Equilibrium Clusters in Concentrated Lysozyme Protein Solutions

We have studied the structure of salt-free lysozyme at 293 K and pH 7.8 using molecular simulations and experimental SAXS effective potentials between proteins at three volume fractions, 0.012, 0.033, and 0.12. We found that the structure of lysozyme near physiological conditions strongly depends on the volume fraction of proteins. The studied lysozyme solutions are dominated by monomers only for <0.012; for the strong dilution 70% of proteins are in a form of monomers. For 0.033 only 20% of proteins do not belong to a cluster. The clusters are mainly elongated. For 0.12 almost no individual particles exits, and branched, irregular clusters of large extent appear. Our simulation study provides new insight into the formation of equilibrium clusters in charged protein solutions near physiological conditions

Influence of activated carbon surface oxygen functionalities on SO2 physisorption – Simulation and experiment

The influence of the gradual oxidation of carbons on SO2 physisorption was studied, by comparison of experimental and simulated SO2 adsorption isotherms. The results confirmed a significant impact of surface groups on the SO2 adsorption. The simulations also revealed a similar, to that observed experimentally, effect of the increase in the percentage of the smallest micropores on adsorption isotherms. The isotherms were analysed using the CMMS model. The conclusion is that this model seems to be a good and sensitive tool for studying SO2 physisorption mechanism since a very good qualitative agreement between the experimental and simulated data was observed

Synergetic effect of carbon nanopore size and surface oxidation on CO2 capture from CO2/CH4 mixtures

We have studied the synergetic effect of confinement (carbon nanopore size) and surface chemistry (the number of carbonyl groups) on CO2 capture from its mixtures with CH4 at typical operating conditions for industrial adsorptive separation (298 K and compressed CO2CH4 mixtures). Although both confinement and surface oxidation have an impact on the efficiency of CO2/CH4 adsorptive separation at thermodynamics equilibrium, we show that surface functionalization is the most important factor in designing an efficient adsorbent for CO2 capture. Systematic Monte Carlo simulations revealed that adsorption of CH4 either pure or mixed with CO2 on oxidized nanoporous carbons is only slightly increased by the presence of functional groups (surface dipoles). In contrast, adsorption of CO2 is very sensitive to the number of carbonyl groups, which can be examined by a strong electric quadrupolar moment of CO2. Interestingly, the adsorbed amount of CH4 is strongly affected by the presence of the co-adsorbed CO2. In contrast, the CO2 uptake does not depend on the molar ratio of CH4 in the bulk mixture. The optimal carbonaceous porous adsorbent used for CO2 capture near ambient conditions should consist of narrow carbon nanopores with oxidized pore walls. Furthermore, the equilibrium separation factor was the greatest for CO2/CH4 mixtures with a low CO2 concentration. The maximum equilibrium separation factor of CO2 over CH4 of ∼18–20 is theoretically predicted for strongly oxidized nanoporous carbons. Our findings call for a review of the standard uncharged model of carbonaceous materials used for the modeling of the adsorption separation processes of gas mixtures containing CO2 (and other molecules with strong electric quadrupolar moment or dipole moment)

The influence of the carbon surface chemical composition on Dubinin-Astakhov equation parameters calculated from SF(6) adsorption data-grand canonical Monte Carlo simulation

Using grand canonical Monte Carlo simulation we show, for the first time, the influence of the carbon porosity and surface oxidation on the parameters of the Dubinin-Astakhov (DA) adsorption isotherm equation. We conclude that upon carbon surface oxidation, the adsorption decreases for all carbons studied. Moreover, the parameters of the DA model depend on the number of surface oxygen groups. That is why in the case of carbons containing surface polar groups, SF(6) adsorption isotherm data cannot be used for characterization of the porosity

Applicability of molecular simulations for modelling the adsorption of the greenhouse gas CF4 on carbons

Tetrafluoromethane, CF4, is powerful greenhouse gas, and the possibility of storing it in microporous carbon has been widely studied. In this paper we show, for the first time, that the results of molecular simulations can be very helpful in the study of CF4 adsorption. Moreover, experimental data fit to the results collected from simulations. We explain the meaning of the empirical parameters of the supercritical Dubinin–Astakhov model proposed by Ozawa and finally the meaning of the parameter k of the empirical relation proposed by Amankwah and Schwarz

The SABRTooth feasibility trial protocol: a study to determine the feasibility and acceptability of conducting a phase III randomised controlled trial comparing stereotactic ablative radiotherapy (SABR) with surgery in patients with peripheral stage I non-small cell lung cancer (NSCLC) considered to be at higher risk of complications from surgical resection.

Background Stage I non-small cell lung cancer (NSCLC) is potentially curable, and surgery is considered to be the standard of care for patients with good performance status and minimal co-morbidity. However, a significant proportion of patients with stage I NSCLC have a poorer performance status and significant medical co-morbidity that make them at higher risk of morbidity and mortality from surgery. Stereotactic ablative radiotherapy (SABR), which uses modern radiotherapeutic techniques to deliver large doses of radiation, has shown superiority over conventional radiotherapy in terms of local control and toxicity and is a standard of care for patients with stage I NSCLC who are at too high risk for surgery. However, it is not known whether surgery or SABR is the most effective in patients with stage I NSCLC who are suitable for surgery but are less fit and at higher risk surgical complications. Previous randomised studies have failed to recruit in this setting, and therefore, a feasibility study is required to see whether a full randomised control trial would be possible. Methods/design SABRTooth is a UK-based, multi-centre, open-label, two-group individually (1:1) randomised controlled feasibility study in patients with peripheral stage I NSCLC considered to be at higher risk from surgical resection. The study will assess the feasibility of conducting a definitive large-scale phase III trial. The primary objective is to assess recruitment rates to provide evidence that, when scaled up, recruitment to a large phase III trial would be possible; the target recruitment being 54 patients in total, over a 21-month period. There are multiple secondary and exploratory objectives designed to explore the optimum recruitment and data collection strategies to help optimise the design of a future phase III trial. Discussion To know whether SABR is a better, equivalent or inferior alternative to surgery for higher risk patients is a key question in lung cancer. Other studies comparing SABR to surgery have closed early due to poor recruitment, and therefore, the SABRTooth feasibility study has been designed around the UK National Health Service (NHS) cancer pathway incorporating many design features in order to maximise recruitment for a future definitive phase III trial

Morphologically disordered pore model for characterization of micro-mesoporous carbons

We present a new morphologically disordered slit-shaped pore (MDSP) model for simulating gas adsorption in micro-mesoporous carbonaceous materials. The MDSP model qualitatively accounts for the inherent roughness of carbon pore walls in accord with the atomistic structural model of LMA10 reference carbon material. The MDSP model is applied to pore size distribution (PSD) calculations from nitrogen adsorption isotherms measured at 77.4 K in the range of pore widths from 0.72 to 40 nm. The MDSP model improves significantly the nitrogen adsorption porosimetry and, being fully atomistic, it is transferable to study various adsorbate-adsorbent systems. Computations of PSD functions for a series of carbonaceous materials, including activated carbon fiber, granular activated carbons, synthetic activated carbons showed that MDSP generates smooth Gaussian-type PSD functions with a well-defined average pore size. Furthermore, PSD functions computed from the MDSP model are free from the artificial gaps in the region of narrow micropores (∼1 nm and ∼2 nm) predicted from the standard slit-shaped pore models with ideal graphite-like walls. MDSP is not only a complementary model to existing approaches, such as quench-solid density functional theory method, but it paves the way to efficient atomistic simulations of various compounds within morphologically disordered carbon nanopores

BLUF Domain Function Does Not Require a Metastable Radical Intermediate State

BLUF (blue light using flavin) domain proteins are an important family of blue light-sensing proteins which control a wide variety of functions in cells. The primary light-activated step in the BLUF domain is not yet established. A number of experimental and theoretical studies points to a role for photoinduced electron transfer (PET) between a highly conserved tyrosine and the flavin chromophore to form a radical intermediate state. Here we investigate the role of PET in three different BLUF proteins, using ultrafast broadband transient infrared spectroscopy. We characterize and identify infrared active marker modes for excited and ground state species and use them to record photochemical dynamics in the proteins. We also generate mutants which unambiguously show PET and, through isotope labeling of the protein and the chromophore, are able to assign modes characteristic of both flavin and protein radical states. We find that these radical intermediates are not observed in two of the three BLUF domains studied, casting doubt on the importance of the formation of a population of radical intermediates in the BLUF photocycle. Further, unnatural amino acid mutagenesis is used to replace the conserved tyrosine with fluorotyrosines, thus modifying the driving force for the proposed electron transfer reaction; the rate changes observed are also not consistent with a PET mechanism. Thus, while intermediates of PET reactions can be observed in BLUF proteins they are not correlated with photoactivity, suggesting that radical intermediates are not central to their operation. Alternative nonradical pathways including a keto–enol tautomerization induced by electronic excitation of the flavin ring are considered

Super-sieving effect in phenol adsorption from aqueous solutions on nanoporous carbon beads

Removal of aromatic contaminants, like phenol, from water can be efficiently achieved by preferential adsorption on porous carbons which exhibit molecular sieving properties. Here, we present nanoporous carbon beads exhibiting an outstanding sieving effect in phenol adsorption from aqueous solution at neutral pH, which is evidenced experimentally and theoretically. The molecular sieving with pure phenol adsorbed phase is achieved by tuning the pore size and surface chemistry of the adsorbent. This study elucidates the essential role of hydrophobic interactions in narrow carbon micropores in removal and clean-up of water from organic pollutants. Furthermore, we suggest a new theoretical approach for evaluation of phenol adsorption capacity that is based on the Monte Carlo simulation of phenol adsorption with the relevance to the pore size distribution function determined by the density functional theory method from low temperature nitrogen adsorption