de Pablo Group

Jonathan K. Whitmer

  • Postdoctoral Researcher

  • Contact:
  • Office Location:

    Searle Laboratory 105
    5735 South Ellis Avenue
    Chicago, IL 60637

Jonathan Whitmer grew up in Wilson, Kansas, and attended Kansas State University in Manhattan, Kansas, where he was a dual major in mathematics and physics as well as a Goldwater Scholar. He then attended the University of Illinois and received MS and PhD degrees in physics working with Erik Luijten (now at Northwestern University). Following his PhD, Whitmer moved to the University of Wisconsin-Madison Department of Chemical and Biological Engineering as a postdoctoral researcher. Currently, he is a postdoctoral scientist at Argonne National Laboratory.

Jon Whitmer’s research interests lie in the dynamics and thermodynamics of soft condensed matter, which encompasses industrially relevant colloidal and polymeric systems, as well as biological materials. His graduate research and postgraduate research have addressed the behavior of colloidal particles in solution, the behavior of dilute polymer solutions, and liquid crystalline materials. The outlines below give a flavor of his current research in each field.

  • Equilibrium and Nonequilibrium Polyelectrolytes: Much in the world exists out of equilibrium. Weather patterns develop and disperse; cells grow and multiply; combustion engines turn molecular bonds into usable energy. Manufacturing processes utilize shear, compression, extrusion, and flow to manipulate materials. At molecular scales exist glasses, comprising the solid-like phases of most synthetic polymers, and proteins, whose delicately-balanced folding is often irreversibly disrupted upon addition of salt or heat. In the particular case of soft materials, systematic study of nonequilibrium phenomena is daunting, with many length and timescales which must be simultaneously resolved. Strong electrostatic forces arising from Coulombic charge and hydrodynamic coupling due to motion in solvent exist alongside solvation and entropic interactions, competing and conspiring to yield intriguing, largely unexplained phenomena. Everything in these systems moves, and history of motion matters. This is particularly important for processing and presentation applications related to genomic analysis. Jon’s work in this area exists in two thrusts: (1) developing coarse-grained models capable of resolving the important mechanical and thermodynamic aspects of DNA at length scales from nanometers to microns, and (2) studying the effects of confinement and flow on suspensions of genome-length DNA.
  • Liquid Crystalline Gels, Elastomers, and Sensors: Liquid crystals comprise phases of matter consisting of orientable molecules, referred to as mesogens, exhibiting properties intermediate between those of solids and liquids. They exhibit orientational ordering, and varying degrees of positional ordering that engender anisotropic mechanical, electric properties. Importantly, orientational ordering in these systems creates Schlieren textures that are not visible to the naked eye but may be easily observed via polarized light microscopy. Distinct degrees of positional order are associated with different mesophases, referred to as isotropic, nematic, or smectic, to name a few. Through their interaction with surfaces or interfaces, these mesophases can include defects, regions of space where the orientation of the liquid crystal changes abruptly. The unique interactions between liquid crystal mesophases and polarized light form the basis for liquid-crystal display technology. Liquid crystal mesophases can be manipulated through the application of external fields, including surface fields, and they may incorporate defects that, owing to their topological charge and shape, have a unique signature in polarized microscopy. The ability of adsorbed impurities at a liquid crystal interface to alter these mesophases and any associated defects forms the basis of liquid-crystal based devices for detection of pathogens, including viruses and toxins. It is often desirable to combine the optical response of liquid crystals with the structural properties and enhanced stability of solids. Two methods that are able to solidify these materials include gelation of embedded colloids (which engenders soft solidity to the material) and polymeric crosslinking (which couples the mesogens to a rubber matrix. Colloids and nanoparticles within a liquid crystalline phase will create defects, and the system will seek minimization of its overall free energy by overlapping these defects. Here, his interests are in (1) designing better sensors by understanding and priming the surface—elastic instabilities which underly anchoring transitions, (2) utilizing colloid-in-liquid crystal gels to create soft solids which retain nematic response, and (3) elucidating the physics underlying the soft-elastic ordering transitions in liquid-crystalline polymers.
  • Colloidal Clustering and Assembly: Self-assembling structures are standard in nature; the delicate dance of functionally specific protein and nucleic acid macromolecules makes life possible. These are often only kinetically stabilized—if one perturbs the system through addition of salt or heat, the structure is denatured, transitioned to its thermodynamic ground state, and rendered useless. In the nascent discipline of molecular engineering, such structures are designed from the top down using molecular and macromolecular constituents. For instance, disordered colloidal solids have desirable properties as stable low-density solids that enhance (e.g.) food texture and shelf-life, while crystalline arrangements are desirable for photonic applications. The resulting structures may, as with proteins, be kinetically or thermodynamically stable. Simulation and theory have shown that kinetic trapping can often determine the final ordered structure into which the particles assemble. Proper prediction of these structures requires the understanding of both suspension thermodynamics and the effect of transient and processing flows on the particle assemblies. Jon is interested in (1) the nucleation of colloidal clusters in equilibrium and nonequilibrium situations, (2) the cluster and crystal structures formed by patchy colloidal particles, and (3) designing particulate systems that can be used to self-assemble into arbitrary structures.

Adaptive enhanced sampling by force-biasing using neural networks

Guo, Ashley Z., et al. "Adaptive enhanced sampling by force-biasing using neural networks." The Journal of chemical physics 148.13 (2018): 134108.

In Silico Measurement of Elastic Moduli of Nematic Liquid Crystals

Sidky, Hythem, Juan J. de Pablo, and Jonathan K. Whitmer. "In Silico Measurement of Elastic Moduli of Nematic Liquid Crystals." Physical review letters 120.10 (2018): 107801.

Ssages: Software suite for advanced general ensemble simulations

Sidky, Hythem, et al. "Ssages: Software suite for advanced general ensemble simulations." The Journal of chemical physics 148.4 (2018): 044104.

Sculpting bespoke mountains: Determining free energies with basis expansions

Whitmer, Jonathan K., et al. "Sculpting bespoke mountains: Determining free energies with basis expansions." The Journal of chemical physics 143.4 (2015): 044101.

Chirality-selected phase behaviour in ionic polypeptide complexes

Perry, Sarah L., et al. "Chirality-selected phase behaviour in ionic polypeptide complexes." Nature communications 6 (2015): 6052.

Basis Function Sampling: A New Paradigm for Material Property Computation

J. K. Whitmer, C. Chiu, A. A. Joshi, and J. J. de Pablo. Basis Function Sampling. PRL. 2014. Vol. 113, Pg. 190602.

Coarse-grained modeling of DNA curvature

G. S. Freeman, D. M. Hinckley, J. P. Lequieu, J. K. Whitmer, and J. J. de Pablo. Coarse-grained modeling of DNA curvature. JCP. 2014. Vol. 141, Pg. 165103.

Surface Adsorption in Nonpolarizable Atomic Models

J. K. Whitmer, A. A. Joshi, R. J. Carlton, N. L. Abbott and J. J. de Pablo. Surface Adsorption in Nonpolarizable Atomic Models. J. Chem. Theory Comput.. 2014. Vol. 10, Pg. 5616-5624.

DNA shape dominates sequence affinity in nucleosome formation

Freeman, Gordon S., et al. "DNA shape dominates sequence affinity in nucleosome formation." Physical review letters 113.16 (2014): 168101.

Interfacial Tension of Polyelectrolyte Complex Coacervate Phases

J. Qin, D. Priftis, R. Farina, S. L. Perry, L. Leon, J. Whitmer, K. Hoffmann, M. Tirrell, and J. J. de Pablo . Interfacial Tension of Polyelectrolyte Complex Coacervate Phases. ACS Macro Letters. 2014. Vol. 3, Pg. 565-568.

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