Transport of DNA in hydrophobic microchannels: a dissipative particle dynamics simulation

Ranjith, S. Kumar; Patnaik, B.S.V.; Vedantam, Srikanth

doi:10.1039/c3sm53035c

Cited by 19 publications

(7 citation statements)

References 49 publications

(73 reference statements)

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“…Detailed validation of FDPD formulation is presented in this section. This method is shown to capture hydrodynamics of suspensions accurately . The FDPD model validation of RBC mechanics and dynamics is discussed below.…”

Section: Resultsmentioning

confidence: 99%

The dynamics of a healthy and infected red blood cell in flow through constricted channels: A DPD simulation

Hoque

Anand

Patnaik

2018

Numer Methods Biomed Eng

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Understanding the dynamics of red blood cell (RBC) motion under in silico conditions is central to the development of cost-effective diagnostic tools. Specifically, unraveling the relationship between the rheological properties and the nature of shape change in the RBC (healthy or infected) can be extremely useful. In case of malarial infection, RBC progressively loses its deformability and tends to occlude the microvessel. In the present study, detailed mesoscopic simulations are performed to investigate the deformation dynamics of an RBC in flow through a constricted channel. Specifically, the manifestation of viscous forces (through flow rates) on the passage and blockage characteristics of a healthy red blood cell (hRBC) vis-á-vis an infected red blood cell (iRBC) are investigated. A finite-sized dissipative particle dynamics framework is used to model plasma in conjunction with a discrete model for the RBC. Instantaneous wall boundary method was used to model no-slip wall boundary conditions with a good control on the near-wall density fluctuations and compressibility effects. To investigate the microvascular occlusion, the RBC motion through 2 types of constricted channels, viz, (1) a tapered microchannel and (2) a stenosed-type microchannel, were simulated. It was observed that the deformation of an infected cell was much less compared with a healthy cell, with an attendant increase in the passage time. Apart from the qualitative features, deformation indices were obtained. The deformation of hRBC was sudden, while the iRBC deformed slowly as it traversed through the constriction. For higher flow rates, both hRBC and iRBC were found to undergo severe deformation. Even under low flow rates, hRBC could easily traverse past the constricted channel. However, for sufficiently slow flow rates (eg, capillary flows), the microchannel was found to be completely blocked by the iRBC.

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Section: Resultsmentioning

confidence: 99%

The dynamics of a healthy and infected red blood cell in flow through constricted channels: A DPD simulation

Hoque

Anand

Patnaik

2018

Numer Methods Biomed Eng

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“…When DNA translocates through a nanometer‐size pore in the ionic solution with an external electric field, the types and concentration of ions and pore diameter will affect the DNA translocation time, as mentioned already in the work of Kowalczyk and co‐workers (Figure B) through all‐atom molecular dynamics simulations . Ranjith et al . were able to separate DNA chains of different lengths by designing the hydrophobicity of the walls.…”

Section: Transport Of Some Soft Matter Systemsmentioning

confidence: 90%

Section: Transport Of Some Soft Matter Systemsmentioning

confidence: 99%

Simulating Transport of Soft Matter in Micro/Nano Channel Flows with Dissipative Particle Dynamics

Yang

Zhu

et al. 2018

Advcd Theory and Sims

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The flow-induced transport of various soft matter systems through a fluidic channel has recently attracted great interest due to its significance ranging from the understanding of several chemical and biological processes to potential industrial and technical applications. Dynamic simulation and modeling can yield an insight into the detailed conformational, dynamical, and transport properties of soft matter systems, which is necessary to understand the transport properties of biological macromolecules in living organisms. As a mesoscopic particles-based simulation technique, dissipative particle dynamics (DPD) has quickly been adopted as a promising approach for simulating dynamic and rheological properties of simple and complex fluids as well as the events taking place inside the fluidic channels. Here, the DPD method widely used in predicting the channel flow containing various soft matter systems is reviewed. The general aspect and basic formulations of DPD are introduced, and different boundary conditions are presented for wall-bounded flows. In addition, the models based on DPD developed to simulate flow-induced transport through fluidic channels for some typical soft matter systems are discussed, including red blood cells, vesicles, polymers, and biomacromolecules. Finally, the future directions to signify the framework in enhancing the design of novel functional systems and beyond are discussed.

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“…Moreover, the numerical simulation of hydrodynamics plays a major role in the understanding of dynamics of fluid flow through stripped channels. The numerical prediction of the hydrodynamics of slipping and sticking surfaces was carried out by different numerical strategies such as molecular dynamics (Cottin-Bizonne et al, 2004), lattice Boltzmann method (Benzi et al, 2006;Harting et al, 2010), dissipative particle dynamics (Ranjith et al, 2014Ranjith, 2015), and computational fluid dynamics (Davies et al, 2006;Haase et al, 2013;Maynes and Crockett, 2014).…”

Section: Introductionmentioning

confidence: 99%

Numerical simulation of liquid–gas interface formation in long superhydrophobic microchannels with transverse ribs and grooves

Joseph¹,

Mathew²,

Krishnaraj³

et al. 2019

Exp. Comput. Multiph. Flow

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Superhydrophobic microchannels have evolved recently as an accepted strategy to mitigate the hydrodynamic resistance tendered in micro-constrictions. In this work, hydrodynamics of a hydrophobic microchannel realized by entrapping air in the cavities located between transversely oriented ribs is numerically investigated. An interface formed between the liquid and air/vapor in the confinement facilitates a resistance free slipping surface for the flowing water. The shape of the meniscus is determined by the pressure difference between air and liquid and is classified as convex, flat, and concave depending on the protrusion angle. Several applications require a long hydrophobic channel in which the liquid pressure decreases lengthwise; consequently the interface shape changes as well. In this regard, a mathematical model is proposed to predict the protrusion angle at a specific distance from the inlet of microchannel. This is incorporated in the computational fluid dynamics (CFD) simulations to define the static geometry of the interface which is varying throughout the length of the channel. Moreover, the boundary is treated as a combination of flat no-slip and curved shear-free regions to mimic the ribs and cavities. Further, the evolution of interface morphology is captured using the volume-of-fluid (VOF) scheme by considering a static contact angle at the solid surface to check the validity of the suggested model. Dynamically evolved protrusion angle is measured for various liquid-gas interface pressures and it is observed that the theoretical scaling proposed by Laplace and Young is well obeyed. Though CFD-VOF simulation scheme is an effective tool for predicting the pressure dependent liquid-gas meniscus and concurrent hydrodynamics of the ribbed microchannel, it is resource intensive. The present study demonstrates that the developed model for static boundary may be adopted alternatively to predict the hydrodynamics of a long hydrophobic microchannel by saving computational resources. Keywordshydrophobic microchannel ribbed channel volume-of-fluid simulation liquid-gas interface

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Transport of DNA in hydrophobic microchannels: a dissipative particle dynamics simulation

Cited by 19 publications

References 49 publications

The dynamics of a healthy and infected red blood cell in flow through constricted channels: A DPD simulation

The dynamics of a healthy and infected red blood cell in flow through constricted channels: A DPD simulation

Simulating Transport of Soft Matter in Micro/Nano Channel Flows with Dissipative Particle Dynamics

Numerical simulation of liquid–gas interface formation in long superhydrophobic microchannels with transverse ribs and grooves

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