Higher-order structure of DNA determines its positioning in cell-size droplets under crowded conditions

Background It is becoming clearer that living cells use water/water (w/w) phase separation to form membraneless organelles that exhibit various important biological functions. Currently, it is believed that the specific localization of biomacromolecules, including DNA, RNA and proteins in w/w microdroplets is closely related to their bio-activity. Despite the importance of this possible role of micro segregation, our understanding of the underlying physico-chemical mechanism is still unrefined. Further research to unveil the underlying mechanism of the localization of macromolecules in relation to their steric conformation in w/w microdroplets is needed. Principal findings Single-DNA observation of genome-size DNA (T4 GT7 bacteriophage DNA; 166kbp) by fluorescence microscopy revealed that DNAs are spontaneously incorporated into w/w microdroplets generated in a binary aqueous polymer solution with polyethylene glycol (PEG) and dextran (DEX). Interestingly, DNAs with elongated coil and shrunken conformations exhibit Brownian fluctuation inside the droplet. On the other hand, tightly packed compact globules, as well as assemblies of multiple condensed DNAs, tend to be located near the interface in the droplet. Conclusion and significance The specific localization of DNA molecules depending on their higher-order structure occurs in w/w microdroplet phase-separation solution under a binary aqueous polymer solution. Such an aqueous solution with polymers mimics the crowded conditions in living cells, where aqueous macromolecules exist at a level of 30–40 weight %. The specific positioning of DNA depending on its higher-order structure in w/w microdroplets is expected to provide novel insights into the mechanism and function of membraneless organelles and micro-segregated particles in living cells.

Field Implementation of In-Depth Conformance Gel Treatment Prior to Starting an ASP Flooding Pilot

Mature carbonate reservoirs under waterflood in Kuwait suffer from relatively low oil recovery due to poor volumetric sweep efficiency, both areal, vertically, and microscopically. An Alkaline-Surfactant-Polymer (ASP) pilot using a regular five-spot well pattern is in progress targeting the Sabriyah Mauddud (SAMA) reservoir in pursuit of reserves growth and production sustainability. SAMA suffers from reservoir heterogeneities mainly associated with permeability contrast which may be improved with a conformance treatment to de-risk pre-mature breakthrough of water and chemical EOR agents in preparation for subsequent ASP injection and to improve reservoir contact by the injected fluids. Each of the four injection wells in the SAMA ASP pilot was treated with a chemical conformance improvement formulation. A high viscosity polymer solution (HVPS) of 200 cP was injected prior to a gelant formulation consisting of P300 polymer and X1050 crosslinker. After a shut-in period, wells were then returned to water injection. Injection of high viscosity polymer solution (HVPS) at the four injection wells showed no increase in injection pressure and occurred higher than expected injection rates. Early breakthrough of polymer was observed at SA-0561 production well from three of the four injection wells. No appreciable change in oil cut was observed. HVPS did not improve volumetric sweep efficiency based on the injection and production data. Gel treatment to improve the volumetric conformance of the four injection wells resulted in all the injection wells showing increased of injection pressure from approximately 3000 psi to 3600 psi while injecting at a constant rate of approximately 2,000 bb/day/well. Injection profiles from each of the injection well ILTs showed increased injection into lower-capacity zones and decreased injection into high-capacity zones. Inter-well tracer testing showed delayed tracer breakthrough at the center SA-0561 production well from each of the four injection wells after gel placement. SA-0561 produced average daily produced temperature increased from approximately 40°C to over 50°C. SA-0561 oil cuts increased up to almost 12% from negligible oil sheen prior to gel treatments. Gel treatment improved volumetric sweep efficiency in the SAMA SAP pilot area.

Polymer in-Situ Rheology in Carbonate Reservoirs

A large, untapped EOR potential may be extracted by extending polymer flooding to carbonate reservoirs. However, several challenges are encountered in carbonates due to generally more heterogeneous rock and lower permeability. In addition, high salinity may lead to high polymer retention. Here we show how in-situ viscosity varies with permeability and heterogeneity in carbonate rock from analysis of core flood results and combined with review of data available in literature. In-situ rheology experiments were performed on both carbonate outcrop and reservoir cores with a range in permeabilities. The polymer used was a high ATBS content polyacrylamide (SAV10) which tolerates high temperature and high salinity. Some cores were aged with crude oil to generate non-water-wet, reservoir representative wettability conditions. These results are compared to a compilation of literature data on in-situ rheology for predominantly synthetic polymers in various carbonate rock. A systematic approach was utilized to derive correlations for resistance factor, permeability reduction and in-situ viscosity as a function of rock and polymer properties. Polymer flooding is applied to improve sweep efficiency that may occur due to reservoir heterogeneities (large permeability contrasts, anisotropy, thief zones) or adverse mobility ratio (high mobility contrast oil-brine). In flooding design, the viscosity of the polymer solution in the reservoir, the in-situ viscosity, is an essential parameter as this is tuned to correct the mobility difference and to improve sweep. The viscosity is estimated from rheometer/viscometer measurements or, better, measured in laboratory core flood experiments. However, upscaling core flood experiments to field is challenging. Core flood experiments measure differential pressure, which is the basis for the resistance factor, RF, that describes the increased resistance to flow for polymer relative to brine. However, the pressure is also influenced by several other factors such as the permeability reduction caused by adsorption and retention of polymer in the rock, the tortuosity of the rock and the viscosity of the flowing polymer solution. Deduction of in-situ viscosity is straight forward using Darcy's law but the capillary bundle model that is the basis for applying this law fails for non-Newtonian fluids. This is particularly evident in carbonate rock. Interpretation of in-situ rheology experiments can therefore be misleading if the wrong assumptions are made. Polymer flooding in carbonate reservoirs has a large potential for increased utilization of petroleum reserves at a reduced CO2 footprint. In this paper we apply learnings from an extensive core flood program for a polymer flood project in the UAE and combine this with reported literature data to generate a basis for interpretation of in-situ rheology experiments in carbonates. Most importantly, we suggest a methodology to screen experiments and select data to be used as basis for modelling polymer flooding. This improves polymer flood design, optimize the polymer consumption, and thereby improve project economy and energy efficiency.

Expanding Polymer Injectivity Tests on a Second Giant Carbonate UAE Oil Reservoir at High Salinity & High Temperature Conditions.

Over the last few years, ADNOC has systematically investigated a new polymer-based EOR scheme to improve sweep efficiency in high temperature and high salinity (HTHS) carbonate reservoirs in Abu Dhabi (Masalmeh et al., 2014). Consequently, ADNOC has developed a thorough de-risking program for the new EOR concept in these carbonate reservoirs. The de-risking program includes extensive laboratory experimental studies and field injectivity tests to ensure that the selected polymer can be propagated in the target reservoirs. A new polymer with high 2-acrylamido-tertiary-butyl sulfonic acid (ATBS) content was identified, based on extensive laboratory studies (Masalmeh, et al., 2019, Dupuis, et al., 2017, Jouenne 2020), and an initial polymer injectivity test (PIT) was conducted in 2019 at 250°F and salinity >200,000 ppm, with low H2S content (Rachapudi, et al., 2020, Leon and Masalmeh, 2021). The next step for ADNOC was to extend polymer application to harsher field conditions, including higher H2S content. Accordingly, a PIT was designed in preparation for a multi-well pilot This paper presents ADNOC's follow-up PIT, which expands the envelope of polymer flooding to dissolve H2S concentrations of 20 - 40 ppm to confirm injectivity at representative field conditions and in situ polymer performance. The PIT was executed over five months, from February 2021 to July 2021, followed by a chase water flood that will run until December 2021. A total of 108,392 barrels of polymer solution were successfully injected during the PIT. The extensive dataset acquired was used to assess injectivity and in-depth mobility reduction associated with the new polymer. Preliminary results from the PIT suggest that all key performance indicators have been achieved, with a predictable viscosity yield and good injectivity at target rates, consistent with the laboratory data. The use of a down-hole shut-in tool (DHSIT) to acquire pressure fall-off (PFO) data clarified the near-wellbore behaviour of the polymer and allowed optimisation of the PIT programme. This paper assesses the importance of water quality on polymer solution preparation and injection performance and reviews operational data acquired during the testing period. Polymer properties determined during the PIT will be used to optimise field and sector models and will facilitate the evaluation of polymer EOR in other giant, heterogeneous carbonate reservoirs, leading to improved recovery in ADNOC and Middle East reservoirs.

Research on the Influence of Sodium Ion on Mechanism of Polymer Solution Viscosity Loss

The researches on the influence of sodium ion on mechanism of polymer solution viscosity loss were conducted. Scanning electron microscopy was used to analyze the polymer microstructure. Molecular dynamics simulation was employed to reveal the influence of sodium ion on the polymer molecular configuration. The results shown: the polymer viscosity loss was more than 70% when the concentration of sodium ion was above 4000 mg/L. The results of microstructure and molecular conformation analysis indicated that the main reason of viscosity loss was the electrostatic attraction between sodium ion and negatively charged groups of polymer molecule chains, which cause compression of polymer molecular chain. The coil and shrinkage of polymer molecular chain led to the breakage of the spatial network structure of macromolecules.

Emergence of uniform linearly-arranged micro-droplets entrapping DNA and living cells through water/water phase-separation

Living cells maintain their lives through self-organization in an environment crowded with a rich variety of biological species. Recently, it was found that micro-droplets containing biomacromolecules, which vary widely in size, are generated accompanied by water/water phase-separation by simple mechanical mixing of an aqueous solution with binary polymers. Here, we report that cell-sized droplets of nearly the same size are generated as a linear array within a glass capillary upon the introduction of a binary polymer solution of polyethylene glycol (PEG) and dextran (DEX). Interestingly, when DNA molecules are added to the polymer solution, stable droplets entrapping DNA molecules are obtained. Similarly, living cells are entrapped spontaneously for the linearly-arranged cell-sized droplets. This simple method for generating micro-droplets entrapping DNA and also living cells is expected to stimulate further study on the self-construction of protocells and micro organoids.

Fluctuation In the Phase Transition Temperature of Poly (NIPAAm-co-HEMA-co-DMAMVA)-Post-guanine Affected by Hydrophilic/hydrophobic Interaction: Fabrication and Characterizations

The phase separation and transition temperature of poly (N-isopropylacrylamide) have been developed by the terpolymerization with new pH-responsive monomer and highly hydrophilic 2-Hydroxyethyl methacrylate. The new monomer based on vanillin is called 2-((dimethylamino)methyl)-4-formyl-6-methoxyphenyl acrylate (DMAMVA), and is investigated by chemical methods (1H, 13C NMR, FTIR, and mass spectroscopy). Terpolymers of dual-responsive thermo-pH with functional groups were fabricated via free radical polymerization of N-isopropylacrylamide (NIPAAm), 10 mol% 2-Hydroxyethyl methacrylate (HEMA), and 5, 10, and 20 mol% DMAMVA. A selected terpolymer was used for post-polymerization with guanine via click reaction and the formation of an imine between the aldehyde group of DMAMVA and the amine group of guanine. All terpolymer and post-terpolymer are chemically evaluated. The physical properties have been implemented by GPC (molecular weight and dispersity), DSC (glass transition temperature Tg), TGA (steps of degradation), and SEM (morphological features). The fluctuations in phase transition temperature Tc or the lower critical solution temperature LCST of the polymer solution in different pH solutions have been performed by two methods, first, the turbidity test by UV-Vis-spectroscopy, second, by micro-DSC for aqueous polymer solution. This work will be extended for more applications in bio-separation technology.