Molecular dynamics study on thermal dehydration process of epsomite (MgSO4.7H2O)

Water vapour sorption in salt hydrates is one of the most promising means of compact, low loss and long-term solar heat storage in the built environment. Among all, epsomite (MgSO4·7H2O) excels for its high-energy storage density and vast availability. However, in practical applications, the slow kinetics and evident structural changes during hydration and dehydration significantly jeopardise the heat storage/recovery rate. A molecular dynamics (MD) study is carried out to investigate the thermal properties and structural changes in the thermal dehydration process of the epsomite. The MD simulation is carried out at 450 K and a vapour pressure of 20 mbar, in accordance with experimental heat storage conditions. The study identifies the dehydration as multiple stages from the initial quick water loss and collapse of the crystal framework to the adsorption of water molecules, which inhibits complete dehydration. Further, the anisotropic diffusion behaviour supports the important role of the porous matrix structure in the heat and mass transfer process. The enthalpy changes, partial densities, mass diffusion coefficients of water and radial distribution functions are calculated and compared with corresponding experimental data to support the conclusions

Quantum chemical analysis of the structures of MgSO4 hydrates

Magnesium sulfate salts can form hydrated compounds with up to seven degree of hydration with an energy exchange of the order of 2.8GJ/m3 [1]. In addition, this salt is abundant in nature and thus this material is a potential candidate for storing energy in seasonal heat storage systems. One of the main issues in using this material for seasonal heat storage system is its slow kinetics and low extent of water take-up under normal atmospheric conditions [2]. In addition, the salt undergoes considerable changes in its crystalline structure during hydration and dehydration, and often they encounter the formation of cracks and pores in the crystal structure [3]. This significantly affects the efficiency of the salt in storing energy and also reusability of the material. A molecular level investigation is necessary to understand the process of hydration and dehydration in detail. Presence of an extensive network of hydrogen bonds in MgSO4.7H2O crystal is identified by Allan Zalkin et al [4]. Significant delocalization of hydrogen atoms within the hydrogen bonds are reported in the study. The 7th water molecule in a hepta-hydrate crystal is captured in the interstitial space within the crystals due to coulombic forces and they are very easily removable. Thus modeling a stable molecule of magnesium sulfate hepta hydrate is difficult. So we undertake the hexa hydrated magnesium sulfate to study the equilibrium molecular structure. The hydrogen bonds present in the structure, which stabilizes the molecule, is a focus of attention in this study. In addition, we report Natural Bond Orbital (NBO) [5] charges of Mg and S as a function of degree of hydration in this study. The NBO analysis gives information about electronic occupations in the molecule. In addition, the variation of the natural charges give information about the nature of inters atomic interactions involved in the hydration process of magnesium sulfates. The hydration process is accompanied by a considerable amount of energy exchange with the surroundings. In addition, significant changes in the crystal structure are predicted to happen during hydration. The binding of a water molecule on a slab of magnesium sulfate will resemble the hydration phenomena of a real crystal. Maslyuk et al [6] have performed such an analysis on kieserite structures and found the influence of hydrogen bonds during hydration. A similar study has done towards the last part of this account, which gives important information about hydration process of magnesium sulfate crystal

Transient behavior in Single-File Systems

We have used Monte-Carlo methods and analytical techniques to investigate the influence of the characteristics, such as pipe length, diffusion, adsorption, desorption and reaction rates on the transient properties of Single-File Systems. The transient or the relaxation regime is the period in which the system is evolving to equilibrium. We have studied the system when all the sites are reactive and when only some of them are reactive. Comparisons between Mean-Field predictions, Cluster Approximation predictions, and Monte Carlo simulations for the relaxation time of the system are shown. We outline the cases where Mean-Field analysis gives good results compared to Dynamic Monte-Carlo results. For some specific cases we can analytically derive the relaxation time. Occupancy profiles for different distribution of the sites both for Mean-Field and simulations are compared. Different results for slow and fast reaction systems and different distribution of reactive sites are discussed.Comment: 18 pages, 19 figure

A DFT based equilibrium study on the hydrolysis and the dehydration reactions of MgCl 2

Magnesium chloride hydrates are characterized as promising energy storage materials in the builtenvironment. During the dehydration of these materials, there are chances for the release of harmful HCl gas, which can potentially damage the material as well as the equipment. Hydrolysis reactions in magnesium chloride hydrates are subject of study for industrial applications. However, the information about the possibility of hydrolysis reaction, and its preference over dehydration in energy storage systems is still ambiguous at the operating conditions in a seasonal heat storage system. A density functional theory level study is performed to determine molecular structures, charges, and harmonic frequencies in order to identify the formation of HCl at the operating temperatures in an energy storage system. The preference of hydrolysis over dehydration is quantified by applying thermodynamic equilibrium principles by calculating Gibbs free energies of the hydrated magnesium chloride molecules. The molecular structures of the hydrates (n = 0, 1, 2, 4, and 6) of MgCl2 are investigated to understand the stability and symmetry of these molecules. The structures are found to be noncomplex with almost no meta-stable isomers, which may be related to the faster kinetics observed in the hydration of chlorides compared to sulfates. Also, the frequency spectra of these molecules are calculated, which in turn are used to calculate the changes in Gibbs free energy of dehydration and hydrolysis reactions. From these calculations, it is found that the probability for hydrolysis to occur is larger for lower hydrates. Hydrolysis occurring from the hexa-, tetra-, and dihydrate is only possible when the temperature is increased too fast to a very high value. In the case of the mono-hydrate, hydrolysis may become favorable at high water vapor pressure and at low HCl pressure

Interplay between Anomalous Transport and Catalytic Reaction Kinetics in Single-File Nanoporous Systems

Functionalized nanoporous materials have broad utility for catalysis applications. However, the kinetics of catalytic reaction processes in these systems can be strongly impacted by the anomalous transport. The most extreme case corresponds to single-file diffusion for narrow pores in which species cannot pass each other. For conversion reactions with a single-file constraint, traditional mean-field-type reaction-diffusion equations fail to capture the initial evolution of concentration profiles, and they cannot describe the scaling behavior of steady-state reactivity. Hydrodynamic reaction-diffusion equations accounting for the single-file aspects of chemical diffusion can describe such initial evolution, but additional refinements are needed to incorporate fluctuation effects controlling, for example, steady-state reactivity localized near pore openings. For polymerization reactions with a single-file constraint, initial behavior depends strongly on system details such as catalytic site loading and reaction rate. However, long-time behavior often involves the formation of a dominant large polymer near each end of the pore, initially within the pore but subsequently partly extruding. In this partial extrusion regime, the kinetics is governed by the special features of the random walk describing the motion of the end of the partly extruded polymer, noting that this extruded end must return within the pore for further growth

Transcriptome-Wide Binding Sites for Components of the Saccharomyces cerevisiae Non-Poly(A) Termination Pathway: Nrd1, Nab3, and Sen1

RNA polymerase II synthesizes a diverse set of transcripts including both protein-coding and non-coding RNAs. One major difference between these two classes of transcripts is the mechanism of termination. Messenger RNA transcripts terminate downstream of the coding region in a process that is coupled to cleavage and polyadenylation reactions. Non-coding transcripts like Saccharomyces cerevisiae snoRNAs terminate in a process that requires the RNA–binding proteins Nrd1, Nab3, and Sen1. We report here the transcriptome-wide distribution of these termination factors. These data sets derived from in vivo protein–RNA cross-linking provide high-resolution definition of non-poly(A) terminators, identify novel genes regulated by attenuation of nascent transcripts close to the promoter, and demonstrate the widespread occurrence of Nrd1-bound 3′ antisense transcripts on genes that are poorly expressed. In addition, we show that Sen1 does not cross-link efficiently to many expected non-coding RNAs but does cross-link to the 3′ end of most pre–mRNA transcripts, suggesting an extensive role in mRNA 3′ end formation and/or termination

The P-Loop Domain of Yeast Clp1 Mediates Interactions Between CF IA and CPF Factors in Pre-mRNA 3′ End Formation

Cleavage factor IA (CF IA), cleavage and polyadenylation factor (CPF), constitute major protein complexes required for pre-mRNA 3′ end formation in yeast. The Clp1 protein associates with Pcf11, Rna15 and Rna14 in CF IA but its functional role remained unclear. Clp1 carries an evolutionarily conserved P-loop motif that was previously shown to bind ATP. Interestingly, human and archaean Clp1 homologues, but not the yeast protein, carry 5′ RNA kinase activity. We show that depletion of Clp1 in yeast promoted defective 3′ end formation and RNA polymerase II termination; however, cells expressing Clp1 with mutant P-loops displayed only minor defects in gene expression. Similarly, purified and reconstituted mutant CF IA factors that interfered with ATP binding complemented CF IA depleted extracts in coupled in vitro transcription/3′ end processing reactions. We found that Clp1 was required to assemble recombinant CF IA and that certain P-loop mutants failed to interact with the CF IA subunit Pcf11. In contrast, mutations in Clp1 enhanced binding to the 3′ endonuclease Ysh1 that is a component of CPF. Our results support a structural role for the Clp1 P-loop motif. ATP binding by Clp1 likely contributes to CF IA formation and cross-factor interactions during the dynamic process of 3′ end formation

CPF-Associated Phosphatase Activity Opposes Condensin-Mediated Chromosome Condensation

International audienceFunctional links connecting gene transcription and condensin-mediated chromosome condensation have been established in species ranging from prokaryotes to vertebrates. However, the exact nature of these links remains misunderstood. Here we show in fission yeast that the 3′ end RNA processing factor Swd2.2, a component of the Cleavage and Polyadenylation Factor (CPF), is a negative regulator of condensin-mediated chromosome condensation. Lack of Swd2.2 does not affect the assembly of the CPF but reduces its association with chromatin. This causes only limited, context-dependent effects on gene expression and transcription termination. However, CPF-associated Swd2.2 is required for the association of Protein Phosphatase 1 PP1Dis2 with chromatin, through an interaction with Ppn1, a protein that we identify as the fission yeast homologue of vertebrate PNUTS. We demonstrate that Swd2.2, Ppn1 and PP1Dis2 form an independent module within the CPF, which provides an essential function in the absence of the CPF-associated Ssu72 phosphatase. We show that Ppn1 and Ssu72, like Swd2.2, are also negative regulators of condensin-mediated chromosome condensation. We conclude that Swd2.2 opposes condensin-mediated chromosome condensation by facilitating the function of the two CPF-associated phosphatases PP1 and Ssu72

Molecular dynamics study on thermal dehydration process of epsomite (MgSO4.7H2O)

Water vapour sorption in salt hydrates is one of the most promising means of compact, low loss and long-term solar heat storage in the built environment. Among all, epsomite (MgSO4·7H2O) excels for its high-energy storage density and vast availability. However, in practical applications, the slow kinetics and evident structural changes during hydration and dehydration significantly jeopardise the heat storage/recovery rate. A molecular dynamics (MD) study is carried out to investigate the thermal properties and structural changes in the thermal dehydration process of the epsomite. The MD simulation is carried out at 450 K and a vapour pressure of 20 mbar, in accordance with experimental heat storage conditions. The study identifies the dehydration as multiple stages from the initial quick water loss and collapse of the crystal framework to the adsorption of water molecules, which inhibits complete dehydration. Further, the anisotropic diffusion behaviour supports the important role of the porous matrix structure in the heat and mass transfer process. The enthalpy changes, partial densities, mass diffusion coefficients of water and radial distribution functions are calculated and compared with corresponding experimental data to support the conclusions