(4fz) Complex Interfaces As the Future of Understanding Soft and Biological Matter

Complex interfaces are the future of soft-matter applications ranging from biomedicine to wearable electronics. Interfacial stresses and transport phenomena control the behavior of biological membranes, the optical and electronic properties of colloidal crystals, and the bulk mechanics of soft composites. To guide future applications in these areas, there is a pressing demand not only for a deeper understanding of the physics and chemistry of interfacial systems, but also for new computational platforms to enable their rapid simulation. I am uniquely qualified to lead these research efforts, by combining my expertise in interfacial soft matter, advanced training in numerical methods and applied mathematics, and successful record of collaboration with a range of experimentalists. My proposed research program spans three specific themes:

(1) Fast, efficient computational modeling of inhomogeneous fluid interfaces

Particle- and surfactant-laden interfaces are ubiquitous in formulated products, petroleum fluids, and advanced technologies. Understanding their self-assembly and phase structure, which are integral to their mechanical and transport properties, demands the advancement of highly sophisticated computer simulations. To date, the simulation of “interfacial” systems has not advanced to the same degree as in “bulk” systems due to the increased complexity in modeling multiple fluid phases with non-local interactions, which requires specialized knowledge. The combination of my theoretical training and expertise in large-scale, high-performance computing will enable me to lead the state of the art in computational modeling of many-body systems at the interface between two fluids, including charged species. To this end, my group will build upon existing open-source, GPU-enabled molecular dynamics platforms (e.g., HOOMD, LAMMPS, GROMACS) and employ data-driven modeling techniques to answer long-outstanding questions: (i) What are the correct “effective” pair potentials for interface-trapped particles, as a function of their size, charge, and anisotropy? (ii) How to predict the complex phase morphologies of self-assembling fluids at interfaces, which are ubiquitous in colloidal and biological systems?

(2) Identifying the mechanisms of membrane permeabilization by antimicrobial peptides

Antimicrobial peptides (AMPs) selectively target and penetrate prokaryotic cell membranes without damaging eukaryotes. These represent one of the last frontiers of potential antibiotics in an age where antibiotic resistance is accelerating while pharmaceutical development of new antibiotics is waning. Over the last ten years, the induction of negative gaussian curvature (NGC) in membranes by AMPs has been identified as a good predictor for antimicrobial potency and has enabled the discovery of new peptide sequences. What remains unclear, however, is how the NGC-inducing ability of AMPs is linked to their proposed modes of action – i.e., how they effectively permeate and destabilize prokaryotic cell membranes via “barrel-stave”, “carpet”, or “toroidal-pore” mechanisms. Although AMP-induced membrane permeabilization and destabilization occurs over the course of seconds to minutes in experiments, current modeling approaches based on molecular dynamics (MD) are limited to much smaller time scales (pico- to nano-seconds). My critical new hypothesis is that curvature-mediated peptide-peptide interactions triggered by NGC in membranes is a key factor to explaining the membrane-penetrating ability of AMPs over these “long” time scales. My recent work on curvature- and electrostatically-mediated interactions in fluid interfaces and membranes allows me to investigate this hypothesis by employing a unique combination of MD simulations and coarse-grained, continuum-mechanical models of peptide-membrane systems.

(3) Liquid-in-solid soft composites: from interface-driven phase separation to bulk mechanics

Dispersed liquid fillers in soft solids are commercially employed as strain gauges for flexible, wearable electronics and serve as “model systems” for tissues and condensed biological matter. The interplay between solid elasticity and interfacial tension in liquid-in-solid materials has been shown to impact phase-separation kinetics (nucleation and growth) as well as bulk transport properties (elastic modulus, dielectric permittivity). An outstanding question, with broad implications in the field of composite materials, is how the nonlinear elasticity of the solid matrix impacts the growth of liquid droplets and their deformation under shear. My expertise in visco-elastic mechanics and finite-element modeling makes me ideally suited to address this question through a nonlinear finite elements (FEM)-based approach. My group will develop a scalable computational platform for simulating liquid dispersions in soft solids, to address a number of pertinent problems in the field: (i) How does hyperelasticity impact droplet coarsening during nucleation and growth? (ii) What is the mechanical origin of load-cycling hysteresis (in elastic modulus and dielectric permittivity) when a liquid-in-solid composite is subjected to a macroscopic deformation (shear or extension)?

Research Experience:

PhD, Stanford University: My PhD training under Prof. Eric Shaqfeh gave me an unparalleled expertise in boundary / finite element simulations and matched asymptotic expansions for studying the mechanics of soft and biological matter. I employed these techniques to investigate vesicle flow in microfluidic channels [7-9], a model system for single-cell microfluidic manipulation, sorting, and drug-loading. Up until that point, models for single- and multi-particle flow in microchannels were mostly limited to rigid particles and droplets. As a simple model for real biological cells, vesicles are droplets with an outer enclosing membrane that gives rise to unique, nonlinear flow physics. I showed, for the first time, that vesicle motion can be arrested in non-circular channels through a novel tank-treading mechanism. This non-intuitive effect, verified by experiments [9], is caused by a symmetry-breaking flow in vesicle membranes that does not emerge in droplets. Since publication, my work has been cited in related work on blood flow and the motion of eggs through the oviduct.

Post-doc, UC Santa Barbara: In my post-doctoral work under Profs. Todd Squires and Joseph Zasadzinski, I developed continuum-scale models of heterogeneous lung surfactant monolayers, specifically focusing on the role of surface curvature. The pulmonary alveolus is a highly curved, geometrically complex structure whose air-water interface is rich in lung surfactant. To date, however, virtually all physicochemical experiments and theories are based on planar, Langmuir monolayers, and therefore unable to capture physiologically relevant curvatures. Building upon classical theories for monolayer phase coexistence, I showed that surface curvature qualitatively changes the shape morphology of condensed domains in lung surfactant monolayers [5]. This is significant, for the domain microstructure impacts the partitioning of fatty acids, cholesterol, and proteins in the lung. I also demonstrated that solid-like domain elasticity gives rise to a new mode of interaction between domains in curved surfaces [1,4], which had previously been controversial in the colloidal physics literature.

Selected Publications:

[1] J. M. Barakat and T. M. Squires. Gaussian-curvature-mediated interactions of elastic inclusions in fluid membranes. in prep.

[2] C. Valtierrez-Gaytan, J. M. Barakat, C. Kohler, K. Kieu, B. L. Stottrup, and J. A. Zasadzinski. Epitaxy-induced morphological transitions in phospholipid monolayers. in prep.

[3] J. M. Barakat, Z. R. Hinton, N. J. Alvarez, and T. W. Walker. Surface-tension effects in oscillatory squeeze-flow rheometry. submitted.

[4] J. M. Barakat and T. M. Squires. Capillary force on an ‘inert’ colloid: a physical analogy to dielectrophoresis. Soft Matter. 17, 3417-3442. 2021. doi: 10.1039/d0sm02143a

[5] J. M. Barakat and T. M. Squires. Shape morphology of dipolar domains in planar and spherical monolayers. J. Chem. Phys. 152 (23), 234701. 2020. doi: 10.1063/5.0009667

[6] M. R. Hakim*, J. M. Barakat*, X. Shi, E. S. G. Shaqfeh, and G. G. Fuller. Evaporation-driven solutocapillary flow of thin liquid films over curved substrates. Phys. Rev. Fluids 4, 034002. 2019. doi: 10.1103/PhysRevFluids.4.034002 (∗ = co-first author)

[7] J. M. Barakat, S. M. Ahmmed, S. A. Vanapalli, and E. S. G. Shaqfeh. Pressure-driven flow of a vesicle through a square microchannel. J. Fluid Mech. 861, 447-483. 2019. doi: 10.1017/jfm.2018.887

[8] J. M. Barakat and E. S. G. Shaqfeh. Stokes flow of vesicles in a circular tube. J. Fluid Mech. 851, 606-635. 2018. doi: 10.1017/jfm.2018.533

[9] J. M. Barakat and E. S. G. Shaqfeh. The steady motion of a closely fitting vesicle in a tube. J. Fluid Mech.835, 721-761. 2018. doi: 10.1017/jfm.2017.743

Honors & Awards:

2020 NIH F32 Ruth L. Kirchstein Postdoctoral Fellowship

2016 Young Researchers’ Travel Support Award for the 24^th ICTAM

2014 Outstanding Teaching Assistant in the Department of Chemical Engineering

2013 NSF Graduate Research Fellowship

Teaching Interests:

My aim as an educator is to foster the same level of passion and curiosity that drove me to pursue a career in STEM. I served as a Teaching Assistant (TA) in three courses, one at Columbia, where I was the first undergraduate TA in the department, and two courses at Stanford. For my graduate TA work, I was recognized as an Outstanding Teaching Assistant by the department. As Outreach Officer of the Stanford Polymer Collective, I led numerous STEM outreach efforts in the community by organizing science workshops for elementary and high school students of diverse backgrounds (Stanford Splash and Bay Area Science Festival). As a future faculty member, I am ideally suited to teach foundational courses in transport phenomena, thermodynamics, and mathematical methods. Drawing upon my unique expertise, I aim to contribute special topics courses in the subjects of Capillarity and Interfacial Phenomena and Complex Fluids and Soft Solids. Finally, I am a proponent of diversified teaching tools (e.g., active learning) as well as modernizing chemical engineering curricula through advanced computer programming.