Modelling DNA extension and fragmentation in contractive microfluidic devices: a Brownian dynamics and computational fluid dynamics approach

Wu, Shuyi; Li, Chuang; Zheng, Quanshui; Xu, Luping

doi:10.1039/c8sm00863a

Cited by 11 publications

(7 citation statements)

References 69 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In laminar flows, considerable progress has been made in the modelling and simulation of polymer scission (e.g. Cascales & de la Torre 1991, 1992Hsieh, Park & Larson 2005;Sim, Khomami & Sureshkumar 2007;Wu et al 2018). However, the knowledge gained from the study of laminar flows cannot be directly applied to turbulent flows because of the different properties of the strain rate, and consequently of the flow-induced polymer stretching, in the two types of flows.…”

Section: Introductionmentioning

confidence: 99%

Polymer scission in turbulent flows

et al. 2021

View full text Add to dashboard Cite

show abstract

Section: Introductionmentioning

confidence: 99%

Polymer scission in turbulent flows

et al. 2021

View full text Add to dashboard Cite

show abstract

“…Figure a shows that the fan-shaped flat liquid jets near nozzles broke up into small droplets, which is similar to the previous studies. − The size of the liquid sheet increased as the KGM concentration increased, indicating that adding KGM inhibited the breakup of liquid jets. The length of a liquid jet is shown in Figure b, and the average liquid jet length increased from 3.21 to 6.22 cm as the KGM concentration increased from 0 to 0.25% (Figure c,d).…”

Section: Resultsmentioning

confidence: 99%

“…The simulation method was reported in previous studies ,, (Supporting Information, Sections S11–S13). Briefly, the multi-scale simulation method combining computational fluid dynamics (CFD) and Brownian dynamics simulation (BD) was used to simulate the dynamic behavior of a single KGM molecule in flow fields.…”

Section: Materials and Methodsmentioning

confidence: 99%

“…However, for larger systems with a mesoscopic scale, these numerical methods were limited by huge time and economic costs. Recently, the computational fluid dynamics-Brown dynamic (CFD-BD) method was developed by using a bead-spring model to simulate polymer chains and using the Langevin equation to simulate the conformational evolution of macromolecules in flow fields. , This effective coarse-grained numerical method is appropriate for the dynamic simulation of long molecular chains (∼10 μm) over a long time (∼10 ms) during the spraying process. From the perspective of the energy model of macromolecules, the polymer can store energy during molecular stretching and release energy during molecular shrinking.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Adding Konjac Glucomannan for Enhancing the Whole Spraying Performance on Superhydrophobic and Hydrophilic Surfaces

Zhang

et al. 2023

ACS Appl. Mater. Interfaces

Self Cite

View full text Add to dashboard Cite

Spraying is a common way to coat solutions onto surfaces evenly. Improving spraying effectiveness can avoid wasting solutions and reduce pollution. In this study, a trace amount of natural polysaccharide, konjac glucomannan (KGM), was added into solutions to regulate the spraying performances including the breakup of liquid jets, size of produced droplets, and collision and spreading of droplets on both superhydrophobic and hydrophilic surfaces. The shear viscosity, extensive viscosity, and surface tension of the KGM solutions were tested. The results of spraying experiments showed that adding KGM inhibited the liquid jet from breaking into small droplets, avoided the breakage of droplets on superhydrophobic surfaces, and promoted the spreading of liquid films on hydrophilic surfaces. The numerical simulation showed the stretching of single macromolecules and quantified the energy stored in molecular chains in a shear-dominated flow field during the spreading of droplets on surfaces and an elongationaldominated flow field during the breakage of a liquid bridge. The storage and dissipation of energy during the stretching and relaxing of KMG macromolecules were important origins of the increase in the colloid viscosity and molecular mechanisms of the effect of the KGM additive on spraying performances. This study provided an understanding and a strategy for optimization and application of spraying additives.

show abstract

“…Furthermore, it was shown that pDNA was more susceptible to shear-induced degradation in low ionic strength solvents, such as ultrapure pDNA lysates, or mixed solvents with a fractional water content . Despite these important insights, the rotating shear disk device used to generate shear in those experiments did not accurately reproduce the numerous interfaces and spatially dependent shear fields encountered in an increasing number of pDNA formulations. − …”

Section: Introductionmentioning

confidence: 99%

Effects of Microfluidic Shear on the Plasmid DNA Structure: Implications for Polymeric Gene Delivery Vectors

et al. 2023

View full text Add to dashboard Cite

Microfluidic manufacturing of advanced gene delivery vectors necessitates consideration of the effects of microfluidic shear forces on the structural integrity of plasmid DNA (pDNA). In this paper, we expose pDNA to variable shear forces in a two-phase, gas–liquid microfluidic reactor and apply gel electrophoresis to analyze the products of on-chip shear-induced degradation. The effects of shear rate, solvent environment, pDNA size, and copolymer complexation on shear-induced degradation are investigated. We find that small naked pDNA (pUC18, 2.7 kb) exhibits shear rate-dependent shear degradation in the microfluidic channels in a mixed organic solvent (dioxane/water/acetic acid; 90/10/<0.1 w/w/w), with the extents of both supercoil isoform relaxation and complete fragmentation increasing as the maximum shear rates increase from 4 × 105 to 2 × 106 s–1. However, over the same range of shear rates, the same pDNA sample shows no evidence of microfluidic shear-induced degradation in a pure aqueous environment. Quiescent control experiments in the same mixed organic solvent prove that a combination of solvent and shear forces is involved in the observed shear-induced degradation. Furthermore, we show that shear degradation effects in mixed organic solvents can be significantly attenuated by complexation of pDNA with the block copolymer polycaprolactone-block-poly(2-vinylpyridine) prior to exposure to microfluidic shear. Finally, we demonstrate that medium (pDSK519, 8.1 kb) and large (pRK290, 20 kb) naked pDNA are more sensitive to shear-induced microfluidic degradation in the mixed organic solvent environment than small pDNA, with both plasmids showing complete fragmentation even at the lowest shear rate, although we found no evidence of shear-induced damage in water for the largest investigated naked pDNA even at the highest flow rate. The resulting understanding of the interplay of the solvent and shear effects during microfluidic processing should inform microfluidic manufacturing routes to new gene therapy formulations.

show abstract

Modelling DNA extension and fragmentation in contractive microfluidic devices: a Brownian dynamics and computational fluid dynamics approach

Abstract: We simulated the thorough process of DNA fragmentation in microfluidics. The conformation of DNA preconditioned by shear flow and the strain rate of elongational flow are two critical parameters for DNA fragmentation.

Cited by 11 publications

References 69 publications

Polymer scission in turbulent flows

Polymer scission in turbulent flows

Adding Konjac Glucomannan for Enhancing the Whole Spraying Performance on Superhydrophobic and Hydrophilic Surfaces

Effects of Microfluidic Shear on the Plasmid DNA Structure: Implications for Polymeric Gene Delivery Vectors

Contact Info

Product

Resources

About