Cracking and buckling: defect driven mechanics of collagen and DNA
Presented by Dr. Keir Neuman
Laboratory of Single Molecule Biophysics, National Heart, Lung, and Blood Institute
National Institutes of Health
Defects in macroscopic beams decrease the mechanical stability and promote buckling and cracking under compressive and torsional stress. For example, a twisted hose will buckle and form an interwound plectoneme at a pre-formed kink. At the microscopic scale of biological polymers such as collagen and DNA, defects on the scale of thermal energy can result in unusual behaviors with important physiological consequences. I will describe a spontaneous periodic buckling phenomenon in fibrillar type I collagen that exposes the otherwise impervious surface of collagen to binding and degradation by matrix metalloproteinases (MMPs). These spontaneous defects migrate over the surface of the collagen while maintaining their periodicity that far exceeds the intrinsic length scales of collagen. The dynamic yet periodic defects can be explained with a simple internal strain model that provides a mechanistic explanation for the inhibition of MMP degradation by the application of external load. Defects in DNA occur spontaneously due to damage and errors in replication or repair. We find that supercoiling can localize a single mismatch in many thousands of base-pairs of DNA and we propose that this may be a mechanism to facilitate mismatch and damage recognition by repair enzymes. Furthermore, the unusual buckling kinetics at mismatches and the direct observation of an intermediate state provide strong evidence supporting a recently proposed torsional buckling pathway.
Keir Neuman graduated cum laude with a B.A. in physics and applied math from the University of California, Berkeley in 1994 and received his Ph.D. in physics from Princeton University in 2002. He did postdoctoral research with Steven Block at Stanford University from 2002 to 2004, and was a Human Frontiers Fellow with David Bensimon and Vincent Croquette at the Laboratoire de Physique Statistique at the École Normale Supérieure in Paris, France from 2004 to 2007. Dr. Neuman joined the NHLBI as a tenure-track Investigator in 2007 and was promoted to senior investigator in 2015. Dr. Neuman is a member of the Biophysical Society, the Optical Society of America, and the American Physical Society.
Critical Ruga Structures for Molecular Self-Assembly and Adhesion/Friction Control in Soft Materials
Presented by Professor Kyung-Suk Kim
Director of the Center for Advanced Materials Research, Professor of Engineering
Morphologies and electronic states of solid surfaces are often used to control guided self-assembly of molecules as well as adhesion and friction in bio and nanotechnology. Here, we first present nanomechanical analysis of peculiar crinkle-ruga formation in multilayer graphene. The ‘crinkle’ is one of subcritical ruga structures, and a quantum-flexoelectric crinkle in graphene was discovered recently [1-3]. The quantum-flexoelectric crinkle in graphene localizes electric surface line-charge within 0.86 nm width along crinkle valleys and ridges. Controlling the charge localization, the crinkle is used as a molecular manipulator. The graphene crinkles attract and align bio-molecules, or nano-particles. Herein, we present detailed mechanisms of critical crinkle formation in graphene, which is revealed by quantum/continuum hybrid analysis. Then, presented are verifications of the crinkle formation and associated self-assembly of molecules with an AFM atomic lattice interferometry . In addition, also presented will be how multi-scale ruga structures control adhesion and friction in soft-material structures.
 M. Kothari, M. H. Cha and K.-S. Kim, “Critical curvature localization in graphene. I. Quantum- flexoelectricity effect,” Proceedings of the Royal Society A. doi: 10.1098/rspa.2018.0054, 2018.
 M. Kothari, M. H. Cha, V. Lafevre and K.-S. Kim, “Critical curvature localization in graphene. II. Nonlocal flexoelectricity-dielectricity coupling, Proceedings of the Royal Society A. doi: 10.1098/rspa.2018-0671, 2018.
 R. Li, M. Kothari, A. Landauer, M. Cha, H. Kwon, & K.-S. Kim, “A New Subcritical Nanostructure of Graphene—Crinkle-Ruga Structure and Its Novel Properties,” MRS Advances, 1-7. doi:10.1557/adv.2018.432, 2018.
 B. K. Jang, J. Kim, H. J. Lee, K .-S. Kim, C. Wang, “Device and method for measuring distribution of atomic resolution deformation,” United States Patent, Patent Number 9,003,561: issued on April 7, 2015.
Kyung-Suk Kim has 38 years of experience as an engineering scientist and is currently Professor of Engineering at Brown University. He received his Ph.D. (1980) in Solid Mechanics from Brown University. He taught at TAM Department, University of Illinois, Urbana-Champaign for 9 years until he joined Brown as Professor of Engineering in 1989. He served as a board member (2012-2015) and the Representative of the Society of Engineering Science (SES) to U.S. National Committee for Theoretical and Applied Mechanics (2016-2018). His research interests are in scale-bridging mechanics, and nano and micromechanics of solids. Through his research on dynamic properties of solids, adhesion and friction, ruga mechanics of soft materials and stability of nanostructures, he has invented numerous new scientific instruments, including various interferometers, and analytical methods. He has advised more than 40 Ph.D. students and postdocs. His work has been recognized through various awards including the Melville Medal (1981), JEP best paper award (1999), the Drucker Medal from ASME (2016), the John Simon Guggenheim Fellowship (1996), the Ho-Am Prize in Engineering (2005), the Kwan-Ak Distinguished Alumni Award of Seoul National University (2012), and the Engineering Science Medal from the Society of Engineering Science (2012). His research on “New Math for Designer Wrinkles” was selected as one (# 30) of the Top 100 Science Stories, in Discover (2015). He will deliver the William, M. Murray Lecture of the Society of Experimental Mechanics in 2019.
Control of Reaction Fronts for Rapid Energy-Efficient Manufacturing of Multifunctional Polymers and Composites
Presented by Professor Nancy R. Sottos
Department of Materials Science and Engineering &
The Beckman Institute for Advanced Science and Technology
University of Illinois at Urbana Champaign
Reaction-diffusion processes are versatile, yet underexplored methods for manufacturing that provide unique opportunities to control the spatial properties of materials, achieving order through broken symmetry. The mathematical formalism and derivation of equations coupling reaction and diffusion were presented in the seminal paper by Alan Turing [Phil. Trans. R. Soc. Lond. B 237, 37,1952], which describes how random fluctuations can drive the emergence of pattern and structure from initial uniformity. Inspired by reaction-diffusion systems in nature, this talk describes a new manufacturing platform technology predicated on the exploitation of an autocatalytic (self-propagating) polymerization reaction occurring in a system undergoing reaction and diffusion of its ingredients. The system uses the exothermic release of energy to provide a positive feedback to the reaction. In turn, this stimulates further exothermic energy release, and a self-propagating reaction “front” that rapidly moves through the material – a process called frontal polymerization. The self-sustained propagation of a reaction wave through the material gives rise to entirely new ways of manufacturing high performance composites using rapid, energy efficient methods at greatly reduced costs, including 3D printing of thermosetting polymers and composites. Controlling the reaction wave by simple thermal perturbations gives rise to symmetry breaking events that can enable complex, emergent pattern formation and control over growth, topology, and shape.
Nancy Sottos is the Donald B. Willet Professor of Engineering in the Department of Materials Science and Engineering and the Beckman Institute at the University of Illinois Urbana-Champaign. Sottos started her career at Illinois in 1991 after earning a Ph.D. from the University of Delaware. Her research interests include self-healing polymers and advanced composites, mechanochemically active polymers, tailored interfaces and novel materials for energy storage. Sottos’ research and teaching awards include the ONR Young Investigator Award, Scientific American’s SciAm 50 Award, the Hetényi Best Paper Award in Experimental Mechanics, the M.M. Frocht and B.J. Lazan Awards from the Society for Experimental Mechanics, the Daniel Drucker Eminent Faculty Award, an IChemE Global Research Award and the Society of Engineering Science Medal. She is a Fellow of the Society of Engineering Science and the Society for Experimental Mechanics.
4:10 pm Presentation
“Formation of Compound Droplets by Turbulent Buoyant Oil Jet and Plume”
Presented by XINZHI XUE (Adviser: Prof. Katz)
Buoyant jet and plume are important in many engineering and environmental applications. In the regime of high Reynolds and Ohnesorge number, knowledge breakup of a liquid jet in another immiscible liquid is limited, however, it is relevant to e.g., to oil well blowout on the sea floor. In this study, refractive index matched silicone oil and sugar water are used as surrogate to crude oil and seawater. Their density, viscosity ratio, and interfacial tension are closely matched with the original liquids. Simultaneous planar laser-induced fluorescence and particle image velocimetry are applied to dissect the jet center plane for flow visualization, as well as quantitative concentration and velocity measurements. Initially, the oil jet entrains water layers as the shear layer rolls up along the jet periphery. While a few droplets form in this process, the primary fragmentation of oil to ligaments occurs 6-12 and 7-13 nozzle diameters downstream of the nozzle at Re=1358 and 2122, respectively. In both cases, compound droplets, containing multiple water droplets, some with smaller oil droplets, form regularly. The origin of some of the encapsulated water droplets can be traced back to the entrained water ligaments. They persist for at least up to 30 nozzle diameters – the current measurement range. Random forest-based segmentation is applied to measure the compound droplet statistics, showing that this phenomenon increases the overall interfacial area by 23% and 15% for Re=1358 and 2122, respectively, increasing with droplet size. The interior water droplets are also less deformed than the exterior oil droplets and ligaments, indicating that the interior interfaces are subjected to less shear. Such longer-lived quiescent interfaces might facilitate increased biochemical interaction between the oil and the water.
4:35 pm Presentation
“Vortex Shedding from a Circular Cylinder in Shear-Thinning Carreau Fluids”
Presented by SHANTANU BAILOOR (Advisers: Profs. Mittal & Zaki)
Results from numerical simulations of two-dimensional, shear-thinning Carreau fluid flow over an unconfined circular cylinder are presented in this paper. Parametric sweeps are performed over the various Carreau model parameters, and trends of the time-averaged force coefficients and vortex characteristics are reported. In general, increased shear-thinning results in lower viscous forces on the body but greater pressure forces, resulting in a complex non-monotonic drag response. Lift forces generally increased with shear-thinning due to the dominant pressure contribution. The decrease in fluid viscosity also led to shorter vortex formation lengths and the consequent rise in the Strouhal frequency of vortex shedding. It is expected that these results will be useful for verification of computational models of unsteady non-Newtonian flows.
*Reception to be held directly afterwards, lobby area of Mudd Hall
Presented by Professor Michael Sheetz, Ph.D., Director
Mechanobiology Institute of Singapore, National University of Singapore and
Department of Biological Sciences, Columbia University
Since repeated tissue damage correlates with increased risk of cancer, there could be a correlation between tissue regeneration and cancer in that they involve growth in adult tissues. Indeed microRNA-21 levels are upregulated in both tissue regeneration and cancer. miRNA-21 causes depletion of several proteins but particularly, tropomyosin (Tpm) 2.1 depletion blocks rigidity sensing and causes growth on soft surfaces. In over forty cancer cell lines tested, at least 75% were missing major components of the rigidity sensing complex (about 60% had low Tpm 2.1). The rigidity sensing complex (about 2 m in length) contracts matrix adhesions by ~100nm; and if the force generated is greater than ~25 pN, then adhesions are reinforced and cells can grow (Wolfenson et al., 2016. Nat Cell Bio. 18:33). However, if the surface is soft and matrix force low, then the rigidity sensor in normal cells causes apoptosis by DAPK1 activation (Qin et al., 2018 BioRxiv. 320739). Transformed cancer cells lack rigidity-sensing contractions and grow on soft surfaces. Restoration of rigidity sensing in cancer cells by normalizing cytoskeletal protein levels (most often by restoring Tpm 2.1 levels) restores rigidity-dependent growth (Yang, B. et al., 2018 BioRxiv. 221176). Surprisingly, we find that cyclic mechanical stretch of transformed cancer cells activates apoptosis through calpain-dependent apoptosis. Restoring rigidity sensing in transformed cancer cells blocked stretch-induced apoptosis and caused rigidity-dependent growth (Tijore et al., 2018 BioRxiv. 491746). Conversely, normal cells become stretch-sensitive for apoptosis after transformation by depleting rigidity sensors through Tpm2.1 kockdown or knockdown of other tumor suppressor proteins needed for rigidity sensing. Thus, it seems that stretch sensitivity is a weakness of many cancer cell lines and this is related to the transformed cell state and not to the tissue type or other factors. Depletion of the rigidity mechanosensor to allow regenerative growth can lead to sustained loss of mechanosensing that enables cancerous growth.
Professor Michael Sheetz is a cell biologist at Columbia University and a Distinguished Professor and the founding Director of the Mechanobiology Institute at the National University of Singapore. He pioneered mechanobiology and biomechanics. In 1968, Sheetz earned a bachelor’s degree at Albion College, and in 1972 received his Ph.D. at the California Institute of Technology. In 1985 he became a professor of cell biology and physiology at the Washington University in St. Louis, Missouri. Since 1990 he is the William R. Kenan, Jr. Professor of Cell Biology at Columbia University, New York. He has also been a professor at Duke University.
4:10 pm Presentation
“Turbulent Flow over Fractal Urban-Like Topography: Prognostic Roughness Model for Unresolved Generations”
Presented by XIAOWEI ZHU (Adviser: Prof. Zaki)
Urban-like topographies are composed of a wide spectrum of topographic elements, which results in a multiscale, fractal-like surface height distribution. Computational modeling of turbulent flows responding to fractal-like geometries poses unique challenges, especially when the number of self-similar generations renders a spectrum of the constituent wavelengths ﬁner than the computer mesh resolution. In the background of large-eddy simulation (LES), high-resolution multiscale topography needs to be spatially ﬁltered to obtain a resolved topography to be directly used in LES. The eﬀects of the subgrid-scale topography need to be modeled. Inspired by the self-similar nature of the topography, we modeled the effects of these truncated topographic modes based on the behaviors of the large-scale geometry. Firstly, the iterated function system (IFS) was used to construct urban-like, fractal geometries. And five fractal dimensions were used to investigate the parameterization of unresolved generations. Secondly, we quantiﬁed the momentum deficit associated with changing attributes (such as fractal dimension and generation), which enabled a posteriori deduction of roughness length parameters needed to model aerodynamic surface stress. We further showed that aerodynamic stress associated with the descendant, sub-generation elements can be parameterized, with only the first few generations resolved on the computational mesh. Finally, a logarithmic law-based roughness model was proposed for the unresolved, sub-generation topographic elements.
Energy optimization in human walking
Presented by Professor Max Donelan
Biomedical Physiology & Kinesiology, Simon Fraser University
Perhaps the most general principle underlying human movement is that people prefer to move in ways that minimize their energetic cost. Although aspects of this preference are likely established over evolutionary and developmental timescales, we recently discovered that the nervous system can continuously optimize cost in real-time. Here I will present our new research focused on uncovering the mechanisms underlying the initiation of this optimization, as well as its process. Our collective findings indicate that energetic cost is not just an outcome of movement, but also plays a central role in continuously shaping it. I will also briefly touch on two other aspects of my research program – bionic energy harvesting and the scaling of control.
Max Donelan is a Professor of Biomedical Physiology & Kinesiology at Simon Fraser University in Vancouver, British Columbia. He received his Ph.D. in Integrative Biology from Berkeley in 2001 under the mentorship of Dr. Rodger Kram and Dr. Art Kuo. He completed his postdoctoral work in Neuroscience at the University of Alberta under the mentorship of Dr. Keir Pearson. Max has held Career Investigator awards from the Michael Smith Foundation for Health Research and the Canadian Institutes of Health Research. In addition to his fundamental research program, he has spun-out companies to commercialize his energy harvesting and wearable technology inventions, and is a scientific advisor to Nike Inc. Max is currently a visiting professor in Bioengineering at Stanford.
In His Own Words: I study how people and other animals move, and then apply what I find to help our society. I mostly study walking in people, and mostly pretty fundamental things about the back-and-forth relationship between how we walk and the energy we require to do so. But I also like to study big and small animals, and how their size affects how they control their movements. This comparative work has led me to study kangaroo tails, crocodile gallops, and elephant nerves, to name a few. In the course of my research, I have invented exoskeletons that harvest electrical energy from our movements, devices that stabilize people as they walk, and an iPhone app that controls people’s running pace with music. Others have used my work to develop new ways of rehabilitating people’s gait, and new ways of controlling their walking robots.
4:10 pm Presentation
“State Estimation in Turbulent Circular-Couette Flows”
Presented by MENGZE WANG (Adviser: Prof. Zaki)
The flow state of turbulent circular-Couette flow is very sensitive to initial conditions and the start-up process. For example, slowly increasing the rotational speed or suddenly accelerating it to the target value can lead to different transitional flow structures, such as stationary and wavy Taylor vortices, which persist in the turbulent regime. As a result, in numerical simulations, it is difficult to prescribe appropriate initial conditions that achieve a target flow state. Furthermore, due to the chaotic nature of turbulence, quantitative comparison between experimental measurements and simulations is challenging. This problem is addressed using an adjoint-variational state-estimation algorithm. By combining simulations with limited measurements, we predict the appropriate initial condition that tracks the correct flow state. A symmetric projector is proposed to guarantee that the initial condition is divergence free. We first consider estimation of turbulent flow with noise-free coarse-grained velocity data. The algorithm achieves more than 50% error reduction compared to space-time interpolation, with a better prediction of large-scale structures and vorticity. We subsequently demonstrate that the estimation accuracy is robust to measurement noise. Finally, a more challenging case is investigated, in which the measurements are composed of the velocity field far from the wall and the wall shear stress.
“Numerical Simulation of the Non-Equal Sized Coalescence-Induced Self-Propelled Droplets”
Presented by XIANYANG (TOM) CHEN (Adviser: Prof. Tryggvason)
In general, external energy is needed to remove liquid from a solid wall during cooling by dropwise condensation. However, experiments have shown that in some cases droplets can propel themselves from the wall, without any external energy, due to the coalescence-induced conversion of surface energy to kinetic energy. Several authors have reported scaling analysis combined with an energy balance of kinetic energy, surface energy and viscous energy, to estimate whether the droplets can be self-propelled or not. Here, we uses numerical simulation to describe the coalescence and self-propelling for non-equal sized droplets, based on a finite-volume/front-tracking method and the Generalized Navier Boundary Condition (GNBC) to model the moving contact lines. We find that a slightly smaller contact angle (165°) will give a larger out-of-plane jumping velocity than superhydrophobic surface (with a contact angle of 180°). Further decreasing the contact angles is believed to result in “immobile coalescence”. The speed of the moving contact line does not influence the spontaneous removal process as long as it is large enough to let the contact areas detach in time. Non-equal sized drops are much more difficult to be spontaneously removed from a wall compared to equal-sized ones. Two spherical drops with a diameter ratio of 2.0, possesses 60% usable energy compared of equal- sized ones and only 0.5% of the total released energy can be effectively used for out-of-plane jumping.
Shock wave focusing to achieve high energy concentration
Presented by Professor Veronica Eliasson
Structural Engineering, University of California San Diego
A shock wave is a thin discontinuous region over which fluid properties abruptly change from one state to another. Shock wave focusing occurs frequently both in nature and in a variety of man-made applications. It takes place when a shock wave propagates through a non-uniform or moving media, reflects from curved surfaces or through reflections with other shock waves. Extreme conditions created at the focal region – resulting in very high pressures and temperatures – can be either beneficial as in the case of shock wave lithotripsy or inertial confinement fusion or detrimental as in the case of superbooms (a type of sonic boom). As the shock wave emerges from the focal region, after the shock focusing event, the shape of the shock is often fundamentally altered. Therefore, a deeper understanding of the shock focusing process, and how to control it, is critical to fully understand its consequences and how to best enhance or mitigate it as needed depending on the application at hand. In this talk I will introduce our newest experimental setup that has the capability to produce multiple simultaneous shock waves in two or three dimensions with a turn around time between consecutive experiments that is under two minutes. Ultra-high-speed photography coupled with schlieren techniques are used to probe the shock dynamic events, and in particular, the transition from regular to irregular reflections.
Veronica Eliasson received her Ph.D. in Mechanics at the Royal Institute of Technology, Stockholm, Sweden, in 2007. After a postdoctoral appointment at Graduate Aerospace Laboratories, California Institute of Technology, she became a faculty member at University of Southern California in 2009. In 2016 Dr. Eliasson moved from USC to the Structural Engineering Department at University of California, San Diego. Dr. Eliasson’s research interests are in the area of experimental mechanics and include shock wave dynamics, high strain rate impacts and fracture mechanics.
4:10 pm Presentation
“Distinct Modes of Unsteadiness in a Separating Turbulent Boundary Layer”
Presented by WEN WU (Profs. Rajat Mittal & Charles Meneveau)
Flow separation is ubiquitous in external as well as internal aerodynamics: wings and fuselages at high angles-of-attack, flow past external objects, shock-wave/boundary layer interactions, diffusers, corners, and junctions are just a few examples of this kind of flow. The separated flow is typically unsteady across a broad range of frequencies. In addition to high-frequency unsteadiness associated with turbulent fluctuations, the flow also displays a low frequency “breathing” or “flapping” mode and a higher frequency “shedding” mode. These unsteady models lead to many issues in applications, such as degradation of system performance and aerodynamic noise. They also bring additional difficulties for the prediction and control of these flows due to the complexity of intermittency. Better and more sophisticated tools are required for analysis of these unsteady modes. We generate a realistic separation bubble via adverse pressure gradient induced by a prescribed suction profile and perform direct numerical simulation of a turbulent boundary layer (Re=500) separated by this APG. The resulting flow exhibits two distinct unsteady modes frequencies separated by a factor of three. The higher-frequency motion scales well with the characteristics of a canonical plane mixing layer, corresponding to the generation of quasi two-dimensional spanwise vortices by KH instability. The lower frequency mode is more difficult to characterize but the use of dynamic mode decomposition (DMD) indicates that the low-frequency mode is associated with elongated streamwise vortices, the scale of which agrees well with the Görtler vortices generated due to curvature effects in the flow.
4:35 pm Presentation
“Effect of Different Axial Casing Groove Geometries on the Performance and Efficiency of a Compressors”
Presented by SUBHRA SHANKHA KOLEY (Adviser: Prof. Katz)
The impact of varying the geometry of axial casing grooves were investigated by carrying out performance tests and flow measurements. It has been shown in earlier studies that skewed semi-circular grooves installed near the blade leading edge (LE) have multiple effects on the flow structure, including ingestion of the tip leakage vortex (TLV), suppression of backflow vortices, and periodic variations of flow angle. To determine which of these phenomena is a key contributor, the present study examines the impact of several grooves, all with the same inlet geometry, but with outlets aimed at different directions. The “U” grooves that have circumferential exits aimed against the direction of blade rotation, achieve the highest stall margin improvement of well above 60%, but cause a 2.0% efficiency loss near the best efficiency point (BEP). The “S” grooves, which have exits aimed with the blade rotation, achieve a relatively moderate stall margin improvement of 36%, but they do not reduce the BEP efficiency. Other grooves, which are aligned with and against the flow direction at the exit from upstream inlet guide vanes, achieve lower improvements. These trends suggest that causing high periodic variations in flow angle around the blade leading edge is particularly effective in extending the stall margin, but also reduces the peak efficiency. In contrast, maintaining low flow angles near the LE achieves more moderate improvement in stall margin, without the maximum efficiency loss. Hence, of the geometries tested, the S grooves appear to have the best overall impact on the machine performance. In order to further elucidate the flow we are conducting flow visualization experiments using cavitation which will be followed by PIV measurements to get an quantitative estimation of the flow.