Bulletin of the American Physical Society
APS March Meeting 2021
Volume 66, Number 1
Monday–Friday, March 15–19, 2021; Virtual; Time Zone: Central Daylight Time, USA
Session M12: Self-Organization in Biological Systems: Subcellular to Tissue Scales IIFocus Live
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Sponsoring Units: DBIO DSOFT Chair: Francesca Serra, Johns Hopkins University Moumita Das, Rochester Institute of Technology |
Wednesday, March 17, 2021 11:30AM - 12:06PM Live |
M12.00001: Designing the Morphology of Separated Phases in Multicomponent Liquid Mixtures Invited Speaker: Andrej Kosmrlj Phase separation of multicomponent liquid mixtures plays an integral part in many processes ranging from industry to cellular biology. While the physics of binary and ternary liquid mixtures is well-understood, the thermodynamic properties of N-component mixtures with N>3 have remained relatively unexplored. This makes it challenging to understand how cells control concentrations of molecules and their interactions to navigate phase diagrams to achieve target structures. To address this issue, we developed novel algorithms for constructing phase diagrams and for predicting the morphology of separated phases. To determine the number of coexisting phases and their compositions, we developed a new algorithm for constructing complete phase diagrams, based on numerical convexification of the discretized free energy landscape. Furthermore, we developed a graph theory approach to predict the topology of coexisting phases from a given set of surface energies (forward problem), enumerate all topologically distinct morphologies, and reverse engineer conditions for surface energies that produce the target morphology (inverse problem). |
Wednesday, March 17, 2021 12:06PM - 12:18PM Live |
M12.00002: Soft nanotubes confining adhensive elastic nanoparticles Zeming Wu The mechanical interaction between soft membrane nanotubes and confined elastic nanoparticles plays essential roles in numerous cellular activities. The aim of this work is to theoretically analyze the interaction between soft nanotubes with various membrane tension and confined nanoparticles with different bending rigidities, and covering the cases of a single particle and multiple particles of spatial periodicity. Depending on the adhesion energy and bending rigidity ratios, a rich variety characteristic interaction states are determined, and the corresponding wrapping phase diagrams are determined. Based on perturbation analysis at small tube deformation and configurational assumptions of catenoid, torus, and one-sheeted hyperboloid at more general tube deformation, we have also obtained analytical solutions on the wrapping of rigid spherical nanoparticles in soft tubes. This study enriches our knowledge on the diversity of membrane tubules in morphologies and structures. |
Wednesday, March 17, 2021 12:18PM - 12:30PM Live |
M12.00003: Dielectrophoresis characterization of Neuroblastoma cells Samaneh Rikhtehgaran, Babak Mosavati, Luc T Wille, Jianning Wei, E Sarah Du This work presents a dielectrophoresis-based method for a label-free noninvasive characterization of neuroblastoma cells. Dielectrophoresis (DEP) is a frequency movement of polarized particles under the spatially nonuniform electric field. Particle can either be attracted to the highest electric field regions (positive DEP) or repulsed away from those regions (negative DEP). The DEP force experienced by the particle depends on the dielectric properties of both particle and the surrounding medium. To demonstrate the method, human neuroblastoma SH-SY5Y cells were analyzed. The SH-SY5Y cell line has been widely used as an in vitro cell model for the study of neurodegenerative diseases. The microfluidic device for DEP characterization consists of an interdigitated ITO electrode chip (50 µm gap and 100 µm band) and a Polydimethylsiloxane (having dimensions of 15*10.63 mm2 in area and 7.48 mm depth). Cell suspension (106 cells/ml) are loaded into the well and electrodes are energized using a signal generator. A sinusoidal AC voltage of Vpp = 10.0 V peak-to-peak and a frequency range 100 kHz-122 MHz are applied. Consequently, by fitting the dielectrophoretic spectra of these cells to a single shell model we will obtain electrical properties of the cells. |
Wednesday, March 17, 2021 12:30PM - 12:42PM Live |
M12.00004: Synchronization and noise in arrays of hydrodynamically coupled cilia Anton Solovev Motile cilia on ciliated epithelia in mammalian airways, brain ventricles and oviduct |
Wednesday, March 17, 2021 12:42PM - 12:54PM Live |
M12.00005: Sensing Cell Shape at the Micron Scale with Reaction-Diffusion Amit Singh, Brian Camley Some dividing cells sense their shape by becoming polarized along their long axis. Polarity is often modeled by a reaction-diffusion system describing the proteins from the Rho GTPase family cycling between active membrane-bound forms and inactive cytosolic forms (a "wave-pinning" model). Does shape-sensing emerge from wave-pinning? We simulate wave-pinning on a curved surface and show that high-activity domains migrate to peaks and troughs of the surface. For smooth surfaces, a simple rule of minimizing the domain perimeter while keeping its area fixed predicts the final position of the domain and its shape. We find that as the surface becomes rough, the domains of the wave-pinning model are more robust in finding the peaks and troughs than predicted by the minimization rule. Why? The minimization rule models a sharp interface between the high and low activity regions whereas the wave-pinning model has a finite interface width. By changing the Rho GTPase diffusivity we can change the interface width and thus the robustness of the shape-sensing of the domains. |
Wednesday, March 17, 2021 12:54PM - 1:06PM Live |
M12.00006: Nanofluidic Device for Measuring the Surface Charge of Extracellular Vesicles via a Tunable Electrostatic Landscape Seyed Imman Isaac Hosseini, Zezhou Liu, Walter Reisner, Sara Mahshid Extracellular vesicles (EVs) play an essential role in intercellular communication. EV surface charge can be used to probe EV surface chemistry and bioconjugation, including surface proteins and sialic acid groups. Surface charge influences different biological processes associated with the EVs, such as cellular uptake and cytotoxicity [1]. Here, we propose a nanofluidic device to perform simultaneous size and charge measurement of EVs. Our device consists of a lattice of electrostatic potential wells embedded in a nanoslit. The nanoslit is interfaced to a thin membrane lid that can be deflected via applied pressure, varying the degree of confinement experienced by the EVs. Using the single molecule electrometry approach developed by the Krishnan group [2], we can use quantification of the EV diffusive dynamics in the lattice, as a function of confinement, to obtain EV size and charge. We apply our device to demonstrate that EVs generated from glioblastoma multiforme (GBM) cells have a lower surface charge compared to EVs generated from GBM normal counterparts (Normal Human Astrocyte, NHA) cells. |
Wednesday, March 17, 2021 1:06PM - 1:18PM Live |
M12.00007: Delay-induced transitions in swarmalator clusters Nicholas Blum, Kevin O'Keeffee, Oleg Kogan We investigate the role of delay in the collective dynamics of swarmalators introduced recently by O’Keeffe, Hong, and Strogatz. Addition of delay into the system of swarmalators was motivated by the biology of early embryonic development. The delay leads to a rich phenomenology, which includes two new collective states. In one of them, all particles in a swarm execute decaying radial oscillations completely in phase with each other. After these oscillations decay, the swarm becomes a static quasi-crystal. We call this the “breathing” state. The other collective state is one in which particles close to the surface of the swarm execute non-decaying convective motions. We call it the “surface boiling” state. For a range of negative phase coupling strengths, there is a transition from the boiling to the breathing state as delay time is increased. |
Wednesday, March 17, 2021 1:18PM - 1:30PM Live |
M12.00008: Numerical simulation of dielectrophoretic behavior of neuroblastoma cells Babak Mosavati, Samaneh Rikhtehgaran, E Sarah Du, Jianning Wei Dielectrophoresis (DEP) is the motion of particles caused by polarization effects in a nonuniform electric field. It has been widely used as a label-free technique for dielectric characterization of biological cells. This work presents a numerical simulation of neuroblastoma cell DEP using the finite element method. COMSOL Multiphysics software is used to analyze the electrical field generated by microelectrodes in a microfluidic chamber. DEP forces exerted on cells are calculated using a simplified spherical shell model and Maxwell’s stress tensor. The latter provides electrostatic force distribution on cell membranes that mimics the actual physics of a cell surrounded by an electrically conductive medium. The model is validated by comparing the simulation results of cell trajectories with the experimentally observed DEP response of neuroblastoma cells cultured from SH-SY5Y cell line in a microfluidic chamber. To induce DEP, ITO electrodes (10 wide and 50 inter-electrode spacing) deposited on the glass substrate of the chamber are energized by a sinusoidal waveform ofpeak-to-peak in a frequency range of 100 kHz-122 MHz. Additionally, a parametric study is performed to investigate the effects of voltage level, frequency, and cell size on the DEP response of cells. |
Wednesday, March 17, 2021 1:30PM - 1:42PM Live |
M12.00009: Inducing Integer Charge Topological Defects in Cell Monolayers Kirsten Endresen, MinSu Kim, Francesca Serra Many cells, when confined on 2-dimensional substrates, align with their neighbors and arrange as nematic liquid crystals (LCs). As in LCs, topological defects are also present in cell monolayers, and these regions of disorder impact the behavior of cells [1,2]. We induce alignment of fibroblasts (3T6) via contact guidance with boundary conditions that induce topological defects with integer topological charge on micropatterned substrates [3]. By varying the height of ridges, we change the anchoring strength which sets the direction for cell alignment and study the effect on cell alignment. We identify two different cell configurations near topological defects with azimuthal symmetry, where cells are able to change not only their alignment, but also their shape. We also vary the initial seeding concentration of cells, which changes the density of cells in their initial configuration, where at high initial density the cells can get frozen into misaligned configurations. [1] K Kawaguchi et al. Nature 545, 327 (2017) [2] TB Saw et al. Nature 544, 212 (2017) [3] K Endresen et al. arXiv: 1912.03271 [cond-mat.soft] 2019. |
Wednesday, March 17, 2021 1:42PM - 1:54PM Live |
M12.00010: The roles of patchy attractions and Brownian motion in fundamental biological processes in a model cell Jennifer Hofmann, Roseanna Zia Microscopic forces and physical phenomena at the colloidal scale are involved with fundamental processes inside living cells. Examples of such phenomena include Brownian motion and deterministic forces between constituents of the cellular milieu. In order to faithfully represent interactions between proteins, in particular, computational models must take into account the orientation-dependence (i.e. “patchiness”) of attractions and binding events. To connect these microscopic forces to whole-cell functions, we use coarse-grained patchy simulations to study key biological processes, including translation elongation, in a model prokaryotic cell. We examine the relationship between the attractive potential strength relative to Brownian motion (used in colloidal simulations) and the equilibrium dissociation constant, Kd, a metric used to describe the binding affinity of biological macromolecules in experiments. Here, we present our results investigating the structure and dynamics of these coarse-grained systems, probing the inseparable connection between colloidal-scale transport and biological function. |
Wednesday, March 17, 2021 1:54PM - 2:06PM Live |
M12.00011: Physics-based modeling of whole-cell function: colloidal fundamentals to life-essential processes Roseanna Zia, Drew Endy, Akshay Maheshwari, Emma del Carmen Gonzalez Gonzalez, Alp M Sunol A grand challenge of systems biology is an understanding of cells so complete that all cellular behavior can be determined from the composition and dynamics of constituent biomolecules. But connecting single-molecule to cellular behavior requires bridging processes that operate over nanoseconds and nanometers to those spanning minutes and microns. Yet the physical details of this intermediate realm are largely abstracted away in whole-cell kinetics models. Colloidal-scale physics bridges this gap and can reveal the relationship between physics and biological function. We demonstrate this by proposing that colloidal mechanisms regulate mRNA translation in E. Coli. We built a novel bio-colloidal modeling framework with nanometer resolution that explicitly and represents the transport and reaction dynamics of individual biomolecules as they interact and react over whole-cell-function time scales. We showed that Brownian motion is essential but insufficient to recover experimentally measured elongation rates; we proposed other colloidal physics mechanisms that close the gap. This is a general framework for discovering how colloid physics predict biological behavior. |
Wednesday, March 17, 2021 2:06PM - 2:18PM Live |
M12.00012: Physical scaling of size and shape in an early diverging animal Pranav Vyas, Matthew S Bull, Hongquan Li, Manu Prakash In most animals, identified as self-organizing multicellular clonal clusters with complex tissue architectures, size control is strictly encoded as a part of the developmental program. These mechanisms however evolved to work in concert with material and environmental physical constraints, thus resulting in apparent scaling laws comparing size and measurable features of form across organisms. Using an early diverging animal with highly regenerative tissue architecture, we ask how size and shape of the earliest freely growing multicellular clusters would have been regulated in the absence of strictly encoded plans. We utilize high-throughput scanning microscopy to collect long term temporal datasets on the growth trajectories of individual organisms to identify scaling laws governing measurable changes in shape metrics with size. We then utilize physical and chemical perturbations to understand robustness of these trajectories and find attractors in shape spaces. Finally, using computational modelling of self-organized growth of discrete networks, we provide theoretical insights into the observed laws and open up space for exploration of further complexity. |
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