Arushi Prakash

PhD Candidate | ChemE | University of Washington, Seattle

Research Synopsis - Proteins, polymers, and nanoparticles self-assemble in complex ways into structures like fibrils that cause Alzheimer's disease, mesh structures for use as hydrogels, and nanotubes for catalysis, respectively. These assemblies occur in solution and at interfaces. By modeling assembly processes using physics-based simulations (all-atom molecular dynamics simulations and advanced sampling methods), I am interested in providing mechanistic insights into these processes. Further, I am also interested in developing methods and protocols to improve simulations of these systems.

Training - I am a Ph.D. candidate in the Department of Chemical Engineering at the University of Washington (UW), where I work with two fantastic advisors - Jagjeet and Janice Bindra Endowed Associate Professor Jim Pfaendtner at UW and Senior Scientist Christopher J. Mundy at the Pacific Northwest National Laboratory - and a wonderful research group. My work is supported by the Materials Synthesis and Simulation Across Scales (MS3) Initiative at PNNL. Right before heading UW in 2014, I completed my undergraduate degree in Chemical Engineering from Birla Institute of Technology & Science, Pilani, India

Link to CV

Updates -
Mar 2018 : Successfully passed my Candidacy Exam!
Feb 2018 : GeekWire's coverage of the NW IMPACT association between UW and PNNL article
Jan 2018 : Recognition by UW's Society of Women Engineers at their annual banquet picture
Nov 2017 : My work is featured in the video for the MS3 Initiative at PNNL here
Aug 2017 : Made it to the cover of the Journal of Physical Chemistry C! here

Project Descriptions

Modeling Electrolyte and Surface Interaction

Most theories of colloidal association only account for dilute concentration limits. I want to understand how concentrated solutions behave, explore how microscopic details of their association may affect macroscopic association forces. For this, I simulate electrolytes (NaCl and KCl) at different concentrations in solutions and near surfaces (ideal mica surface). From this simulations, I can recover the free energy of association of electrolytes with other electrolyte atoms, water, and surfaces.

Publications:

  • A Prakash, J Pfaendtner, J Chun, CJ Mundy,Quantifying the Molecular-Scale Aqueous Response to the Mica Surface, Journal of Physical Chemistry C, 2017

    • Modelling Non-canonical Peptide Assemblies

    Peptoids are a new class of biopolymers that have shown promise as chemical scaffolds drug carriers, antimicrobial coatings, anticancer compounds, and antibiotics. I want to understand how peptoids assemble into membrane structures in solution and on the mica surface. For this, I work on improving existing force fields, and modeling large-scale assemblies, and calculating kinetics of small oligomer formations.

    Publications: (*Co-first authors)

  • X. Ma, S. Zhang, F. Jiao, C. J. Newcomb, Y. Zhang, A. Prakash, Z. Liao, M. D. Baer, C. J. Mundy, J. Pfaendtner, A. Noy, C-L. Chen, J. J. Yoreo. Tuning crystallization pathways through sequence engineering of biomimetic polymers, Nature Materials, 2017
  • K Sprenger*, A Prakash*, J Pfaendtner,Investigating the role of phosphorylation in silica binding peptides with molecular dynamics simulations, Langmuir, 2017

    • Modeling Protein Adsorption

    Biomineralization is a complex process by which sponges grow ornate silica exoskeletons, bones and teeth are formed. The interaction of proteins with inorganic surfaces is central to these phenomena. I model the interaction of the R5 peptide with silica surfaces, and SN15 peptide with hydroxyapatite surfaces, and model peptide-surface systems to understand these processes better.

    Publications: (*Co-first authors)

  • K Sprenger*, A Prakash*, J Pfaendtner,Investigating the role of phosphorylation in silica binding peptides with molecular dynamics simulations, Langmuir, 2017
  • A Prakash, M Baer, CJ Mundy, J Pfaendtner, Peptoid backbone flexibility dictates its interaction with water and surfaces: A molecular dynamics investigation, Biomacromolecules, 2018
  • A Prakash*, K Sprenger*, J Pfaendtner,Essential slow degrees of freedom in protein-surface simulations: A metadynamics investigation, Biochemical and Biophysical Research Communications, 2017

    • Metadynamics biasing

    Improvement of Enhanced Sampling Methods

    Molecular dynamics simulations of complex systems can get trapped in metastable states. To effectively sample these systems, I am developing enhanced sampling (metadynamics-based) methods and protocols that are able to bias multiple degrees of freedom of the system.

    Publications: (*Co-first authors)

  • A Prakash*, CD Fu*, M Bonomi, J Pfaendtner, Biasing Smarter, Not Harder, By Partitioning Collective Variables Into Families, In preparation

    • Publications

    *Co-first authors

    1. A Prakash*, CD Fu*, M Bonomi, J Pfaendtner, Biasing Smarter, Not Harder, By Partitioning Collective Variables Into Families, In preparation
    2. A Prakash, M Baer, CJ Mundy, J Pfaendtner, Peptoid backbone flexibility dictates its interaction with water and surfaces: A molecular dynamics investigation, Biomacromolecules, 2018
    3. K Sprenger*, A Prakash*, J Pfaendtner,Investigating the role of phosphorylation in silica binding peptides with molecular dynamics simulations, Langmuir, 2017
    4. A Prakash, J Pfaendtner, J Chun, CJ Mundy,Quantifying the Molecular-Scale Aqueous Response to the Mica Surface, Journal of Physical Chemistry C, 2017
    5. A Prakash*, K Sprenger*, J Pfaendtner,Essential slow degrees of freedom in protein-surface simulations: A metadynamics investigation, Biochemical and Biophysical Research Communications, 2017
    6. X. Ma, S. Zhang, F. Jiao, C. J. Newcomb, Y. Zhang, A. Prakash, Z. Liao, M. D. Baer, C. J. Mundy, J. Pfaendtner, A. Noy, C-L. Chen, J. J. Yoreo. Tuning crystallization pathways through sequence engineering of biomimetic polymers, Nature Materials, 2017

    Presentations

    Oral Presentations

    1. A Prakash, M Baer, CJ Mundy, J Pfaendtner, “Aggregation and Self-Assembly of Biomimetic Polymers at Interfaces”, AIChE Annual Meeting, 2017, Minnesota
    2. A Prakash, CJ Mundy, M Baer, J Pfaendtner, “Understanding the behavior of peptoids with classical molecular dynamics and enhanced sampling (Metadynamics)”, Pacific Northwest National Laboratory, 2016, Richland, WA [Invited]

    Poster Presentations

    1. A Prakash, K Sprenger, J Pfaendtner, “Investigating Biosilification by Silaffin Peptide R5 With Parallel Tempering Metadynamics in the Well-Tempered Ensemble”, RARE, 2017, Agra, India
    2. A Prakash, K Sprenger, J Pfaendtner, “Protein Adsorption on Surfaces: The Role of Forcefield and Surface Ions”, AIChE Annual Meeting, 2017, Minnesota
    3. A Prakash, M Baer, CJ Mundy, J Pfaendtner, “What affects peptoid assembly?”, Peptoid Summit, 2017, Berkeley
    4. A Prakash, K Sprenger, J Pfaendtner, “Exhaustive sampling of protein-surface interactions using classical molecular dynamics and metadynamics” Graduate Women and Postdoc Forum at D.E. Shaw Research, 2017, New York
    5. A Prakash, CJ Mundy, M Baer, J Pfaendtner, “Using Metadynamics to understand the multi-dimensional free energy landscape of peptoid self-assembly”, Gordon Research Conference on Computational Chemistry, 2016, Girona, Spain
    6. A Prakash, CJ Mundy, M Baer, J Pfaendtner, “Electrolytes at the muscovite (001) interface: A molecular dynamics study”, 251st ACS National Meeting & Exposition, 2016, San Diego, CA
    7. A Prakash, M Baer, CJ Mundy, J Pfaendtner, “Understanding the behavior of peptoids with classical molecular dynamics and metadynamics”, UW Chemical Engineering Graduate Student Symposium, 2016, Seattle, WA

    Awards

    • 2018. Nominated for Student Teaching Award, College of Engineering, UW
    • 2018. SWE Outstanding Female Award in Chemical Engineering
    • 2017. AIChE Women’s Initiative Committee Travel Award
    • 2016. Materials Computation Center Travel Award
    • 2016. Travel Award for ACS Environmental Interfaces Symposium
    • 2013. UGC-NRC Research Fellowship