Effects of a Free Adsorbate Boundary on the Description of an Argon Adsorbed Film on Graphite below the Bulk Triple Point

Monte Carlo simulations have been carried out to study argon adsorption on graphite at temperatures below the bulk triple point temperature, T_tr^(bulk) = 83.8 K. Two models for graphite have been used to investigate the effects of an adsorbate patch with a free boundary on the layering temperatures, the two-dimensional (2D)-triple point and the 2D-critical point for the three adsorbate layers on the surface. The first model (S-model) has a planar surface of infinite extent in the two directions parallel to the surface, and the second is a finite (2D-patch model). Although simulations using both models describe the characteristic temperatures, only the 2D-patch model can represent the experimental isotherms accurately, and the condensation pressures at which first-order transitions occur, while simulations with the S-model yield many unphysical substeps that are not observed experimentally in the first layer adsorbate, which leads to a poor description of higher adsorbate layers. These results support the interpretation that boundary growth of an adsorbate patch is the mechanism for argon adsorption at temperatures below the bulk triple point temperature. Combining the results derived from this simulation study for temperatures below the bulk triple point temperature, with results reported in the literature for temperatures above T_tr^(bulk) and experimental data, we have constructed a generic pattern for the adsorption isotherms of simple gases on graphite at temperatures ranging from well below the bulk triple point temperature up to the bulk critical temperature, a comprehensive description not widely recognized in the literature.

Transcriptome analysis of blastoderms exposed to prolonged egg storage and short periods of incubation during egg storage

BACKGROUND

Cool temperature egg storage prior to incubation is a common practice in the broiler industry; however, prolonged egg storage causes increased embryonic mortality and decreased hatchability and growth in surviving chicks. Exposing eggs to short periods of incubation during egg storage (SPIDES) reduces the adverse consequences of prolonged storage. SPIDES increases blastodermal cell viability by reducing apoptosis, though the counteracting mechanisms are unclear. To define the impact of prolonged storage and SPIDES, transcriptome analysis compared gene expression from blastoderms isolated from eggs exposed to the following treatments: control (CR, stored at 17 °C for 4 days), prolonged storage (NSR, stored at 17 °C for 21 days), SPIDES (SR, stored at 17 °C for 21 days with SPIDES), and incubated control (C2, stored at 17 °C for 4 days followed by incubation to HH (Hamburger-Hamilton) stage 2, used as the ideal standard development) (n = 3/group). Data analysis was performed using the CLC Genomics Workbench platform. Functional annotation was performed using DAVID and QIAGEN Ingenuity Pathway Analysis.

RESULTS

In total, 4726 DEGs (differentially expressed genes) were identified across all experimental group comparisons (q < 0.05, FPKM> 20, |fold change| > 1.5). DEGs common across experimental comparisons were involved in cellular homeostasis and cytoskeletal protein binding. The NSR group exhibited activation of ubiquitination, apoptotic, and cell senescence processes. The SR group showed activation of cell viability, division, and metabolic processes. Through comparison analysis, cellular respiration, tRNA charging, cell cycle control, and HMBG1 signaling pathways were significantly impacted by treatment and potential regulatory roles for ribosomal protein L23a (RPL23A) and MYC proto-oncogene, BHLH transcription factor (MYC) were identified.

CONCLUSIONS

Prolonged egg storage (NSR) resulted in enriched cell stress and death pathways; while SPIDES (SR) resulted in enriched basic cell and anti-apoptotic pathways. New insights into DNA repair mechanisms, RNA processing, shifts in metabolism, and chromatin dynamics in relation to egg storage treatment were obtained through this study. Although egg storage protocols have been examined through targeted gene expression approaches, this study provided a global view of the extensive molecular networks affected by prolonged storage and SPIDES and helped to identify potential upstream regulators for future experiments to optimize egg storage parameters.

Characterization of non-graphitized carbon blacks: a model with surface crevices

Experimental isotherms for argon and nitrogen adsorption on two non-graphitized carbon substrates, Carbopack B and Cabot BP280, do not obey Henry's Law in the range of pressures accessible to the most sensitive MKS pressure transducers. At high pressures, close to the bulk coexistence pressure (P0), the isotherms at temperatures below the bulk triple point temperature cross the P0 axis at a finite loading, a behaviour which is interpreted as incomplete wetting. It was found that the adsorbed density at P0 for Cabot BP280 is lower than that for Carbopack B which is, in turn, only slightly lower than that for the highly graphitized Carbopack F, suggesting that there is a long-range effect of the surface structure in non-graphitized carbon blacks, in the accumulation of higher layers, especially for Cabot BP280. We have carried out extensive Monte Carlo simulations to compare experimental observations with a molecular model for substrate surfaces decorated with crevices of molecular dimensions. From the analysis of the experimental data, it was found that the typical width of crevices is of the order of 0.65-0.9 nm. In the high pressure region, the crossing of the P0 axis by isotherms at temperatures below the bulk triple point temperature can be explained by an adsorbate structure which is less dense and more disordered than the fcc structure of the bulk crystal, with a consequent raising of the coexistence pressure between the adsorbate and the gas phase above P0. Adsorbate loading at the point where the isotherm crosses the P0 axis for Cabot BP280 is lower than for Carbopack B which can be attributed to a higher concentration of crevices leading to a lower adsorbate density and an irregular arrangement of atoms at the interface separating the adsorbed phase and the gas phase. This results in weaker gas-adsorbate interactions which supresses the build-up of higher layers. We suggest that the use of the adsorbed density at the bulk coexistence pressure, at temperatures below the bulk triple point temperature, can be a useful tool for assessing the presence and concentration of surface crevices on non-graphitized carbon black.

A simulation study of the low temperature phase diagram of the methane monolayer on graphite: a test of potential energy functions

The TraPPE-EH model reveals the two patterns of commensurate monolayer and the mechanism of commensurate–incommensurate transition in a certain temperature range.

On the canonical isotherms for bulk fluid, surface adsorption and adsorption in pores: A common thread

Kinetic Monte Carlo simulated isotherms calculated in the canonical ensemble, at temperatures below the critical temperature, for bulk fluid, surface adsorption and adsorption in a confined space, show a van der Waals (vdW) loop with a vertical phase transition between the rarefied and dense spinodal points at the co-existence chemical potential, µ_co. Microscopic examination of the state points on this loop reveals features that are common to these systems. At state points with chemical potentials greater than μ_co the microscopic configurations show clusters, which coalesce to form two co-existing phases along the vertical section of the loop (the coexistence line). As more molecules are added, the dense region expands at the expense of the rarefied region, to the point where the rarefied region becomes spherical (cylindrical for 2D-systems) with a curvature greater than that of the coexisting phases. This results in a decrease of chemical potential from µ_co to the liquid spinodal point where the rarefied region disappears. With a further increase in loading, the chemical potential and the density increase. The existence of a vdW loop is the microscopic reason for the hysteresis observed in the grand canonical isotherm, where the adsorption and desorption boundaries of the hysteresis loop are first-order transitions, enclosing the vertical section of the vdW loop of the canonical isotherm. However, a first-order transition is rarely observed in experiments where transitions are usually steep, but not vertical. From our extensive simulations, we provide two possible reasons: (1) the finite extent of the system and (2) the existence of high energy sites that localize the clusters. In the first case, the desorption branch, and in the second case the adsorption branch, either comes close to, or collapses onto the coexistence line. When both occur, the hysteresis loop disappears and the isotherm is reversible, as often observed experimentally.

On the growth of argon clusters on a weak adsorbent decorated with patches

Much attention has been paid to understanding the clustering mechanism of water adsorbed on carbonaceous adsorbents. Adsorbed water forms clusters around strong sites, such as functional groups and surface defects, and these clusters then coalesce if the strong sites are sufficiently close to each other. Simulations of water adsorption are notoriously time consuming because of the slow relaxation of the strongly-directional hydrogen bonds. Our objective in this paper is to gain a better insight into clustering and coalescence of water, without incurring large computing overheads. To this end we have chosen argon as an adsorbate, and a substrate that is a very weak adsorbent for argon. To mimic functional groups, the substrate surface is decorated with strongly adsorbing patches. The adsorbate forms nano-clusters with convex surfaces at pressures greater than the saturation vapour pressure. When these clusters are sufficiently close to each other, they coalescence to form larger fused clusters, and there is a decrease in the equilibrium pressure. The relationship between the radius of curvature of the developed nano-clusters and the equilibrium pressure follows the functional form of the Kelvin equation, but the energy parameterγv_M is smaller than the bulk value, implying that the clusters have a smaller cohesive energy.

Nonwetting/Prewetting/Wetting Transition of Ammonia on Graphite

Simulations of ammonia adsorption on graphite were carried out over a range of temperatures to investigate the transition from nonwetting to wetting. The process is governed by a subtle interplay between the various interactions in the system and the temperature. At temperatures below the bulk triple point, the system is nonwetting; above the triple point, we observed continuous wetting, preceded by a prewetting region in which the so-called thin-to-thick film transition occurs. This system serves as an excellent example of wetting/nonwetting behavior in an associating fluid as a function of temperature because the heat of sublimation (or condensation) is greater than the isosteric heat of adsorption at zero loading. The nonwetting-to-wetting transition (NW/W) is also strongly affected by the adsorbate-adsorbate interaction, which becomes important when this contribution to the isosteric heat is of a similar magnitude to the heat of condensation. An appropriate indicator of a NW/W transition at a given loading is therefore the difference between the isosteric heat and the heat of sublimation (or condensation). Our simulation results show the "thin-to-thick" film transition in the temperature range between 195 and 240 K, which has not been previously explained. Above 240 K, continuous wetting occurs. This study provides a basis for a better understanding of adsorption in a range of systems because ammonia is an intermediate between simple molecules, such as argon, and strongly associating fluids, such as water.

On the transition from partial wetting to complete wetting of methanol on graphite

Excellent agreement with experiment for methanol adsorption on graphitized carbon black at low temperatures by Monte Carlo simulation. Incomplete wetting and complete wetting are observed at a range of temperatures above the triple point.

The role of adsorbate size on adsorption of Ne and Xe on graphite

We have carried out an extensive grand canonical Monte Carlo simulation to investigate the adsorption of neon and xenon on graphite. The adsorbate collision diameters of neon and xenon are smaller and greater respectively, than the commensurate graphite lattice spacing λ=3×3R30⁰ of 0.426 nm. Simulated isotherms and isosteric heats were obtained using a graphite model that has been shown to describe successfully the adsorbate transitions for krypton, methane and nitrogen by Prasetyo et al. (2017), which have collision diameters close to λ. Neon does not exhibit commensurate (C) packing because the gain in the intermolecular potential interactions in the incommensurate (IC) packing when molecules move away from carbon hexagon centres, does not compensate for the increase in the solid-fluid potential energy. Xenon, on the other hand, exhibits IC packing because its molecular size is greater than λ. Nevertheless, at a sufficiently high chemical potential, the first layer of xenon changes from the IC to C packing (in contrast to what is observed for krypton, nitrogen and methane). This transition occurs because the decrease in the xenon intermolecular interactions is sufficiently compensated by the increase in the solid-fluid interaction, and the increase in the fluid-fluid interactions between molecules in the first layer and those in the second layer. This finding is supported by the X-ray diffraction study by Mowforth et al. (1986) and Morishige et al. (1990).

Water adsorption on carbon - A review

Water adsorption on carbonaceous materials has been studied increasingly in the recent years, not only because of its impact on many industrial processes, but also motivated by a desire to understand, at a fundamental level, the distinctive character of directional interactions between water molecules, and between water molecules and other polar groups, such as the functional groups (FGs) at the surfaces of graphene layers. This paper presents an extensive review of recent experimental and theoretical work on water adsorption on various carbonaceous materials, with the aim of gaining a better understanding of how water adsorption in carbonaceous materials relates to the concentration of FGs, their topology (arrangement of the groups) and the structure of the confined space in porous carbons. Arising from this review we are able to propose mechanisms for water adsorption in carbonaceous materials as the adsorbate density increases. The intricate interplay between the roles of FGs and confinement makes adsorption of water on carbon materials very different from that of other simple molecules.

Computational methodology for determining textural properties of simulated porous carbons

We have refined and improved the computational efficiency of the TriPOD technique, used to determine the accessible characteristics of porous solids with a known configuration of solid atoms. Instead of placing a probe molecule randomly, as described in the original version of the TriPOD method (Herrera et al., 2011), we implemented a scheme for dividing the porous solid into 3D-grids and computing the solid-fluid potential energies at these grid points. We illustrate the potential of this technique in determining the total pore volume, the surface area and the pore size distribution of various molecular models of porous carbons, ranging from simple pore models to a more complex simulated porous carbon model; the latter is constructed from a canonical Monte Carlo simulation of carbon microcrystallites of various sizes.

On the microscopic origin of the temperature evolution of isosteric heat for methane adsorption on graphite

Evolution of the isosteric heat of methane adsorption on graphite with temperature.

Effects of Surface Structure and Temperature on the Surface Mediation, Layer Concentration and Molecular Projection Area: Adsorption of Argon and Nitrogen onto Graphitized Thermal Carbon Black

This paper is devoted to an investigation of the effects of surface structure (structure-less or structured) on the description of the adsorption isotherm and the isosteric heat of nitrogen and argon adsorption onto graphitized thermal carbon black. It was found that the surface structure had little effect on the adsorption of either argon or nitrogen at 77 K and 87.3 K. The variation of the monolayer coverage concentration was also investigated as well as the concentrations of higher layers as a function of pressure and temperature. Finally, the commonly used values for the molecular projection area of nitrogen and argon for graphitized thermal carbon black (16.2 Å2 and 13.8 Å2) were revisited. For this material, a value of 15.5 Å2 is recommended for nitrogen at 77 K, while for the case of argon at the same temperature the recommended values of 13.8 Å2 and 12.94 Å2 are suggested for the reduced pressure range (0.1–0.2P/P0) and (0.25–0.35P/P0), respectively. A value of 14 Å2 for argon at 87.3 K is suggested for the BET plot over the reduced pressure range of 0.1–0.2P/P0.

A GCMC simulation and experimental study of krypton adsorption/desorption hysteresis on a graphite surface

Adsorption isotherms and isosteric heats of krypton on a highly graphitized carbon black, Carbopack F, have been studied with a combination of Monte Carlo simulation and high-resolution experiments at 77K and 87K. Our investigation sheds light on the microscopic origin of the experimentally observed, horizontal hysteresis loop in the first layer, and the vertical hysteresis-loop in the second layer, and is found to be in agreement with our recent Monte Carlo simulation study (Diao et al., 2015). From detailed analysis of the adsorption isotherm, the latter is attributed to the compression of an imperfect solid-like state in the first layer, to form a hexagonally packed, solid-like state, immediately following the first order condensation of the second layer. To ensure that capillary condensation in the confined spaces between microcrystallites of Carbopack F does not interfere with these hysteresis loops, we carried out simulations of krypton adsorption in the confined space of a wedge-shaped pore that mimics the interstices between particles. These simulations show that, up to the third layer, any such interference is negligible.

On the explanation of hysteresis in the adsorption of ammonia on graphitized thermal carbon black

The entropic effect of temperature dominates the adsorption behaviours of ammonia from spill-over to clustering on the basal plane of graphite.

Structure–activity correlation in transfection promoted by pyridinium cationic lipids

The efficiency of transfection of a plasmid DNA promoted by a series of pyridinium lipids is correlated with molecular parameters of the lipids.

Adsorption on ordered and disordered duplex layers of porous anodic alumina

We have carried out systematic experiments and numerical simulations of the adsorption on porous anodic aluminum oxide (AAO) duplex layers presenting either an ordered or a disordered interconnecting interface between the large (cavity) and small (constriction) sections of the structured pores. Selective blocking of the pore openings resulted in three different pore topologies: open structured pores, funnel pores, and ink-bottle pores. In the case of the structured pores having an ordered interface, the adsorption isotherms present a rich phenomenology characterized by the presence of two steps in the condensation branch and the opening of one (two) hysteresis loops during evaporation for the ink-bottle (open and funnel) pores. The isotherms can be obtained by summing the isotherms measured on uniform pores having the dimensions of the constrictions or of the cavities. The numerical analysis of the three different pore topologies indicates that the shape of the junction between the two pore sections is only important for the adsorption branch. In particular, a conic junction which resembles that of the AAO pores represents the experimental isotherms for the open and funnel pores better, but the shape of the junction in the ink bottle pores does not matter. The isotherms for the duplex layers with a disordered interface display the same general features found for the ordered duplex layers. In both cases, the adsorption branches coincide and have two steps which are shifted to lower relative pressures compared to those for the ordered duplex. Furthermore, the desorption branches comprise hysteresis loops much wider than those of the ordered duplex layers. Overall, this study highlights the important role played by morphologies where there are interconnections between large and small pores.

Existence of ultrafine crevices and functional groups along the edge surfaces of graphitized thermal carbon black

Adsorption of different gases on graphitized thermal carbon black (GTCB) has been studied with a new molecular model to examine the consequences of micropore crevices and functional groups at the junctions between adjacent basal planes. Adsorption was simulated in the Grand Canonical Monte Carlo ensemble and the theoretical Henry constants were calculated by Monte Carlo volume integration over the Boltzmann factor of the solid-fluid potential. The simulation results are in good agreement with high-resolution experimental isotherms for argon on mineralogical graphite measured by Lopez-Gonzalez et al.1 From detailed inspection of the argon isotherms at extremely low coverages, we find two distinct Henry law regions, separated by a plateau (suggesting saturation of the stronger sites) that spans over a few decades of pressure. The first Henry law region is attributed to adsorption in the ultrafine crevices at the junctions between two adjacent basal planes, and the second region corresponds to adsorption on the basal plane, as confirmed by the theoretical Henry constant. The simulated isosteric heat and snapshots of molecular configurations show that argon adsorbs preferentially in the ultrafine crevices where there is a deep potential well due to overlap from the opposite pore walls. Similar behavior was found for other nonassociating fluids (Ar, N2, and CO2); however, for associating fluids (NH3 and H2O), the strong sites for adsorption and nucleation come from the combined effects of functional groups and ultrafine crevices, since the latter cannot alone account for the observed adsorption.

Hysteresis loop and scanning curves of argon adsorption in closed-end wedge pores

The hysteresis loop and scanning curves for argon adsorbed in a wedge pore with one end closed are studied with grand canonical Monte Carlo simulation. We have found multiple hysteresis loops for pores with either the narrow end or the wider end closed. In pores with the narrow end closed, adsorption and desorption exhibits a two-stage sequence of rapid change, followed by a gradual change in adsorbate density. The pore can be divided into zones of commensurate packing and junctions of incommensurate packing. A striking feature is that the sequence of these two stages is opposite for the adsorption and desorption processes. This can be explained by cohesion in the adsorbate, in which a steep condensation process is associated with the zones and a steep evaporation process is associated with the junctions between them. For pores with the wider end closed, the processes of adsorption and desorption from various zones are correlated with each other. In pores with the narrow end closed, the scanning curves trace reversibly along the segment of the isotherm, where the isotherm shows gradual change, and when the scanning curve reaches a point between the gradual change segment and the sharp change segment, the scanning curve crosses from one boundary of the hysteresis loop to the corresponding point on the other boundary. This indicates that the condensation and evaporation states are not affected by scanning but that, in scanning across the hysteresis loop, the adsorbate passes through a sequence of metastable states as the distribution of density is rearranged, without any significant change in the overall density. In contrast, for pores with the wider end closed, both the descending curve from a partially filled pore and the ascending curve are identical to the desorption branch of the corresponding pore with its narrow end closed.