Post Doctoral Associates
Dr. Gaddiel Ouaknin
My research interests include computational mechanics, soft matter, shape optimization, parallel algorithms, and stochastic calculus. During my PhD, using polymer field theory and level set methods, I developed shape optimization algorithms for predicting the phases of polymeric materials with a free surface. Previously, in my postdoc, I developed parallel algorithms on distributed memory architecture for Accelerated Stokesian Dynamics (ASD) to simulate large-scale stochastic particle systems correlated through hydrodynamic interactions. Recently, as a research engineer, I developed a novel algorithm for fast and accurate computation of correlated Brownian motion of particles in a Stokes flow with many-body hydrodynamic interactions with near- and far-field interactions. I am also interested in stochastic calculus theory and applications.
I am a Ph.D. student in the Chemical Engineering Department, and my research interests include colloidal systems, complex fluids, and rheology. My work supports our challenge to understand the physics inside living cells. The first step in this lofty goal is understanding of the hydrodynamics of intracellular transport. To this end, I utilize our group’s newly developed and evolving computational model, where confinement and particle shape, size, and interactions are aimed toward rigorous modeling of the key transport processes in a model cell. My study focuses on the dynamics of a confined polydisperse suspension where particles interact via many-body hydrodynamic and lubrication interactions, as well as via attractive and repulsive interactions, as they undergo colloidal-scale transport driven by thermal fluctuations and by deterministic forces (as would be generated by the towing of molecular motors). Our approach combines the non-equilibrium statistical mechanics and low-Reynolds number hydrodynamics theory with Confined Stokesian Dynamics simulations. My goal is to understand the changes in particle configuration, motion, phase behavior, and self-organization that can arise as a result of the interplay between microscopic forces, changes in concentration, confinement, and active motion.
Brian K. Ryu
I am a Ph.D. student in the department of Chemical Engineering and my research interests lie in computational methods for colloidal soft matter. The goal of my current research is to develop a framework for studying the time-dependent thermodynamic phase behavior of colloidal material and gels. Colloidal systems express a range of equilibrium and non-equilibrium states that arise from interparticle interactions. By dynamically controlling states through repeated quench-anneal protocols, we envision that a wide range of new materials can be created. In my study, we aim to sculpt and design new colloidal soft matter with desirable mechanical and transport properties. Furthermore, we seek computational methods to characterize structure, dynamics, rheology, and transport properties of colloidal soft matter for applications in personal protective equipment, biomaterials, and biophysics.
Alp M. Sunol
I am a Ph.D. student in Chemical Engineering at Stanford University. My primary research interest is the theoretical and computational study of soft matter and complex fluids. The goal of my research is to better understand how physics at the colloidal scale regulates cellular function and fitness. While modeling of cellular behavior is robust in atomistic-scale structural biology, with little time evolution, and in kinetics-based systems-biology, which abstracts away space, many cellular processes operate over colloidal length scales, where interparticle interactions and particle motion play central and nontrivial roles in whole-cell behavior. In my research, I leverage our group's expertise in simulating colloidal suspensions to develop physics-based computational models, which are used to understand how colloidal scale interactions at different biological conditions affect spatial organization and transport dynamics of molecules inside cells. These models account for Brownian motion, many-body hydrodynamic and lubrication interactions, electrostatic interactions, confinement, polydispersity, and physiochemical forcing.
J. Galen Wang
I am a Ph.D. student in Mechanical Engineering from Cornell University, currently in residence at Stanford. I have a broad interest in fluid dynamics, especially in complex fluids and their rheology. My focus is on the non-equilibrium phase behaviors of colloidal glasses, which can form when the colloidal concentration is “quenched” rapidly to bypass crystallization. Prior theories have focused on seeking a metastable equilibrium description of the colloidal glass transition, yet the underlying physics of this process remains unclear. In my project, we trigger the colloidal glass transition via a novel particle-size quench utilizing large-scale dynamic simulation, and with collaboration from experimentalists in the McKenna Group at Texas Tech University I have developed several algorithms that mimic experiments. In my simulations I am monitoring the detailed structural, dynamical and rheological quantities during the concentration quenches and the following aging processes, and have found that self-diffusion emerging over distinct length scales plays a key role in the colloidal glass transition. My goal is to reveal the mechanistic origin of the colloidal glass transition and to develop models for non-equilibrium phase transitions, ultimately advancing designs of non-equilibrium materials and deepening our understanding of biological processes.
My goal is operational mastery of living matter, sufficient to construct cells and control their dynamics. Such engineering capacity would have major implications for distributed and personalized biotechnology and medicine. As an MD/PhD student in the Bioengineering department working jointly with Drs. Roseanna Zia and Drew Endy, I am working towards operational mastery by bridging the fields of colloidal physics and synthetic biology. While cells have so far largely been understood based on mechanistic models of single molecules and spatially-abstracted phenomenological models of biological functions, developments at the frontier of synthetic biology suggest that such biochemistry-centric approaches are not enough to enable the construction of cells. In my current projects I am thus developing theoretical, modeling, and experimental frameworks grounded in colloidal physics and statistical mechanics for systematically elucidating how, beyond their biochemistry, molecules physically organize to produce whole-cell biological functions essential for life. Feel free to contact me -- I'm always happy to chat!
I am a Ph.D. student in the department of Chemical Engineering, and my research interests lie at the intersection of biology, suspension mechanics, and complex fluids. With my work, I am interested in how colloidal-scale physics inform and orchestrate biological processes inside of cells. In pursuing this question, I leverage our group's expertise in simulating dense colloidal dispersions (via Brownian and Stokesian Dynamics methods) to study the interplay between many-body hydrodynamic and lubrication interactions, electrostatic attractions, Brownian forces, polydispersity, and confinement. One major benefit of colloidal-scale models is their ability to scale to biologically relevant timescales which all-atom models are too computationally intensive to reach. Although care must be taken to accurately represent biomacromolecular interactions at a coarse-grained colloidal level, colloidal modeling represents a powerful tool to better understand the physics of biological function.
Corinne G. Weeks
I am a Ph.D. student in the Department of Chemical Engineering with a broad interest in developing theories to describe the macroscopic behaviors of complex fluids. My current project focuses on studying heterogeneous suspensions, where particle concentrations and shear rates can vary throughout the suspension. These variations can impart macroscale behaviors and properties fundamentally different from homogeneous suspensions. Prior attempts to model heterogeneous behaviors were often phenomenological in nature and limited to specific flow types. I aim to develop a broadly applicable theory relating macroscopic properties in heterogeneous suspensions such as the stress and viscosity to microscopic particle configurations by extending a theoretical framework recently developed in our group to non-dilute suspensions, allowing for the study of behaviors such as shear thickening and thinning, memory effects, and strong non-uniformities in heterogeneous suspensions. Ultimately, this will permit the quantitative predictions of suspension behavior during industrially and biologically relevant heterogeneous flows, such as pressure driven flow through a pipe.
I am a PhD student in the department of Chemical Engineering, and my research interests include theoretical and computational study of soft matter and complex fluids. Specifically, my work examines the colloidal glass transition. In colloids, changes in solids volume fraction or the strength of interparticle attractions relative to Brownian motion determine the phase. Increasing the concentration of hard-sphere suspensions can trigger a liquid-to-solid phase transition, resulting in the formation of a crystal. However, in some cases, crystallization fails, and the material solidifies in an amorphous structure without a well-defined thermodynamic transition; it vitrifies into a glass. Recent work in the Zia group has shown that relaxation in colloidal glasses occurs via self-diffusion and persists up to near maximum packing with no divergence in relaxation time. However, size polydispersity is known to modulate the volume fraction at which vitrification begins. In my work, I aim to elucidate the role of size polydispersity in the dynamics of the glass transition and develop a framework to investigate what movement mechanisms allow continued relaxation in colloidal glasses.
I am a Ph.D. student in Mechanical Engineering at Stanford University. I am interested in the physics of colloidal dispersions, and the computational and theoretical techniques used to model them. Currently, I am working on implementing size polydispersity into our group's parallel Accelerated Stokesian Dynamics code, which will be useful in elucidating aspects of the colloidal glass transition, among other applications. In addition, most theoretical and computational studies of colloidal suspensions have considered only spherical particles. I am interested in the role of particle shape in determining suspension behavior, and plan to apply machine learning methods towards this goal.
I am an undergraduate student at Cornell University studying chemical engineering. This summer I am working on simulating confined Brownian suspensions to explore how microscopic forces and processes at the colloidal scale may regulate whole-cell function via flow. By utilizing the physics-based computational models developed by the group, I will systematically evaluate the impact of diverse biological conditions and active motion on spatial organization and transport properties of molecules in a cell.
I am an undergraduate student at UCLA studying computational and systems biology with a minor in mathematics. This summer, I am participating in research at Stanford as a part of the Stanford Undergraduate Research Fellowship program. My work investigates the effect of nonspecific interactions between peptides on the amyloid nucleation process by using dynamic colloidal simulation.
Past Post Doctoral Associates
Dr. Monica E. A. Zakhari, currently Assistant Professor at Eindhoven University of Technology
Dr. Nicholas J. Hoh, currently Senior Data Scientist at Intuit
Dr. Poornima Padmanabhan, currently Assistant Professor at Rochester Institute of Technology
Past Graduate Students
Dr. Derek E. Huang, currently a postdoctoral scholar at the National Institute of Science and Technology
Dr. Benjamin E. Dolata, currently a postdoctoral scholar at Georgetown University
Dr. Lilian C. Johnson, currently a postdoctoral scholar at the National Institute of Science and Technology
Dr. Christian Aponte-Rivera, currently a postdoctoral scholar at Duke University
Dr. Henry Chu, currently Assistant Professor at the University of Florida
Dr. Benjamin Landrum, currently in R&D at Intel
Dr. Ritesh P. Mohanty, currently a Senior Scientist at Corning
Dr. Yu Su, currently a Senior Scientist at Google