Study on Hydrate Phase Equilibrium Diagram of Methane Containing System Based on Thermodynamic Model

Natural gas hydrate is a potential energy source in the future, which widely occurs in nature and industrial activities, and its formation and decomposition are identified by phase equilibrium. The calculation of multicomponent gas phase equilibrium is more complex than that of single component gas, which depends on the accurate model characterized by enthalpy and free energy. Based on the Kvamme-Tanaka statistical thermodynamic model, theoretical and experimental methods were used to predict and verify the phase equilibrium of pure methane hydrate and carbon dioxide hydrate in the temperature range of 273.17–289.05 K. The phase equilibrium curves of methane-containing gases such as CH4+CO2,CH4+C2H6,CH4+H2S and CH4+CO2+H2S under different mole fractions were drawn and analyzed, and the decomposition or formation enthalpy and free energy of hydrate were calculated. The results show that, the phase equilibrium curves of the methane containing systems is mainly related to the guest molecule type and the composition of gas. The evolution law of phase equilibrium pressure of different gases varies with composition and temperature, and the phase splitting of CO2 at the quadruple point affects the phase equilibrium conditions. Due to the consideration of the interaction between the motion of guest molecules and the vibration of crystal lattice, the model exhibits a good performance, which is quantified in terms of mean square error (MSE) with respect to the experimental data. The magnitudes of MSE percent are respectively 1.2, 4.8, 15.12 and 9.20 MPa2 for CH4+CO2, CH4+C2H6, CH4+H2S and CH4+CO2+H2S systems, and the values are as low as 3.57 and 1.32 MPa2 for pure methane and carbon dioxide, respectively. This study provides engineers and researchers who want to consult the diagrams at any time with some new and accurate experimental data, calculated results and phase equilibrium curves. The research results are of great significance to the development and utilization of gas hydrate and the flow safety prediction of gas gathering and transportation.

EVAP: A two-photon imaging tool to study conformational changes in endogenous Kv2 channels in live tissues

A primary goal of molecular physiology is to understand how conformational changes of proteins affect the function of cells, tissues, and organisms. Here, we describe an imaging method for measuring the conformational changes of the voltage sensors of endogenous ion channel proteins within live tissue, without genetic modification. We synthesized GxTX-594, a variant of the peptidyl tarantula toxin guangxitoxin-1E, conjugated to a fluorophore optimal for two-photon excitation imaging through light-scattering tissue. We term this tool EVAP (Endogenous Voltage-sensor Activity Probe). GxTX-594 targets the voltage sensors of Kv2 proteins, which form potassium channels and plasma membrane–endoplasmic reticulum junctions. GxTX-594 dynamically labels Kv2 proteins on cell surfaces in response to voltage stimulation. To interpret dynamic changes in fluorescence intensity, we developed a statistical thermodynamic model that relates the conformational changes of Kv2 voltage sensors to degree of labeling. We used two-photon excitation imaging of rat brain slices to image Kv2 proteins in neurons. We found puncta of GxTX-594 on hippocampal CA1 neurons that responded to voltage stimulation and retain a voltage response roughly similar to heterologously expressed Kv2.1 protein. Our findings show that EVAP imaging methods enable the identification of conformational changes of endogenous Kv2 voltage sensors in tissue.

The sequence–ensemble relationship in fuzzy protein complexes

Intrinsically disordered proteins (IDPs) interact with globular proteins through a variety of mechanisms, resulting in the structurally heterogeneous ensembles known as fuzzy complexes. While there exists a reasonable comprehension on how IDP sequence determines the unbound IDP ensemble, little is known about what shapes the structural characteristics of IDPs bound to their targets. Using a statistical thermodynamic model, we show that the target-bound ensembles are determined by a simple code that combines the IDP sequence and the distribution of IDP–target interaction hotspots. These two parameters define the conformational space of target-bound IDPs and rationalize the observed structural heterogeneity of fuzzy complexes. The presented model successfully reproduces the dynamical signatures of target-bound IDPs from the NMR relaxation experiments as well as the changes of interaction affinity and the IDP helicity induced by mutations. The model explains how the target-bound IDP ensemble adapts to mutations in order to achieve an optimal balance between conformational freedom and interaction energy. Taken together, the presented sequence–ensemble relationship of fuzzy complexes explains the different manifestations of IDP disorder in folding-upon-binding processes.

Technical Note: Classical and statistical thermodynamic treatment of adsorption and desorption kinetics and rates

Adsorption and desorption represent the initial processes of the interaction of gas species with the condensed phase. It has important implications for evaluating heterogeneous (gas-to-solid) and multiphase chemical kinetics involved in catalysis, environmental interfaces, and, in particular, aerosol particles. When describing gas uptake, gas-to-particle partitioning, and the chemical transformation of aerosol particles the desorption lifetime is a crucial parameter to assess the underlying chemical kinetics such as surface reaction and surface-to-bulk transfer. The desorption lifetime, in turn, depends on the desorption free energy which is affected by the chosen adsorbate model and standard states. To assess the impact of those conditions on desorption energy and, thus, desorption lifetime, we provide a complete classical and statistical thermodynamic treatment of the adsorption and desorption process considering transition state theory for two typically applied adsorbate models, the 2D ideal gas and the 2D ideal lattice gas, the latter being equivalent to Langmuir adsorption. Both models apply to solid and liquid substrate surfaces. We derive the thermodynamic and microscopic relationships for adsorption and desorption equilibrium constants, adsorption and desorption rates, first-order adsorption and desorption rate coefficients, and the corresponding pre-exponential factors. Although, some of these derivations can be found in the literature, this study aims to bring all derivations into one place to facilitate the interpretation and analysis of desorption energies for their application in multiphase chemical kinetics. This exercise allows for a microscopic interpretation of the underlying processes including the surface accommodation coefficient and highlights the importance of the choice of adsorbate model and standard states when analyzing and interpreting adsorption and desorption processes. We demonstrate how the choice of adsorbate model choice affects equilibrium surface concentrations and coverages, desorption rates, and decay of the adsorbate species with time. In addition, we show how those results differ when applying a concentration- or activity-based description. Our treatment demonstrates that the pre-exponential factor can differ by orders of magnitude depending on the choice of adsorbate model with similar effects on the desorption lifetime, yielding significant uncertainties in the desorption energy. Furthermore, uncertainties in surface coverage and assumptions in standard surface coverage can lead to significant changes in desorption energies derived from measured desorption rates. Providing a comprehensive thermodynamic and microscopic representation aims to guide theoretical and experimental assessments of desorption energies and estimate potential uncertainties in applied desorption energies and corresponding desorption lifetimes important for improving our understanding of multiphase chemical kinetics.

Short Range Order Modeling in Alloys

The Short and Long Range Orders in alloys can be considered based on a new expression for the combinatorial factor. This expression is more convenient and intuitive than the traditionally used form and can be directly applied to reproduce the results of several good known statistical-thermodynamic models that usually are considered completely independent or even inconsistent.The short list includes quasichemical theory, associated solution model, surrounded atom model, cluster site approximation.As result, the formalism and interpretation of these models are significantly clarified, allowing simultaneously to identify and fix several long standing errors that otherwise could be left unnoticed.Multicomponent generalization of listed models is also critically simplified.For the systems experiencing a phase transition, the advanced version of theory provides a mechanism allowing to reproduce the correct critical temperature of conversion and at the same time to increase significantly the precision of thermodynamic functions.

Analysis of Tandem Repeat Protein Folding Using Nearest-Neighbor Models

Cooperativity is a hallmark of protein folding, but the thermodynamic origins of cooperativity are difficult to quantify. Tandem repeat proteins provide a unique experimental system to quantify cooperativity due to their internal symmetry and their tolerance of deletion, extension, and in some cases fragmentation into single repeats. Analysis of repeat proteins of different lengths with nearest-neighbor Ising models provides values for repeat folding (ΔGi) and inter-repeat coupling (Δ Gi-1, i). In this article, we review the architecture of repeat proteins and classify them in terms of Δ Gi and Δ Gi-1, i; this classification scheme groups repeat proteins according to their degree of cooperativity. We then present various statistical thermodynamic models, based on the 1D-Ising model, for analysis of different classes of repeat proteins. We use these models to analyze data for highly and moderately cooperative and noncooperative repeat proteins and relate their fitted parameters to overall structural features. Expected final online publication date for the Annual Review of Biophysics, Volume 50 is May 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.