1
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Nguyen T, Manikantan H. Cross-streamline migration and near-wall depletion of elastic fibers in micro-channel flows. SOFT MATTER 2024; 20:1725-1735. [PMID: 38285458 DOI: 10.1039/d3sm01499a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2024]
Abstract
The complex dynamics of elastic fibers in viscous fluids are central to many biological and industrial systems. Fluid-structure interactions underlying these dynamics govern the shape and transport of flexible fibers, and understanding these interactions can help tune flow properties in applications such as microfluidic separation, printing and clogging. In this work, we use slender-body theory to study micromechanical dynamics that arise from the coupling between the elastic backbone of a fiber and the local straining flow that contributes to filament flipping and cross-streamline migration. The resulting transverse drift is unbiased in either direction in simple shear flow. However, a non-uniform shear rate results in bias towards regions of high shear, which we connect to the shape transitions during flips. We discover a depletion layer that forms near the boundaries of pressure-driven channel flow due to the competition between such a cross-streamline drift and steric exclusion from the walls. Finally, we develop scaling laws for the curvature of filaments during flip events, demonstrating the origin of the drift bias in non-uniform flows, and confirm this behavior from our simulations. Put together, these results shed light on the role of a local and dominant coupling between elasticity and viscous resistance in dictating long-term dynamics and transport of elastic fibers in confined flows.
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Affiliation(s)
- Thomas Nguyen
- Department of Chemical Engineering, University of California Davis, Davis, CA 95616, USA.
| | - Harishankar Manikantan
- Department of Chemical Engineering, University of California Davis, Davis, CA 95616, USA.
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2
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Dutta S, Sing CE. Brownian dynamics simulations of bottlebrush polymers in dilute solution under simple shear and uniaxial extensional flows. J Chem Phys 2024; 160:044901. [PMID: 38258921 DOI: 10.1063/5.0177113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 01/01/2024] [Indexed: 01/24/2024] Open
Abstract
We study the dynamics of bottlebrush polymer molecules in dilute solutions subjected to shear and uniaxial extensional flows using Brownian dynamics simulations with hydrodynamic interaction (HI). Bottlebrush polymers are modeled using a coarse-grained representation, consisting of a set of beads interacting pairwise via a purely repulsive potential and connected by finitely extensible nonlinear springs. We present the results for molecular stretching, stress, and solution viscosity during the startup of flow as well as under steady state as a function of side chain length while keeping the backbone length fixed. In extensional flow, the backbone fractional extension and the first normal stress difference decrease with an increase in side chain length at a fixed Weissenberg number (Wi). Using simulation results both in the presence of and in the absence of HI, we show that this is primarily a consequence of steric interaction resulting from the dense grafting of side chains. In shear flow, we observe a shear-thinning behavior in all cases, although it becomes less pronounced with increasing side chain length. Furthermore, nonmonotonicity in the backbone fractional extension is observed under shear, particularly at high Wi. We contextualize our simulation results for bottlebrush polymers with respect to existing studies in the literature for linear polymers and show that the unique dynamical features characterizing bottlebrush polymers arise on account of their additional molecular thickness due to the presence of densely grafted side chains.
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Affiliation(s)
- Sarit Dutta
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 S Mathews Avenue, Urbana, Illinois 61801, USA
| | - Charles E Sing
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 S Mathews Avenue, Urbana, Illinois 61801, USA
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3
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Nguyen AH, Kania S, Oztekin A, Webb EB. Predicting reaction behavior of tethered polymers in shear flow. J Chem Phys 2023; 159:174907. [PMID: 37929865 DOI: 10.1063/5.0168440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 10/17/2023] [Indexed: 11/07/2023] Open
Abstract
Kinetics of force-mediated chemical reactions of end-tethered polymers with varying chain length N in varying shear rate flow γ̇ are explored via coarse-grained Brownian dynamics simulations. At fixed γ̇, force F along a polymer increases linearly with N as previously predicted; however, contrary to existing theory, the F(N) slope increases for N above a transition length that exhibits minimal dependence on γ̇. Force profiles are used in a stochastic model of a force-mediated reaction to compute the time for x percent of a polymer population to experience a reaction, tx. Observations are insensitive to the selected value of x in that tx data for varying N and γ̇ can be consistently collapsed onto a single curve via appropriate scaling, with one master curve for systems below the transition N (small N) and another for those above (large N). Different force scaling for small and large N results in orders of magnitude difference in force-mediated reaction kinetics as represented by the population response time. Data presented illustrate the possibility of designing mechano-reactive polymer populations with highly controlled response to flow across a range in γ̇.
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Affiliation(s)
- Anh Hung Nguyen
- Department of Mechanical Engineering and Mechanics, Lehigh University, Bethlehem, Pennsylvania 18015, USA
| | - Sagar Kania
- Department of Mechanical Engineering and Mechanics, Lehigh University, Bethlehem, Pennsylvania 18015, USA
| | - Alparslan Oztekin
- Department of Mechanical Engineering and Mechanics, Lehigh University, Bethlehem, Pennsylvania 18015, USA
| | - Edmund B Webb
- Department of Mechanical Engineering and Mechanics, Lehigh University, Bethlehem, Pennsylvania 18015, USA
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4
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Radhakrishnan K, Singh SP. Compression of a confined semiflexible polymer under direct and oscillating fields. Phys Rev E 2023; 108:014501. [PMID: 37583203 DOI: 10.1103/physreve.108.014501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 06/19/2023] [Indexed: 08/17/2023]
Abstract
The folding transition of biopolymers from the coil to compact structures has attracted wide research interest in the past and is well studied in polymer physics. Recent seminal works on DNA in confined devices have shown that these long biopolymers tend to collapse under an external field, which is contrary to the previously reported stretching of the chain. In this work, we capture the compression of a confined semiflexible polymer under direct and oscillating fields using a coarse-grained computer simulation model in the presence of long-range hydrodynamics. In the case of a semiflexible polymer chain, the inhomogeneous hydrodynamic drag from the center to the periphery of the coil couples with the chain bending to cause a swirling movement of the chain segments, leading to structural intertwining and compaction. Contrarily, a flexible chain of the same length lacks such structural deformation and forms a well-established tadpole structure. While bending rigidity profoundly influences the chain's folding favorability, we also found that subject to the direct field, chains in stronger confinements exhibit substantial compaction, contrary to the one in moderate confinements or bulk where such compaction is absent. However, an alternating field within an optimum frequency can effectuate this compression even in moderate or no confinement. This field-induced collapse is a quintessential hydrodynamic phenomenon, resulting in intertwined knotted structures even for shorter chains, unlike other spontaneous knotting experiments where it happens exclusively for longer chains.
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Affiliation(s)
- Keerthi Radhakrishnan
- Department of Physics, Indian Institute of Science Education and Research, Bhopal 462 066, Madhya Pradesh, India
| | - Sunil P Singh
- Department of Physics, Indian Institute of Science Education and Research, Bhopal 462 066, Madhya Pradesh, India
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5
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Xu S, Wang Z, Yu Y, Zhu Q, Zhang X. Conformations and dynamic behaviors of confined wormlike chains in a pressure-driven flow. E-POLYMERS 2022. [DOI: 10.1515/epoly-2022-0073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Abstract
The conformations and dynamic behaviors of wormlike chains confined by a slit in a pressure-driven flow were investigated using dissipative particle dynamics method. The wormlike chains exhibit varying conformations due to the varying shear stresses across the slit. The wormlike chain solution can be well described by the power-law fluid, and the power-law index decreases with the increase in chain rigidity. We also presented that the wormlike chain undergoes tumbling motion in the vicinity of the wall in the presence of pressure-driven flow. We also found that the wormlike chains can migrate both away from the wall and slightly away from the slit center, and the migration away from the slit center increases as the chain rigidity is increased because of hydrodynamic interactions induced in a more rigid wormlike chain.
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Affiliation(s)
- Shaofeng Xu
- School of Mechatronics and Energy Engineering, NingboTech University , Ningbo , 315000 , China
| | - Ziheng Wang
- Faculty of Mechanical Engineering and Automation, Zhejiang Sci-Tech University , Hangzhou , 310000 , China
| | - Yifan Yu
- School of Mechanical Engineering, Zhejiang University , Hangzhou , 310000 , China
| | - Qiaohui Zhu
- School of Mechanical Engineering, Zhejiang University , Hangzhou , 310000 , China
| | - Xuechang Zhang
- School of Mechatronics and Energy Engineering, NingboTech University , Ningbo , 315000 , China
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6
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Singh S, Subramanian G, Ansumali S. Two-fluid kinetic theory for dilute polymer solutions. Phys Rev E 2022; 106:044501. [PMID: 36397464 DOI: 10.1103/physreve.106.044501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 09/07/2022] [Indexed: 06/16/2023]
Abstract
We provide a Boltzmann-type kinetic description for dilute polymer solutions based on two-fluid theory. This Boltzmann-type description uses a quasiequilibrium based relaxation mechanism to model collisions between a polymer dumbbell and a solvent molecule. The model reproduces the desired macroscopic equations for the polymer-solvent mixture. The proposed kinetic scheme leads to a numerical algorithm which is along the lines of the lattice Boltzmann method. Finally, the algorithm is applied to describe the evolution of a perturbed Kolmogorov flow profile, whereby we recover the major elastic effect exhibited by a polymer solution, specifically, the suppression of the original inertial instability.
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Affiliation(s)
- Shiwani Singh
- Mathematics Institute, University of Warwick, Coventry CV4 7AL, United Kingdom
- Engineering Mechanics Unit, JNCASR, Jakkur, Bangalore 560064, India
| | | | - Santosh Ansumali
- Engineering Mechanics Unit, JNCASR, Jakkur, Bangalore 560064, India
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7
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Dynamical and Structural Properties of Comb Long-Chain Branched Polymer in Shear Flow. Int J Mol Sci 2022; 23:ijms231911290. [PMID: 36232591 PMCID: PMC9569657 DOI: 10.3390/ijms231911290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 09/21/2022] [Accepted: 09/21/2022] [Indexed: 11/16/2022] Open
Abstract
Using hybrid multi-particle collision dynamics (MPCD) and a molecular dynamics (MD) method, we investigate the effect of arms and shear flow on dynamical and structural properties of the comb long-chain branched (LCB) polymer with dense arms. Firstly, we analyze dynamical properties of the LCB polymer by tracking the temporal changes on the end-to-end distance of both backbones and arms as well as the orientations of the backbone in the flow-gradient plane. Simultaneously, the rotation and tumbling behaviors with stable frequencies are observed. In other words, the LCB polymer undergoes a process of periodic stretched–folded–stretched state transition and rotation, whose period is obtained by fitting temporal changes on the orientation to a periodic function. In addition, the impact induced by random and fast motions of arms and the backbone will descend as the shear rate increases. By analyzing the period of rotation behavior of LCB polymers, we find that arms have a function in keeping the LCB polymer’s motion stable. Meanwhile, we find that the rotation period of the LCB polymer is mainly determined by the conformational distribution and the non-shrinkable state of the structure along the velocity-gradient direction. Secondly, structural properties are numerically characterized by the average gyration tensor of the LCB polymer. The changes in gyration are in accordance with the LCB polymer rolling when varying the shear rate. By analyzing the alignment of the LCB polymer and comparing with its linear and star counterparts, we find that the LCB polymer with very long arms, like the corresponding linear chain, has a high speed to reach its configuration expansion limit in the flow direction. However, the comb polymer with shorter arms has stronger resistance on configuration expansion against the imposed flow field. Moreover, with increasing arm length, the comb polymer in shear flow follows change from linear-polymer-like to capsule-like behavior.
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8
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Perez Ocampo L, Weiss LB, Jardat M, Likos CN, Dahirel V. Electroosmotic Flow Induced Lift Forces on Polymer Chains in Nanochannels. ACS POLYMERS AU 2022; 2:245-256. [PMID: 35971422 PMCID: PMC9372999 DOI: 10.1021/acspolymersau.1c00058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
A major objective
of research in nanofluidics is to achieve better
selectivity in manipulating the fluxes of nano-objects and in particular
of biopolymers. Numerical simulations allow one to better understand
the physical mechanisms at play in such situations. We performed hybrid
mesoscale simulations to investigate the properties of polymers under
flows in slit pores at the nanoscale. We use multiparticle collision
dynamics, an algorithm that includes hydrodynamics and thermal fluctuations,
to investigate the properties of fully flexible and stiff polymers
under several types of flow, showing that Poiseuille flows and electroosmotic
flows can lead to quantitatively and qualitatively different behaviors
of the chain. In particular, a counterintuitive phenomenon occurs
in the presence of an electroosmotic flow: When the monomers are attracted
by the solid surfaces through van der Waals forces, shear-induced
forces lead to a stronger repulsion of the polymers from these surfaces.
Such focusing of the chain in the middle of the channel increases
its flowing velocity, a phenomenon that may be exploited to separate
different types of polymers.
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Affiliation(s)
- Lisbeth Perez Ocampo
- Sorbonne Université, CNRS, Physico-chimie des électrolytes et nano-systèmes interfaciaux, PHENIX, F-75005 Paris, France
| | - Lisa B. Weiss
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Marie Jardat
- Sorbonne Université, CNRS, Physico-chimie des électrolytes et nano-systèmes interfaciaux, PHENIX, F-75005 Paris, France
| | - Christos N. Likos
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Vincent Dahirel
- Sorbonne Université, CNRS, Physico-chimie des électrolytes et nano-systèmes interfaciaux, PHENIX, F-75005 Paris, France
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9
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Peng B, Yang Z, Yang L, Chen J, Liu L, Wang D. Reducing the Solvent Quality Gives Rise to the Outward Migration of a Star Polymer in Poiseuille Flow. Macromolecules 2022. [DOI: 10.1021/acs.macromol.2c00031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Bo Peng
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China
- University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Zhenyue Yang
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China
| | - Li Yang
- State Key Laboratory of Environment-friendly Energy Materials, School of Material Science and Engineering, Southwest University of Science and Technology, Mianyang 621010, P. R. China
| | - Jizhong Chen
- Guangdong University of Technology, Guangzhou, Guangdong 510006, P. R. China
| | - Lijun Liu
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China
| | - Dapeng Wang
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China
- University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
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10
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Kim DY, Lee JB, Lee DY. Selective Localization of Nanofiller on Mechanical Properties of Poly(lactic acid)/Poly(butylene adipate- co-terephthalate) Nanocomposites via the Surface Energy and Melt Blending Technique. Macromolecules 2022. [DOI: 10.1021/acs.macromol.1c02074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Do Young Kim
- Department of Polymer Science and Engineering, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Jae Bin Lee
- Department of Polymer Science and Engineering, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Dong Yun Lee
- Department of Polymer Science and Engineering, Kyungpook National University, Daegu 41566, Republic of Korea
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11
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Radhakrishnan K, Singh SP. Collapse of a Confined Polyelectrolyte Chain under an AC Electric Field. Macromolecules 2021. [DOI: 10.1021/acs.macromol.1c00637] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Keerthi Radhakrishnan
- Department of Physics, Indian Institute of Science Education and Research Bhopal, Bhopal 462066, Madhya Pradesh, India
| | - Sunil P. Singh
- Department of Physics, Indian Institute of Science Education and Research Bhopal, Bhopal 462066, Madhya Pradesh, India
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12
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Smith KM, Hsiao LC. Migration and Morphology of Colloidal Gel Clusters in Cylindrical Channel Flow. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:10308-10318. [PMID: 34403581 DOI: 10.1021/acs.langmuir.1c01287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
We report the cluster-level structural parameters of colloidal thermogelling nanoemulsions in channel flow as a function of attractive interactions and local shear stress. The spatiotemporal evolution of the gel microstructure is obtained by directly visualizing the dispersed phase near the edge of a cylindrical channel. We observe the flow of the nanoemulsion gels in a range of radial positions (r) and shear stresses between 70 and 220 Pa, finding that the r-dependent cluster sizes are due to a balance between shear forces that yield bonds and attractive interactions that rebuild the inter-colloid bonds. In addition, the largest clusters appear to be affected by confinement and accumulate toward the central axis of the channel, resulting in a volume fraction gradient. Cluster size and volume fraction variabilities are most prominent when the attractive interactions are the strongest. Specifically, a distinct transition from sparse, fluidized clusters near the walls to concentrated, large clusters toward the center is observed. These two structural states coincide with a velocity-based transition from higher shear rates near the walls to lower shear rates toward the center of the channel. We find a compounding effect where larger gel clusters, formed under strong attractions and low shear stresses, are susceptible to shear-induced migration that intensifies r-dependent heterogeneity and deviations in the flow behavior from predictive models.
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Affiliation(s)
- Kristine M Smith
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Lilian C Hsiao
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
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13
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Liu A, Yang Z, Liu L, Chen J, An L. Role of Functionality in Cross-Stream Migration, Structures, and Dynamics of Star Polymers in Poiseuille Flow. Macromolecules 2020. [DOI: 10.1021/acs.macromol.0c00699] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Aiqing Liu
- College of Chemistry, Jilin University, Changchun 130012, People’s Republic of China
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People’s Republic of China
| | - Zhenyue Yang
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People’s Republic of China
| | - Lijun Liu
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People’s Republic of China
| | - Jizhong Chen
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People’s Republic of China
- University of Science and Technology of China, Hefei 230026, People’s Republic of China
| | - Lijia An
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People’s Republic of China
- University of Science and Technology of China, Hefei 230026, People’s Republic of China
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14
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Valley BE, Crowell AD, Butler JE, Ladd AJC. Electro-hydrodynamic extraction of DNA from mixtures of DNA and bovine serum albumin. Analyst 2020; 145:5532-5538. [PMID: 32608411 DOI: 10.1039/d0an00961j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
We report separation of genomic DNA (48 kbp) from bovine serum albumin (BSA) by the electro-hydrodynamic coupling between a pressure-driven flow and a parallel electric field. Electro-hydrodynamic extraction exploits this coupling to trap DNA molecules at the entrance of a microfluidic contraction channel, while allowing proteins and salts to be flushed from the device. Samples (10 μL) containing λ-DNA (1 ng) and BSA (0.3 mg) were injected directly into the device and convected to the contraction channel entrance by a flowing buffer solution. The DNA remains trapped in this region essentially indefinitely, while proteins and salts are eluted. The effectiveness of the concept has been assessed by fluorescence measurements of DNA and BSA concentrations. Electro-hydrodynamic extraction in a single-stage device was found to enhance the concentration of DNA 40-fold, while reducing the BSA concentration by four orders of magnitude. The relative concentrations of DNA to BSA at the contraction channel entrance can be as large as 1.5 : 1, corresponding to an A260/280 ratio of 1.9. The maximum yield of DNA from a salt-free solution is 50%, while salted (150 mM) solutions have a lower yield (38%).
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Affiliation(s)
- Benjamin E Valley
- Department of Chemical Engineering, University of Florida, Gainesville, FL, USA.
| | - Anne D Crowell
- Department of Chemical Engineering, University of Florida, Gainesville, FL, USA.
| | - Jason E Butler
- Department of Chemical Engineering, University of Florida, Gainesville, FL, USA.
| | - Anthony J C Ladd
- Department of Chemical Engineering, University of Florida, Gainesville, FL, USA.
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15
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Lin TY, Klass SH, Francis MB, Shaqfeh ESG. Extravasation of PEGylated Spherical Nanoparticles through a Circular Pore of Similar Size. Macromolecules 2020. [DOI: 10.1021/acs.macromol.0c00187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tiras Y. Lin
- Department of Mechanical Engineering, Stanford University, Stanford, California 94305, United States
| | - Sarah H. Klass
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Matthew B. Francis
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Eric S. G. Shaqfeh
- Department of Mechanical Engineering, Stanford University, Stanford, California 94305, United States
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
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16
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Słowicka AM, Stone HA, Ekiel-Jeżewska ML. Flexible fibers in shear flow approach attracting periodic solutions. Phys Rev E 2020; 101:023104. [PMID: 32168723 DOI: 10.1103/physreve.101.023104] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 01/03/2020] [Indexed: 11/07/2022]
Abstract
The three-dimensional dynamics of a single non-Brownian flexible fiber in shear flow is evaluated numerically, in the absence of inertia. A wide range of ratios A of bending to hydrodynamic forces and hundreds of initial configurations are considered. We demonstrate that flexible fibers in shear flow exhibit much more complicated evolution patterns than in the case of extensional flow, where transitions to higher-order modes of characteristic shapes are observed when A exceeds consecutive threshold values. In shear flow, we identify the existence of an attracting steady configuration and different attracting periodic motions that are approached by long-lasting rolling, tumbling, and meandering dynamical modes, respectively. We demonstrate that the final stages of the rolling and tumbling modes are effective Jeffery orbits, with the constant parameter C replaced by an exponential function that either decays or increases in time, respectively, corresponding to a systematic drift of the trajectories. In the limit of C→0, the fiber aligns with the vorticity direction and in the limit of C→∞, the fiber periodically tumbles within the shear plane. For moderate values of A, a three-dimensional meandering periodic motion exists, which corresponds to intermediate values of C. Transient, close to periodic oscillations are also detected in the early stages of the modes.
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Affiliation(s)
- Agnieszka M Słowicka
- Institute of Fundamental Technological Research, Polish Academy of Sciences, Pawińskiego 5b, 02-106 Warsaw, Poland
| | - Howard A Stone
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, New Jersey 08544, USA
| | - Maria L Ekiel-Jeżewska
- Institute of Fundamental Technological Research, Polish Academy of Sciences, Pawińskiego 5b, 02-106 Warsaw, Poland
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17
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Li L, Cao Q, Liu H, Gu Z, Yu Y, Huang F, Zuo C. Transport of polymer-modified nanoparticles in nanochannels coated with polymers. RSC Adv 2019; 9:38944-38951. [PMID: 35540675 PMCID: PMC9075939 DOI: 10.1039/c9ra08365k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 11/18/2019] [Indexed: 12/30/2022] Open
Abstract
Using molecular dynamics simulations based on explicit-solvent model, we study migration of polymer-modified nanoparticles through nanochannels coated with polymers. The polymers densely grafted on the spherical nanoparticle and the channel surface form spherical polymer brush (SPB) and planar polymer brush (PPB), respectively. The migration of the neutral polymer-modified nanoparticle is driven by electroosmotic flow (EOF). The effects of the electric field strength and the SPB–PPB interaction on polymer conformations and transport dynamics of the SPB are explored. The migration velocity of the SPB reduces as the interaction between the SPB and the PPB increases. For strong SPB–PPB interaction, the directional migration of the SPB can be triggered only after the electric field strength exceeds a critical value. The high EOF velocity forces the center of mass of the spherical nanoparticle to keep near the central region of the channel due to high shear rate close to the brush–fluid interface. Unlike electrophoresis of charged polymer-grafted spherical particles, the SPB adopts a more extended conformation in the plane perpendicular to the EOF direction. Using molecular dynamics simulations based on explicit-solvent model, we study migration of polymer-modified nanoparticles through nanochannels coated with polymers.![]()
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Affiliation(s)
- Lujuan Li
- College of Mechanical and Electrical Engineering, Jiaxing University Jiaxing 314001 P. R. China
| | - Qianqian Cao
- College of Mechanical and Electrical Engineering, Jiaxing University Jiaxing 314001 P. R. China
| | - Hao Liu
- College of Mechanical and Electrical Engineering, Jiaxing University Jiaxing 314001 P. R. China
| | - Zhiqing Gu
- College of Mechanical and Electrical Engineering, Jiaxing University Jiaxing 314001 P. R. China
| | - Ying Yu
- College of Mechanical and Electrical Engineering, Jiaxing University Jiaxing 314001 P. R. China
| | - Fengli Huang
- College of Mechanical and Electrical Engineering, Jiaxing University Jiaxing 314001 P. R. China
| | - Chuncheng Zuo
- College of Mechanical and Electrical Engineering, Jiaxing University Jiaxing 314001 P. R. China
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18
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Setaro AC, Underhill PT. Dumbbell kinetic theory for polymers in a combination of flow and external electric field. Phys Rev E 2019; 100:052501. [PMID: 31869926 DOI: 10.1103/physreve.100.052501] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Indexed: 06/10/2023]
Abstract
Combining Poiseuille flow with an external electric field is a demonstrated method to drive transverse migration in capillary electrophoresis. Despite both computational and experimental studies, a number of questions about how to best model polymers under these conditions remains. Attempts have been made to develop a kinetic theory for a bead-spring dumbbell model, but these have only been accurate at low electric field strength and have not captured the nonmonotonic relationship between migration and electric field strength. In this paper, we revisit the development of a kinetic theory for a bead-spring dumbbell in a combination of parabolic flow and an external electric field. The resultant theory yields a compact formula that predicts polymer concentration profiles that agree excellently with our Brownian dynamics simulations including the aforementioned nonmonotonic relationship. Furthermore, we compare our theoretical results to experimental data and find that our model nearly quantitatively predicts the position of the maximum in migration.
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Affiliation(s)
- Angelo C Setaro
- The Howard P. Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
| | - Patrick T Underhill
- The Howard P. Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
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19
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Role of Hydrodynamic Interactions in the Deformation of Star Polymers in Poiseuille Flow. CHINESE JOURNAL OF POLYMER SCIENCE 2019. [DOI: 10.1007/s10118-020-2346-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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20
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Weiss LB, Likos CN, Nikoubashman A. Spatial Demixing of Ring and Chain Polymers in Pressure-Driven Flow. Macromolecules 2019. [DOI: 10.1021/acs.macromol.9b01629] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Lisa B. Weiss
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Christos N. Likos
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Arash Nikoubashman
- Institute of Physics, Johannes Gutenberg University Mainz, Staudingerweg 7, 55128 Mainz, Germany
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21
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Dong C, Kania S, Morabito M, Zhang XF, Im W, Oztekin A, Cheng X, Webb EB. A mechano-reactive coarse-grained model of the blood-clotting agent von Willebrand factor. J Chem Phys 2019; 151:124905. [PMID: 31575216 DOI: 10.1063/1.5117154] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The von Willebrand Factor (vWF) is a large blood glycoprotein that aids in hemostasis. Within each vWF monomer, the A2 domain hosts a cleavage site for enzyme ADAMTS13, which regulates the size of vWF multimers. This cleavage site can only be exposed when an A2 domain unfolds, and the unfolding reaction energy landscape is highly sensitive to the force conditions on the domain. Based on previous optical tweezer experimental results, we advance here a new activated A2 monomer model (AA2MM) for coarse-grained modeling of vWF that accurately represents the force-based probabilistic change between the unfolded/refolded states. A system of springs is employed to mimic the complex mechanical response of vWF monomers subject to pulling forces. AA2MM was validated by comparing monomer scale simulation results to data from prior pulling experiments on vWF monomer fragments. The model was further validated by comparing multimer scale Brownian dynamics simulation results to experiments using microfluidic chamber microscopy to visualize tethered vWF proteins subject to flow. The A2 domain unfolding reaction was studied in bulk flow simulations (pure shear and elongation flow), giving evidence that elongational flow drives the vWF size regulation process in blood. The mechanoreactive, coarse-grained AA2MM accurately describes the complex mechanical coupling between human blood flow conditions and vWF protein reactivity.
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Affiliation(s)
- Chuqiao Dong
- Department of Mechanical Engineering and Mechanics, Lehigh University, Bethlehem, Pennsylvania 18015, USA
| | - Sagar Kania
- Department of Mechanical Engineering and Mechanics, Lehigh University, Bethlehem, Pennsylvania 18015, USA
| | - Michael Morabito
- Department of Mechanical Engineering and Mechanics, Lehigh University, Bethlehem, Pennsylvania 18015, USA
| | - X Frank Zhang
- Department of Mechanical Engineering and Mechanics, Lehigh University, Bethlehem, Pennsylvania 18015, USA
| | - Wonpil Im
- Department of Bioengineering, Lehigh University, Bethlehem, Pennsylvania 18015, USA
| | - Alparslan Oztekin
- Department of Mechanical Engineering and Mechanics, Lehigh University, Bethlehem, Pennsylvania 18015, USA
| | - Xuanhong Cheng
- Department of Bioengineering, Lehigh University, Bethlehem, Pennsylvania 18015, USA
| | - Edmund B Webb
- Department of Mechanical Engineering and Mechanics, Lehigh University, Bethlehem, Pennsylvania 18015, USA
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22
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Cho M, Hong SO, Lee SH, Hyun K, Kim JM. Effects of Ionic Strength on Lateral Particle Migration in Shear-Thinning Xanthan Gum Solutions. MICROMACHINES 2019; 10:E535. [PMID: 31443169 PMCID: PMC6723194 DOI: 10.3390/mi10080535] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 08/08/2019] [Accepted: 08/12/2019] [Indexed: 01/22/2023]
Abstract
Viscoelastic fluids, including particulate systems, are found in various biological and industrial systems including blood flow, food, cosmetics, and electronic materials. Particles suspended in viscoelastic fluids such as polymer solutions migrate laterally, forming spatially segregated streams in pressure-driven flow. Viscoelastic particle migration was recently applied to microfluidic technologies including particle counting and sorting and the micromechanical measurement of living cells. Understanding the effects on equilibrium particle positions of rheological properties of suspending viscoelastic fluid is essential for designing microfluidic applications. It has been considered that the shear-thinning behavior of viscoelastic fluid is a critical factor in determining the equilibrium particle positions. This work presents the lateral particle migration in two different xanthan gum-based viscoelastic fluids with similar shear-thinning viscosities and the linear viscoelastic properties. The flexibility and contour length of the xanthan gum molecules were tuned by varying the ionic strength of the solvent. Particles suspended in flexible and short xanthan gum solution, dissolved at high ionic strength, migrated toward the corners in a square channel, whereas particles in the rigid and long xanthan gum solutions in deionized water migrated toward the centerline. This work suggests that the structural properties of polymer molecules play significant roles in determining the equilibrium positions in shear-thinning fluids, despite similar bulk rheological properties. The current results are expected to be used in a wide range of applications such as cell counting and sorting.
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Affiliation(s)
- Mira Cho
- Department of Energy Systems Research, Ajou University, Suwon 16499, Korea
| | - Sun Ok Hong
- Department of Energy Systems Research, Ajou University, Suwon 16499, Korea
| | - Seung Hak Lee
- School of Chemical and Biomolecular Engineering, Pusan National University, Busan 46241, Korea
| | - Kyu Hyun
- School of Chemical and Biomolecular Engineering, Pusan National University, Busan 46241, Korea.
| | - Ju Min Kim
- Department of Energy Systems Research, Ajou University, Suwon 16499, Korea.
- Department of Chemical Engineering, Ajou University, Suwon 16499, Korea.
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23
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Abstract
The interfacial physics of complex liquids under flow remains a long-standing problem in fluid mechanics that is important for fields ranging from lubrication to nanofluidics. Liquids containing small amounts of high-molecular weight polymers are found to flow through channels faster than expected, a phenomenon attributed to the formation of boundary depletion layers that relaxes the no-slip boundary condition and allows the bulk of the fluid to slip past the walls. This work provides the most direct measurement to date of the dimension and composition of depletion layers of a polymer solution under flow. We anticipate extending this approach to help understand fluid dynamics in different regimes, such as flow in nanoconfinement and turbulence. Complex liquids flow through channels faster than expected, an effect attributed to the formation of low-viscosity depletion layers at the boundaries. Characterization of depletion layer length scale, concentration, and dynamics has remained elusive due in large part to the lack of suitable real-space experimental techniques. The short length scales associated with depletion layers have traditionally prohibited direct imaging. By overcoming this limitation via adaptations of stimulated emission depletion (STED) microscopy, we directly measure the concentration profile of polymer solutions at a nonadsorbing wall under Poiseuille flow. Using this approach, we 1) confirm the theoretically predicted concentration profile governed by entropically driven depletion, 2) observe depletion layer narrowing at low to intermediate shear rates, and 3) report depletion layer composition that approaches pure solvent at unexpectedly low shear rates.
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24
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Wang Y, Morabito M, Zhang XF, Webb E, Oztekin A, Cheng X. Shear-Induced Extensional Response Behaviors of Tethered von Willebrand Factor. Biophys J 2019; 116:2092-2102. [PMID: 31103230 DOI: 10.1016/j.bpj.2019.04.025] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 04/03/2019] [Accepted: 04/22/2019] [Indexed: 10/26/2022] Open
Abstract
We perform single-molecule flow experiments using confocal microscopy and a microfluidic device for shear rates up to 20,000 s-1 and present results for the shear-induced unraveling and elongation of tethered von Willebrand factor (VWF) multimers. Further, we employ companion Brownian dynamics simulations to help explain details of our experimental observations using a parameterized coarse-grained model of VWF. We show that global conformational changes of tethered VWF can be accurately captured using a relatively simple mechanical model. Good agreement is found between experimental results and computational predictions for the threshold shear rate of extension, existence of nonhomogenous fluorescence distributions along unraveled multimer contours, and large variations in extensional response behaviors. Brownian dynamics simulations reveal the strong influence of varying chain length, tethering point location, and number of tethering locations on the underlying unraveling response. Through a complex molecule like VWF that naturally adopts a wide distribution of molecular size and has multiple binding sites within each molecule, this work demonstrates the power of tandem experiment and simulation for understanding flow-induced changes in biomechanical state and global conformation of macromolecules.
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Affiliation(s)
- Yi Wang
- Department of Materials Science and Engineering, Bethlehem, Pennsylvania
| | - Michael Morabito
- Department of Mechanical Engineering and Mechanics, Bethlehem, Pennsylvania
| | - X Frank Zhang
- Department of Mechanical Engineering and Mechanics, Bethlehem, Pennsylvania; Department of Bioengineering, Lehigh University, Bethlehem, Pennsylvania.
| | - Edmund Webb
- Department of Mechanical Engineering and Mechanics, Bethlehem, Pennsylvania
| | - Alparslan Oztekin
- Department of Mechanical Engineering and Mechanics, Bethlehem, Pennsylvania
| | - Xuanhong Cheng
- Department of Materials Science and Engineering, Bethlehem, Pennsylvania; Department of Bioengineering, Lehigh University, Bethlehem, Pennsylvania.
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25
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Xu S, Lou Y, He P, Wang X, Wang J. Effect of solvent quality on Poiseuille flow of polymer solutions in microchannels: A dissipative particle dynamics study. J Appl Polym Sci 2019. [DOI: 10.1002/app.47345] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Shaofeng Xu
- Ningbo Institute of Technology; Zhejiang University; Zhejiang China
- Department of Mechanical Engineering; Northwestern University; Evanston Illinois 60208
| | - Yinghou Lou
- Ningbo Institute of Technology; Zhejiang University; Zhejiang China
| | - Ping He
- Ningbo Institute of Technology; Zhejiang University; Zhejiang China
| | - Xiangyang Wang
- Ningbo Institute of Technology; Zhejiang University; Zhejiang China
| | - Jiugen Wang
- School of Mechanical Engineering; Zhejiang University; Zhejiang China
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26
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Wu S, Li C, Zheng Q, Xu L. Modelling DNA extension and fragmentation in contractive microfluidic devices: a Brownian dynamics and computational fluid dynamics approach. SOFT MATTER 2018; 14:8780-8791. [PMID: 30338769 DOI: 10.1039/c8sm00863a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Fragmenting DNA into short pieces is an essential manipulation in many biological studies, ranging from genome sequencing to molecular diagnosis. Among various DNA fragmentation methods, microfluidic hydrodynamic DNA fragmentation has huge advantages especially in terms of handling small-volume samples and being integrated into automatic and all-in-one DNA analysis equipment. Despite the fast progress in experimental studies and applications, a systematic understanding of how DNA molecules are distributed, stretched and fragmented in a confined microfluidic field is still lacking. In this work, we investigate the extension and fragmentation of DNA in a typical contractive microfluidic field, which consists of a shear flow-dominated area and an elongational flow-dominated area, using the Brownian dynamics-computational fluid dynamics method. Our results show that the shear flow at the straight part of the microfluidic channel and the elongational flow at the contractive bottleneck together determine the performance of DNA fragmentation. The average fragment size of DNA decreases with the increase of the strain rate of the elongational flow, and the upstream shear flow can significantly precondition the conformation of DNA to produce shorter and more uniform fragments. A systematic study of the dynamics of DNA fragmentation shows that DNA tends to break at the mid-point when the strain rate of elongational flow is small, and the breakage point largely deviates from the midpoint as the strain rate increases. Our simulation of the thorough DNA fragmentation process in a realistic microfluidic field agrees well with experimental results. We expect that our study can shed new light on the development of future microfluidic devices for DNA fragmentation and integrated DNA analysis devices.
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Affiliation(s)
- Shuyi Wu
- Center for Nano and Micro Mechanics, School of Aerospace Engineering, Tsinghua University, Beijing, China.
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27
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Montes RJ, Butler JE, Ladd AJC. Trapping DNA with a high throughput microfluidic device. Electrophoresis 2018; 40:437-446. [DOI: 10.1002/elps.201800287] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 09/08/2018] [Accepted: 09/10/2018] [Indexed: 01/17/2023]
Affiliation(s)
- Ryan J. Montes
- Department of Chemical Engineering University of Florida Gainesville FL USA
| | - Jason E. Butler
- Department of Chemical Engineering University of Florida Gainesville FL USA
| | - Anthony J. C. Ladd
- Department of Chemical Engineering University of Florida Gainesville FL USA
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28
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Palmer TL, Espås TA, Skartlien R. Effects of polymer adsorption on the effective viscosity in microchannel flows: phenomenological slip layer model from molecular simulations. J DISPER SCI TECHNOL 2018. [DOI: 10.1080/01932691.2018.1467776] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Teresa Lynne Palmer
- University of Stavanger, Stavanger, Norway
- IOR Centre of Norway, Stavanger, Norway
- Institute for Energy Technology, Kjeller, Norway
| | - Thomas Asadi Espås
- Institute for Energy Technology, Kjeller, Norway
- University of Manchester, Oxford Rd, Manchester, UK
| | - Roar Skartlien
- Institute for Energy Technology, Kjeller, Norway
- Ugelstad Lab., NTNU, Norwegian University of Science and Technology, Trondheim, Norway
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29
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Affiliation(s)
- Anthony J.C. Ladd
- Chemical Engineering Department, University of Florida , Gainesville, FL, USA
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30
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Nir G, Chetrit E, Vivante A, Garini Y, Berkovich R. The role of near-wall drag effects in the dynamics of tethered DNA under shear flow. SOFT MATTER 2018; 14:2219-2226. [PMID: 29451293 DOI: 10.1039/c7sm01328k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We utilized single-molecule tethered particle motion (TPM) tracking, optimized for studying the behavior of short (0.922 μm) dsDNA molecules under shear flow conditions, in the proximity of a wall (surface). These experiments track the individual trajectories through a gold nanobead (40 nm in radius), attached to the loose end of the DNA molecules. Under such circumstances, local interactions with the wall become more pronounced, manifested through hydrodynamic interactions. To elucidate the mechanical mechanism that affects the statistics of the molecular trajectories of the tethered molecules, we estimate the resting diffusion coefficient of our system. Using this value and our measured data, we calculate the orthogonal distance of the extended DNA molecules from the surface. This calculation considers the hydrodynamic drag effect that emerges from the proximity of the molecule to the surface, using the Faxén correction factors. Our finding enables the construction of a scenario according to which the tension along the chain builds up with the applied shear force, driving the loose end of the DNA molecule away from the wall. With the extension from the wall, the characteristic times of the system decrease by three orders of magnitude, while the drag coefficients decay to a plateau value that indicates that the molecule still experiences hydrodynamic effects due to its proximity to the wall.
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Affiliation(s)
- Guy Nir
- Dep. of Genetics, Harvard Medical School, Boston, MA 02115, USA. and Department of Physics and Institute of Nanotechnology, Bar Ilan University, Ramat Gan 52900, Israel
| | - Einat Chetrit
- Department of Chemical-Engineering, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel.
| | - Anat Vivante
- Department of Physics and Institute of Nanotechnology, Bar Ilan University, Ramat Gan 52900, Israel
| | - Yuval Garini
- Department of Physics and Institute of Nanotechnology, Bar Ilan University, Ramat Gan 52900, Israel
| | - Ronen Berkovich
- Department of Chemical-Engineering, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel. and The Ilze Katz Institute for Nanoscience and Technology, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
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31
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Singh SP, Gompper G, Winkler RG. Steady state sedimentation of ultrasoft colloids. J Chem Phys 2018; 148:084901. [PMID: 29495770 DOI: 10.1063/1.5001886] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The structural and dynamical properties of ultra-soft colloids-star polymers-exposed to a uniform external force field are analyzed by applying the multiparticle collision dynamics technique, a hybrid coarse-grain mesoscale simulation approach, which captures thermal fluctuations and long-range hydrodynamic interactions. In the weak-field limit, the structure of the star polymer is nearly unchanged; however, in an intermediate regime, the radius of gyration decreases, in particular transverse to the sedimentation direction. In the limit of a strong field, the radius of gyration increases with field strength. Correspondingly, the sedimentation coefficient increases with increasing field strength, passes through a maximum, and decreases again at high field strengths. The maximum value depends on the functionality of the star polymer. High field strengths lead to symmetry breaking with trailing, strongly stretched polymer arms and a compact star-polymer body. In the weak-field-linear response regime, the sedimentation coefficient follows the scaling relation of a star polymer in terms of functionality and arm length.
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Affiliation(s)
- Sunil P Singh
- Indian Institute of Science Education and Research Bhopal, Bhopal By pass Road Bhauri, Bhopal 462 066, Madhya Pradesh, India
| | - Gerhard Gompper
- Theoretical Soft Matter and Biophysics, Institute for Advanced Simulation and Institute of Complex Systems, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Roland G Winkler
- Theoretical Soft Matter and Biophysics, Institute for Advanced Simulation and Institute of Complex Systems, Forschungszentrum Jülich, D-52425 Jülich, Germany
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32
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Lin TY, Saadat A, Kushwaha A, Shaqfeh ESG. Effect of Length on the Dynamics of Wall Tethered Polymers in Shear Flow. Macromolecules 2017. [DOI: 10.1021/acs.macromol.7b02032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tiras Y. Lin
- Department
of Mechanical Engineering, ‡Department of Chemical Engineering,
and §Institute for
Computational and Mathematical Engineering, Stanford University, Stanford, California 94305, United States
| | - Amir Saadat
- Department
of Mechanical Engineering, ‡Department of Chemical Engineering,
and §Institute for
Computational and Mathematical Engineering, Stanford University, Stanford, California 94305, United States
| | - Amit Kushwaha
- Department
of Mechanical Engineering, ‡Department of Chemical Engineering,
and §Institute for
Computational and Mathematical Engineering, Stanford University, Stanford, California 94305, United States
| | - Eric S. G. Shaqfeh
- Department
of Mechanical Engineering, ‡Department of Chemical Engineering,
and §Institute for
Computational and Mathematical Engineering, Stanford University, Stanford, California 94305, United States
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33
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Weiss LB, Nikoubashman A, Likos CN. Topology-Sensitive Microfluidic Filter for Polymers of Varying Stiffness. ACS Macro Lett 2017; 6:1426-1431. [PMID: 35650806 DOI: 10.1021/acsmacrolett.7b00768] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The separation of polymers based on their size, rigidity, and topology is an essential but also highly challenging task for nanoscience and engineering. Using hybrid molecular dynamics simulations that correctly take into account hydrodynamics, we have designed microfluidic channels for separating linear from ring polymers in dilute solutions. We establish that the transport velocity of the polymers is independent of their topology and rigidity when the channel walls are smooth and repulsive. However, when the walls are decorated with attractive spots arranged on lines parallel to the flow, ring polymers exhibit an order of magnitude higher transport velocity compared to linear chains. The spots induce a homeotropic-like reorientation of ring polymers close to walls leading to a tank treading motion along them, whereas linear chains are immobilized upon adsorption. This mechanism becomes more enhanced with increasing polymer rigidity. The presented technique holds thus promise for reliably separating nanoparticles based on their topology.
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Affiliation(s)
- Lisa B. Weiss
- Faculty
of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Arash Nikoubashman
- Institute
of Physics, Johannes Gutenberg University Mainz, Staudingerweg
7, 55128 Mainz, Germany
| | - Christos N. Likos
- Faculty
of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria
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34
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Abstract
Nanomaterials have been widely used in the design of drug delivery platforms. This work computationally explores the vascular dynamics of nanoworms as drug carriers within blood flow by considering the effects of nanoworm length, stiffness, and local physiological conditions such as hematocrit. We found that nanoworms with length of 8 μm and moderate stiffness are the optimal choice as drug carriers for circulating within normal vascular network due to their lower near wall margination. Compared to those of spherical rigid particles, these nanoworms demonstrate significant demargination behaviors at hematocrit 20%, induced by the local hydrodynamic interactions. Specifically, the interactions between nanoworms and red blood cells create asymmetrical local flow fields, resulting in the demargination of nanoworms. In addition, the flexibility of nanoworms enables them to conform to the deformed shape of red blood cells under shear flow, leading to their high concentration within the core region of vessels. Therefore, the long blood circulation time of nanoworms can be partially attributed to their demargination behaviors and intertwinement with red blood cells. According to these simulation results, tuning the length and stiffness of nanoworms is the key to design drug carries with reduced near wall margination within normal vascular networks and extend their blood circulation time.
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Affiliation(s)
- Huilin Ye
- Department of Mechanical Engineering, University of Connecticut, 191 Auditorium Road, Unit 3139, Storrs, Connecticut 06269, United States
| | - Zhiqiang Shen
- Department of Mechanical Engineering, University of Connecticut, 191 Auditorium Road, Unit 3139, Storrs, Connecticut 06269, United States
| | - Le Yu
- Department of Materials Science and Engineering, University of Connecticut, 97 North Eagleville Road, Unit 3136, Storrs, Connecticut 06269, United States
| | - Mei Wei
- Department of Materials Science and Engineering, University of Connecticut, 97 North Eagleville Road, Unit 3136, Storrs, Connecticut 06269, United States.,Institute of Materials Science, University of Connecticut, 97 North Eagleville Road, Unit 3136, Storrs, Connecticut 06269, United States
| | - Ying Li
- Department of Mechanical Engineering, University of Connecticut, 191 Auditorium Road, Unit 3139, Storrs, Connecticut 06269, United States.,Institute of Materials Science, University of Connecticut, 97 North Eagleville Road, Unit 3136, Storrs, Connecticut 06269, United States
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35
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Pawłowska S, Nakielski P, Pierini F, Piechocka IK, Zembrzycki K, Kowalewski TA. Lateral migration of electrospun hydrogel nanofilaments in an oscillatory flow. PLoS One 2017; 12:e0187815. [PMID: 29141043 PMCID: PMC5687761 DOI: 10.1371/journal.pone.0187815] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 10/26/2017] [Indexed: 12/31/2022] Open
Abstract
The recent progress in bioengineering has created great interest in the dynamics and manipulation of long, deformable macromolecules interacting with fluid flow. We report experimental data on the cross-flow migration, bending, and buckling of extremely deformable hydrogel nanofilaments conveyed by an oscillatory flow into a microchannel. The changes in migration velocity and filament orientation are related to the flow velocity and the filament's initial position, deformation, and length. The observed migration dynamics of hydrogel filaments qualitatively confirms the validity of the previously developed worm-like bead-chain hydrodynamic model. The experimental data collected may help to verify the role of hydrodynamic interactions in molecular simulations of long molecular chains dynamics.
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Affiliation(s)
- Sylwia Pawłowska
- Department of Biosystems and Soft Matter, Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland
| | - Paweł Nakielski
- Department of Biosystems and Soft Matter, Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland
| | - Filippo Pierini
- Department of Biosystems and Soft Matter, Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland
| | - Izabela K. Piechocka
- Department of Biosystems and Soft Matter, Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland
| | - Krzysztof Zembrzycki
- Department of Biosystems and Soft Matter, Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland
| | - Tomasz A. Kowalewski
- Department of Biosystems and Soft Matter, Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland
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36
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Nikoubashman A, Howard MP. Equilibrium Dynamics and Shear Rheology of Semiflexible Polymers in Solution. Macromolecules 2017. [DOI: 10.1021/acs.macromol.7b01876] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Arash Nikoubashman
- Institute of Physics, Johannes Gutenberg University Mainz, Staudingerweg 7, 55128 Mainz, Germany
| | - Michael P. Howard
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
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37
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Chien W, Chen YL. Confinement, curvature, and attractive interaction effects on polymer surface adsorption. J Chem Phys 2017; 147:064901. [DOI: 10.1063/1.4996738] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Affiliation(s)
- Wei Chien
- Institute of Physics, Academia Sinica, Taipei, Taiwan
- Department of Physics, National Taiwan University, Taipei, Taiwan
| | - Yeng-Long Chen
- Institute of Physics, Academia Sinica, Taipei, Taiwan
- Department of Physics, National Taiwan University, Taipei, Taiwan
- Department of Chemical Engineering, National Tsing-Hua University, Hsinchu, Taiwan
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38
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Zhao X, Li J, Jiang X, Karpeev D, Heinonen O, Smith B, Hernandez-Ortiz JP, de Pablo JJ. ParallelO(N) Stokes’ solver towards scalable Brownian dynamics of hydrodynamically interacting objects in general geometries. J Chem Phys 2017; 146:244114. [DOI: 10.1063/1.4989545] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Affiliation(s)
- Xujun Zhao
- Mathematics and Computer Science Division, Argonne National Laboratory, Lemont, Illinois 60439, USA
- Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA
| | - Jiyuan Li
- Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA
| | - Xikai Jiang
- Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA
| | - Dmitry Karpeev
- Mathematics and Computer Science Division, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - Olle Heinonen
- Materials Science Division, Argonne National Laboratory, Lemont, Illinois 60439, USA
- Northwestern-Argonne Institute for Science and Engineering, Evanston, Illinois 60208, USA
| | - Barry Smith
- Mathematics and Computer Science Division, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - Juan P. Hernandez-Ortiz
- Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA
- Departmento de Materiales, Universidad Nacional de Colombia, Sede Medellin, Colombia
| | - Juan J. de Pablo
- Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA
- Materials Science Division, Argonne National Laboratory, Lemont, Illinois 60439, USA
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39
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Palmer TL, Baardsen G, Skartlien R. Reduction of the effective shear viscosity in polymer solutions due to crossflow migration in microchannels: Effective viscosity models based on DPD simulations. J DISPER SCI TECHNOL 2017. [DOI: 10.1080/01932691.2017.1306784] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- T. L. Palmer
- Department of Petroleum Technology, University of Stavanger, Stavanger, Norway
- IOR Centre of Norway, Norway
| | - G. Baardsen
- Department of Process Technology, Institute for Energy Technology, Kjeller, Norway
- Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Oslo, Oslo, Norway
| | - R. Skartlien
- IOR Centre of Norway, Norway
- Department of Process Technology, Institute for Energy Technology, Kjeller, Norway
- Department of Chemical Engineering, Ugelstad Lab., NTNU, Trondheim, Norway
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40
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Debnath T, Ghosh PK, Nori F, Li Y, Marchesoni F, Li B. Diffusion of active dimers in a Couette flow. SOFT MATTER 2017; 13:2793-2799. [PMID: 28345093 DOI: 10.1039/c7sm00356k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We study the 3D dynamics of an elastic dimer consisting of an active swimmer bound to a passive cargo, both suspended in a Couette flow. Using numerical simulations, we determine the diffusivity of such an active dimer in the presence of long-range hydrodynamic interactions for different values of its self-propulsion speed and the Couette flow. We observe that the effect of hydrodynamic interactions is greatly enhanced under the condition that self-propulsion is strong enough to contrast the shear flow. The magnitude of the effect grows with the size of the dimer's constituents relative to their distance, which makes it appreciable under experimental conditions.
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Affiliation(s)
- Tanwi Debnath
- Department of Chemistry, University of Calcutta, Kolkata 700009, India
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41
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Qian W, Doi K, Kawano S. Effects of Polymer Length and Salt Concentration on the Transport of ssDNA in Nanofluidic Channels. Biophys J 2017; 112:838-849. [PMID: 28297643 PMCID: PMC5355498 DOI: 10.1016/j.bpj.2017.01.027] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 01/23/2017] [Accepted: 01/24/2017] [Indexed: 11/25/2022] Open
Abstract
Electrokinetic phenomena in micro/nanofluidic channels have attracted considerable attention because precise control of molecular transport in liquids is required to optically and electrically capture the behavior of single molecules. However, the detailed mechanisms of polymer transport influenced by electroosmotic flows and electric fields in micro/nanofluidic channels have not yet been elucidated. In this study, a Langevin dynamics simulation was used to investigate the electrokinetic transport of single-stranded DNA (ssDNA) in a cylindrical nanochannel, employing a coarse-grained bead-spring model that quantitatively reproduced the radius of gyration, diffusion coefficient, and electrophoretic mobility of the polymer. Using this practical scale model, transport regimes of ssDNA with respect to the ζ-potential of the channel wall, the ion concentration, and the polymer length were successfully characterized. It was found that the relationship between the radius of gyration of ssDNA and the channel radius is critical to the formation of deformation regimes in a narrow channel. We conclude that a combination of electroosmotic flow velocity gradients and electric fields due to electrically polarized channel surfaces affects the alignment of molecular conformations, such that the ssDNA is stretched/compressed at negative/positive ζ-potentials in comparatively low-concentration solutions. Furthermore, this work suggests the possibility of controlling the center-of-mass position by tuning the salt concentration. These results should be applicable to the design of molecular manipulation techniques based on liquid flows in micro/nanofluidic devices.
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Affiliation(s)
- Weixin Qian
- Department of Mechanical Science and Bioengineering, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka, Japan
| | - Kentaro Doi
- Department of Mechanical Science and Bioengineering, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka, Japan.
| | - Satoyuki Kawano
- Department of Mechanical Science and Bioengineering, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka, Japan.
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42
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Lüsebrink D, Cerdà JJ, Sánchez PA, Kantorovich SS, Sintes T. The behavior of a magnetic filament in flow under the influence of an external magnetic field. J Chem Phys 2016; 145:234902. [DOI: 10.1063/1.4971860] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- Daniel Lüsebrink
- IFISC (UIB-CSIC) Instituto de Física Interdisciplinar y Sistemas Complejos, Campus UIB, 07122 Palma de Mallorca, Spain
| | - Joan J. Cerdà
- IFISC (UIB-CSIC) Instituto de Física Interdisciplinar y Sistemas Complejos, Campus UIB, 07122 Palma de Mallorca, Spain
| | - Pedro A. Sánchez
- Faculty of Physics, Universität Wien, Boltzmanngasse 5, 1090 Wien, Austria
| | | | - Tomás Sintes
- IFISC (UIB-CSIC) Instituto de Física Interdisciplinar y Sistemas Complejos, Campus UIB, 07122 Palma de Mallorca, Spain
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43
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Farutin A, Piasecki T, Słowicka AM, Misbah C, Wajnryb E, Ekiel-Jeżewska ML. Dynamics of flexible fibers and vesicles in Poiseuille flow at low Reynolds number. SOFT MATTER 2016; 12:7307-7323. [PMID: 27507620 DOI: 10.1039/c6sm00819d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The dynamics of flexible fibers and vesicles in unbounded planar Poiseuille flow at low Reynolds number is shown to exhibit similar basic features, when their equilibrium (moderate) aspect ratio is the same and vesicle viscosity contrast is relatively high. Tumbling, lateral migration, accumulation and shape evolution of these two types of flexible objects are analyzed numerically. The linear dependence of the accumulation position on relative bending rigidity, and other universal scalings are derived from the local shear flow approximation.
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44
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Hsiao KW, Schroeder CM, Sing CE. Ring Polymer Dynamics Are Governed by a Coupling between Architecture and Hydrodynamic Interactions. Macromolecules 2016. [DOI: 10.1021/acs.macromol.5b02357] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Kai-Wen Hsiao
- Department
of Chemical and Biomolecular Engineering, University of Illinois Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Charles M. Schroeder
- Department
of Chemical and Biomolecular Engineering, University of Illinois Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Charles E. Sing
- Department
of Chemical and Biomolecular Engineering, University of Illinois Urbana−Champaign, Urbana, Illinois 61801, United States
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45
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Friedrich SM, Liu KJ, Wang TH. Single Molecule Hydrodynamic Separation Allows Sensitive and Quantitative Analysis of DNA Conformation and Binding Interactions in Free Solution. J Am Chem Soc 2016; 138:319-27. [PMID: 26684193 PMCID: PMC4812671 DOI: 10.1021/jacs.5b10983] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Limited tools exist that are capable of monitoring nucleic acid conformations, fluctuations, and distributions in free solution environments. Single molecule free solution hydrodynamic separation enables the unique ability to quantitatively analyze nucleic acid biophysics in free solution. Single molecule fluorescent burst data and separation chromatograms can give layered insight into global DNA conformation, binding interactions, and molecular distributions. First, we show that global conformation of individual DNA molecules can be directly visualized by examining single molecule fluorescent burst shapes and that DNA exists in a dynamic equilibrium of fluctuating conformations as it is driven by Poiseuille flow through micron-sized channels. We then show that this dynamic equilibrium of DNA conformations is reflected as shifts in hydrodynamic mobility that can be perturbed using salt and ionic strength to affect packing density. Next, we demonstrate that these shifts in hydrodynamic mobility can be used to investigate hybridization thermodynamics and binding interactions. We distinguish and classify multiple interactions within a single sample, and demonstrate quantification amidst large concentration differences for the detection of rare species. Finally, we demonstrate that these differences can resolve perfect complement, 2 bp mismatched, and 3 bp mismatched sequences. Such a system can be used to garner diverse information about DNA conformation and structure, and potentially be extended to other molecules and mixed-species interactions, such as between nucleic acids and proteins or synthetic polymers.
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Affiliation(s)
- Sarah M. Friedrich
- Biomedical Engineering Department, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218
| | - Kelvin J. Liu
- Biomedical Engineering Department, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218
| | - Tza-Huei Wang
- Biomedical Engineering Department, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218
- Mechanical Engineering Department, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218
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46
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Atwi A, Hijazi A, Khater A. Simulations of the PDF functions for dilute colloidal suspensions of molecular particles flowing in mesopores with rough surface boundaries. COLLOID JOURNAL 2016. [DOI: 10.1134/s1061933x16010038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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47
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Uematsu Y. Nonlinear electro-osmosis of dilute non-adsorbing polymer solutions with low ionic strength. SOFT MATTER 2015; 11:7402-7411. [PMID: 26274546 DOI: 10.1039/c5sm01507c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Nonlinear electro-osmotic behaviour of dilute non-adsorbing polymer solutions with low salinity is investigated using Brownian dynamics simulations and a kinetic theory. In the Brownian simulations, the hydrodynamic interaction between the polymers and a no-slip wall is considered using the Rotne-Prager approximation of the Blake tensor. In a plug flow under a sufficiently strong applied electric field, the polymer migrates toward the bulk, forming a depletion layer thicker than the equilibrium one. Consequently, the electro-osmotic mobility increases nonlinearly with increasing electric field and becomes saturated. This nonlinear mobility does not depend qualitatively on the details of the rheological properties of the polymer solution. Analytical calculations using the kinetic theory for the same system quantitatively reproduce the results of the Brownian dynamics simulation well.
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Affiliation(s)
- Yuki Uematsu
- Department of Physics, Kyoto University, Kyoto 606-8502, Japan.
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48
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Słowicka AM, Wajnryb E, Ekiel-Jeżewska ML. Dynamics of flexible fibers in shear flow. J Chem Phys 2015; 143:124904. [PMID: 26429038 DOI: 10.1063/1.4931598] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Dynamics of flexible non-Brownian fibers in shear flow at low-Reynolds-number are analyzed numerically for a wide range of the ratios A of the fiber bending force to the viscous drag force. Initially, the fibers are aligned with the flow, and later they move in the plane perpendicular to the flow vorticity. A surprisingly rich spectrum of different modes is observed when the value of A is systematically changed, with sharp transitions between coiled and straightening out modes, period-doubling bifurcations from periodic to migrating solutions, irregular dynamics, and chaos.
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Affiliation(s)
- Agnieszka M Słowicka
- Institute of Fundamental Technological Research, Polish Academy of Sciences, Pawińskiego 5b, 02-106 Warsaw, Poland
| | - Eligiusz Wajnryb
- Institute of Fundamental Technological Research, Polish Academy of Sciences, Pawińskiego 5b, 02-106 Warsaw, Poland
| | - Maria L Ekiel-Jeżewska
- Institute of Fundamental Technological Research, Polish Academy of Sciences, Pawińskiego 5b, 02-106 Warsaw, Poland
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49
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Ranjith SK. Mesoscopic simulation of single DNA dynamics in rotational flows. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2015; 38:89. [PMID: 26314257 DOI: 10.1140/epje/i2015-15089-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2015] [Revised: 06/11/2015] [Accepted: 06/22/2015] [Indexed: 06/04/2023]
Abstract
In this numerical study, the transport and dynamics of an isolated DNA in rotational flow generated in a microchannel have been investigated using dissipative particle dynamics. Often, inertial flow through microchannels with a sudden change in surface structure facilitates a re-circulation or vortex region. The conformation and mobility of the bio-polymer under the influence of such rotating fluid inside a square cavity of the microchannel is analyzed. The flexible polymer chain is found to migrate towards the rotating region and follows the vortex streamline. The orientation, size and tumbling period of polymer strands are affected by the strength of the microvortex. At elevated flow rates, the macromolecule prefers to remain inside the vortex and a hydrodynamic trap is formed. Moreover, residence time of the single molecule in the microcavity is significantly influenced by the chain length and flow strength. Further, it has been demonstrated that, such entrapment duration can be strategically altered by modifying the hydrophobicity of the microchannel.
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Affiliation(s)
- S Kumar Ranjith
- Micro/nanofluidics Research Laboratory, Department of Mechanical Engineering, College of Engineering Trivandrum, Govermnet of Kerala, 695016, Thiruvananthapuram, India,
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50
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Lee J, Kim Y, Lee S, Jo K. Visualization of large elongated DNA molecules. Electrophoresis 2015; 36:2057-71. [PMID: 25994517 DOI: 10.1002/elps.201400479] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 03/08/2015] [Accepted: 04/27/2015] [Indexed: 12/26/2022]
Abstract
Long and linear DNA molecules are the mainstream single-molecule analytes for a variety of biochemical analysis within microfluidic devices, including functionalized surfaces and nanostructures. However, for biochemical analysis, large DNA molecules have to be unraveled, elongated, and visualized to obtain biochemical and genomic information. To date, elongated DNA molecules have been exploited in the development of a number of genome analysis systems as well as for the study of polymer physics due to the advantage of direct visualization of single DNA molecule. Moreover, each single DNA molecule provides individual information, which makes it useful for stochastic event analysis. Therefore, numerous studies of enzymatic random motions have been performed on a large elongated DNA molecule. In this review, we introduce mechanisms to elongate DNA molecules using microfluidics and nanostructures in the beginning. Secondly, we discuss how elongated DNA molecules have been utilized to obtain biochemical and genomic information by direct visualization of DNA molecules. Finally, we reviewed the approaches used to study the interaction of proteins and large DNA molecules. Although DNA-protein interactions have been investigated for many decades, it is noticeable that there have been significant achievements for the last five years. Therefore, we focus mainly on recent developments for monitoring enzymatic activity on large elongated DNA molecules.
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Affiliation(s)
- Jinyong Lee
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Mapogu, Seoul, Republic of Korea
| | - Yongkyun Kim
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Mapogu, Seoul, Republic of Korea
| | - Seonghyun Lee
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Mapogu, Seoul, Republic of Korea
| | - Kyubong Jo
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Mapogu, Seoul, Republic of Korea
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