The investigation of the average diameter of the SiO2 nanoparticles effect on the oil displacing efficiency from the pore in the rock formation using nanosuspension as a displacing agent

The numerical investigation of the nanofluid flow, which displaced the oil, in a microchannel was carried out. The effect of the average diameter of the SiO2 nanoparticles on the oil displacing efficiency by nanofluids for different sizes of microchannel at various Reynolds numbers was studied. A T-shaped microchannel with a vertical channel, called a pore channel, which imitated the pore in the rock formation was considered as a computational domain. The main flow channel width and height were 200 µm. The width and height of the pore channel were varied in the range from 100 µm to 800 µm. The Reynolds number varied from 0.1 to 100. The oil recovery coefficient, which is defined as the ratio of the displacing volume of oil from the pore to the volume of the pore was considered as the main studied characteristic. The nanofluid is considered a single-phase fluid with experimentally obtained properties. The mass concentration of SiO2 nanoparticles was 0.5%. The average diameters of nanoparticles were 5 nm, 18 nm, and 50 nm. It was found, that the oil recovery coefficient increased with a decrease in the average diameter of nanoparticles. It was obtained that the nanofluid can enhance the oil recovery several times compared to pure water.

Filtering pore chanels distribution density in Western Siberia

It is well known that information on filter channels distribution density can be obtained based on the data of core samples capillary studies in laboratory conditions. The curve of the fractional participation of pore channels in filtration, as a rule, is obtained by numerical processing of the capillary studies results. In this study, using a generalized mathematical model of capillary curves, an analytical solution is obtained for filtration channels distribution density by size in the conditions of Western Siberia reservoirs. The work shows that the main share in the filtration is taken by pore channels, the sizes of which are close to the maximum value. The density function of the filtering channels is mainly determined by the maximum radius and heterogeneity of the pore channel size distribution. Keywords: capillary pressure curve; generalized model; distribution density; filtering channels.

Vicia faba TPC1, a genetically encoded variant of the vacuole Two Pore Channel 1, is hyperexcitable

To fire action-potential-like electrical signals, the vacuole membrane requires the depolarization-activated two-pore channel TPC1, also called Slowly activating Vacuolar SV channel. The TPC1/SV channel, encoded by the TPC1 gene, functions as a voltage-dependent and Ca2+-regulated potassium channel. TPC1 currents are activated by a rise in cytoplasmic Ca2+ but blocked by luminal Ca2+. In search for species-dependent functional TPC1 channel variants, we studied polymorphic amino acids contributing to luminal Ca2+ sensitivity. We found that the acidic residues Glu457, Glu605 and Asp606 of the Ca2+-sensitive Arabidopsis AtTPC1 channel were neutralized by either asparagine or alanine in Vicia faba and many other Fabaceae as well. When expressed in the Arabidopsis loss-of-AtTPC1 function background, the wild type VfTPC1 was hypersensitive to vacuole depolarization and insensitive to blocking luminal Ca2+. When AtTPC1 was mutated for the three VfTPC1-homologous polymorphic site residues, the Arabidopsis At-VfTPC1 channel mutant gained VfTPC1-like voltage and luminal Ca2+ insensitivity that together made vacuoles hyperexcitable. These findings indicate that natural TPC1 channel variants in plant families exist which differ in vacuole excitability and very likely respond to changes in environmental settings of their ecological niche.

Functional Analyses of the Two Distinctive Types of Two-Pore Channels (TPCs) and the Slow Vacuolar Channel in Marchantia polymorpha

The two-pore channel (TPC) family is widely conserved in eukaryotes. Many vascular plants, including Arabidopsis and rice, possess a single TPC gene which functions as a slow vacuolar (SV) channel—voltage-dependent cation-permeable channel located in the vacuolar membrane (tonoplast). On the other hand, a liverwort Marchantia polymorpha genome encodes three TPC homologs: MpTPC1 is similar to TPCs in vascular plants (type 1 TPC), while MpTPC2 and MpTPC3 are classified into a distinctive group (type 2 TPC). Phylogenetic analysis suggested that the type 2 TPC emerged before the land colonization in plant evolution and was lost in vascular plants and hornworts. All of the three MpTPCs were shown to be localized at the tonoplast. We generated knockout mutants of tpc1, tpc2, tpc3, and tpc2 tpc3 double mutant by CRISPR/Cas9 genome editing and performed patch-clamp analyses of isolated vacuoles. The SV channel activity was abolished in the Mptpc1 loss-of-function mutant (Mptpc1-1KO), while Mptpc2-1KO, Mptpc3-1KO, and Mptpc2-2/tpc3-2KO double mutant exhibited similar activity to the wild type, indicating that MpTPC1 (type 1) is solely responsible for the SV channel activity. Activators of mammalian TPC channels, PI(3,5)P2, and, NAADP, did not affect the ion channel activity of any MpTPCs. These results indicate that the type 1 TPCs, which are well conserved in all land plant species, encode the SV channel, while the type 2 TPCs likely encode other tonoplast cation channel(s) distinct from the SV channel and animal TPC channels.

Effect of Viscosity Action and Capillarity on Pore-Scale Oil–Water Flowing Behaviors in a Low-Permeability Sandstone Waterflood

Water flooding technology is an important measure to enhance oil recovery in oilfields. Understanding the pore-scale flow mechanism in the water flooding process is of great significance for the optimization of water flooding development schemes. Viscous action and capillarity are crucial factors in the determination of the oil recovery rate of water flooding. In this paper, a direct numerical simulation (DNS) method based on a Navier–Stokes equation and a volume of fluid (VOF) method is employed to investigate the dynamic behavior of the oil–water flow in the pore structure of a low-permeability sandstone reservoir in depth, and the influencing mechanism of viscous action and capillarity on the oil–water flow is explored. The results show that the inhomogeneity variation of viscous action resulted from the viscosity difference of oil and water, and the complex pore-scale oil–water two-phase flow dynamic behaviors exhibited by capillarity play a decisive role in determining the spatial sweep region and the final oil recovery rate. The larger the viscosity ratio is, the stronger the dynamic inhomogeneity will be as the displacement process proceeds, and the greater the difference in distribution of the volumetric flow rate in different channels, which will lead to the formation of a growing viscous fingering phenomenon, thus lowering the oil recovery rate. Under the same viscosity ratio, the absolute viscosity of the oil and water will also have an essential impact on the oil recovery rate by adjusting the relative importance between viscous action and capillarity. Capillarity is the direct cause of the rapid change of the flow velocity, the flow path diversion, and the formation of residual oil in the pore space. Furthermore, influenced by the wettability of the channel and the pore structure’s characteristics, the pore-scale behaviors of capillary force—including the capillary barrier induced by the abrupt change of pore channel positions, the inhibiting effect of capillary imbibition on the flow of parallel channels, and the blockage effect induced by the newly formed oil–water interface—play a vital role in determining the pore-scale oil–water flow dynamics, and influence the final oil recovery rate of the water flooding.

COV-Drug Target interaction server for Covid-19 Drug Repurposing

The outbreak of the novel coronavirus disease COVID-19, caused by the SARS-CoV-2 virus has killed over 5 million people to date. So, there is an urgent requirement for new and effective medications that can treat the disease caused by SARS-CoV-2. To find new drugs, identification of drug targets is necessary (Chen et al., 2016). Number of research studies have identified therapeutic targets such as helicases, transmembrane serine protease 2, cathepsin L, cyclin G-associated kinase, adaptor associated kinase 1, two-pore channel, viral virulence factors, 3-chymotrypsin-like protease, suppression of excessive inflammatory response, inhibition of viral membrane, nucleocapsid, envelope, and accessory proteins, and inhibition of endocytosis. Here we present a web enabled tool which helps in ranking the COVID-19 drugs based upon underlying molecular targets. The users are allowed to give drugs in SMILE format and the tools will provide the list of relevant targets related to COVID-19.

Artificial Intelligence-Driven Algorithm for Drug Effect Prediction on Atrial Fibrillation: An in silico Population of Models Approach

Background: Antiarrhythmic drugs are the first-line treatment for atrial fibrillation (AF), but their effect is highly dependent on the characteristics of the patient. Moreover, anatomical variability, and specifically atrial size, have also a strong influence on AF recurrence.Objective: We performed a proof-of-concept study using artificial intelligence (AI) that enabled us to identify proarrhythmic profiles based on pattern identification from in silico simulations.Methods: A population of models consisting of 127 electrophysiological profiles with a variation of nine electrophysiological variables (GNa, INaK, GK1, GCaL, GKur, IKCa, [Na]ext, and [K]ext and diffusion) was simulated using the Koivumaki atrial model on square planes corresponding to a normal (16 cm2) and dilated (22.5 cm2) atrium. The simple pore channel equation was used for drug implementation including three drugs (isoproterenol, flecainide, and verapamil). We analyzed the effect of every ionic channel combination to evaluate arrhythmia induction. A Random Forest algorithm was trained using the population of models and AF inducibility as input and output, respectively. The algorithm was trained with 80% of the data (N = 832) and 20% of the data was used for testing with a k-fold cross-validation (k = 5).Results: We found two electrophysiological patterns derived from the AI algorithm that was associated with proarrhythmic behavior in most of the profiles, where GK1 was identified as the most important current for classifying the proarrhythmicity of a given profile. Additionally, we found different effects of the drugs depending on the electrophysiological profile and a higher tendency of the dilated tissue to fibrillate (Small tissue: 80 profiles vs Dilated tissue: 87 profiles).Conclusion: Artificial intelligence algorithms appear as a novel tool for electrophysiological pattern identification and analysis of the effect of antiarrhythmic drugs on a heterogeneous population of patients with AF.

The investigation of the efficiency of oil displacing from the pore in the rock formation depending on the width and height of the pore using nanosuspension as a displacing agent

The numerical investigation of the two-phase fluid flow in a microchannel was carried out. The effect of the pore width and height on the oil displacing efficiency by nanofluids for various Reynolds numbers was studied. The computational domain was a T-shaped microchannel with a horizontal main flow channel and a vertical channel that imitated the pore in the rock formation, called a pore channel. The main channel width and height were 200 µm, and the pore channel width and height were varied in the range from 100 µm to 800 µm. The Reynolds number was varied from 0.1 to 100. The main studied characteristic was the oil recovery coefficient, defined as the ratio of the volume of oil remaining in the pore to the volume of the pore. That characteristic, obtained for a case, when the nanofluid was used as a displacing agent, was compared to the similar one obtained for a case, when pure water was used as a displacing agent. A single-phase fluid with properties, determined experimentally, was considered the nanofluid. The mass concentrations of SiO2 nanoparticles were 0.25% and 0.5%. The average diameter of nanoparticles was equal to 5 nm. It was found, that the oil recovery coefficient increased with an increase in width of the pore channel and a decrease in its height. It was obtained that the nanofluid can enhance the oil recovery in several times as compared to pure water. It was also found that the main factor affecting the efficiency of oil recovery is the contact angle of wetting.

Voltage-gating and cytosolic Ca2+ activation mechanisms of Arabidopsis two-pore channel AtTPC1

Arabidopsis thaliana two-pore channel AtTPC1 is a voltage-gated, Ca2+-modulated, nonselective cation channel that is localized in the vacuolar membrane and responsible for generating slow vacuolar (SV) current. Under depolarizing membrane potential, cytosolic Ca2+ activates AtTPC1 by binding at the EF-hand domain, whereas luminal Ca2+ inhibits the channel by stabilizing the voltage-sensing domain II (VSDII) in the resting state. Here, we present 2.8 to 3.3 Å cryoelectron microscopy (cryo-EM) structures of AtTPC1 in two conformations, one in closed conformation with unbound EF-hand domain and resting VSDII and the other in a partially open conformation with Ca2+-bound EF-hand domain and activated VSDII. Structural comparison between the two different conformations allows us to elucidate the structural mechanisms of voltage gating, cytosolic Ca2+ activation, and their coupling in AtTPC1. This study also provides structural insight into the general voltage-gating mechanism among voltage-gated ion channels.

Topology and Contribution to the Pore Channel Lining of Plasma Membrane-Embedded Shigella flexneri Type 3 Secretion Translocase IpaB

Type 3 secretion systems are nanomachines employed by many bacteria, including Shigella , which deliver into human cells bacterial virulence proteins that alter cellular function in ways that promote infection. Delivery of Shigella virulence proteins occurs through a pore formed in human cell membranes by the IpaB and IpaC proteins.