TALKS
A locally corrected multiblob method with hydrodynamically matched grids for the Stokes mobility problem
Anna Broms, Mattias Sandberg (KTH Royal Institute of Technology), Anna-Karin Tornberg (KTH Royal Institute of Technology)
Abstract:
Inexpensive numerical methods are key to enabling simulations of systems of a large number of particles of different shapes in Stokes flow. Several different approximate methods have been introduced for this purpose. We study the accuracy of the multiblob method for solving the deterministic Stokes mobility problem in free space, where the 3D geometry of a particle surface is discretised with spherical blobs and the pair-wise interaction between blobs is described by the RPY-tensor. The aim is to investigate and improve on the magnitude of the error in the resulting Stokes mobility matrix using two different techniques: an optimisation procedure to find an optimal grid of blobs and a pair-correction inspired by Stokesian dynamics. The optimisation of the grid with a certain number of blobs is done to match the hydrodynamics of a single model particle, alone in the fluid, with the motivation that for large particle-particle distances, this self-interaction for each particle dominates the global coupling present for all particles in the fluid. We can choose to match rotational or translational properties of the model particle, or both, with the centers of the blobs placed on a geometric surface interior to the surface of the model particle. With a small error in the self-interaction, more accurate computations for well-separated particles can be obtained, even with coarse blob-resolutions of the particle surfaces, and the self-interaction error sets the precise error level. The pair-correction is local and cheap-to-apply, allowing for a further reduced error level for distant particles, but more importantly, improves on the error substantially also for moderately separated particles and particles in close proximity. Two different types of geometries are considered: spheres and axisymmetric rods with smooth caps. The error in the mobility matrix is quantified for particles of varying inter-particle distances for systems containing a few particles, comparing to an accurate solution based on a second kind BIE-formulation where the quadrature error is controlled by employing quadrature by expansion (QBX).
Active rotating particles in confined and structured environments
Juan L. Aragones, Paula Magrinya (Universidad Autonoma de Madrid), Galor Geva (Universidad Autonoma de Madrid), Pablo Llombart (Universidad Autonoma de Madrid), Laura R. Arriaga (Universidad Autonoma de Madrid)
Abstract:
In this work, we study the dynamics of active rotating particles confined either in vesicles or in structured environments to develop strategies for controlling the transport of colloidal systems. Magnetic particles that rotate under the actuation of an external rotating magnetic field generate flows and when encapsulated in giant vesicles, the flow confinement leads to the rotation of the vesicle, and its ultimate translation on a substrate. Moreover, we show that the transport properties of the confined particle and rotating vesicle strongly depends on the mechanical properties of the vesicle membrane. Alternatively, the flow generated by the active particles can be confined in a structured array of obstacles, leading to the transport of particles through the array. We show that the trajectories of the particles in the array of obstacles can be dynamically controlled and widely depend on the order of the obstacles. Both systems may enable the design of materials with defined and controlled transport properties.
Activity-induced instabilities and emergent patterns in active suspensions
Ignacio Pagonabarraga (CECAM HQ)
Abstract:
Active suspensions can displace in a liquid medium in which they are suspended as a result of nonequilibrium processes, such as chemical reactions, or inhomogeneous thermal heating. These are intrinsically out of equilibrium systems, which makes them very versatile, with a natural tendency to self-assemble. Due to their small size, these out of equilibrium dynamical states generates flows that induce long range hydrodynamic interactions. These interactions have profound effects in the transport and assembly of colloidal suspensions.
I will analyze the role that hydrodynamics play in the rectification mechanism that leads to their motion, as well as the possibility that hydrodynamic instabilities lead to novel estates of self-propulsion. I will discuss the impact that these mechanisms have in the emergence of patterns and different type of morhological structures in model active suspensions. I will combine theoretical simple models and computer simulations to gain insight in the role of hydrodynamics in these out of equilibrium system.
Collective motion of torque-dipolar micro-swimmers
Enkeleida Lushi (New Jersey Institute of Technology)
Abstract:
We present a model and simulations for micro-swimmers that take into account the counter-rotation of the body and flagella, as seen in motile bacteria or spermatozoa. The disturbance fluid flow of one such swimmer now contains a torque-dipole singularity in addition to the well-known force-dipolar singularity. The linear analysis of the coarse-grained model shows an instability for a range of parameters, which we summarise in a phase diagram. Lastly, we show large-scale simulations of torque-dipolar micro-swimmers and illustrate the collective behavior in the regions of parameter space indicated by the stability analysis.
Detecting temporal correlations in hopping dynamics in Lennard–Jones liquids
Vittoria Sposini, Aleksei V. Chechkin (University of Potsdam), Igor M. Sokolov (Humboldt University Berlin), Sándalo Roldán-Vargas (University of Granada)
Abstract:
Lennard–Jones mixtures represent one of the popular systems for the study of glass–forming liquids. Spatio/temporal heterogeneity and rare (activated) events are at the heart of the slow dynamics typical of these systems. Such slow dynamics is characterised by the development of a plateau in the mean–squared displacement at intermediate times, accompanied by a non–Gaussianity in the displacement distribution identified by exponential tails. Single–particle motion of glass–forming liquids is usually interpreted as an alternation of rattling within the local cage and cage–escape motion and therefore can be described as a sequence of waiting times and jumps. In this talk I will discuss the emergence of temporal anti–correlations among waiting times, which become more and more pronounced when lowering the temperature.
Dynamics and distributions of cells in blood flow
Michael Graham (University of Wisconsin-Madison)
Abstract:
As they flow, red blood cells migrate toward the center of a blood vessel, leaving a so-called cell-free layer at the vessel wall, while white blood cells and platelets are preferentially found near the walls, a segregration phenomenon called margination. We present direct simulations of blood flow as well as mechanistic theory that aim to describe and understand these phenomena. We also describe collaborative work with the laboratory of Wilbur Lam that demonstrates the importance of these phenomena in medicine.
To disentangle effects of shape, size, and deformability, with first describe direct simulations of multicomponent suspensions of deformable capsules. Observations indicate that margination can be driven by contrasts of size, stiffness or shape – for example, a trace component of stiff or small particles will marginate in a suspension whose majority component is large and soft. A simple theory based on pair -collisions and wall-induced migration predicts, in good agreement with experiments and our simulations, that the cell-free layer thickness follows a master curve with confinement ratio and volume fraction. It also predicts several regimes of segregation, depending on the value of a dimensionless “margination parameter” that combines the effects of collisions and migration.
These segregation phenomena have important physiological and clinical consequences. Treatment of patients with drugs such as dexamethasone or epinephrine lead to softening of white blood cells, and thus to their demargination. In blood disorders such as sickle cell disease and iron deficiency anemia, the diseased cells are smaller and stiffer than heathy red blood cells, and our simulations predict that these cells will strongly marginate. We also predict that that these marginated cells generate large shear stress fluctuations on the vessel walls, a phenomenon that may explain clinical observations of vascular inflammation in persons with these disorders.
Effects of virus morphology on their translational and rotational diffusion
Nicolas Moreno, Daniela Moreno-Chaparro (Basque Center for Applied Mathematics), Florencio Balboa Usabiaga (Basque Center for Applied Mathematics), Marco Ellero (Basque Center for Applied Mathematics)
Abstract:
Enveloped viruses possess a characteristic morphology constituted by an envelope decorated with spike proteins localised on the surface. Spike proteins are responsible for specific virus/cell interactions and binding. However, they can provide relevant information about the microrheological features of the viruses. Here, we investigate the passive transport of enveloped viruses to elucidate the effect of their morphology on their infectivity. The translational and rotational diffusivity of the virions were computed using the rigid multiblob method (RMB). Virions of different spike morphology and number (SARS-CoV-2, HIV, Herpes, Influenza) were investigated. We identified that the diffusion of the virus significantly reduces for viruses with bulkier spikes. Moreover, the mobility reached a saturation condition, where increasing the spikes number no longer affected their diffusion. Our findings indicate that the diffusional mechanisms of SARS-CoV-2 are controlled by the characteristic size and distribution of its spikes. Remarkably, the evidence suggests that the low number of spikes in viruses such as SARS-CoV-2 stems from geometrical constraints preserved in a variety of viruses with a larger number of spikes. These findings can provide tools for designing microrheological devices to screen, detect, and characterise viruses.
Filament simulation with applications to cilia dynamics
Eric Keaveny (Imperial College London)
Abstract:
In this talk, I will provide an overview of a recently developed framework to simulate the motion of flexible filaments in viscous fluids. The framework relies on a combination of numerical techniques such as implicit geometric time integration and quasi-Newton methods and can interface with a wide variety of hydrodynamic models developed by the community, including matrix-free methods. I will present results from simulations where we use the methodology to explore the coordinated motion of active filaments. In particular, I will highlight how the coordinated state changes with the topology of the surface to which the filaments are attached, and whether or not the surface is fixed or free to move.
Load-dependent friction between particles induces shear-thinning behaviour : simulations and experiments
François Peters, Laurent Lobry (InPhyNi (University Côte d'Azur)), Elisabeth Lemaire (InPhyNi (University Côte d'Azur))
Abstract:
The last decades have seen the emergence of the idea that contact between particles has a strong influence on the rheological behaviour of non-Brownian suspensions. In particular, friction between contacting particles induces strongly enhanced viscosity, bringing the viscosity from numerical simulations to the level of experimental data. In addition, together with the inclusion of repulsive forces that hinder contact, taking friction into account allowed to explain the long-standing issue of Discontinuous Shear Thickening in non-Brownian suspensions as a transition from frictionless to frictional contacts as the repulsive forces are overcome [1].
In light of the strong influence of friction on non-Brownian suspension rheology, the question of the precise nature of frictional contact interactions arises. Up to now, most of the particle scale computational studies have indeed only considered standard Coulomb friction, according to which solid contact involves a constant friction coefficient. In the present work, a modified contact law is considered, where the friction coefficient depends on the normal force between particles. The idea is that, due to the low force level experienced by contacting particles in a sheared non-Brownian suspension, contact occurs only through a small number of asperities, so that the friction coefficient decreases as load increases. With the help of particle scale simulations using this contact law, we provide an explanation of the long-standing issue of the shear-thinning behaviour that is often observed in non-Brownian suspensions rheology [2]. In addition, a simple model is built from the simulation data, that allows to compute the suspension viscosity with only the contact law as an input. In order to validate this approach, experiments have been performed using an AFM that allowed to measure the friction coefficient between contacting particles [3]. The latter as been found to decrease with load, and the viscosity computed from the experimental friction law displays shear-thinning behaviour, in quantitative agreement with experimental measurements.
Reference
[1]R. Seto, R. Mari, J. Morris, M. Denn, Phys. Rev. Lett., 111, 218301 (2013)
[2]L. Lobry, E. Lemaire, F. Blanc, S. Gallier, F. Peters, J. Fluid Mech., 860, 682-710 (2018)
[3]M. Arshad, A. Maali, C. Claudet, L. Lobry, F. Peters, E. Lemaire, Soft Matter, 17, 6088-6097 (2021)
Macromolecules in hydrodynamic flows: the effect of flexibility, anisotropy, and geometry
Marisol Ripoll, Carlos A. R. Medina (Forschungszentrum Jülich)
Abstract:
The flow behavior of macromolecules with different degrees of anisotropy and flexibility leads to numerous interesting questions with a large number practical applications. The characterization of the molecule conformations is not trivial from an experimental viewpoint, and it has important implications in the rheological or phoretic behavior of the system. By means of mesoscopic simulations it is possible to investigate the properties of such systems in the presence and in the absence of hydrodynamic simulations, what allows us to quantify their importance. In this talk, we will discuss first the induced periodic deformation of flexible helices, and ring polymers in shear flow, and show how the presence of hydrodynamic interactions induces a vorticity displacement on chiral molecules [1] and a vorticity swelling on ring polymers [2]. In contrast to shear flow, in the presence of a temperature gradient, anisotropic, or flexible macromolecules do not get deformed, nor oriented, unless they are completely or partially fixed [3]. We will show then how a temperature gradient induces an osmotic flow close to anisotropic fixed particles [4], the spinning of stiff helicoidal macromolecules, and the elongation of flexible macromolecules [5].
[1] Run Li, G. Gompper, M. Ripoll, Macromolecules, 2021, 54, 812
[2] M. Liebetreu, M. Ripoll, C. N. Likos, ACS Macro Lett. 2018, 7, 447
[3] Z. Tan, M. Yang, M. Ripoll, Soft Matter, 2017, 13, 7283
[4] Z. Tan, M. Yang, M. Ripoll, Phys. Rev. App., 2019, 11, 054004
[5] C. A. R. Medina, M. Ripoll, preprint, 2022
Magnetorheology in Pulsed & Triaxial Fields
Juan de Vicente, coauthors: G. Camacho, J. R. Morillas, M. Terkel, A. Rodríguez-Barroso, Ó. Martínez-Cano (University of Granada)
Abstract:
Conventional magnetorheological (MR) fluids are colloidal suspensions prepared by dispersion of magnetisable particles in non-magnetic liquid carriers. Interestingly, they exhibit a remarkable rheological change (so-called MR effect) upon the application of a magnetic field. The reason for this is the magnetic field-guided colloidal assembly of the dispersed magnetisable particles. The self-assembly can be controlled through the field configuration (DC, AC or combinations) and most of the investigations reported in the literature focus on DC fields. In this communication we show that the use of AC fields alone or in combination of DC fields are capable to generate exotic structures with enhanced MR effect (i.e. larger viscoelastic moduli and yield stresses).
First, a device is constructed to measure the MR effect under homogeneous magnetic fields in saturation. The device optimization is done using magnetostatic Finite Element Method simulations. Also, Computational Fluid Dynamics simulations are performed and validated against experiments and theoretical calculations. Magnetostatic simulations on model dipolar lattices are carried out in a wide range of particle concentrations at saturation and results compared to experimental ones. Deviations between simulations and experiments are presumably due to a lower compactness and the presence of defects in the field-generated structures. This hypothesis is supported by particle level simulations and experiments under pulsed magnetic fields.
Second, a triaxial magnetic field generator is built to operate up to frequencies of 4 kHz and preliminary experimental data are reported on the directed self-assembly and rheological evaluation of model MR fluids. Bigger aggregates are formed, and the MR effect is subsequently enhanced, by subjecting MR fluids to carefully controlled intervals of uniaxial DC fields and precession fields in the velocity gradient direction. Experimental results are found to be in good qualitative agreement with particle-level simulations and videomicroscopy observations.
Acknowledgements:
This work was supported by ERDF, FEDER, MICINN AE EQC2019-005529-P and PID2019-104883GB-I00 projects, Junta de Andalucía P18-FR-2465 and A-FQM-396-UGR20 projects, FPU20/04357, BES-2017-079891, (EF-ST)-H2020-MSCA-IF-2017 (Grant 795318) and (EFST)-H2020-MSCA-IF-2020 (Grant 101030666) fellowships.
Mapping articulated microswimmers to phoretic particles
Florencio Balboa Usabiaga, Harinadha Gidituri (BCAM - Basque Center for Applied Mathematics), Gökberk Kabacaoğlu (2) (Bilkent University, Ankara), Marco Ellero (BCAM - Basque Center for Applied Mathematics)
Multi-scale models and experiments for interparticle interactions in nanoparticle aggregates
Pietro Asinari, Paola Tiberto (INRiM)
Abstract:
Interparticle interactions in aggregates are essential in determining the long-lasting stability of nanoparticle suspensions and hence the accumulation of nanoparticles in tissues, which is critical in therapeutic applications, as well as in toxicity assessments. For example, dipolar interaction markedly modifies the way a tissue is heated by an assembly of embedded nanoparticles in magnetic hyperthermia treatments. A second example might be that aggregation free energy of nanoparticles is among the physical descriptors used by Quantitative Structure-Activity Relationship models (QSAR) to finally predict toxicity. In this talk, we will present models and experiments for describing and characterising interparticle interactions and their impact on toxicity assessments and therapeutic applications. Firstly, we introduce a multi-scale modelling protocol: starting from ab initio Density Functional Theory (DFT) to get an accurate determination of the energetics and electronic structure, we switch to classical Molecular Dynamics (MD) simulations to calculate the Potential of Mean Force (PMF) for the connection of two identical nanoparticles in water [1]. Next, we discuss the heating efficiency of an assembly of magnetic nanoparticles under an alternating driving field by using rate equations with the aim of clarifying the factors affecting their performance as tracers in magnetic particle imaging (MPI) [2].
Reference
[1]G. Mancardi, M. Alberghini, N. Aguilera-Porta, M. Calatayud, P. Asinari, E. Chiavazzo, Nanomaterials, 12, 217 (2022)
[2]G. Barrera, P. Allia, P. Tiberto, ACS Appl. Nano Mater., 5, 2699-2714 (2022)
Nano-hydrodynamics and the slip boundary condition
Pep Español (UNED)
Abstract:
The interstitial gap between colloidal particles in concentrated or aggregated suspensions may be on the nanometer scale. It is then a question of whether at such scales the equations of hydrodynamic are applicable. We construct from first principles a simple theory for discrete non-local hydrodynamics near parallel solid walls that describes the irreversible solid-liquid interaction through extended friction forces entering the equations of motion[1,2]. The resolution of this discrete theory can be varied reaching the continuum limit at high resolutions. However, we show that at high-resolution non-Markovian effects are detectable, particularly near the walls. This precludes a Markovian theory for the description of the dynamics of the fluid density layering near the walls. The discrete non-local theory is used to derive the slip boundary condition for its corresponding approximate local theory, with a microscopic expression for the slip length. We assess the slip boundary condition through MD simulations of an unsteady plug flow.
References
[1]D. Duque-Zumajo, J. de la Torre, D. Camargo, P. Español, Phys. Rev. E, 100, 062133 (2019)
[2]J. de la Torre, D. Duque-Zumajo, D. Camargo, P. Español, Phys. Rev. Lett., 123, 264501 (2019)
Neural Network Based Reduced Model for Stokesian Particulate Flows
Gokberk Kabacaoglu (Bilkent University)
Stokesian particulate flows describe the hydrodynamics of rigid or deformable particles in the zero Reynolds number regime. Due to highly nonlinear fluid-structure interaction dynamics, moving interfaces, and multiple scales, numerical simulations of such flows are challenging and expensive. I will present our machine-learning-augmented reduced model for fast simulations of such flows. Besides, I will show how the reduced model enables us study optimal microfluidic device design for dense suspensions of deformable particles.
Our goal is to design a deterministic lateral displacement (DLD) device to sort same-size biological cells by their deformability, in particular to sort red blood cells by their viscosity contrast between the fluid in the interior and the exterior of the cells. A DLD device optimized for efficient cell sorting enables rapid medical diagnoses of several diseases such as malaria since infected cells are stiffer than their healthy counterparts. In this context, I will first describe an integral equation formulation that delivers optimal complexity solvers for this type of problems. Despite its excellent theoretical properties, our integral equation solver remains prohibitively expensive for optimization and uncertainty quantification. I will then summarize our efforts to reduce the computational costs, starting from low-resolution discretization, domain truncation, and model reduction.
Model reduction is used to accelerate the action of specific and very expensive nonlinear operators. The final scheme blends ultra low-resolution solvers (who on their own cannot resolve the flow), several regression neural networks, and an operator time-stepping scheme, which we introduced to specifically enable the use of surrogate models. We have used our methodology successfully for flows that are completely different from the flows in the training dataset.
This is a joint work with George Biros at the University of Texas at Austin.
Reference
[1]G. Kabacaoğlu, G. Biros, Phys. Rev. E, 99, 063313 (2019)
Optical forces and complex suspensions
Manuel Marques (Universidad Autonoma de Madrid)
Abstract:
In this talk I review the origin of optical forces and how they can be used to create and manipulate complex suspensions. First, I will describe some key concepts on optical forces in arbitrary particles, like the Maxwell stress energy tensor. Then, I will focus on the dipole approximation, and I will analyze in detail the forces on particles with size much smaller than the radiation wavelength [1-3]. I will show how this force affects the dynamics of complex systems made up of isolated particles [4,5], dimmers [6], and suspensions of several particles, and how these problems are tackled through the so-called discrete dipole approximation and the Green dyadic tensor. Finally, I will show some examples of control of diffusion and collective dynamics using standing waves [7], isotropic random electromagnetic fields [8,9], and generation of active motion using nonreciprocal optical forces [10].
Reference
[1]T. Boyer, Phys. Rev. A, 7, 1832-1840 (1973)
[2]P. Chaumet, M. Nieto-Vesperinas, Opt. Lett., 25, 1065 (2000)
[3]S. Albaladejo, M. Marqués, M. Laroche, J. Sáenz, Phys. Rev. Lett., 102, 113602 (2009)
[4]S. Albaladejo, M. Marqués, F. Scheffold, J. Sáenz, Nano Lett., 9, 3527-3531 (2009)
[5]S. Albaladejo, M. Marqués, J. Sáenz, Opt. Express, 19, 11471 (2011)
[6]J. Luis-Hita, J. Sáenz, M. Marqués, ACS Photonics, 3, 1286-1293 (2016)
[7]R. Delgado-Buscalioni, M. Meléndez, J. Luis-Hita, M. Marqués, J. Sáenz, Phys. Rev. E, 98, 062614 (2018)
[8]V. Pastor, M. Marqués, Phys. Rev. A, 97, 053837 (2018)
[9]J. Luis-Hita, M. Marqués, R. Delgado-Buscalioni, N. de Sousa, L. Froufe-Pérez, F. Scheffold, J. Sáenz, Phys. Rev. Lett., 123, 143201 (2019)
[10]J. Luis-Hita, J. Sáenz, M. Marqués, ACS Photonics, 9, 1008-1014 (2022)
Physical Virology with Atomic Force Microscopy: seeing and touching viruses and protein cages
Pedro J de Pablo (Autonomous University of Madrid)
Abstract:
The basic architecture of a virus consists of the capsid, a shell made up of repeating protein subunits, which packs, shuttles and delivers their genome at the right place and moment. Viral particles are endorsed with specific physicochemical properties which confer to their structures certain meta-stability whose modulation permits fulfilling each task of the viral cycle. These natural designed capabilities have impelled using viral capsids as protein containers of artificial cargoes (drugs, polymers, enzymes, minerals) with applications in biomedical and materials sciences. Both natural and artificial protein cages have to protect their cargo against a variety of physicochemical aggressive environments, including molecular impacts of highly crowded media, thermal and chemical stresses, and osmotic shocks. Viral cages stability depend not only on the ultimate structure of the external capsid, which rely on the interactions between protein subunits, but also on the nature of the cargo. During the last decade our lab has focused on the study of protein cages with Atomic Force Microscopy (AFM). We are interested in stablishing links of their mechanical properties with their structure and function. In particular, mechanics provide information about the cargo storage strategies of both natural and virus-derived protein cages. Mechanical fatigue has revealed as a nanosurgery tool to unveil the strength of the capisd subunit bonds . This allows to unveil ageing effects on virus structures (6), in a similar way to ageing in materials science.
References
Passive and active particle dynamics in complex fluids
Gwynn Elfring (University of British Columbia)
Abstract
There is a rich history in the literature on the effects of particles in Newtonian flows, but when the suspending fluid is also complex, as it is in many applications from environmental flows such as avalanches or mudslides, to energy applications such as down-hole scenarios in the oilfield, to biophysical flows such as cells in the human body, the rheology of these suspensions is far less understood. Particles can interact with nonlinear non-Newtonian stresses in these complex suspensions to significantly alter flows and an ongoing effort is to characterize and understand these effects.
In this talk, I will discuss a number of instances where particles suspended in complex fluids lead to markedly different dynamics and rheology for microhydrodynamic flows. For example, particles suspended in a Newtonian fluid will increase the apparent viscosity of the fluid, called the Einstein viscosity; however, if instead the suspending fluid is shear-thinning, the higher strain-rates induced by the particles will also produce a competing apparent reduction of the viscosity and for a dilute suspension of particles in a weakly shear-thinning fluid, these combined effects lead to modified Einstein viscosity. I will also discuss how active particles (biological or otherwise) can display completely different behaviour in complex fluids, such as reciprocal swimmers that in a Newtonian fluid would not produce net motion but in a complex fluid move and whose motion is directly coupled with the non-Newtonian rheology of the fluid. Finally, I will raise some of the fundamental difficulties involved in porting methods developed for the modelling and simulation of suspensions in Newtonian fluids, both passive and active, to tackle the problem of suspensions in non-Newtonian fluids.
Sculpting vesicles with active particles
Dmitry Fedosov, Masoud Hoore (Forschungszentrum Juelich), Clara Abaurrea-Velasco (Forschungszentrum Juelich), Hanumantha Vutukuri (University of Twente), Thorsten Auth (Forschungszentrum Juelich), Jan Vermant (ETH Zuerich), Gerhard Gompper (Forschungszentrum Juelich)
Abstract:
Biological cells are able to generate intricate structures and respond to external stimuli, sculpting their membrane from inside. Simplified biomimetic systems can aid in understanding the principles which govern these shape changes and elucidate the response of the cell membrane under strong deformations. We employ a combined simulation and experimental approach to investigate different non-equilibrium shapes and active shape fluctuations of vesicles enclosing self-propelled particles [1]. Interestingly, the most pronounced shape changes are observed at relatively low particle loadings, starting with the formation of tether-like protrusions to highly branched, dendritic structures. At high volume fractions, globally deformed vesicle shapes are observed. The obtained state diagram of vesicles sculpted by active particles predicts the conditions under which local internal forces can generate dramatic cell shape changes. Finally, we will discuss challenges and limitations in modelling such complex systems.
References
Simulating dense suspensions: how far can we go with discrete element methods?
Christopher Ness (University of Edinburgh)
Abstract:
This contribution will review recent progress in establishing the discrete element method as a tool for studying dense suspension rheology. We will discuss what physics can and cannot be included in such models and what their advantages and disadvantages are.
Simulating fluctuating fiber suspensions
Brennan Sprinkle, Ondrej Maxian (NYU), Aleksandar Donev (NYU)
Abstract:
The stochastic nature of sub-cellular processes coupled with the ever-changing topology of cytoskeletal networks make the microscopic dynamics of a cell difficult or impossible to carefully interrogate through lab measurements or existing simulation techniques. In this talk I'll present a novel method capable of simulating microscopic fiber networks, with a particular focus on the cellular cytoskeleton. The numerical method I’ll describe leverages fast linear algebra and carefully designed temporal integration to simulate the Brownian dynamics of flexible, fluctuating, inextensible microfilament suspensions with Linear complexity. The method treats fibers as curves on the unit sphere so that strict inextensibility is maintained as they evolve - and I'll describe how this approach is used to ensure that both inextensibility and detailed ballance are maintined as the system evolves. I'll also briefly describe how we can use these simulations to study the Rheology of fiberous gels.
Simulating magnetization cycles of magnetic nanoparticles for biosensing
Pablo Palacios Alonso, Elena Sanz-de Diego (iMdea nanocicencia), Sedef Özel (iMdea nanocicencia), Fracisco J. Terán (iMdea nanocicencia), Rafael Delgado Buscalioni (Universidad Autónoma de Madrid)
Abstract:
Nowadays, there are an increasing number of applications based on magnetic nanoparticles (MNP) suspended in a solution. In this complex fluid the Brownian displacements of the MNPs are coupled by long ranged hydrodynamic and magnetic interactions. Here we present an efficient scheme for simulating this kind of systems implemented in a high-performance GPU code (UAMMD) [1]. By solving these complex dynamics this tool permits to simulate multitude of experimental systems.
We have used our implementation to simulate the dynamics of magnetic nanoparticles under the effect of an AC magnetic field. This problem is the basis of a novel biomarker detection technique named AC magnetometry [2] in which the changes of the AC magnetization cycles of the particles when they interact with the target biomolecule are used to detect their presence. Depending on the valence of the analyte the changes in the cycles are due to the modification of the surface if the valence is equal to one or due to the formation of cross-linking structures if the valence is equal or higher than to. First, we have simulated the magnetization cycles of different particles when they interact with a monovalent analyte obtaining an excellent agreement with the experimental measurements and now, we are studying the cycles of particles when they interact with a divalent analyte leading to the formation of cross-linking structures. In this second system hydrodynamic and magnetic couplings between the particles are very relevant.
References
[1]https://github.com/RaulPPelaez/UAMMD/
[2]https://patentscope.wipo.int/search/en/detail.jsf?docId=WO2019092131
Simulating suspensions of passive and active articulated bodies in Stokes flow
Blaise Delmotte, Florencio Balboa Usabiaga (2) ((2) Basque Center for Applied Mathematics)
Abstract:
An articulated body is defined as a finite number of rigid bodies connected in an arbitrary fashion by a set of constraints that limit the relative motion between pairs of bodies. Such a general definition encompasses a wide variety of situations in the microscopic world, from bacteria to synthetic micro-swimmers, but it is also encountered when discretising inextensible bodies, such as filaments or membranes. Simulating suspensions of such articulated bodies requires to solve hydrodynamic interactions between large collections of objects of arbitrary shape while satisfying the multiple constraints that connect them. We identify three main challenges in this task: (1) limiting the cost of the hydrodynamic solves, (2) reducing the number of degrees of freedom in the system, (3) enforcing the constraints within machine precision at each time-step. To address the first challenge we propose a formalism that combines the body mobility problem with a velocity formulation of the constraints, resulting in a mixed mobility-resistance problem. While resistance problems are known to scale badly with the particle number, our preconditioned iterative solver is not sensitive to the system size, therefore allowing to study large suspensions with quasilinear computational cost. In order to reduce the number of degrees of freedom in the system, we extend the well-known robot- arm model to the more general case of hybrid chains, so that only one reference position and the bodies orientations are needed to track an articulated body. Finally, we pre- vent any constraint violation, e.g. due to discrete time-integration errors, by correcting the particles’ positions and orientations at the end of each time-step. Our correction procedure, based on a nonlinear minimisation algorithm, is negligible in terms of com- putational cost and preserves the accuracy of the time-integration scheme. We illustrate the capacity of our method by simulating large suspensions of fully resolved bacteria interacting near a no-slip boundary.
Simulating the magnetization dynamics of magnetic nanoparticles for biomedical applications
Jonathan Leliaert, Daniel Ortega (Condensed Matter Physics, University of Cadiz, Cadiz, Spain), Javier Ortega-Julia (Ghent University), Annelies Coene (Ghent University)
Abstract:
Magnetic nanoparticles are increasingly employed in biomedical applications such as disease detection and tumor treatment. To ensure a safe and efficient operation of these applications, a complete understanding of the particle dynamics is required. In this talk, I will present the results of two simulation studies in which we model the particles' magnetization (and in one case also the rotational) dynamics.
Firstly [1], a magnetic characterization technique is presented in which the particles are excited by specific pulsed time-varying magnetic fields. This way, we can selectively excite nanoparticles of a given size so that the resulting measurement gives direct information on the size distribution without the need for any a priori assumptions or complex postprocessing procedures to decompose the measurement signal, which contrasts state-of-the-art magnetic characterization techniques. The possibility to selectively excite certain particle types opens up perspectives in “multicolor” particle imaging, where different particle types need to be imaged independently within one sample.
Secondly [2], building on previous theoretical work, we present an equation to estimate the heat dissipation of individual, interacting particles at nonzero temperature that perform both field-induced and thermal switching. After validating this equation, we investigate a system of interacting particles with different anisotropies.
Our results indicate that the generated heat becomes more homogeneously distributed at larger fields. We believe that this homogenization of the particle heating will help to achieve a more homogenized heating of tumours during hyperthermia treatments. The use of the proposed equation would simplify the selection process of optimum nanoparticle distributions leading to optimal tumour heating. Its simplicity and flexibility also allow it to be integrated into multi-scale, multiphysics simulations to accurately assess the magnetic hyperthermia therapy without impacting the overall computational time.
Reference
[1]A. Coene, J. Leliaert, Sensors, 20, 3882 (2020)
Simulations of dense suspensions of rough polydisperse particles with a tribological variable-friction coefficient model
Jose Antonio Ruiz-Lopez, Sagaya Prasanna Kumar (Basque Centre for Applied Mathematics), Adolfo Vázquez-Quesada (Autonomous University of Madrid), Juan de Vicente (University of Granada), Marco Ellero (Basque Centre for Applied Mathematics)
Some curious rheology of suspensions with non-Newtonian matrices
Roger Tanner (University of Sydney)
Abstract:
Whilst progress has been made with the mechanics of non-colloidal suspensions with Newtonian matrices the introduction of non-Newtonian matrix fluids presents new challenges.
For all matrix types the availability of experimental data for comparison with computations is generally limited to:
- 1. Steady shear viscosity
- 2. Normal stress differences- N1 and N2
- 3. Uniaxial elongational flow (Planar extensions are too hard)
- 4. Unsteady shear flows: Reversing shears and sinusoidal oscillations.
In the present talk it is assumed that the particles are rigid spheres of equal size and that Brownian motion can be neglected. Examining each case in turn, 1 and 2 are steady viscometric flows and there have been several sets of experiments and several approaches by computation including some from members of this Workshop. For non-Newtonian matrices it is usual to assume in computations that the matrix fluid can be described by a single-mode Oldroyd-B model or a closely related model. It seems progress is being made.
Turning to case 3 (uniaxial extensional flows) there are few experiments and no computations as far as I know. For the experiments reported here the viscoelastic matrix fluid seems to be well described by a single-mode Oldroyd-B model. However experiments on suspensions show a dramatic (O(10)) increase in the elongational viscosity even for a mere 5% volume fraction of spheres. From this curious result it appears that the single-mode Oldroyd-B model is inadequate, and an explanation is given.
For case 4, we show the effect of matrix viscoelasticity on the Gadala-Maria/Acrivos reversing strain eaperiments. We also examine the G’, G” results for the suspensions. They do not resemble a single-mode response.
In conclusion, one sees the necessity of being very careful in selecting a model for computation.
Steady and wave contractions of biological gels
Alex Mogilner (New York University)
Abstract:
Many events in cell and developmental biology depend on contraction of actomyosin gels. In live cells, these contractions are so complicated that biophysicists resorted to reconstruction of the contraction events in cell extract bubbles. In small bubbles, a continuous, steady centripetal contraction evolves, while in larger bubbles, periodic waves of contraction develop. I will demonstrate that the steady-to-wave transition can be explained by a balance of the actomyosin gel assembly and gel movements. Furthermore, this phenomenon depends on complex density-dependent mechanical properties of the actomyosin gel.
Study of the rheology of non-colloidal suspensions with inter-particle slip boundary conditions
Adolfo Vázquez-Quesada, Sagaya Savarimuthu Prassana Kumar (BCAM), Marco Ellero (BCAM)
Abstract:
Nowadays, computational simulations have allowed to reproduce and explain many of the mechanisms in complex fluids. Despite advances, there are still not well-understood mechanisms, even for the simplest case of a suspension of spherical non-colloidal (no thermal noise) particles in a Newtonian solvent. For example, these systems show shear-thinning in experiments [1], .i.e. viscosity decreases with increasing shear stress, while a mild shear-thickening is typically obtained in frictionless simulations [2]. Some explanations for the thinning include "hidden" high-shear rates non-Newtonian effects of the solvet [3], elastic-to-plastic deformation in contact asperities [4] and, more recently adhesive effects [5]. Another possible explanation for the shear-thinning phenomenon is that the no-slip condition is not appropriate anymore to describe the interaction between close spheres [6, 7], leading to a slip-induced shear-thinning on the overall suspensions [8, 9].
Specifically, we propose here a reduction of the viscosity of the solvent at the gaps between close particles. A bi-viscous model [10] is used to calculate the lubrication force, to get us to a slip model with a non-constant slip length along the surface of the particles [9]. By tuning the parameters of this model, experimental results of a sphere approaching a planar wall [11] can be reproduced. The modified lubrication force is also introduced in a fast lubrication dynamics model [12] to study the rheology of dense suspensions, showing that the shear-thinning observed in experiments can be reproduced qualitatively. Finally, introduction of particles roughness in combination with slip is proposed as a possible mechanism to obtain quatitative agreement.
[1] Tanner, R. I. (2015). Journal of Non-Newtonian Fluid Mechanics, 222, 18-23.
[2] Vázquez-Quesada, A., & Ellero, M. (2016). Journal of Non-Newtonian Fluid Mechanics, 233, 37-47.
[3] Vázquez-Quesada, A., Tanner, R. I., & Ellero, M. (2016). Physical review letters, 117(10), 108001.
[4] Lobry, L., Lemaire, E., Blanc, F., Gallier, S., & Peters, F. (2019). Journal of Fluid Mechanics, 860, 682-710.
[5] Ge, Z., Martone, R., Brandt, L., & Minale, M. (2021). Physical Review Fluids, 6(10), L101301.
[6] Zhu, Y., & Granick, S. (2002). Physical review letters, 88(10), 106102.
[7] Zhu, Y., & Granick, S. (2001). Physical review letters, 87(9), 096105.
[8] Kroupa, M., Soos, M., & Kosek, J. (2017). Physical Chemistry Chemical Physics, 19(8), 5979-5984.
[9] Vázquez-Quesada, A., Espanol, P., & Ellero, M. (2018). Physical Review Fluids, 3(12), 123302.
[10] Gartling, D. K., & Phan-Thien, N. (1984). Journal of Non-Newtonian fluid mechanics, 14, 347-360.
[11] Neto, C., Craig, V. S. J., & Williams, D. R. M. (2003). The European Physical Journal E, 12(1), 71-74.
[12] Kumar, S. P., Vázquez-Quesada, A., & Ellero, M. (2020). Journal of Non-Newtonian Fluid Mechanics, 281, 10431
The relationship between the potential of mean force and the second fluctuation theorem
Tanja Schilling, Fabian Glatzel (University of Freiburg)
Abstract:
The underdamped, non-linear, generalized Langevin equation is widely used to model coarse-grained dynamics. We show under which approximations this equation can be obtained from the Hamiltonian dynamics of the underlying microscopic system and in which cases it makes sense to introduce a potential of mean force. We demonstrate the implications of our derivation for the structure of memory terms and their connection to generalized fluctuation-dissipation relations. We show, in particular, that the widely used, simple structure which contains a potential of mean force, a memory term which is linear in the observable, and a fluctuating force which is related to the memory term by a fluctuation-dissipation relation, is neither exact nor can it, in general, be derived as a controlled approximation to the exact dynamics.
The rising velocity of a slowly pulsating bubblein a shear-thinning fluid
Marco De Corato, Yannis Dimakopoulos (University of Patras), John Tsamopoulos (University of Patras)
Abstract:
Highly viscous non-Newtonian fluids are commonly found in many industrial applications. During their processing, these fluids can trap small bubbles, which can remain suspended for a very long time due to the high viscosity of the surrounding fluid, even in the absence of yield stress. These air pockets may result in poor quality of the final product, reduced mechanical properties, bacterial contamination of personal care products, or intermittent flow regimes in microfluidics.
Bubble dynamics driven by periodic pressure change is emerging as a potential route to promote bubble removal from complex fluids by locally changing their viscosity or yielding the surrounding material. These methods exploit the mechanical stresses imparted by pulsating bubbles to locally yield the material or reduce its viscosity to enhance the release of bubbles.
In this talk, I will discuss the rising motion of small bubbles that undergo contraction, expansion, or oscillation in a shear-thinning fluid. Using a perturbation expansion and numerical simulations, I will show how the shear-thinning properties of the fluid couple with the volumetric oscillations to drastically increase the rising speed of the bubble. Finally, I will compare the numerical results with recent experiments, which demonstrate the importance of the elastic response of the fluid.
References
[1]M. De Corato, Y. Dimakopoulos, J. Tsamopoulos, Physics of Fluids, 31, 083103 (2019)
Transient flows and migration in granular suspensions: key role of Reynolds-like dilatancy
Romain Mari, Shivakumar Athani (Université Grenoble-Alpes, CNRS), Bloen Metzger (Aix Marseille Université & CNRS), Yoel Forterre (Aix Marseille Université & CNRS)
Abstract:
Non-Brownian suspensions have a non-Newtonian rheology, albeit a simple one, as stresses are linear in the shear rate. However in many relevant applications, these suspensions do not remain homogeneous, as dilation and migration phenomena affect the distribution of suspended particles. Predicting the stress levels observed during these phenomena remains challenging. In this work we simulate dilation in dense suspensions with Discrete Element Method under a varying imposed pressure on the particle phase. We show that a two-phase model incorporating a Reynolds-like dilatancy law, which prescribes the dilation rate of the suspension over a typical strain scale, quantitatively captures the suspension dilation/compaction over the whole range of parameters investigated. Together with the Darcy flow induced by the pore pressure gradient during dilation or compaction, this Reynolds-like dilatancy implies that the early stress response of the suspension is nonlocal, with a nonlocal length scale L which scales with the particle size and diverges algebraically at jamming. In regions affected by L, the stress level is fixed, not by the steady-state rheology, but by the Darcy fluid pressure gradient resulting from the dilation/compaction rate. Our results extend the validity of the Reynolds-like dilatancy flow rule, initially proposed for jammed suspensions, to flowing suspension below jamming, thereby providing a unified framework to describe dilation and shear-induced migration. They pave the way for understanding more complex unsteady flows of dense suspensions, such as impacts, transient avalanches or the impulsive response of shear-thickening suspensions.
Understanding enhanced rotational dynamics of active probes in rod suspensions
Joost de Graaf, Meike Bos (Utrecht University), Clara Abaurrea-Velasco (Utrecht University), Narinder Narinder (University of Konstanz), Clemens Bechinger (University of Konstanz)
Abstract:
Synthetic active particles (APs) have received considerable interest for biomedical applications and as model systems for non-equilibrium dynamics. However, because an AP's motion strongly depends on the properties of the surrounding liquid, it can additionally serve as a microrheological probe for the properties of the surrounding medium [1,2]. APs in Newtonian media have been studied in great detail, but much less is known when these particles move in complex fluids. Such a fluid's nonlinear rheological properties can lead to a drastically enhanced rotational diffusion (ERD) coefficient [1-3].
In this oral presentation, we study the motion of an AP in a polydisperse quasi-two-dimensional suspension of colloidal rods. Compared to previous studies [1,2], wherein we embedded APs in a spherical colloid suspension, the use of rods allows us to unlock a new mode of fast, local structural dynamics. This dynamics enabled a comprehensive understanding of the mechanism underlying ERD. Combining simulations and experiment, we conclude that minute microstructural fluctuations of rods in near contact with the AP, together with the probe's active motion, generate a fluctuating torque on the AP eventually leading to ERD. These fluctuations can be connected to a local stress relaxation, which may be used in the continuum formalism that was proposed [1,3,4] to capture ERD. Our work thus unifies the previously disjoint continuum and particle-based descriptions for this phenomenon. Beyond the rheological characterization abilities of APs, our findings are important to understand the dynamics of microorganisms in their natural (typically viscoelastic) habitat.
Reference
[1]C. Lozano, J. Gomez-Solano, C. Bechinger, Nat. Mater., 18, 1118-1123 (2019)
[2]C. Abaurrea-Velasco, C. Lozano, C. Bechinger, J. de Graaf, Phys. Rev. Lett., 125, 258002 (2020)
[3]J. Gomez-Solano, A. Blokhuis, C. Bechinger, Phys. Rev. Lett., 116, 138301 (2016)
[4]N. Narinder, C. Bechinger, J. Gomez-Solano, Phys. Rev. Lett., 121, 078003 (2018)
Understanding the Shear Rheology of Particle Suspensions in Viscoelastic Fluids using Computational Simulation
Eric Shaqfeh, Anika Jain (Stanford University), Anni Zhang (Stanford University), Neo Boon Siong (Stanford University)
Abstract:
Rigid or flexible particles suspended in viscoelastic fluids are ubiquitous in the food industry (e.g. pastes), industrial molding applications (all composites and 3-D printed parts), the energy industry (e.g. fracking fluids), and biological fluids (i.e. swimming of bacteria in mucous). A real breakthrough in this area has been the development of 3D computational simulations of such viscoelastic suspensions including particle motion and particle level resolution of the elastic flow fields. My group has been active in developing such simulations using the immersed boundary formalism, including unstructured grids and parallelized algorithms. In this talk, we will use these methods to examine two different, but related problems: 1) the shear rheology of rigid, spherical particles suspended in so-called ``Boger fluids’’ which modestly shear thin and 2) the shear rheology of spherical particles suspended in strongly shear thinning solutions (as an initial model for synovial fluid therapy). We will demonstrate that the concentration parameter β
is critical in understanding the contributions to the extra stress in such suspensions. These contributions naturally are divided into the stresslet and particle-induced fluid stress (PIFS) and we will discuss particle-interaction effects on both. In particular, the PIFS is controlled by the particle stress field around any given single particle, at least for concentrations up to 10%, and for small β this flow is qualitatively different than the Newtonian flow field. Experiments and simulations show that in the latter case, the particle contribution to the extra shear stress may shear thin, in contrast to the strong thickening that is observed in the case of suspending Boger fluids.
Reference
[1]A. Jain, E. Shaqfeh, Journal of Rheology, 65, 1269-1295 (2021)