Permeation Pathway Research Articles

Exploring Flexibility and Folding Patterns Throughout Time in Voltage Sensors.

The voltage-sensing domain (VSD) is a module capable of responding to changes in the membrane potential through conformational changes and facilitating electromechanical coupling to open a pore gate, activate proton permeation pathways, or promote enzymatic activity in some membrane-anchored phosphatases. To carry out these functions, this module acts cooperatively through conformational changes. The VSD is formed by four transmembrane segments (S1-S4) but the S4 segment is critical since it carries positively charged residues, mainly Arg or Lys, which require an aqueous environment for its proper function. The discovery of this module in voltage-gated ion channels (VGICs), proton channels (Hv1), and voltage sensor-containing phosphatases (VSPs) has expanded our understanding of the principle of modularity in the voltage-sensing mechanism of these proteins. Here, by sequence comparison and the evaluation of the relationship between sequence composition, intrinsic flexibility, and structural analysis in 14 selected representatives of these three major protein groups, we report five interesting differences in the folding patterns of the VSD both in prokaryotes and eukaryotes. Our main findings indicate that this module is highly conserved throughout the evolutionary scale, however: (1) segments S1 to S3 in eukaryotes are significantly more hydrophobic than those present in prokaryotes; (2) the S4 segment has retained its hydrophilic character; (3) in eukaryotes the extramembranous linkers are significantly larger and more flexible in comparison with those present in prokaryotes; (4) the sensors present in the kHv1 proton channel and the ciVSP phosphatase, both of eukaryotic origin, exhibit relationships of flexibility and folding patterns very close to the typical ones found in prokaryotic voltage sensors; and (5) archaeal channels KvAP and MVP have flexibility profiles which are clearly contrasting in the S3-S4 region, which could explain their divergent activation mechanisms. Finally, to elucidate the obscure origins of this module, we show further evidence for a possible connection between voltage sensors and TolQ proteins.

Influence of hygiene tissue paper used as an additive on the physicochemical and mechanical properties of CO2-cured belite-rich cement paste

The present study investigated the fresh, hardened, and physicochemical properties of CO2-cured belite-rich cement (BRC) paste incorporating hygiene tissue paper (HTP) as an additive. HTP was added at 0.5% and 1.0% by wt. of BRC paste. The BRC paste was prepared at a water-to-cement ratio of 0.4 and cured under water and carbonation. The results demonstrated that upon carbonation, the incorporation of HTP at 1.0% increases the CO2 uptake and compressive strength of specimens by 18.60% and 22.29%, respectively. A pore structure analysis shows a decrease in the threshold pore size diameter with an increase in the HTP content for CO2-cured samples. An SEM analysis revealed precipitation and impregnation of calcites in and around the HTP microfiber particles. The incorporation of HTP under water curing on the other hand did not significantly influence the strength or the physicochemical properties. It was observed that HTP contributes to improving the properties of CO2-cured BRC paste in two ways; the porous structure of HTP provides pathways for the deep permeation of CO2 into the matrix, and the surface of HTP offers an additional area for calcite precipitation.

Multi-scale dissolution dynamics for carbon sequestration in carbonate rock samples

Carbon dioxide (CO2) sequestration in porous, sedimentary reservoirs is a key technology to mitigate emissions of anthropogenic CO2 and curb irreversible climate change. The abundance of carbonate formations, both as saline aquifers and hydrocarbon reservoirs, makes future CO2 storage in carbonate formations highly likely. The weak carbonic acid that forms when CO2 dissolves in water will, however, interact with highly reactive carbonate. Preferential flow paths may form during dissolution or calcite precipitation may reduce injectivity - both processes significantly impacting reservoir sweep efficiency. Hence, understanding the dynamics of the dissolution processes and their influence on flow properties is necessary to safely store CO2 in carbonate formations. Darcy and sub-Darcy scale dissolution kinetics were here assessed in carbonate core plugs with and without pre-existing highly permeable pathways, during multiphase flow and under relevant storage conditions.Darcy-scale dissolution and precipitation data (injectivity changes, effluent analysis and mass loss) confirmed that CO2 and brine co-injections altered the carbonate rock structure on Darcy scale, but could not determine the cause of change. Multi-modal imaging was applied to independently quantify structural changes with computed tomography (CT) and aqueous flow characteristics with positron emission tomography (PET), thereby determining injectivity dependence on local flow patterns. Formation of high permeability pathways, which was expected due to rock dissolution, was only observed in cores with pre-existing open fractures, where reactive flow was limited to the fracture plane. A good correlation between the two imaging modules was found: areas of higher porosity yielded a low-density CT signal (i.e. high number of voids present) and a high PET signal density (i.e. large volume of traced fluid present). Loss of injectivity suggested local changes in the flow pattern due to blocking of pore throats by moving particles or secondary precipitation or mineralization of dissolved ions. High-resolution PET imaging revealed cementation, that was also visible using micro-CT, hence determining sub-Darcy local flow obstructions that led to decreased Darcy scale injectivity. Multi-modal imaging, where core characteristics, such as large vugs and cementation, can be independently determined by complementary modalities, may therefore be a useful tool to quantify reactive flow and resulting dissolution in rock samples.

Oscillating electric field assisted nano-incised graphene kirigami for ultrahigh-performance water desalination membrane

Benefiting from the single-atom thickness, dense honeycomb structure, nano-size pores, and adjustable selection capability, graphene kirigami (GK) is expected to be a promising candidate for the membrane of water desalination. However, due to the low bending stiffness of the GK structure, the fluctuation in incision size and the accumulation of salt ions around the incisions always limit the GK membrane from higher water desalination efficiency. In this study, we adopted an oscillating electric field to improve the water desalination efficiency of nano-incised GK via molecular dynamic (MD) simulation. The results reveal that with the oscillating electric field's assistance, the water permeability of the GK membrane achieves 1351.6 L/m2/h/bar theoretically under the condition of 100 % salt rejection, 5.9–7.1 times higher than the reported nano-porous graphene membrane and 2–5 orders of magnitude higher than the existing reverse osmosis membranes. The oscillating electric field can enhance the water desalination efficiency of the proposed GK membranes mainly by alleviating the structural fluctuation of the GK membrane and dredging the permeation pathway for water molecules. The considerable potential of the oscillating electric field-assisted GK membrane reported by this study will attract great attention in the field of water separation and purification.

Bioturbated strata in the Upper Cretaceous Aruma Formation, central Saudi Arabia: An analog for aquifers and hydrocarbon reservoirs with large burrows

The upper Cretaceous Aruma Formation in Central Saudi Arabia exhibits Thalassinoides-bearing strata resembling a bioturbated carbonate reservoir with large burrows. These burrows possess distinct stratigraphic characteristics. Certain intervals within the formation feature open or partially filled Thalassinoides, creating three-dimensional permeability pathways, while others contain Thalassinoides filled with low-permeability sediments. This comprehensive study investigates the paleoenvironment, ichnological features, bulk permeability influence, and stratigraphic variations of these bioturbated intervals. Incorporating field observations, laboratory analyses (including petrography, geochemical assessments, petrophysical measurements, and computed tomography scanning [CT]), we present the division of the studied interval into three biogenically influenced fluid flow media (BIFM 1–3). BIFM 1 comprises solution-enlarged open Thalassinoides (average shaft diameter: 5 cm) hosted within a mud-dominated matrix. BIFM 2 consists of Thalassinoides with mud-dominated infills (average shaft diameter: 3 cm) embedded in a dolomite matrix. BIFM 3 exhibits compacted open Thalassinoides. These BIFM units demonstrate burrow percentages ranging from 10% to 45%, featuring interconnected networks. The identified units reflect diverse depositional settings, ranging from open marine to restricted lagoon, and distinct stratigraphic positions. By highlighting the sedimentological and stratigraphic controls on the petrophysical properties of carbonate strata containing Thalassinoides with large burrows, this research contributes to the prediction of super-permeability zones in analogous settings.

Fabrication of highly selective PEBA mixed matrix membranes by incorporating metal-organic framework MIL-53 (Al) for the pervaporation separation of pyridine-water mixture

Pyridine is generally found in the effluents from the synthesis of paints, rubber chemicals, vitamins, and pesticides. This study focused on improving the pervaporation (PV) performance of polyether block-amide (PEBA-2533) membranes cast on polyvinylidene fluoride (PVDF) substrate, by incorporating the MIL-53 (Al) particles to prepare mixed matrix membranes (MMMs) for pyridine separation from the aqueous solution. MIL-53 (Al) has a larger aperture size (8.5 Å) than the molecular size of the pyridine (6.0 Å), which could allow pyridine molecules to efficiently pass through its channels. The coadjacent MIL-53 particles created relatively continuous permeation pathways for the penetrants in the MMMs, which substantially enhanced the separation performance. Impressively, the resultant MMMs displayed superior pyridine separation performance at complex conditions. At 65 °C and 0.5 wt% pyridine aqueous solution, the separation factor and pyridine flux of PEBA/PVDF membrane were 17.3 and 143.5 g m−2 h−1, which were improved using MIL-53@PEBA/PVDF MMMs to 48.1 and 226.9 g m−2 h−1, respectively. Owing to the enhanced pyridine affinity, hydrophobic property, and thermal robustness, the resultant MMMs overcame the inherent trade-off between selectivity and permeability, and also displayed the promising long-term stability. These findings may provide valuable insights for developing novel MMMs with superior separation performance.

Identification of a drug binding pocket in TMEM16F calcium-activated ion channel and lipid scramblase

The dual functions of TMEM16F as Ca2+-activated ion channel and lipid scramblase raise intriguing questions regarding their molecular basis. Intrigued by the ability of the FDA-approved drug niclosamide to inhibit TMEM16F-dependent syncytia formation induced by SARS-CoV-2, we examined cryo-EM structures of TMEM16F with or without bound niclosamide or 1PBC, a known blocker of TMEM16A Ca2+-activated Cl- channel. Here, we report evidence for a lipid scrambling pathway along a groove harboring a lipid trail outside the ion permeation pore. This groove contains the binding pocket for niclosamide and 1PBC. Mutations of two residues in this groove specifically affect lipid scrambling. Whereas mutations of some residues in the binding pocket of niclosamide and 1PBC reduce their inhibition of TMEM16F-mediated Ca2+ influx and PS exposure, other mutations preferentially affect the ability of niclosamide and/or 1PBC to inhibit TMEM16F-mediated PS exposure, providing further support for separate pathways for ion permeation and lipid scrambling.

PTEX helps efficiently traffic haemoglobinases to the food vacuole in Plasmodium falciparum.

A key element of Plasmodium biology and pathogenesis is the trafficking of ~10% of the parasite proteome into the host red blood cell (RBC) it infects. To cross the parasite-encasing parasitophorous vacuole membrane, exported proteins utilise a channel-forming protein complex termed the Plasmodium translocon of exported proteins (PTEX). PTEX is obligatory for parasite survival, both in vitro and in vivo, suggesting that at least some exported proteins have essential metabolic functions. However, to date only one essential PTEX-dependent process, the new permeability pathways, has been described. To identify other essential PTEX-dependant proteins/processes, we conditionally knocked down the expression of one of its core components, PTEX150, and examined which pathways were affected. Surprisingly, the food vacuole mediated process of haemoglobin (Hb) digestion was substantially perturbed by PTEX150 knockdown. Using a range of transgenic parasite lines and approaches, we show that two major Hb proteases; falcipain 2a and plasmepsin II, interact with PTEX core components, implicating the translocon in the trafficking of Hb proteases. We propose a model where these proteases are translocated into the PV via PTEX in order to reach the cytostome, located at the parasite periphery, prior to food vacuole entry. This work offers a second mechanistic explanation for why PTEX function is essential for growth of the parasite within its host RBC.

Tire-Derived Transformation Product 6PPD-Quinone Induces Mortality and Transcriptionally Disrupts Vascular Permeability Pathways in Developing Coho Salmon.

Urban stormwater runoff frequently contains the car tire transformation product 6PPD-quinone, which is highly toxic to juvenile and adult coho salmon (Onchorychus kisutch). However, it is currently unclear if embryonic stages are impacted. We addressed this by exposing developing coho salmon embryos starting at the eyed stage to three concentrations of 6PPD-quinone twice weekly until hatch. Impacts on survival and growth were assessed. Further, whole-transcriptome sequencing was performed on recently hatched alevin to address the potential mechanism of 6PPD-quinone-induced toxicity. Acute mortality was not elicited in developing coho salmon embryos at environmentally measured concentrations lethal to juveniles and adults, however, growth was inhibited. Immediately after hatching, coho salmon were sensitive to 6PPD-quinone mortality, implicating a large window of juvenile vulnerability prior to smoltification. Molecularly, 6PPD-quinone induced dose-dependent effects that implicated broad dysregulation of genomic pathways governing cell-cell contacts and endothelial permeability. These pathways are consistent with previous observations of macromolecule accumulation in the brains of coho salmon exposed to 6PPD-quinone, implicating blood-brain barrier disruption as a potential pathway for toxicity. Overall, our data suggests that developing coho salmon exposed to 6PPD-quinone are at risk for adverse health events upon hatching while indicating potential mechanism(s) of action for this highly toxic chemical.

Loss of cystatin C regulates permeability and inflammatory pathways in retina.

Cystatin C has been linked to inflammation in other diseases, such as epilepsy and Alzheimer's disease. These studies were designed to investigate whether Cystatin C regulates retinal inflammation and permeability. To address this question, we used Cystatin C knockout mice in a retinal ischemia/reperfusion model to determine whether Cystatin C regulated retinal damage, as well as inflammatory mediators and retinal permeability. To support the mouse work, we also used primary retinal endothelial cells cultured in normal and high glucose. Ischemia/reperfusion in Cystatin C knockout mice caused increased formation of degenerate capillaries. Loss of Cystatin C increased fluorescein leakage in the retina, which was accompanied by reduced levels of zonula occludin 1 (ZO-1) and occludin proteins. When REC were grown in high glucose, recombinant Cystatin C decreased retinal permeability, while Cystatin C siRNA increased dextran flux compared to high glucose alone. Recombinant Cystatin C decreased levels of interleukin-1-beta (IL-1β) and high mobility group box 1 (HMGB1) levels. In conclusion, loss of Cystatin C increased vascular damage in response to ischemia/reperfusion. Cystatin C regulated permeability and inflammatory mediators in the retina in response to stressors. Cystatin C offers a new target for retinal disease therapeutic development.

#5983 PULMONARY INVOLVEMENT IN AUTOSOMAL DOMINANT POLYCYSTIC KIDNEY DISEASE

Abstract Background and Aims Autosomal dominant policystic kidney disease (ADPKD) is the most common genetic kidney disease. It is caused by mutations in PKD1 and PKD2 genes, which encode for polycystin-1 (PC-1) and polycystin-2 (PC-2), two proteins localized in the primary cilia which regulate calcium permeability and cellular signaling pathways. The major phenotype of the disease is the formation of multiple cysts in the kidneys but in many cases it also involves other organs like heart, brain and lungs. The latters are not yet well studied; some papers report a higher prevalence of bronchiectasis in ADPKD patients compared to the general population; morover, one work describes the absence of PC-1 in motile cilia of ADPKD pts compared to controls, who actually do express the protein. Based on available literature, we hypothesized that the PC-1 and PC-2 could have a role also in motile cilia. Exaled nasal nitric oxide (nNO) is an indirect marker of cilia dysfunction, standardized for the screening of primary ciliary dyskinesia, a motile ciliopathy, in which very low levels of nNO are found because of the entrapment of NO in the abundant stagnant mucus. Method We recruited 27 patients with ADPKD and 25 randomly selected controls. We compared nNO measurements between the two groups, stratifying for truncated mutations and eGFR. After stratification according to ADPKD genetic mutation, we analyzed separately each of the two subgroups with the control group. Results nNO levels were no different in ADPKD patients compared with healthy controls (mean ± standard deviation: 850±240 vs 923±290; P = .3). However in sub-group analysis, lower nNO measurements were found in patients with truncated mutation (769±164) compared to the control group (924±290, P = .05). No association was observed between renal functions expressed as eGFR and nNO levels. Discussion Overall nNO levels did not differ in ADPKD individuals compared to controls, although lower nNO measurements were observed in ADPKD patients exhibiting a truncated mutation. Conclusion Even at the edge of the statistical significance (P = .05), given it's confirmed in a wider population, this finding could signify that pts who carry a more aggressive genotype (PKD-1 truncated mutation) may not express polycystins in motile cilia; this aspect is in line with the verified knowledge that this kind of mutation ends up in the total absence of the protein. On the other hand, pts with a missense mutation may still express the protein in motile cilia, therefore without any functional impairment.

Constructing high-performance GO membrane with pore-adjustable polymer nanoparticles

Desalination of textile wastewater is an effective measure to reduce environmental pollution and realize resource reuse. Graphene oxide (GO) membrane is regarded as one of the first choices for textile wastewater desalination due to its chemical resistance, strong mechanical properties, and adjustable interlayer channels. Here, we propose a polyaniline (PANI) particle incorporation strategy and use the dedoping effect of polyaniline to provide an additional permeation pathway through one-step alkali treatment to accelerate water molecule transport. Polyaniline (PANI) doped with polystyrene sulfonic acid (PSS) nanoparticles were synthesized and incorporated into GO membranes, followed by crosslinking of glutaraldehyde (GA) for stability and alkali treatment for more porosity generation. The as-prepared BGO/PANI-PSS membrane with 30% PANI-PSS addition displayed a flux of 70.4 LMH/bar, 99.3%, and 4.8% rejection for Congo red and NaCl, respectively, exhibiting 5.9 times higher permeability than that of GO membrane with similar dye rejection. This work provides a facile strategy for designing GO composite membranes for dye/salt separation.

IL-22-Activated MUC13 Impacts on Colonic Barrier Function through JAK1/STAT3, SNAI1/ZEB1 and ROCK2/MAPK Signaling.

Overexpression of the transmembrane mucin MUC13, as seen in inflammatory bowel diseases (IBD), could potentially impact barrier function. This study aimed to explore how inflammation-induced MUC13 disrupts epithelial barrier integrity by affecting junctional protein expression in IBD, thereby also considering the involvement of MUC1. RNA sequencing and permeability assays were performed using LS513 cells transfected with MUC1 and MUC13 siRNA and subsequently stimulated with IL-22. In vivo intestinal permeability and MUC13-related signaling pathways affecting barrier function were investigated in acute and chronic DSS-induced colitis wildtype and Muc13-/- mice. Finally, the expression of MUC13, its regulators and other barrier mediators were studied in IBD and control patients. Mucin knockdown in intestinal epithelial cells affected gene expression of several barrier mediators in the presence/absence of inflammation. IL-22-induced MUC13 expression impacted barrier function by modulating the JAK1/STAT3, SNAI1/ZEB1 and ROCK2/MAPK signaling pathways, with a cooperating role for MUC1. In response to DSS, MUC13 was protective during the acute phase whereas it caused more harm upon chronic colitis. The pathways accounting for the MUC13-mediated barrier dysfunction were also altered upon inflammation in IBD patients. These novel findings indicate an active role for aberrant MUC13 signaling inducing intestinal barrier dysfunction upon inflammation with MUC1 as collaborating partner.

Structure and mechanism of oxalate transporter OxlT in an oxalate-degrading bacterium in the gut microbiota

An oxalate-degrading bacterium in the gut microbiota absorbs food-derived oxalate to use this as a carbon and energy source, thereby reducing the risk of kidney stone formation in host animals. The bacterial oxalate transporter OxlT selectively uptakes oxalate from the gut to bacterial cells with a strict discrimination from other nutrient carboxylates. Here, we present crystal structures of oxalate-bound and ligand-free OxlT in two distinct conformations, occluded and outward-facing states. The ligand-binding pocket contains basic residues that form salt bridges with oxalate while preventing the conformational switch to the occluded state without an acidic substrate. The occluded pocket can accommodate oxalate but not larger dicarboxylates, such as metabolic intermediates. The permeation pathways from the pocket are completely blocked by extensive interdomain interactions, which can be opened solely by a flip of a single side chain neighbouring the substrate. This study shows the structural basis underlying metabolic interactions enabling favourable symbiosis.

Ion permeation pathway within the internal pore of P2X receptor channels.

P2X receptor channels are trimeric ATP-activated ion channels expressed in neuronal and non-neuronal cells that are attractive therapeutic targets for human disorders. Seven subtypes of P2X receptor channels have been identified in mammals that can form both homomeric and heteromeric channels. P2X1-4 and P2X7 receptor channels are cation-selective, whereas P2X5 has been reported to have both cation and anion permeability. P2X receptor channel structures reveal that each subunit is comprised of two transmembrane helices, with both N-and C-termini on the intracellular side of the membrane and a large extracellular domain that contains the ATP binding sites at subunit interfaces. Recent structures of ATP-bound P2X receptors with the activation gate open reveal the unanticipated presence of a cytoplasmic cap over the central ion permeation pathway, leaving lateral fenestrations that may be largely buried within the membrane as potential pathways for ions to permeate the intracellular end of the pore. In the present study, we identify a critical residue within the intracellular lateral fenestrations that is readily accessible to thiol-reactive compounds from both sides of the membrane and where substitutions influence the relative permeability of the channel to cations and anions. Taken together, our results demonstrate that ions can enter or exit the internal pore through lateral fenestrations that play a critical role in determining the ion selectivity of P2X receptor channels.

In Silico Prediction of Stratum Corneum Partition Coefficients via COSMOmic and Molecular Dynamics Simulations.

Stratum corneum (SC) is the main barrier of human skin where the inter-corneocytes lipids provide the main pathway for transdermal permeation of functional actives of skin care and health. Molecular dynamics (MD) has been increasingly used to simulate the SC lipid bilayer structure so that the barrier property and its affecting factors can be elucidated. Among reported MD simulation studies, solute partition in the SC lipids, an important parameter affecting SC permeability, has received limited attention. In this work, we combine MD simulation with COSMOmic to predict the partition coefficients of dermatologically relevant solutes in SC lipid bilayer. Firstly, we run MD simulations to obtain equilibrated SC lipid bilayers with different lipid types, compositions, and structures. Then, the simulated SC lipid bilayer structures are fed to COSMOmic to calculate the partition coefficients of the solutes. The results show that lipid types and bilayer geometries play a minor role in the predicted partition coefficients. For the more lipophilic solutes, the predicted results of solute partition in SC lipid bilayers agree well with reported experimental values of solute partition in extracted SC lipids. For the more hydrophilic molecules, there is a systematical underprediction. Nevertheless, the MD/COSMOmic approach correctly reproduces the phenomenological correlation between the SC lipid/water partition coefficients and the octanol/water partition coefficients. Overall, the results show that the MD/COSMOmic approach is a fast and valid method for predicting solute partitioning into SC lipids and hence supporting the assessment of percutaneous absorption of skin care ingredients, dermatological drugs as well as environmental pollutants.

Mechanism underlying delayed rectifying in human voltage-mediated activation Eag2 channel

The transmembrane voltage gradient is a general physico-chemical cue that regulates diverse biological function through voltage-gated ion channels. How voltage sensing mediates ion flows remains unknown at the molecular level. Here, we report six conformations of the human Eag2 (hEag2) ranging from closed, pre-open, open, and pore dilation but non-conducting states captured by cryo-electron microscopy (cryo-EM). These multiple states illuminate dynamics of the selectivity filter and ion permeation pathway with delayed rectifier properties and Cole-Moore effect at the atomic level. Mechanistically, a short S4-S5 linker is coupled with the constrict sites to mediate voltage transducing in a non-domain-swapped configuration, resulting transitions for constrict sites of F464 and Q472 from gating to open state stabilizing for voltage energy transduction. Meanwhile, an additional potassium ion occupied at positions S6 confers the delayed rectifier property and Cole-Moore effects. These results provide insight into voltage transducing and potassium current across membrane, and shed light on the long-sought Cole-Moore effects.

Preliminary Estimation of Geological Structure Based on Relocated Hypocenter of Microearthquake: Case Study at “X” Geothermal Field

Generally, analysis of geological structure in the geothermal field is carried out using remote sensing methods, geological mapping, and gravity analysis. These methods can provide the distribution of geological structure on the surface but cannot provide information on whether the structure is active or not. This study aims to utilize improved hypocenter location which can be used to delineate the distribution of active faults. This is useful for obtain a better interpretation of geological structures in geothermal areas. Hypocenter locations are determined by picking the arrival time of the P-wave and S-wave. This method sometimes leads to uncertainty of hypocenter location due to subjectivity of picking arrival time. The double-difference method is applied with additional input pairing events from waveform cross-correlation (WCC) to overcome the uncertainty of hypocenter location. The result shows 3 microearthquake clusters formed in the western, central, and eastern parts of the “X” Geothermal Field. The cluster formed in the western area shows that there are two orientations of conjugated hypocenter distribution with the orientation of NW-SE and NE-SW. These hypocenters reveal the presence of geological structures which provide permeability pathways for fluids rising in the western part of the geothermal field. Multiplet-clustering analysis in the middle cluster which coincides with the reservoir zone shows two different sub-clusters indicating the possibility of two different sources mechanism working in the area. By integrating all the analysis and hypocenter distribution, these methods provide a better interpretation of structure’s distribution in the “X” Geothermal Field.

Efficient large-scale mechanism-based computation of skin permeability

A drug’s skin permeability is a key quantity within dermatological risk assessment as it quantifies the maximal rate of dermal absorption, under steady state conditions, per unit concentration difference across the skin of a topically applied drug. Given descriptors of the permeant, the vehicle, and skin conditions, this paper adopts a systematic approach to efficiently calculate estimates of a topically applied chemical’s skin permeability based on mechanistic knowledge of permeability across the elements of a fine spatial discretization of the dermal strata. The permeability estimates are obtained by solving a system of linear equations constructed using an electrical resistor network analogy. Being mechanism based, these estimates can account for skin conditions, heterogenous dermal penetration pathways, and the chemical-dependence and spatial dependence of partitioning and diffusivity.The contribution of this work can be viewed as a mechanistic, numerical, extension of the Potts-Guy relation that augments an open-source dermal PBPK model. Moreover, rather than requiring model simulations of steady state conditions, the approach centers on a direct calculation of permeability based on the mechanistic descriptors of the permeation scenario. The calculation method may therefore be directly integrated into parameter identification, optimization, and sensitivity analysis algorithms. We demonstrate the validity of the method by comparing its permeability predictions with previously reported in silico estimates and in vitro measurements. We additionally illustrate the utility of the method towards the analysis of dermal PBPK models using a minimal example that relates overall skin permeability to the interaction between multiple permeation pathways.

Path sampling with memory reduction and replica exchange to reach long permeation timescales

Assessing kinetics in biological processes with molecular dynamics simulations remains a computational and conceptual challenge, given the large time and length scales involved. For kinetic transport of biochemical compounds or drug molecules, the permeability through the phospholipid membranes is a key kinetic property, but long timescales are hindering the accurate computation. Technological advances in high-performance computing therefore need to be accompanied by theoretical and methodological developments. In this contribution, the replica exchange transition interface sampling (RETIS) methodology is shown to give perspective toward observing longer permeation pathways. It is first reviewed how RETIS, a path-sampling methodology that gives in principle exact kinetics, can be used to compute membrane permeability. Next, recent and current developments in three RETIS aspects are discussed: several new Monte Carlo moves in the path-sampling algorithm, memory reduction by reducing pathlengths, and exploitation of parallel computing with CPU-imbalanced replicas. Finally, the memory reduction presenting a new replica exchange implementation, coined REPPTIS, is showcased with a permeant needing to pass a membrane with two permeation channels, either representing an entropic or energetic barrier. The REPPTIS results showed clearly that inclusion of some memory and enhancing ergodic sampling via replica exchange moves are both necessary to obtain correct permeability estimates. In an additional example, ibuprofen permeation through a dipalmitoylphosphatidylcholine membrane was modeled. REPPTIS succeeded in estimating the permeability of this amphiphilic drug molecule with metastable states along the permeation pathway. In conclusion, the presented methodological advances allow for deeper insight into membrane biophysics even if the pathways are slow, as RETIS and REPPTIS push the permeability calculations to longer timescales.