mass exchanges between phases, it is possible to work with universal primary variables to correctly describe gas phase appearance or disappearance. Simple numerical simulations are presented for validation as well as an application of this model to the FORGE benchmark on the cell scale together with a sensitivity analysis guided by physical considerations.

The relationship between philosophy and evidence in education

This article explores the ways that philosophy and evidence interact in the exploration of normative questions in philosophy of education. First, the authors provide a description of reflective equilibrium, a central method in normative philosophizing. They proceed to describe three tasks of normative philosophy, each of which requires engagement with empirical evidence, albeit in different ways: identifying values, assessing institutional arrangements, and guiding policy action. They recommend increased attention from social scientists to the potential contribution of philosophy in setting the agenda for empirical research, and they recommend increased use by philosophers of real-life case studies, which enable philosophers to better understand decision-makers’ feasibility constraints. These recommendations, they argue, can enable both social scientists and philosophers to better equip decision-makers to enact the best policy from among the options available to them.

Equilibrium and kinetic studies for the removal of cationic dye using banana pith

The large quantity of green cull bananas has the potential of being used industrially and, thereby, to improve banana economics and eliminate the large environmental problem presented by banana waste. Wastewaters from textile, cosmetics, printing, dying, food colouring, and paper-making industries are polluted by dyes. The adsorption of basic dye by waste banana pith was investigated by varying dye concentrations, adsorbent dose, particle size and agitation rate. The adsorption capacity was found to be maximum value of removal by using 0.1 g of sorbent with particle size 1mm at mixing speed 200 rpm for initial concentration 25 mg/l to reach value of approximate 89%. The Langmuir, Temkin and Freundlich adsorption models were used for mathematical description of the adsorption equilibrium and it was found that experimental data fitted very well to these models except Langmuir model. Adsorption of dye was applied on (pseudo-first and pseudo-second-order kinetics), and the experimental data was more fitted to pseudo second order. The results of this study showed that banana pith could be employed as effective and low-cost materials for the removal of dyes from aqueous solutions.

Synthesis of bulk ion-imprinted polymers (IIPs) embedded with oleic acid coated Fe<sub>3</sub>O<sub>4</sub> for selective extraction of hexavalent uranium

A selective and reliable method for the extraction of trace quantities of U(VI) by the use of a magnetic U(VI) ion-imprinted polymer (IIP) was developed. In this study, oleic acid (OA) coated magnetite nano-particles were incorporated into the cross-linked polymeric matrix of the selective sorbent, in order to gain the physical advantages of separating the polymers. Many physico-chemical factors influence the adsorption process; uranyl ion uptake ability based on these parameters was investigated. The optimum parameters obtained were sample pH 4,50 mg of the magnetic polymer, a contact time of 45 min and an initial U(VI) concentration of 2 mg·ℓ-1. The adsorption capacities for the magnetic NIP and IIP were found to be 0.95 mg·g1 and 1.21 mg·g-1, respectively. The adsorption behaviour of U(VI) in the presence of other competing metal ions onto the cross-linked magnetic polymers was also examined in binary mixtures and the order of selectivity was found to be U(VI) > Pb(VI) > Ni(II). The resulting magnetic nano-composite polymers were found to be stable up to the sixth cycle of use and reuse. The Freundlich adsorption model was used for the mathematical description of the adsorption equilibrium and the adsorption kinetic data fitted the pseudo-first-order model with R2 > 0.92.Keywords: Bulk, magnetic imprinted polymers, oleic acid, uranium

An Algebraic Description of the Absorption Equilibrium for the Solvay Soda System

Simplified relationships for the equilibrium partial pressure of the gas phase components were presented for the crystallization conditions of sodium bicarbonate in the NaCl–NH3–CO2–H2O system. Based on the partial pressures computed from the validated mixed-solvent-electrolyte (MSE) model, the regression equation coefficients were derived for explicitly correlating the partial pressures with the liquid phase concentrations and temperature in the range of (308.15 to 338.15) K. A good agreement was found between pressures calculated from the algebraic equations and compared with corresponding values computed from the MSE model. The obtained exponential equations can be directly used for the estimation of the equilibrium partial pressures in the process conditions of carbonation columns.

An approximate single fluid 3-dimensional magnetohydrodynamic equilibrium model with toroidal flow

An approximate model for a single fluid three-dimensional (3D) magnetohydrodynamic (MHD) equilibrium with pure isothermal toroidal flow with imposed nested magnetic flux surfaces is proposed. It recovers the rigorous toroidal rotation equilibrium description in the axisymmetric limit. The approximation is valid under conditions of nearly rigid or vanishing toroidal rotation in regions with significant 3D deformation of the equilibrium flux surfaces. Bifurcated helical core equilibrium simulations of long-lived modes in the MAST device demonstrate that the magnetic structure is only weakly affected by the flow but that the 3D pressure distortion is important. The pressure is displaced away from the major axis and therefore is not as noticeably helically deformed as the toroidal magnetic flux under the subsonic flow conditions measured in the experiment. The model invoked fails to predict any significant screening by toroidal plasma rotation of resonant magnetic perturbations in MAST free boundary computations.