Dissipative particle dynamics simulation of field-dependent DNA mobility in nanoslits

Ke, Yan; Chen, Yu Zong; Han, Jongyoon; Liu, Guirong; Wang, Jian‐Sheng; Hadjiconstantinou, Nicolas G.

doi:10.1007/s10404-011-0859-5

Cited by 7 publications

(3 citation statements)

References 28 publications

(28 reference statements)

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“…While DPD is not as computationally efficient as lattice Boltzmann simulations, it is a more flexible method that does not suffer from the numerical instability associated with many lattice Boltzmann applications. DPD facilitates the simulation of complex fluid systems on physically interesting and important length and time scales, including bio-particle and DNA filtering systems [56][57][58].…”

Section: Introductionmentioning

confidence: 99%

Dissipative Particle Dynamics (DPD): An Overview and Recent Developments

Liu

Zhou

et al. 2014

Arch Computat Methods Eng

179

101

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Dissipative particle dynamics (DPD) is a mesoscale particle method that bridges the gap between microscopic and macroscopic simulations. It can be regarded as a coarse-grained molecular dynamics method suitable for larger time and length scales. It has been successfully applied to different areas of interests, especially in modeling the hydrodynamic behavior of complex fluids in mesoscale. This paper presents an overview on DPD including the methodology, formulation, implementation procedure and some related numerical aspects. The paper also reviews the major applications of the DPD method, especially in modeling (1) micro drop dynamics, (2) multiphase flows in microchannels and fracture networks, (3) movement and suspension of macromolecules in micro channels and (4) movement and deformation of single cells. The paper ends with some concluding remarks summarizing the major features and future possible development of this unique mesoscale modeling technique.

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Section: Introductionmentioning

confidence: 99%

Dissipative Particle Dynamics (DPD): An Overview and Recent Developments

Liu

Zhou

et al. 2014

Arch Computat Methods Eng

179

101

View full text Add to dashboard Cite

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“…Alternatively, dissipative particle dynamics (DPD) has proven capabilities for capturing the dynamic and rheological properties of simple and complex fluids, and thus may be deployed to solve the proposed questions at an acceptable accuracy and an affordable computational cost. So far DPD has been successfully applied to investigate biomolecular behavior, such as DNA moving in nanoslits ( 23 ) and endocytosis of liposomes ( 24 ). In this study, we use DPD to gain insight into the interactions between the EG and the glycocalyx of passaging RBCs.…”

Section: Introductionmentioning

confidence: 99%

Cross talk between endothelial and red blood cell glycocalyces via near-field flow

Goligorsky

Luo

2021

Biophysical Journal

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Vascular endothelial cells and circulating red blood cell (RBC) surfaces are both covered by a layer of bushy glycocalyx. The interplay between these glycocalyx layers is hardly measurable and insufficiently understood. This study aims to investigate and qualify the possible interactions between the glycocalyces of RBCs and endothelial cells using mathematical modeling and numerical simulation. Dissipative particle dynamics (DPD) simulations are conducted to investigate the response of the endothelial glycocalyx (EG) to varying ambient conditions. A two-compartment model including EG and flow and a threecompartment model comprising EG, RBC glycocalyx, and flow are established. The two-compartment analysis shows that a relatively fast flow is associated with a predominantly bending motion of the EG, whereas oscillatory motions are predominant in a relatively slow flow. Results show that circulating RBCs cause the contactless deformation of EG. Its deformation is dependent on the chain layout, chain length, bending stiffness, RBC-to-EG distance, and RBC velocities. Specifically, shorter EG chains or RBC-to-EG distance leads to greater relative deflections of EG. Deformation of EG is enhanced when the EG chains are rarefied or RBCs move faster. The bending stiffness maintains stretching conformation of EG. Moreover, a compact EG chain layout and shedding EG chains disturb the neighboring flow field, causing disordered flow velocity distributions. In contrast, the movement of EG chains on RBC surfaces exerts a marginal driving force on RBCs. The DPD method is used for the first time, to our knowledge, in the three-compartment system to explore the cross talk between EG and RBC glycocalyx. This study suggests that RBCs drive the EG deformation via the near-field flow, whereas marginal propulsion of RBCs by the EG is observed. These new, to our knowledge, findings provide a new angle to understand the roles of glycocalyx in mechanotransduction and microvascular permeability and their perturbations under idealized pathophysiologic conditions associated with EG degradation.

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“…And its study has been substantially motivated by the recent development in nanotechnology. Although being ubiquitous in fields such as membrane separation, nano‐confined catalysis, energy conversion, and DNA sequencing, nanofluidics still has many unsettled questions. For instance, Fornasiero et al and Holt et al found that the flow rates of pressure‐driven fluids in the sub‐2‐nm carbon nanotube pores are about three orders‐of‐magnitude greater than those predicted by the no‐slip Hagen–Poiseuille (H‐P) relation.…”

Section: Introductionmentioning

confidence: 99%

Fluid inhomogeneity within nanoslits and deviation from Hagen–Poiseuille flow

Wang

Yang

2016

AIChE Journal

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Recently, the deviation of nano‐confined flows from classical hydrodynamic theories has been frequently reported. In this work, such a flow is theoretically investigated by means of dissipative particle dynamics (DPD) simulation. The simulation results show that the density and viscosity inhomogeneities near solid/fluid interfaces depends on the slit wettability only. Flow enhancement relative to the Hagen–Poiseuille (H‐P) flow occurs together with the flow inhomogeneity. Combining of flow inhomogeneity and the Stokes equation, a theoretical model for flux calculation is established. As the slit being widened, the model can be simplified by gradually eliminating the higher order traces, and be simplified into the model with Navier's slip condition and the well‐known H‐P relation at last. The theoretical results of flux are in good agreement with the simulations by DPD. © 2016 American Institute of Chemical Engineers AIChE J, 63: 834–842, 2017

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Dissipative particle dynamics simulation of field-dependent DNA mobility in nanoslits

Cited by 7 publications

References 28 publications

Dissipative Particle Dynamics (DPD): An Overview and Recent Developments

Dissipative Particle Dynamics (DPD): An Overview and Recent Developments

Cross talk between endothelial and red blood cell glycocalyces via near-field flow

Fluid inhomogeneity within nanoslits and deviation from Hagen–Poiseuille flow

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