An improved hybrid continuum‐atomistic four‐way coupled model for electrokinetics in nanofluidics

Jahromi, Saeed; Amani, E.; Movahed, Saeid

doi:10.1002/elps.201800307

Cited by 10 publications

(7 citation statements)

References 56 publications

(88 reference statements)

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“…In order to neutralize the system, we add the appropriate number of the ions (sodium and chloride) that were added to the system. The periodic boundary conditions (PBCs) were applied to each system in all the spatial directions [47]. Additionally, to solvate the system, the transferable intermolecular potential 3-point (TIP3P) water model was utilized [48].…”

Section: Molecular Dynamics (Md) Simulationmentioning

confidence: 99%

[Retracted] Atomic Scale Interactions between RNA and DNA Aptamers with the TNF‐α Protein

Asadzadeh

Moosavi

Alexandrakis

et al. 2021

BioMed Research International

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Interest in the design and manufacture of RNA and DNA aptamers as apta-biosensors for the early diagnosis of blood infections and other inflammatory conditions has increased considerably in recent years. The practical utility of these aptamers depends on the detailed knowledge about the putative interactions with their target proteins. Therefore, understanding the aptamer-protein interactions at the atomic scale can offer significant insights into the optimal apta-biosensor design. In this study, we consider one RNA and one DNA aptamer that were previously used as apta-biosensors for detecting the infection biomarker protein TNF-α, as an example of a novel computational workflow for selecting the aptamer candidate with the highest binding strength to a target. We combine information from the binding free energy calculations, molecular docking, and molecular dynamics simulations to investigate the interactions of both aptamers with TNF-α. The results reveal that the RNA aptamer has a more stable structure relative to the DNA aptamer. Interaction of aptamers with TNF-α does not have any negative effect on its structure. The results of molecular docking and molecular dynamics simulations suggest that the RNA aptamer has a stronger interaction with the protein. Also, these findings illustrate that basic residues of TNF-α establish more atomic contacts with the aptamers compared to acidic or pH-neutral ones. Furthermore, binding energy calculations show that the interaction of the RNA aptamer with TNF-α is thermodynamically more favorable. In total, the findings of this study indicate that the RNA aptamer is a more suitable candidate for using as an apta-biosensor of TNF-α and, therefore, of greater potential use for the diagnosis of blood infections. Also, this study provides more information about aptamer-protein interactions and increases our understanding of this phenomenon.

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Section: Molecular Dynamics (Md) Simulationmentioning

confidence: 99%

[Retracted] Atomic Scale Interactions between RNA and DNA Aptamers with the TNF‐α Protein

Asadzadeh

Moosavi

Alexandrakis

et al. 2021

BioMed Research International

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“…Since the principal hypothesis underlying equation 5 is that the wall effect is negligible due to the large distance of the drop from it [29,46,47], we can assume that the sheargradient force is the dominant component of the inertial lift in our study. After subtracting the calculated deformation lift based on this equation from the obtained total lift (fig.…”

Section: Resultsmentioning

confidence: 99%

A numerical lift force analysis on the inertial migration of a deformable droplet in steady and oscillatory microchannel flows at different Capillary numbers and oscillation frequencies

Lafzi,

Dabiri

2021

Preprint

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Inertial migration of deformable particles has become appealing in recent years due to its numerous applications in microfluidics and biomedicine. The physics underlying the motion of such particles is contingent upon the presence of lift forces in microchannels. This importance initiated several works to analyze and quantify such forces acting on particles. However, since most of such attempts have focused on solid and non-deformable particles, we extend the lift force analysis for the case of deformable droplets and study the effects of Capillary numbers on their dynamics in this paper. Furthermore, utilizing oscillatory flows as an alternative for steady currents within the microchannels has been proved to be beneficial by introducing new equilibrium positions for the particles. Therefore, the present analysis includes the oscillatory regimes and identifies the effects of oscillation frequencies on lift forces as well. We then propose an expression that mimics the lift force behavior in oscillatory flows accurately. Finally, we introduce a procedure to derive and predict a simple expression for the steady and averaged oscillatory lift for any given combination of Capillary number and oscillation frequency within a continuous range.

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“…Since the droplet in this study has large distances from the wall, the wall effect is negligible compared to the shear gradient force in the inertial lift. 31,33,36 Also, to the best of our knowledge, there is no analytical equation for the shear gradient lift in the literature to date. The drag force is computed based on its physical definition: 37…”

Section: The Shear Gradient Liftmentioning

confidence: 99%

A numerical lift force analysis on the inertial migration of a deformable droplet in steady and oscillatory microchannel flows

Lafzi

Dabiri

2022

Lab Chip

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An improved hybrid continuum‐atomistic four‐way coupled model for electrokinetics in nanofluidics

Cited by 10 publications

References 56 publications

[Retracted] Atomic Scale Interactions between RNA and DNA Aptamers with the TNF‐α Protein

[Retracted] Atomic Scale Interactions between RNA and DNA Aptamers with the TNF‐α Protein

A numerical lift force analysis on the inertial migration of a deformable droplet in steady and oscillatory microchannel flows at different Capillary numbers and oscillation frequencies

A numerical lift force analysis on the inertial migration of a deformable droplet in steady and oscillatory microchannel flows

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