Noncooperative thermodynamics and kinetic models of ligand binding to polymers: Connecting McGhee-von Hippel model with the Tonks gas model

Ligand binding to polymers modifies the physical and chemical properties of the polymers, leading to physical, chemical, and biological implications. McGhee and von Hippel obtained the equilibrium coverage as a function of the ligand affinity, through the computation of the possible binding sites for the ligand. Here, we complete this theory deriving the kinetic model for the ligand-binding dynamics and the associated equilibrium chemical potential, which turns out to be of the Tonks gas model type. At low coverage, the Tonks chemical potential becomes the Fermi chemical potential and even the ideal gas chemical potential. We also discuss kinetic models associated with these chemical potentials. These results clarify the kinetic models of ligand binding, their relations with the chemical potentials, and their range of validity. Our results highlight the inaccuracy of ideal and simplified kinetic approaches for medium and high coverages

Estimation of the temperature of a radiating body by measuring the stationary temperatures of a thermometer placed at different distances

This paper presents a novel method for determining the temperature of a radiating body. The experimental method requires only very common instrumentation. It is based on the measurement of the stationary temperature of an object placed at different distances from the body and on the application of the energy balance equation in a stationary state. The method allows one to obtain the temperature of an inaccessible radiating body when radiation measurements are not available. The method has been applied to the determination of the filament temperature of incandescent lamps of different powers

Reliability of rectified transport: Coherence and reproducibility of transport by open-loop and feedback-controlled Brownian ratchets

Brownian ratchets are small-scale systems which rectify thermal fluctuations to produce a net current of particles. They have inspired many models of molecular motors that perform transport in the noisy environment of living cells. For the most common ratchet systems, this rectification is achieved by means of the switching of a periodic and spatially asymmetric potential (flashing ratchets) or by means of a rocking force (rocking ratchets). The rectification mechanism can be applied without information on the state of the system (open-loop ratchets) or using information on the state of the system (feedback or closed-loop ratchets). In order to characterize the transport, the most used quantity is the mean velocity of the center of mass of the system. However, another important transport attribute that has not received much attention is its quality. Here we analyze the quality of transport by studying the coherence and reproducibility of the transport induced by several representative open-and closed-loop rectification protocols under the maximum mean velocity conditions. We find that for few-particle systems, the best protocol is the rocked feedback protocol, producing the transport of particles with the highest coherence and reproducibility per distance traveled at the maximum mean velocity, while for larger systems it is overtaken by its open-loop counterpart. Our results also show that protocols with similar maximum mean velocities can have quite different coherences and reproducibilities. This highlights the importance of studying the reliability of rectified transport to develop performant synthetic rectification devices. These contributions to the emerging field of reliable transport in noisy environments are expected also to provide insight into the performance of natural molecular motors

Electro-Osmotic Behavior of Polymeric Cation-Exchange Membranes in Ethanol-Water Solutions

The aim of this work is to apply linear non-equilibrium thermodynamics to study the electrokinetic properties of three cation-exchange membranes of different structures in ethanol-water electrolyte solutions. To this end, liquid uptake and electro-osmotic permeability were estimated with potassium chloride ethanol-water solutions with different ethanol proportions as solvent. Current-voltage curves were also measured for each membrane system to estimate the energy dissipation due to the Joule effect. Considering the Onsager reciprocity relations, the streaming potential coefficient was discussed in terms of ethanol content of the solutions and the membrane structure. The results showed that more porous heterogeneous membrane presented lower values of liquid uptake and streaming potential coefficient with increasing ethanol content. Denser homogeneous membrane showed higher values for both, solvent uptake and streaming coefficient for intermediate content of ethanol

The Correlation between the Water Content and Electrolyte Permeability of Cation-Exchange Membranes

The salt permeability through three commercial cation-exchange membranes with different morphologies is investigated in aqueous NaCl solutions. Ion-exchange membranes (IEMs) find application in different processes such as electrodialysis, reverse osmosis, diffusion dialysis, membrane electrolysis, membrane fuel cells and ion exchange bioreactors. The aim of this paper is the experimental determination of the electrolyte permeability in the following membranes: MK-40 membrane, Nafion N324 membrane and Nafion 117 membrane. The latter is selected as being a reference membrane. The effect of an increase in the NaCl concentration in the solutions on membranes transport properties is analyzed. With regard to membranes sorption, a decrease in the water content was observed when the external electrolyte concentration is increased. Concerning permeation through the membranes, the salt permeability increased with concentration for the Nafion 117 membrane and remained nearly constant for the other two membranes. A close relation between the degree of liquid sorption by the membranes and the electrolyte permeability was observed

A non-equilibrium thermodynamics model of multicomponent mass and heat transport in pervaporation processes

The framework of non-equilibrium thermodynamics (NET) is used to derive heat and mass transport equations for pervaporation of a binary mixture in a membrane. In this study, the assumption of equilibrium of the sorbed phase in the membrane and the adjacent phases at the feed and permeate sides of the membrane is abandoned, defining the interface properties using local equilibrium. The transport equations have been used to model the pervaporation of a water-ethanol mixture, which is typically encountered in the dehydration of organics. The water and ethanol activities and temperature profiles are calculated taking mass and heat coupling effects and surfaces into account. The NET approach is deemed good because the temperature results provided by the model are comparable to experimental results available for water-alcohol systems

Transporte gaseoso en membranas poliméricas densas de LLDPE

El objetivo de este trabajo es el estudio experimental de fenómenos de transporte gaseoso en membranas poliméricas densas. Concretamente, se ha estudiado el transporte isotermo de gases puros originado por una diferencia de presión impuesta y mantenida a través de membranas obtenidas de copolimeros de etileno y l-octeno. Los coeficientes de transporte, proporcionales a la razón entre los flujos moleculares y las fuerzas que los provocan, han sido analizados en los distintos límites de presión y temperatura medias. Los experimentos se realizaron tanto en muestras individuales como apilamientos de membranas y tanto en muestras ordinarias, no forzadas, como en membranas sometidas a estiramiento longitudinal o transversal. El estudio de transporte realizado mediante técnicas usuales de previsión variable hubo de ser complementado con estudios exclusivos de las membranas, incluyendo su conducta térmica (técnica de calometría diferencial), óptica (microscopia electrónica de barrido) y viscoelástica (experimentos termomecánicos)

Numerical model of non-isothermal pervaporation in a rectangular channel

A numerical model of non-isothermal pervaporation was developed to investigate the development of the velocity, concentration and temperature fields in rectangular membrane module geometry. The model consists of the coupled Navier-Stokes equations to describe the flow field, the energy equation for the temperature field, and the species convection-diffusion equations for the concentration fields of the solution species. The coupled nonlinear transport equations were solved simultaneously for the velocity, temperature and concentration fields via a finite element approach. Simulation test cases for trichloroethylene/water, ethanol/water and iso-propanol/water pervaporation, under laminar flow conditions, revealed temperature drop axially along the module and orthogonal to the membrane surface. The nonlinear character of the concentration and temperature boundary-layers are most significant near the membrane surface. Estimation of the mass transfer coefficient assuming isothermal assumption conditions can significantly deviate from the non-isothermal predictions. For laminar conditions, predictions of the feed-side mass transfer coefficient converged to predictions from the classical Leveque solution as the feed temperature approached the permeate temperature

Cooperative kinetics of ligand binding to linear polymers

Ligands change the chemical and mechanical properties of polymers. In particular, single strand binding protein (SSB) non-specifically bounds to single-stranded DNA (ssDNA), modifying the ssDNA stiffness and the DNA replication rate, as recently measured with single-molecule techniques. SSB is a large ligand presenting cooperativity in some of its binding modes. We aim to develop an accurate kinetic model for the cooperative binding kinetics of large ligands. Cooperativity accounts for the changes in the affinity of a ligand to the polymer due to the presence of another bound ligand. Large ligands, attaching to several binding sites, require a detailed counting of the available binding possibilities. This counting has been done by McGhee and von Hippel to obtain the equilibrium state of the ligands-polymer complex. The same procedure allows to obtain the kinetic equations for the cooperative binding of ligands to long polymers, for all ligand sizes. Here, we also derive approximate cooperative kinetic equations in the large ligand limit, at the leading and next-to-leading orders. We found cooperativity is negligible at the leading-order, and appears at the next-to-leading order. Positive cooperativity (increased affinity) can be originated by increased binding affinity or by decreased release affinity, implying different kinetics. Nevertheless, the equilibrium state is independent of the origin of cooperativity and only depends on the overall increase in affinity. Next-to-leading approximation is found to be accurate, particularly for small cooperativity. These results allow to understand and characterize relevant ligand binding processes, as the binding kinetics of SSB to ssDNA, which has been reported to affect the DNA replication rate for several SSB-polymerase pairs. (C) 2022 The Author(s). Published by Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology