Turbulent drag reduction and degradation of DNA

Drag Reduction in Turbulent Wall-Bounded Flows of Realistic Polymer Solutions

Suspensions of DNA macromolecules (0.8 wppm, 60 kbp), modeled as finitely extensible nonlinear elastic dumbbells coupled to the Newtonian fluid, show drag reduction up to 27% at friction Reynolds number 180, saturating at the previously unachieved Weissenberg number ≃10^{4}. At a large Weissenberg number, the drag reduction is entirely induced by the fully stretched polymers, as confirmed by the extensional viscosity field. The polymer extension is strongly non-Gaussian, in contrast to the assumptions of classical viscoelastic models.

Prediction and New Insight for the Drag Reduction of Turbulent Flow with Polymers and Its Degradation Mechanism

A physicochemical understanding of the mechanism of turbulent flow drag reduction with polymer and its degradation is of great interest from both science and industry perspectives. Although the correlation based on the Fourier series has been proposed to predict the drag reduction and its degradation, its physical meaning was not clear until now. This letter aims to clarify this issue. We develop a comprehensive model to predict the drag reduction and degradation of polymers in turbulent flow from a chemical thermodynamics and kinetics viewpoint. We demonstrate that the Fourier series employed to predict the drag reduction and its degradation is due to the viscoelastic property of drag-reducing polymer solution, and the phase angle in the model, in physical nature, represents the hysteresis of the polymer in turbulent flow. Besides, our new insight of drag reduction with flexible polymers can also explain why a maximum drag reduction in rotational flow appears before degradation happens.

Optimization of Application Conditions of Drag Reduction Agent in Product Oil Pipelines

Drag reduction performance was studied with a rotating disk instrument in the laboratory, and experiments show that there is an initial rapid growth stage and stability stage for drag reduction ratio change. The higher the rotational speed, the larger the initial drag reduction ratio is; the larger the concentration, the shorter the drag reduction stabilization time is. Under high concentration and high speed, the drag reduction onset time is short. Because of the shear degradation, the Reynolds number should be taken into account during use. Through a comparison of diesel properties after adding agents with national standard, it is confirmed that drag reduction agents could be used in this pipeline.

Effect of guar gum and salt concentrations on drag reduction and shear degradation properties of turbulent flow of water in a pipe

Concentrated solutions of guar gum in water (1000-3000ppm) with and without KCl salt (1000-4000ppm) were injected near the wall for a short period (2.5min) to investigate their effect on drag reduction in turbulent flow of water through a pipe (Re≈17000-45000). Relative to bulk solution, the concentrations of polymer and salt were 50-150ppm and 50-200ppm, respectively. A drag reduction of 71.45% was observed for 3000ppm of biopolymer without salt. Guar gum experienced mechanical degradation under high shear conditions and addition of KCl improved shear stability up to 47% (for Re≈45000). A polymer concentration of 3000ppm and salt concentration of 2000ppm in the injection fluid were found to be optimum for achieving the highest drag reduction with better shear stability. Results indicated that boundary layer injection shows better drag reduction ability than pre-mixed solutions.

Role of Bio-Based Polymers on Improving Turbulent Flow Characteristics: Materials and Application

The remarkable ability of polymeric additives to reduce the level of frictional drag significantly in turbulent flow, even under extremely low dilutions, is known as turbulent drag-reduction behavior. Several bio-polymers have been assessed as promising drag-reducing agents for the potential replacement of high molecular weight synthetic polymers to improve safety and ameliorate environmental concerns. This article reviews the recent advances regarding the impact of several bio-polymer additives on turbulent drag reduction in either pipe or rotating disk flow systems, and their potential applications in the petroleum, biomedical, and agricultural industries.

Applications of Water-Soluble Polymers in Turbulent Drag Reduction

Water-soluble polymers with high molecular weights are known to decrease the frictional drag in turbulent flow very effectively at concentrations of tens or hundreds of ppm. This drag reduction efficiency of water-soluble polymers is well known to be closely associated with the flow conditions and rheological, physical, and/or chemical characteristics of the polymers added. Among the many promising polymers introduced in the past several decades, this review focuses on recent progress in the drag reduction capability of various water-soluble macromolecules in turbulent flow including both synthetic and natural polymers such as poly(ethylene oxide), poly(acrylic acid), polyacrylamide, poly(N-vinyl formamide), gums, and DNA. The polymeric species, experimental parameters, and numerical analysis of these water-soluble polymers in turbulent drag reduction are highlighted, along with several existing and potential applications. The proposed drag reduction mechanisms are also discussed based on recent experimental and numerical researches. This article will be helpful to the readers to understand better the complex behaviors of a turbulent flow with various water-soluble polymeric additives regarding experimental conditions, drag reduction mechanisms, and related applications.

Greater than X kb: a quantitative assessment of preservation conditions on genomic DNA quality, and a proposed standard for genome-quality DNA

Advances in biodiversity genomic sequencing will increasingly depend on the availability of DNA samples-and their quantifiable metadata-preserved in large institutional biorepositories that are discoverable to the scientific community. Improvements in sequencing technology constantly provide longer reads, such that longer fragment length, higher molecular weight, and overall "genome-quality" DNA (gDNA) will be desirable. Ideally, biorepositories should publish numerical scale measurements of DNA quality useful to the user community. However, the most widely used technique to evaluate DNA quality, the classic agarose gel, has yet to be quantified. Here we propose a simple and economical method using open source image analysis software to make gDNA gel images quantifiable, and propose percentage of gDNA "greater than X kb" as a standard of comparison, where X is a band from any widely used DNA ladder with desirably large band sizes. We employ two metadata standards ("DNA Threshold" and "Percent above Threshold") introduced as part of the Global Genome Biodiversity Network (GGBN) Darwin Core extension. We illustrate the method using the traditionally used HindIII ladder and the 9,416 base-pair (bp) band as a standard. We also present data, for two taxa, a vertebrate (fish) and an invertebrate (crab), on how gDNA quality varies with seven tissue preservation methods, time since death, preservation method (i.e. buffers vs. cold temperatures), and storage temperature of various buffers over time. Our results suggest that putting tissue into a buffer prior to freezing may be better than directly into ultra-cold conditions.

Greater than X kb: a quantitative assessment of preservation conditions on genomic DNA quality, and a proposed standard for genome-quality DNA

Advances in biodiversity genomic sequencing will increasingly depend on the availability of DNA samples—and their quantifiable metadata—preserved in large institutional biorepositories that are discoverable to the scientific community. Improvements in sequencing technology constantly provide longer reads, such that longer fragment length, higher molecular weight, and overall “genome-quality” DNA (gDNA) will be desirable. Ideally, biorepositories should publish numerical scale measurements of DNA quality useful to the user community. However, the most widely used technique to evaluate DNA quality, the classic agarose gel, has yet to be quantified. Here we propose a simple and economical method using open source image analysis software to make gDNA gel images quantifiable, and propose percentage of gDNA “greater than X kb” as a standard of comparison, where X is a band from any widely used DNA ladder with desirably large band sizes. We employ two metadata standards (“DNA Threshold” and “Percent above Threshold”) introduced as part of the Global Genome Biodiversity Network (GGBN) Darwin Core extension. We illustrate the method using the traditionally used HindIII ladder and the 9,416 base-pair (bp) band as a standard. We also present data, for two taxa, a vertebrate (fish) and an invertebrate (crab), on how gDNA quality varies with seven tissue preservation methods, time since death, preservation method (i.e. buffers vs. cold temperatures), and storage temperature of various buffers over time. Our results suggest that putting tissue into a buffer prior to freezing may be better than directly into ultra-cold conditions.

Critical considerations for developing nucleic acid macromolecule based drug products

Protein expression therapy using nucleic acid macromolecules (NAMs) as a new paradigm in medicine has recently gained immense therapeutic potential. With the advancement of nonviral delivery it has been possible to target NAMs against cancer, immunodeficiency and infectious diseases. Owing to the complex and fragile structure of NAMs, however, development of a suitable, stable formulation for a reasonable product shelf-life and efficacious delivery is indeed challenging to achieve. This review provides a synopsis of challenges in the formulation and stability of DNA/m-RNA based medicines and probable mitigation strategies including a brief summary of delivery options to the target cells. Nucleic acid based drugs at various stages of ongoing clinical trials are compiled.

Mechanochemistry of Topological Complex Polymer Systems

Although existing since the concept of macromolecules, polymer mechanochemistry is a burgeoning field which attracts great scientific interest in its ability to bias conventional reaction pathways and its potential to fabricate mechanoresponsive materials. We review here the effect of topology on the mechanical degradation of polymer chains and the activation of mechanophores in polymer backbones. The chapter focuses on both experimental and theoretical work carried out in the past 70 years. After a general introduction (Sect. 1), where the concept, the history, and the application of polymer mechanochemistry are briefly described, flow fields to study polymer mechanochemistry are discussed (Sect. 2), results of mechanochemistry study are presented for linear polymers (Sect. 3), cyclic polymers (Sect. 4), graft polymers (Sect. 5), star-shaped polymers (Sect. 6), hyperbranched polymers and dendrimers (Sect. 7), and systems with dynamic topology (Sect. 8). Here we focus on (1) experimental results involving the topological effect on the coil-to-stretch transition and the fracture of the polymer chains, (2) the underlying mechanisms and the key factor that determines the mechanical stability of the macromolecules, (3) theoretical models that relate to the experimental observations, and (4) rational design of mechanophores in complex topology to achieve multiple activations according to the existing results observed in chain degradation.

In-plane rotation classification for coherent X-ray imaging of single biomolecules

We report a new classification scheme with computation complexity well within the capacity of a PC for coherent X-ray imaging of single biomolecules. In contrast to current methods, which are based on data from large scattering angles, we propose to classify the orientations of the biomolecule using data from small angle scattering, where the signals are relatively strong. Further we integrate data to form radial and azimuthal distributions of the scattering pattern to reduce the variance caused by the shot noise. Classification based on these two distributions are shown to successfully recognize not only the patterns from molecules of the same orientation but also those that differ by an in-plane rotation.

DNA hydrodynamic degradation controlled by Kolomogorov length scales in pipe flow

Strict US Food and Drug Administration regulations on contamination levels for DNA therapeutics acceptable for human use complicate the manufacturing process. This study aims to improve therapeutic production through the investigation of the molecular effects of hydrodynamic forces encountered during processing. Results suggest that the strain rate and residence time were not solely responsible for degradation within the system. Instead, turbulent flows at the entrance or developing flow regions dominate especially when the Kolmogorov length scale approaches the stretched molecular length scale. We specifically suggest this for linear genomic DNA and supercoiled plasmid DNA when the ratio of the molecular length to the Kolmogorov length scale must remain smaller than unity to minimize loss of the desired structure. These findings suggest that bioprocessing systems should design expansions and contractions to minimize recirculation and turbulent mixing zones, although, not always possible, careful attention should be paid to pipe surface roughness to ensure that turbulent eddies are not generated in low Reynolds number flows.

Direct observation of single flexible polymers using single stranded DNA()

Over the last 15 years, double stranded DNA (dsDNA) has been used as a model polymeric system for nearly all single polymer dynamics studies. However, dsDNA is a semiflexible polymer with markedly different molecular properties compared to flexible chains, including synthetic organic polymers. In this work, we report a new system for single polymer studies of flexible chains based on single stranded DNA (ssDNA). We developed a method to synthesize ssDNA for fluorescence microscopy based on rolling circle replication, which generates long strands (>65 kb) of ssDNA containing "designer" sequences, thereby preventing intramolecular base pair interactions. Polymers are synthesized to contain amine-modified bases randomly distributed along the backbone, which enables uniform labelling of polymer chains with a fluorescent dye to facilitate fluorescence microscopy and imaging. Using this approach, we synthesized ssDNA chains with long contour lengths (>30 μm) and relatively low dye loading ratios (~1 dye per 100 bases). In addition, we used epifluorescence microscopy to image single ssDNA polymer molecules stretching in flow in a microfluidic device. Overall, we anticipate that ssDNA will serve as a useful model system to probe the dynamics of polymeric materials at the molecular level.

Model systems for single molecule polymer dynamics

Double stranded DNA (dsDNA) has long served as a model system for single molecule polymer dynamics. However, dsDNA is a semiflexible polymer, and the structural rigidity of the DNA double helix gives rise to local molecular properties and chain dynamics that differ from flexible chains, including synthetic organic polymers. Recently, we developed single stranded DNA (ssDNA) as a new model system for single molecule studies of flexible polymer chains. In this work, we discuss model polymer systems in the context of "ideal" and "real" chain behavior considering thermal blobs, tension blobs, hydrodynamic drag and force-extension relations. In addition, we present monomer aspect ratio as a key parameter describing chain conformation and dynamics, and we derive dynamical scaling relations in terms of this molecular-level parameter. We show that asymmetric Kuhn segments can suppress monomer-monomer interactions, thereby altering global chain dynamics. Finally, we discuss ssDNA in the context of a new model system for single molecule polymer dynamics. Overall, we anticipate that future single polymer studies of flexible chains will reveal new insight into the dynamic behavior of "real" polymers, which will highlight the importance of molecular individualism and the prevalence of non-linear phenomena.

Sonochemical preparation of polymer nanocomposites

This review covers sonochemical fabrication of polymer nanocomposites. In addition to its application to the synthesis of various polymeric systems, due to its powerful efficiency, sonochemistry has been widely used not only as the assistant of dispersion for nanomaterials such as carbon nanotubes (CNT) and organophillic clay, but also as a special initiator to enhance polymerization for fabrication of polymer nanocomposites with CNT and metallic nanoparticles. Recent developments in the preparation of multi-walled carbon nanotube/polymer nanocomposites with polystyrene and PMMA, magnetic particle/CNT composites and polymer/clay nanocomposites along with their physical characteristics and potential engineering applications will be introduced. Physical characterizations include morphological, thermal, and rheological properties under either an applied electric or magnetic field.

Universal scaling for polymer chain scission in turbulence

We report that previous polymer chain scission experiments in strong flows, long analyzed according to accepted laminar flow scission theories, were in fact affected by turbulence. We reconcile existing anomalies between theory and experiment with the hypothesis that the local stress at the Kolmogorov scale generates the molecular tension leading to polymer covalent bond breakage. The hypothesis yields a universal scaling for polymer scission in turbulent flows. This surprising reassessment of over 40 years of experimental data simplifies the theoretical picture of polymer dynamics leading to scission and allows control of scission in commercial polymers and genomic DNA.

Properties of microfluidic turbulent mixing revealed by fluorescence lifetime imaging

We present a new method of measurement based on fluorescence lifetime imaging that reveals molecular-scale details of the mixing process in a continuous-flow turbulent microfluidic reactor. Our data provide a glimpse of the cascade to the minimal eddy size, followed by rapid diffusion involving the smallest eddies for final mixing.

Measurements and CFD Modeling of Drag-Reduction Effects

Summary

Computational-fluid-dynamics (CFD) modeling of drag reduction (DR) by polymer additives dissolved in hydrocarbon was carried out in pipe flows and in a rotating shear viscometer. A two-layer turbulence model was applied that described turbulence damping by the molecules of drag-reducing additives (DRAs) in the near-wall regions. The von Karman constant in the near-wall region was used as the model parameter. Extensive measurements of the DR effect for a rotating viscometer were performed at different Reynolds numbers, apparent molar masses, and DRA concentrations. The model with only one fit parameter was able to reproduce the experimental results in both pipe flows and the rotating viscometer. Experimental results were used in relating the model parameter to the relevant physical properties.

Introduction

The phenomenon of DR by low concentrations of long-chain polymers has been widely studied since Toms discovered the effect more than 50 years ago. In long oil pipelines, the pumping capacity can be significantly increased and pumping costs decreased by applying small amounts of DRA. A reduction of up to 70% in pressure loss in pipe flow has been achieved.

The DR effect has mostly been studied in pipe flow because it is the most important application.1–3 With pipe diameters larger than 40 mm, DR effects can also be measured accurately at high Reynolds numbers for high-viscosity (3·10–5 m2/s) oil. How- ever, pipeline construction may be rather expensive and the measurements time-consuming. The advantage of pipe-flow measurements is the large amount of general knowledge about turbulent flow in pipes.

In a spinning wheel consisting of a ring-shaped pipe and equipped with torque-measurement devices, pressure loss can be measured accurately with a small amount of fluid and without degradation losses. One possible drawback of this method is the short liquid-volume length that provides only partial DR effects.

Measurements in a rotating-viscometer-type apparatus have been carried out by, for example, Tong et al.,4 Cadot et al.,5 and Choi et al.6 It is easy to control the turbulent flow conditions in this type of experiment by varying the diameter of the rotating cylinder and the rotational speed.

We have carried out extensive measurements of DR effects in a viscometer equipped with a rotating cylinder in a baffled vessel. DR efficiency was measured with varying polymer molar masses and concentrations as well as rotational speed. The experimental setup is relatively easy to model with CFD.

Although a vast amount of research on DR has been done, the mechanism of the phenomenon is still poorly understood. Lumley,7 Thirumalai and Bhattacharjee,8 and Ryskin9 have presented possible explanations and theoretical analysis.

The commonly approved theory of DR is based on polymer molecules stretching outside the viscous sublayer because of shear forces and the subsequent enhanced damping of the transverse turbulent fluctuations close to the pipe wall.

The polymer chain elongates in an extensional flow if the strain rate exceeds a critical value. The DR effects are related to the polymers' elongation and relaxation properties and depend on polymer characteristics, such as apparent molar mass, molar mass distribution, and chain structure, as well as polymer concentration and shear stresses. Furthermore, fully stretched polymer chains can be degraded by high shear stresses, leading to losses in DR effects.

CFD modeling of the DR effect in turbulent flow is challenging. Attempts to model the DR effect have been made by Hassid and Poreh10 with a one-equation turbulence model, Poreh and Hassid 11 and Patterson et al.12 with a modified k-e model, and Sureshkumar et al.13 with direct numerical simulation.

Turbulence damping should be based on anisotropic turbulence models in which the damping effects are described, in each direction, by polymer DR properties. These models, however, are computationally expensive and, therefore, not suitable for engineering applications.

In this paper, the effect of drag reducers on turbulence has been modeled with an isotropic two-layer turbulence model that employs the one-equation model of Hassid and Poreh10 in the near-wall region and the standard k -e model in the fully turbulent regions. The results of measurements with the rotating viscometer were used to fit the model parameters, and the validity of the model was tested in pipe flows. The developed DR model was incorporated into the commercial CFD code STAR-CD14 for simulating local DR effects in arbitrary flow conditions.

Measurements of DR and Degradation Effects in Hydrocarbon Solvent

Description of Measuring Device.

In this study, the flow conditions necessary to elongate the polymer, the DR efficiency of polymers of various apparent molar masses, and their degradation kinetics have been measured with the rotating shear viscometer shown in Fig. 1.

The vessel is equipped with a rotating cylinder 99 mm in diameter and baffles around the vessel and near the bottom. The rotation speed of the cylinder can be adjusted within the 0- to 3,200-rpm range. The vessel stands on two bottom discs with an annular ball bearing in between, allowing frictionless movement of the upper disc. DR effects can be exactly measured under turbulent conditions by measuring the torque force of the bottom plate against the balance sensor.