(6u) Multiscale Dynamics in Biological Soft Matter and Polymeric Fluids | AIChE

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(6u) Multiscale Dynamics in Biological Soft Matter and Polymeric Fluids

Authors 

Saadat, A. - Presenter, Stanford University

Research Interests:

The overarching theme of my research is to utilize numerical simulations in conjunction with experiments and direct visualization of soft matter dynamics for a bevy of engineering and biological applications. These applications extend beyond simply academic interest and concern human health, bioengineering, and rational design of industrially critical materials.

The platforms that I have developed for my investigations include computational mechanics of complex non-Newtonian fluids and deformable objects (immersed boundary method) and molecular stochastic simulation of polymeric solutions. I exploit high-performance-computing (HPC) and massive large-scale parallelism to accelerate the numerical simulations which are otherwise intractable. Graphical processing units (GPUs) and message passing interface (MPI) are the two computational tools to facilitate parallel computing that I have been using extensively.

A major part of my graduate and postdoctoral research has involved experimental investigation, either directly or through collaboration. In my postdoctoral research, I have been conducting microfluidic experiments and automatic image analysis for quantification of red blood cell biomechanics. In my graduate research, I have studied the dynamics of single comb DNA macromolecules in cross-slot microfluidic hydrodynamic trap and also used linear and nonlinear viscoelastic measurements for characterizing rheological properties of polymer melts.

Research Experience:

Designing Microfluidic Medical Assays

(most recent Postdoctoral research advised by Eric S. G. Shaqfeh for the computational part and Juan Santiago for the experimental part. The project is in collaboration with Stanford Genome Technology Center)

My main objective has been to combine direct microfluidic experiments with computational modeling to design a multi-purpose microfluidic platform which can diagnose morphological and bio-mechanical changes to red blood cells (RBCs) to diagnose Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS), a mysterious disease with no definitive cure which is estimated to affect millions of individuals around the world, and 2 out of 100 children. The platform is designed to accurately measure the cell size and flexibility to diagnose differences between healthy controls and ME/CFS patients. It will identify factors contributing to differences in deformability, namely, the shear resistance of the cytoskeletal spectrin network and cytoplasmic viscosity. In this regard, the simulations are performed for the following specific aims:
1. Optimizing the operational and geometrical features of the micro-channels.
2. Converting cell shape and deformation to the characteristic elastic and viscous properties.

Collective Dynamics of Red Blood Cells (RBCs) in Micro-vasculature

(Postdoctoral research advised by Eric S. G. Shaqfeh)

I studied the effect of RBC deformability and cytoplasmic viscosity on its migration and distribution in small-medium arterioles (20-35 μm). In particular, we addressed the following aims:
1. The effect of RBC deformability on its distribution and clear fluid layer in small arterioles,
2. The impact of cytoplasmic viscosity on cell shapes, migration, and clear fluid layer.
Cell deformability alters in certain pathologies and cytoplasmic viscosity is mostly determined by hemoglobin concentration. Under normal conditions, a red blood cell has an internal viscosity 5-6 times higher compared to the viscosity of the plasma. It was found that the distribution of RBCs in smaller arterioles are subjected to a qualitatively different behavior compared to medium sized arterioles. I also found that the cytoplasmic viscosity significantly reduces the RBC-free layer, changes the concentration distribution of the cells normal to the walls, and slows down the formation of RBC accumulation at the center of the channel. The simulations indicated the formation of rich configurational diversity among the cells, from simple slipper-liked to trilobe and multilobe shapes which have been observed experimentally. Interestingly, the single cell hydrodynamic lift is significantly affected for higher viscosity contrast, whereas two cell collision remains almost unaffected..

Transport of Architecturally Complex Macromolecules in Dilute and Semi-dilute Polymeric Solutions

(PhD research advised by Bamin Khomami in collaboration with Charles M. Schroeder)

I have developed a simulation platform ("BDpack" http://amir-saadat.github.io/BDpack/) on the basis of Brownian dynamics to do high fidelity prediction of both transient and steady-state properties of semi-dilute polymer solutions while including full long range hydrodynamic interactions (HI) and excluded volume effects. The simulation platform is used to study the transport of interacting multiple chains under equilibrium condition and also in shear and planar elongational flow.
I used this platform to study the dynamics of comb polymers in dilute solutions, and the simulation results revealed the significant impact of branches on the unraveling stretching dynamics and also relaxation behavior of comb polymers with respect to the linear chains. Currently, I am continuing the project by investigating the dynamic behavior of architecturally complex macromolecules, in particular comb polymers, in a bath of semi-dilute chains.

Teaching Interests:

Teaching and mentoring younger students are part of my motive to continue working in academia. Throughout my graduate and postdoctoral research, I had the privilege to mentor/supervise four undergraduate students and help them develop the required research skills.

I am interested in teaching courses in the chemical and mechanical engineering syllabi in graduate and undergraduate levels. In particular, fluid and continuum mechanics as applied to medicine/biology, applied numerical methods applied in computational fluid dynamics of soft matter and deformable objects and stochastic simulation of polymers, all of which fit well with my background. I also enjoy teaching many of the undergrad level courses, namely, introductory or advanced fluid mechanics, and finite element method. I am open to accept other topics and not afraid of taking over courses that are not in my area of expertise.

Teaching Experience:

  1. "Numerical Analysis and Linear Algebra" for the 2017 AHPCRC (army high-performance-computing research center) summer institute.
  2. Co-thought graduate level core course "Transport Phenomena" (I also served as a teaching assistant for this course for two consecutive semesters).
  3. "Plastic engineering and polymer processing" (I prepared undergraduate students for graduate level national entrance exam)
  4. Meshing software "Fluent" and "Gambit" for two semesters (practical numerical skills as well as engineering problems)

Selected Awards and Successful Proposals:

  1. July 2017 -- NVIDIA-Stanford ICME grant for leveraging GPU computing ($50,000)
  2. Apr 2019-present -- NSF's XSEDE computational resources (Allocation of computational time equal to ∼$40,000)
  3. Aug 2018-present -- Open Medicine Foundation (OMF) Postdoctoral Scholarship
  4. Feb 2017-Aug 2018 -- Army High-Performance Computing Research Center (AHPCRC) Postdoctoral Scholarship
  5. Feb 2014-Aug 2016 -- Eastman graduate student fellowship from Eastman Chemical Company

Selected Publications:

  1. A. Saadat, C. J. Guido, E. S. G. Shaqfeh, Effect of cytoplasmic viscosity on Red blood cell migration in small arteriole-level confinements, bioarxiv preprint (submitted to Phys. Rev. Fluids Rapid Communications), 2019.
  2. A. Saadat*, C. J. Guido*, G. Iaccarino, E. S. G. Shaqfeh, Immersed-finite-element method for deformable particle suspensions in viscous and viscoelastic media, Phys. Rev. E, 2018, 98, 063316.
  3. J. Mai*, A. Saadat*, B. Khomami, C. M. Schroeder, Stretching Dynamics of Single Comb Polymers in Extensional Flow, Macromolecules, 2018, 51, 1507.
  4. Y. Lin*, A. Saadat*, A. Kushwaha, E. S. G. Shaqfeh, Effect of Length on the Dynamics of Wall Tethered Polymers in Shear Flow, Macromolecules, 2017, 51, 254.
  5. A. Saadat, B. Khomami, Letter to the Editor: BDpack, an Open Source Parallel Brownian Dynamics Simulation Package. Journal of Rheology, 2017, 61, 147-149.
  6. A. Saadat, B. Khomami, A New Bead-Spring Model for Simulation of Semi-Flexible Macromolecules. The Journal of Chemical Physics, 2016, 145, 204902.
  7. A. Saadat, B. Khomami, Matrix-Free Brownian Dynamics Simulation Technique for Semidilute Polymeric Solutions. Physical Review E, 2015, 92, 033307.
  8. A. Saadat, B. Khomami, Molecular Based Prediction of the Extensional Rheology of High Molecular Weight Polystyrene Dilute Solutions: A High-Fidelity Brownian Dynamics Approach. Journal of Rheology, 2015, 59, 1507-1525.
  9. A. Saadat, B. Khomami, Computationally Efficient Algorithms for Incorporation of Hydrodynamic and Excluded Volume Interactions in Brownian Dynamics Simulations: A Comparative Study of the Krylov Subspace and Chebyshev Based Techniques. The Journal of Chemical Physics, 2014, 140, 184903.
  10. A. Saadat, H. Nazockdast, F. Sepehr, M. Mehranpour, Linear and Nonlinear Melt Rheology and Extrudate Swell of Acrylonitrile-Butadiene-Styrene and Organoclay-Filled Acrylonitrile-Butadiene-Styrene Nanocomposite. Polymer Engineering & Science, 2010, 50, 2340-2349.
  11. A. Saadat, H. Nazockdast, F. Sepehr, M. Mehranpour, Viscoelastic Modeling of Extrudate Swell of Acrylonitrile-Butadiene-Styrene/Clay Nanocomposite. Applied Rheology, 2013, 23, 12131.

Topics 

Biological Engineering
Computational Molecular Engineering

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