Flow Alignment Research Articles

Two-fluid model for the breakdown of flow alignment in nematic liquid crystals.

We present a macroscopic two-fluid model to explain the breakdown of flow alignment in nematic liquid crystals under shear flow due to smectic clusters. We find that the velocity difference of the two fluids plays a key role to mediate the time-dependent behavior as soon as a large enough amount of smectic order is induced by flow. For the minimal model it is sufficient to keep the nematic degrees of freedom, the mass density of the smectic clusters and the degree of smectic order, the density, and two velocities as macroscopic variables. While frequently a smectic A or C phase arises at lower temperatures, this is not required for the applicability of the present model. Indeed, as pointed out before by Gähwiller, there are compounds showing a breakdown of flow alignment over a large temperature range and no smectic phase, but a solid phase at lower temperatures. We also demonstrate that, using a one velocity model, there is no coupling under shear flow between induced smectic order and the director orientation in stationary situations thus rendering such a model to be unsuitable to describe the breakdown of flow alignment. In a two-fluid description, flow alignment breaks down and becomes unstable with regard to a space- and time-dependent state due to an induced finite velocity difference. In an Appendix we outline a mesoscopic model to account for the sign change in the anisotropy of the electric conductivity observed in nematics with smectic clusters.

Reference flow: reducing reference bias using multiple population genomes

Most sequencing data analyses start by aligning sequencing reads to a linear reference genome, but failure to account for genetic variation leads to reference bias and confounding of results downstream. Other approaches replace the linear reference with structures like graphs that can include genetic variation, incurring major computational overhead. We propose the reference flow alignment method that uses multiple population reference genomes to improve alignment accuracy and reduce reference bias. Compared to the graph aligner vg, reference flow achieves a similar level of accuracy and bias avoidance but with 14% of the memory footprint and 5.5 times the speed.

Measurement of the charge separation along the magnetic field with Signed Balance Function in 200 GeV Au + Au collisions at STAR

Experimental searches for Chiral Magnetic Effect (CME) in heavy-ion collisions have been going on for a decade, and so far there is no conclusive evidence for its existence. Recently, the Signed Balance Function (SBF), based on the idea of examining the momentum ordering of charged pairs along the in- and out-of-plane directions, has been proposed as a probe of CME. In this approach, a pair of observables is invoked: one is rrest, the out-of-plane to in-plane ratio of ΔB measured in pair's rest frame, where ΔB is the difference between signed balance functions; The other is a double ratio, RB = rrest/rlab, where rlab is a measurement similar to rrest but measured in the laboratory frame. These two observables give opposite responses to the CME-driven charge separation compared to the background correlations arising from resonance flow and global spin alignment. Both rrest and RB being larger than unity can be regarded as a case in favor of the existence of CME. It is found experimentally that rrest, rlab and RB are larger than unity in Au+Au collisions at 200 GeV, and larger than realistic model calculations with no CME implemented. These findings are difficult to be explained by a background-only scenario.

In situ magnetorheological SANS setup at Institut Laue-Langevin

A magnetorheological sample environment is presented that allows for in situ magnetic field and shear flow during small-angle neutron scattering (SANS) measurements and is now available at the Institut Laue-Langevin (ILL). The setup allows performing simultaneous magnetorheological measurements together with the investigation of structural and magnetic changes on the nanometer length scale underlying the rheological response of ferrofluids. We describe the setup consisting of a commercial rheometer and a custom-made set of Helmholtz coils and show exemplarily data on the field and shear flow alignment of a dispersion of hematite nanospindles in water.Graphical abstractA magnetorheological sample environment is presented that allows for in-situ magnetic field and shear flow during Small-Angle Neutron Scattering (SANS) measurements and is now available at the Institut Laue-Langevin (ILL).

Fingerprinting the nonlinear rheology of a liquid crystalline polyelectrolyte

We report on the rheology of isotropic and nematic aqueous solutions of a sulfonated all-aromatic polyamide, poly(2,2′-disulfonyl-4,4′-benzidine terephthalamide) (PBDT), that forms high-aspect-ratio rod-like assemblies. For quiescently isotropic solutions, the concentration dependence of the zero-shear viscosity, longest relaxation time, and terminal modulus shows deviations in comparison to the Doi-Edwards theory for hard rods. For quiescently nematic solutions, we characterize the flow behavior through steady-state and transient nonlinear rheological measurements in conjunction with small-angle neutron scattering under shear. The steady-state flow curve is characterized by two anomalous shear thickening responses, one at moderate shear rates and the other immediately prior to flow alignment at high shear rates. We assign the origin of these shear thickening response to director “kayaking” and “out-of-plane steady” states, using predictions from prior high-resolution numerical simulations of sheared nematic rods. Utilizing transient shear flow reversals and step-down experiments, we characterize the oscillatory response of the nematic director through these flow regimes. When the first normal stress difference is plotted versus the shear stress during a transient step-down, the so-called dynamic stress path, the counterclockwise versus clockwise rotation has previously been shown to reveal the relative dominance of viscous versus elastic contributions to the stress tensor, respectively. Our measurements strongly suggest that the anomalous shear thickening behavior in nematic PBDT solutions arises from viscous stresses developed as the ensemble of rods undergoes periodic oscillatory motion under shear, rather than elastic stresses due to broadening of the orientational distribution function.

DMA 내 막대형 시스 유동 층류화 장치에 의한 샘플 유동 정렬 및 입자 분류 효율 향상

DMA 내 막대형 시스 유동 층류화 장치에 의한 샘플 유동 정렬 및 입자 분류 효율 향상

Probe chiral magnetic effect with signed balance function * * A.H. Tang is supported by the US Department of Energy (DE-AC02-98CH10886, DE-FG02-89ER40531)

In this paper a pair of observables are proposed as alternative ways, by examining the fluctuation of net momentum-ordering of charged pairs, to study the charge separation induced by the Chiral Magnetic Effect (CME) in relativistic heavy ion collisions. They are, the out-of-plane to in-plane ratio of fluctuation of the difference between signed balance functions measured in pair’s rest frame, and the ratio of it to similar measurement made in the laboratory frame. Both observables have been studied with simulations including flow-related backgrounds, and for the first time, backgrounds that are related to resonance's global spin alignment. The two observables have similar positive responses to signal, and opposite, limited responses to identifiable backgrounds arising from resonance flow and spin alignment. Both observables have also been tested with two realistic models, namely, a multi-phase transport (AMPT) model and the anomalous-viscous fluid dynamics (AVFD) model. These two observables, when cross examined, will provide useful insights in the study of CME-induced charge separation.

Observation of transition cascades in sheared liquid crystalline polymers.

We report on the shear rheology of liquid crystalline solutions composed of charged, rodlike polymers that form supramolecular assemblies dispersed in water. Under steady shear, we observe shear thickening behavior, followed by a hesitation in the viscosity accompanied by an extremely narrow range of negative first normal stress difference. The Peclet number (Pe, shear rate normalized by rod rotational diffusivity) for the onset of shear thickening is in agreement with previous, high-resolution numerical simulations of the Doi-Edwards-Hess kinetic theory. We interrogate these dynamic responses through shear step-down experiments, revealing a complex evolution of transient responses. Detailed analysis of the stress transients provides compelling evidence that the principal axis of the rod orientational distribution, the nematic director, undergoes a cascade of transitions and coexistence of periodic states known as kayaking, tumbling, and wagging, before transitioning to steady flow alignment above a critical shear rate.

Integrative analysis for prediction of process-induced, orientation-dependent tensile properties in a stochastic prepreg platelet molded composite

Prepreg platelet molded composite (PPMC) is derived from compression molded pieces of chopped unidirectional prepreg tape. The properties of a stochastic PPMC arise from the meso-structure that develops during processing. This paper describes an integrated methodology for analysis of stochastic PPMC to develop process-structure-property relationships. Flow-induced fiber orientation distributions were predicted using an anisotropic viscous constitutive model implemented in a nonlinear, explicit finite element (FE) solver. The predicted orientation state was validated by CT-based orientation measurements and optical microscopy. A computational framework for simulation of tensile property distributions of a stochastic PPMC by progressive failure analysis is presented. The probabilistic simulation results were statistically validated against experimental data. A FE analysis was developed with an explicitly modeled platelet meso-structure wherein the platelets are treated as a homogeneous orthotropic medium using continuum damage mechanics to model the intraplatelet failure and a cohesive zone model for interlaminar disbonding. Panels were molded using partial charge coverage to induce flow alignment of the fibers. Tensile coupons were excised from the molded panels both along (parallel) and transverse (perpendicular) to the preferential fiber direction to compare the composite effective properties with those reported in the literature for planar random orientation states. The composite tensile properties were found to be strongly dependent on the global orientation state.

Assessing recall of personal sun exposure by integrating UV dosimeter and self-reported data with a network flow framework.

BackgroundMelanoma survivors often do not engage in adequate sun protection, leading to sunburn and increasing their risk of future melanomas. Melanoma survivors do not accurately recall the extent of sun exposure they have received, thus, they may be unaware of their personal UV exposure, and this lack of awareness may contribute towards failure to change behavior. As a means of determining behavioral accuracy of recall of sun exposure, this study compared subjective self-reports of time outdoors to an objective wearable sensor. Analysis of the meaningful discrepancies between the self-report and sensor measures of time outdoors was made possible by using a network flow algorithm to align sun exposure events recorded by both measures. Aligning the two measures provides the opportunity to more accurately evaluate false positive and false negative self-reports of behavior and understand participant tendencies to over- and under-report behavior.Methods39 melanoma survivors wore an ultraviolet light (UV) sensor on their chest while outdoors for 10 consecutive summer days and provided an end-of-day subjective self-report of their behavior while outdoors. A Network Flow Alignment framework was used to align self-report and objective UV sensor data to correct misalignment. The frequency and time of day of under- and over-reporting were identified.FindingsFor the 269 days assessed, the proposed framework showed a significant increase in the Jaccard coefficient (i.e. a measure of similarity between self-report and UV sensor data) by 63.64% (p < .001), and significant reduction in false negative minutes by 34.43% (p < .001). Following alignment of the measures, under-reporting of sun exposure time occurred on 51% of the days analyzed and more participants tended to under-report than to over-report sun exposure time. Rates of under-reporting of sun exposure were highest for events that began from 12-1pm, and second-highest from 5-6pm.ConclusionThese discrepancies may reflect lack of accurate recall of sun exposure during times of peak sun intensity (10am–2pm) that could ultimately increase the risk of developing melanoma. This research provides technical contributions to the field of wearable computing, activity recognition, and identifies actionable times to improve participants’ perception of their sun exposure.

Closing the Mitochondrial Permeability Transition Pore in hiPSC-Derived Endothelial Cells Induces Glycocalyx Formation and Functional Maturation.

SummaryHuman induced pluripotent stem cells (hiPSCs) are used to study organogenesis and model disease as well as being developed for regenerative medicine. Endothelial cells are among the many cell types differentiated from hiPSCs, but their maturation and stabilization fall short of that in adult endothelium. We examined whether shear stress alone or in combination with pericyte co-culture would induce flow alignment and maturation of hiPSC-derived endothelial cells (hiPSC-ECs) but found no effects comparable with those in primary microvascular ECs. In addition, hiPSC-ECs lacked a luminal glycocalyx, critical for vasculature homeostasis, shear stress sensing, and signaling. We noted, however, that hiPSC-ECs have dysfunctional mitochondrial permeability transition pores, resulting in reduced mitochondrial function and increased reactive oxygen species. Closure of these pores by cyclosporine A improved EC mitochondrial function but also restored the glycocalyx such that alignment to flow took place. These results indicated that mitochondrial maturation is required for proper hiPSC-EC functionality.

Two-shape-tensor model for tumbling in nematic polymers and liquid crystals.

Most, but not all, liquid crystals tend to align when subject to shear flow, while most nematic polymeric liquid crystals undergo a tumbling instability, where the director rotates with the flow. The reasons of this instability remain elusive, as it is possible to find similar molecules exhibiting opposite behaviors. We propose a continuum theory suitable for describing a wide range of material behaviors, ranging form nematic elastomers to nematic polymers and nematic liquid crystals, where the material parameters have meaningful physical interpretations and the conditions for tumbling emerge clearly. There are two possible ways to relax the internal stress in a nematic material. The first is the reorganization of the polymer network, the second is the alignment of the network natural axis with respect to the principal direction of the effective strain. We show that tumbling occurs whenever the second mechanism is less efficient than the first. Furthermore, we provide a justification of the experimental fact that at high temperatures, in an isotropic phase, only flow alignment is observed and no tumbling is possible, even in polymers.

Multiparticle collision dynamics for tensorial nematodynamics.

Liquid crystals establish a nearly unique combination of thermodynamic, hydrodynamic, and topological behavior. This poses a challenge to their theoretical understanding and modeling. The arena where these effects come together is the mesoscopic (micron) scale. It is then important to develop models aimed at capturing this variety of dynamics. We have generalized the particle-based multiparticle collision dynamics (MPCD) method to model the dynamics of nematic liquid crystals. Following the Qian-Sheng theory [Phys. Rev. E 58, 7475 (1998)1063-651X10.1103/PhysRevE.58.7475] of nematics, the spatial and temporal variations of the nematic director field and order parameter are described by a tensor order parameter. The key idea is to assign tensorial degrees of freedom to each MPCD particle, whose mesoscopic average is the tensor order parameter. This nematic MPCD method includes backflow effect, velocity-orientation coupling, and thermal fluctuations. We validate the applicability of this method by testing (i) the nematic-isotropic phase transition, (ii) the flow alignment of the director in shear and Poiseuille flows, and (iii) the annihilation dynamics of a pair of line defects. We find excellent agreement with existing literature. We also investigate the flow field around a force dipole in a nematic liquid crystal, which represents the leading-order flow field around a force-free microswimmer. The anisotropy of the medium not only affects the magnitude of velocity field around the force dipole, but can also induce hydrodynamic torques depending on the orientation of dipole axis relative to director field. A force dipole experiences a hydrodynamic torque when the dipole axis is tilted with respect to the far-field director. The direction of hydrodynamic torque is such that the pusher- (or puller-) type force dipole tends to orient along (or perpendicular to) the director field. Our nematic MPCD method can have far-reaching implications not only in modeling of nematic flows, but also to study the motion of colloids and microswimmers immersed in an anisotropic medium.

Robust Planar Odometry Based on Symmetric Range Flow and Multiscan Alignment

This paper presents a dense method for estimating planar motion with a laser scanner. Starting from a symmetric representation of geometric consistency between scans, we derive a precise range flow constraint and express the motion of the scan observations as a function of the rigid motion of the scanner. In contrast to existing techniques, which align the incoming scan with either the previous one or the last selected keyscan, we propose a combined and efficient formulation to jointly align all these three scans at every iteration. This new formulation preserves the advantages of keyscan-based strategies but, is more robust against suboptimal selection of keyscans and the presence of moving objects. An extensive evaluation of our method is presented with simulated and real data in both static and dynamic environments. Results show that our approach is one order of magnitude faster and significantly more accurate than existing methods in all the conducted experiments. With a runtime of about one millisecond, it is suitable for those robotic applications that require planar odometry with low computational cost. The code is available online as a ROS package.

Dissipative versus reversible contributions to macroscopic dynamics: the role of time-reversal symmetry and entropy production

We discuss the time-reversal behavior of dynamic cross-couplings among various hydrodynamic degrees of freedom in liquid crystal systems. Using a standard hydrodynamic description including linear irreversible thermodynamics, we show that the distinct thermodynamic requirements for reversible and irreversible couplings lead to experimentally accessible differences. We critically compare our descriptions with those of existing standard continuum mechanics theories, where time-reversal symmetry is not adequately invoked. The motivation comes from recent experimental progress allowing to discriminate between the hydrodynamic description and the continuum mechanics approach. This concerns the dynamics of Lehmann-type effects in chiral liquid crystals and the dynamic magneto-electric response in ferronematics and ferromagnetic nematics, a liquid multiferroic system. In addition, we discuss the consequences of time-reversal symmetry for flow alignment of the director in nematics (or pretransitional nematic domains) and for the dynamic thermo-mechanical and electro-mechanical couplings in textured nematic liquid crystals.

Enhanced sedimentation of elongated plankton in simple flows

Negatively buoyant phytoplankton play an important role in the sequestration of CO_2 from the atmo-sphere and are fundamental to the health of the world’s fisheries. However, there is still much to discoveron transport mechanisms from the upper photosynthetic regions to the deep ocean. In contrast to intuitive expectations that mixing increases plankton residence time in light-rich regions, recent experimental and computational evidence suggests that turbulence can actually enhance sedimentation of negatively buoyant diatoms. Motivated by these studies we dissect the enhanced sedimentation mechanisms using the simplest possible two-dimensional flows, avoiding expensive computations and obfuscation. In particular, we find that in vertical shear, preferential flow alignment and aggregation in down-welling regions both increase sedimentation, whereas horizontal shear reduces the sedimentation due only to alignment. However the magnitude of the shear does not affect the sedimentation rate. In simple vertical Kolmogorov flow elongated particles also have an enhanced sedimentation speed as they spend more time in down-welling regions of the flow with vertically aligned orientation, an effect that increases with the magnitude of shear. An additional feature is identified in horizontal Kolomogorov flow, whereby the impact of shear-dependent sedimentation speed is to cause aggregation in regions of high-shear where the sedimentation speed is minimum. In cellular flow, there is an increase in mean sedimentation speed with aspect ratio and shear strength associated with aggregation in down-welling regions. Furthermore, spatially projected trajectories can intersect and give rise to chaotic dynamics, which is associated with a depletion of particles within so called retention zones.

Effects of flow on the dynamics of a ferromagnetic nematic liquid crystal.

We investigate the effects of flow on the dynamics of ferromagnetic nematic liquid crystals. As a model, we study the coupled dynamics of the magnetization, M, the director field, n, associated with the liquid crystalline orientational order, and the velocity field, v. We evaluate how simple shear flow in a ferromagnetic nematic is modified in the presence of small external magnetic fields, and we make experimentally testable predictions for the resulting effective shear viscosity: an increase by a factor of 2 in a magnetic field of about 20 mT. Flow alignment, a characteristic feature of classical uniaxial nematic liquid crystals, is analyzed for ferromagnetic nematics for the two cases of magnetization in or perpendicular to the shear plane. In the former case, we find that small in-plane magnetic fields are sufficient to suppress tumbling and thus that the boundary between flow alignment and tumbling can be controlled easily. In the latter case, we furthermore find a possibility of flow alignment in a regime for which one obtains tumbling for the pure nematic component. We derive the analogs of the three Miesowicz viscosities well-known from usual nematic liquid crystals, corresponding to nine different configurations. Combinations of these can be used to determine several dynamic coefficients experimentally.

Flow Preservation of Umbilical Vein for Autologous Shunt and Cardiovascular Reconstruction

Synthetic graft materials are commonly used for shunts and cardiovascular reconstruction in neonates, but are prone to thrombosis and scarring. The umbilical vein is a potential source of autologous, endothelialized tissue for neonatal shunts and tissue reconstruction, but requires preservation before implantation. Umbilical cords were collected in UW solution with antibiotics at 4°C until dissection. Umbilical vein segments were tested for burst pressure before and after 2 weeks of preservation. Umbilical veins segments were preserved under static or flow conditions at 4°C in UW solution with 5% human plasma lysate for 7 days. Veins were evaluated with histopathology, scanning electron microscopy, and platelet adhesion testing. Umbilical veins have no difference in burst pressure at harvest (n= 16) compared with 2 weeks of preservation (n= 11; 431 ± 229 versus 438 ± 244 mm Hg). After 1 week, static and flow-preserved veins showed viability of the vessel segments with endothelium staining positive for CD31, von Willebrand factor, and endothelial nitric oxide synthase. Scanning electron microscopy demonstrated preservation of normal endothelial morphology and flow alignment in the flow-preserved samples compared with cobblestone endothelial appearance and some endothelial cell loss in the static samples. Static samples had significantly more platelet adhesion than flow-preserved samples did. Umbilical veins have adequate burst strength to function at neonatal systemic pressures. Preservation under flow conditions demonstrated normal endothelial and overall vascular morphology with less platelet adhesion compared with static samples. Preserved autologous umbilical veins are potential source for endothelialized shunts or cardiovascular repair tissue for neonates.

QFMatch: multidimensional flow and mass cytometry samples alignment

Part of the flow/mass cytometry data analysis process is aligning (matching) cell subsets between relevant samples. Current methods address this cluster-matching problem in ways that are either computationally expensive, affected by the curse of dimensionality, or fail when population patterns significantly vary between samples. Here, we introduce a quadratic form (QF)-based cluster matching algorithm (QFMatch) that is computationally efficient and accommodates cases where population locations differ significantly (or even disappear or appear) from sample to sample. We demonstrate the effectiveness of QFMatch by evaluating sample datasets from immunology studies. The algorithm is based on a novel multivariate extension of the quadratic form distance for the comparison of flow cytometry data sets. We show that this QF distance has attractive computational and statistical properties that make it well suited for analysis tasks that involve the comparison of flow/mass cytometry samples.

Flow Alignment of Extracellular Vesicles: Structure and Orientation of Membrane-Associated Bio-macromolecules Studied with Polarized Light.

Extracellular vesicles (EVs) are currently in scientific focus, as they have great potential to revolutionize the diagnosis and therapy of various diseases. However, numerous aspects of these species are still poorly understood, and thus, additional insight into their molecular-level properties, membrane-protein interactions, and membrane rigidity is still needed. We here demonstrate the use of red-blood-cell-derived EVs (REVs) that polarized light spectroscopy techniques, linear and circular dichroism, can provide molecular-level structural information on these systems. Flow-linear dichroism (flow-LD) measurements show that EVs can be oriented by shear force and indicate that hemoglobin molecules are associated to the lipid bilayer in freshly released REVs. During storage, this interaction ceases; this is coupled to major protein conformational changes relative to the initial state. Further on, the degree of orientation gives insight into vesicle rigidity, which decreases in time parallel to changes in protein conformation. Overall, we propose that both linear dichroism and circular dichroism spectroscopy can provide simple, rapid, yet efficient ways to track changes in the membrane-protein interactions of EV components at the molecular level, which may also give insight into processes occurring during vesiculation.