| 1. |
- Agrawal, Vipin, 1994-
(författare)
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Shells and filament in flows
- 2022
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The motivation to study elastic structures such as filaments and shells stemmed from its application in the construction of tall buildings, bridges etc. Interest in this field has rekindled in the past decades due to growing interest in understanding biological materials and because of possible applications in nanoscience and medicine. This also poses new challenges as the biological materials show both solid and fluid-like behavior, and in addition, they are active. In this thesis, we study the mechanical properties of shells and filament and their interaction with fluid. The thesis is divided into two themes. First, how to model nano-vesicles and how are the mechanical properties affected if a spherical shell is thermal and active? Second, can non-linear interaction between fluid and filament generate turbulence and hence mixing in the Stokes flow?To model nano-vesicles, we develop an open-source software package - MeMC. The MeMC models nano-vesicles as an elastic objects. It interprets the force-distance data generated by indentation of biological nano-vesicles by atomic force microscopes and uses Monte-Carlo simulations to compute elastic coefficients of a nano-vesicle. Further, we use this code and break the detailed balance in Monte-Carlo simulation - thereby driving the shell active and out of thermal equilibrium - to study the effect of activity on mechanical properties of elastic shells, in particular, buckling. Such a shell typically has either higher (active) or lower (quiescent) fluctuations compared to one in thermal equilibrium depending on how the detailed balance is broken. We show that for the same set of elastic parameters, a shell that is not buckled in thermal equilibrium can be buckled if turned active. Similarly, a shell that is buckled in thermal equilibrium can unbuckle if turned quiescent. Based on this result, we suggest that it is possible to experimentally design microscopic elastic shells whose buckling can be optically controlled.In the next part of the thesis, we visit the problem of mixing in Stokes flow using elastic filament. We study the interaction of the filament with Stokes flow. As it is known, the flow of Newtonian fluid at low Reynolds number is, in general, regular, and time-reversible due to absence of nonlinear effects. For example, if the fluid is sheared by its boundary motion that is subsequently reversed, then all the fluid elements return to their initial positions. Consequently, mixing in microchannels happens solely due to molecular diffusion and is very slow. Here, we show, numerically, that the introduction of a single, freely floating, flexible filament in a time-periodic linear shear flow can break time reversibility and give rise to chaos due to elastic nonlinearities, if the bending rigidity of the filament is within a carefully chosen range. Within this range, not only the shape of the filament is spatiotemporally chaotic, but also the flow is an efficient mixer. We model the filament using the bead-rod model. We consider two different models for the viscous forces: (a) they are modelled by the Rotne-Prager tensor. This incorporates the hydrodynamic interaction between every pair of beads. (b) we consider only the diagonal term of the Rotne-Prager tensor which makes the viscous forces local. In both cases, we find the same qualitative result: the shape of a stiff filament is time-invariant -- either straight or buckled for large enough bending rigidity; it undergoes a period-n bifurcation (n = 2,3, 4, etc) as the filament is made softer; becomes spatiotemporally chaotic for even softer filaments. For case (a) but not for (b) we find that the chaos is suppressed if bending rigidity is decreased further. For (b), in the chaotic phase, we show that the iterative map for the angle, which the end–to–end vector of the filament makes with the tangent its one end, has period three solutions; hence it is chaotic.
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| 2. |
- Bucciarelli, Saskia, et al.
(författare)
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Dramatic influence of patchy attractions on short-time protein diffusion under crowded conditions
- 2016
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Ingår i: Science Advances. - : American Association for the Advancement of Science (AAAS). - 2375-2548. ; 2:12, s. 1601432-1601432
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Tidskriftsartikel (refereegranskat)abstract
- In the dense and crowded environment of the cell cytoplasm, an individual protein feels the presence of and interacts with all surrounding proteins. While we expect this to strongly influence the short-time diffusion coefficient Ds of proteins on length scales comparable to the nearest-neighbor distance, this quantity is difficult to assess experimentally. We demonstrate that quantitative information about Ds can be obtained from quasi-elastic neutron scattering experiments using the neutron spin echo technique. We choose two well-characterized and highly stable eye lens proteins, bovine α-crystallin and γB-crystallin, and measure their diffusion at concentrations comparable to those present in the eye lens. While diffusion slows down with increasing concentration for both proteins, we find marked variations that are directly linked to subtle differences in their interaction potentials. A comparison with computer simulations shows that anisotropic and patchy interactions play an essential role in determining the local short-time dynamics. Hence, our study clearly demonstrates the enormous effect that weak attractions can have on the short-time diffusion of proteins at concentrations comparable to those in the cellular cytosol.
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| 3. |
- Henry, Ewan, et al.
(författare)
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Sorting cells by their dynamical properties
- 2016
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 6
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Tidskriftsartikel (refereegranskat)abstract
- Recent advances in cell sorting aim at the development of novel methods that are sensitive to various mechanical properties of cells. Microfluidic technologies have a great potential for cell sorting; however, the design of many micro-devices is based on theories developed for rigid spherical particles with size as a separation parameter. Clearly, most bioparticles are non-spherical and deformable and therefore exhibit a much more intricate behavior in fluid flow than rigid spheres. Here, we demonstrate the use of cells' mechanical and dynamical properties as biomarkers for separation by employing a combination of mesoscale hydrodynamic simulations and microfluidic experiments. The dynamic behavior of red blood cells (RBCs) within deterministic lateral displacement (DLD) devices is investigated for different device geometries and viscosity contrasts between the intra-cellular fluid and suspending medium. We find that the viscosity contrast and associated cell dynamics clearly determine the RBC trajectory through a DLD device. Simulation results compare well to experiments and provide new insights into the physical mechanisms which govern the sorting of non-spherical and deformable cells in DLD devices. Finally, we discuss the implications of cell dynamics for sorting schemes based on properties other than cell size, such as mechanics and morphology.
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| 4. |
- Henry, Ewan, et al.
(författare)
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Sorting red blood cells by their dynamical properties
- 2016
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Ingår i: 20th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2016. - 9780979806490 ; , s. 786-787
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Konferensbidrag (refereegranskat)abstract
- A combination of mesoscale hydrodynamic simulations and microfluidic experiments are used to explore the use of cells' mechanical and dynamical properties as biomarkers for separation. Dynamic behaviour of red blood cells (RBCs) within deterministic lateral displacement (DLD) devices is investigated within various array geometries and for different viscosity contrasts between the intra- and extra-cellular fluid. We find that the viscosity contrast and associated cell dynamics clearly determine RBC trajectories through DLD devices. Simulation results compare well to experiments and provide new insights into the physical mechanisms which govern the sorting of non-spherical and deformable cells in DLD devices.
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| 5. |
- Hochstetter, Axel, et al.
(författare)
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Deterministic Lateral Displacement : Challenges and Perspectives
- 2020
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Ingår i: ACS Nano. - : American Chemical Society (ACS). - 1936-0851 .- 1936-086X. ; 14:9, s. 10784-10795
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Forskningsöversikt (refereegranskat)abstract
- The advent of microfluidics in the 1990s promised a revolution in multiple industries from healthcare to chemical processing. Deterministic lateral displacement (DLD) is a continuous-flow microfluidic particle separation method discovered in 2004 that has been applied successfully and widely to the separation of blood cells, yeast, spores, bacteria, viruses, DNA, droplets, and more. Deterministic lateral displacement is conceptually simple and can deliver consistent performance over a wide range of flow rates and particle concentrations. Despite wide use and in-depth study, DLD has not yet been fully elucidated or optimized, with different approaches to the same problem yielding varying results. We endeavor here to provide up-to-date expert opinion on the state-of-art and current fundamental, practical, and commercial challenges with DLD as well as describe experimental and modeling opportunities. Because these challenges and opportunities arise from constraints on hydrodynamics, fabrication, and operation at the micro- and nanoscale, we expect this Perspective to serve as a guide for the broader micro- and nanofluidic community to identify and to address open questions in the field.
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| 6. |
- Holm, Stefan H., et al.
(författare)
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Microfluidic Particle Sorting in Concentrated Erythrocyte Suspensions
- 2019
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Ingår i: Physical Review Applied. - 2331-7019. ; 12:1
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Tidskriftsartikel (refereegranskat)abstract
- An important step in diagnostics is the isolation of specific cells and microorganisms of interest from blood. Since such bioparticles are often present at very low concentrations, throughput needs to be as high as possible. In addition, to ensure simplicity, a minimum of sample preparation is important. Therefore, sorting schemes that function for whole blood are highly desirable. Deterministic lateral displacement (DLD) devices have proven to be very precise and versatile in terms of a wide range of sorting parameters. To better understand how DLD devices perform for blood as the hematocrit increases, we carry out measurements and simulations for spherical particles in the micrometer range which move through DLD arrays for different flow velocities and hematocrits ranging from pure buffer to concentrated erythrocyte suspensions mimicking whole blood. We find that the separation function of the DLD array is sustained even though the blood cells introduce a shift in the trajectories and a significant dispersion for particles whose diameters are close to the critical size in the device. Simulations qualitatively replicate our experimental observations and help us identify fundamental mechanisms for the effect of hematocrit on the performance of the DLD device.
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| 7. |
- Hong, Liang, et al.
(författare)
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Structure and Dynamics of a Compact State of a Multidomain Protein, the Mercuric Ion Reductase
- 2014
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Ingår i: Biophysical Journal. - : Elsevier BV. - 1542-0086 .- 0006-3495. ; 107:2, s. 393-400
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Tidskriftsartikel (refereegranskat)abstract
- The functional efficacy of colocalized, linked protein domains is dependent on linker flexibility and system compaction. However, the detailed characterization of these properties in aqueous solution presents an enduring challenge. Here, we employ a novel, to our knowledge, combination of complementary techniques, including small-angle neutron scattering, neutron spin-echo spectroscopy, and all-atom molecular dynamics and coarse-grained simulation, to identify and characterize in detail the structure and dynamics of a compact form of mercuric ion reductase (MerA), an enzyme central to bacterial mercury resistance. MerA possesses metallochaperone-like N-terminal domains (NmerA) tethered to its catalytic core domain by linkers. The NmerA domains are found to interact principally through electrostatic interactions with the core, leashed by the linkers so as to subdiffuse on the surface over an area close to the core C-terminal Hg(II)-binding cysteines. How this compact, dynamical arrangement may facilitate delivery of Hg(II) from NmerA to the core domain is discussed.
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| 8. |
- Liu, Xiaoyan, et al.
(författare)
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Wrapping anisotropic microgel particles in lipid membranes : Effects of particle shape and membrane rigidity
- 2023
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - 0027-8424. ; 120:30
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Tidskriftsartikel (refereegranskat)abstract
- Cellular engulfment and uptake of macromolecular assemblies or nanoparticles via endocytosis can be associated to both healthy and disease-related biological processes as well as delivery of drug nanoparticles and potential nanotoxicity of pollutants. Depending on the physical and chemical properties of the system, the adsorbed particles may remain at the membrane surface, become wrapped by the membrane, or translocate across the membrane through an endocytosis-like process. In this paper, we address the question of how the wrapping of colloidal particles by lipid membranes can be controlled by the shape of the particles, the particle–membrane adhesion energy, the membrane phase behavior, and the membrane-bending rigidity. We use a model system composed of soft core–shell microgel particles with spherical and ellipsoidal shapes, together with phospholipid membranes with varying composition. Confocal microscopy data clearly demonstrate how tuning of these basic properties of particles and membranes can be used to direct wrapping and membrane deformation and the organization of the particles at the membrane. The deep-wrapped states are more favorable for ellipsoidal than for spherical microgel particles of similar volume. Theoretical calculations for fixed adhesion strength predict the opposite behavior-wrapping becomes more difficult with increasing aspect ratio. The comparison with the experiments implies that the microgel adhesion strength must increase with increasing particle stretching. Considering the versatility offered by microgels systems to be synthesized with different shapes, functionalizations, and mechanical properties, the present findings further inspire future studies involving nanoparticle–membrane interactions relevant for the design of novel biomaterials and therapeutic applications.
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| 9. |
- Myung, Jin Suk, et al.
(författare)
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Weak Shape Anisotropy Leads to a Nonmonotonic Contribution to Crowding, Impacting Protein Dynamics under Physiologically Relevant Conditions
- 2018
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Ingår i: The Journal of Physical Chemistry Part B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106. ; 122
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Tidskriftsartikel (refereegranskat)abstract
- The effect of a nonspherical particle shape on the dynamics in crowded solutions presents a significant challenge for a comprehensive understanding of interaction and structural relaxation in biological and soft matter. We report that small deviations from a spherical shape induce a nonmonotonic contribution to the crowding effect on the short-time cage diffusion compared with spherical systems, using molecular dynamics simulations with mesoscale hydrodynamics of a multiparticle collision dynamics fluid in semidilute systems with volume fractions smaller than 0.35. We show that the nonmonotonic effect due to anisotropy is caused by the combination of a reduced relative mobility over the entire concentration range and a looser and less homogeneous cage packing of nonspherical particles. Our finding stresses that nonsphericity induces new complexity, which cannot be accounted for in effective sphere models, and is of great interest in applications such as formulations as well as for the fundamental understanding of soft matter in general and crowding effects in living cells in particular.
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| 10. |
- Zhang, Z., et al.
(författare)
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Deformability-based sorting of red blood cells in deterministic lateral displacement devices
- 2016
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Ingår i: 20th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2016. - 9780979806490 ; , s. 788-789
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Konferensbidrag (refereegranskat)abstract
- Mesoscopic simulations with two-dimensional (2D) models have been performed to elucidate the dynamics of deformable red blood cells (RBCs) in deterministic lateral displacement (DLD) devices. Several shapes of posts, including circular, diamond, square and triangular structures and RBCs with different rigidities are considered. In comparison to rigid particles, the deformable RBCs exhibit much more complex dynamics within a DLD device, which not only brings additional complications but also provides new separation mechanisms (e.g., based on cell deformability). Further simulation results reveal that the post geometry which induces more cell deformation can be applied to effectively sort RBCs based on their rigidity.
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