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CBE Research Opportunities

Research Opportunities in Chemical and Biomolecular Engineering for Undergraduates

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Engineering Multifunctional Nanoparticles for Targeted Drug Delivery in Cancer

Modern cancer therapeutics are typically developed to aim at key pathways and proteins that are critical to the survival and progression of malignant cells. Nevertheless, they are still associated with undesirable side effects due to nonspecific toxicity that non-targeted tissue and organs experience. In recent years,nanoparticle (NP) based drug delivery systems that carry drugs to tumor in body have greatly improved the efficacy of traditional therapeutics, while decreasing the associated systemic toxicities. NPs with a diameter of 10-200 nm can selectively target and preferentially home at the tumor site via the enhanced permeability and retention (EPR) effect. More complex NPs, such as multiple drug carriers (for combination therapy) and coatings of targeting elements for receptors on cancer cells, have also been engineered to improve the overall outcome by overcoming problems associated with tumor tissue targeting and penetration, drug resistance, cellular uptake and circulation half-life.

We use NPs to target Multiple myeloma (MM), a B-cell malignancy characterized by proliferation of monoclonal plasma cells in the bone marrow (BM) and is the second most common type of blood cancer in the U.S. Despite the recent advances in treatment strategies and the emergence of novel therapies, it still remains incurable. A major factor that contributes to development of drug resistance in MM is the interaction of MM cancer cells with the BM microenvironment. It has been demonstrated that the adhesion of MM cells to the BM stroma via α4β1 integrins leads to cell adhesion mediated drug resistance (CAM-DR), which enables MM cells to gain resistance to drugs such as doxorubicin (Dox)–a 1st line chemotherapeutic in the treatment of MM. To over come this problem, the clinicians apply combination therapy, which is the simultaneous use of two complementary chemotherapeutic agents during treatment. One caveat of this treatment method has been that it is almost impossible to attain the critical stoichiometry at the tumor that is necessary to achieve this synergistic drug effect when conventional methods of chemotherapy is used. Here, we seek to overcome this challenge by using an engineering approach for targeted drug delivery. The overall objective of this proposed project is to engineer “smart” nanoparticles that will deliver and exert the cytotoxic effects of the chemotherapeutic agents on MM cells, and at the same time do it in such a manner to overcome CAMDR for improved patient outcome. To enable this, we will engineer micellar nanoparticles that will be (i) functionalized with α4β1-antagonist peptides as well as Dox and carfilzomib drug conjugates, and (ii) designed to show the adhesion inhibitory and the cytotoxic effects in a temporal sequence. When the nanoparticles are delivered to the MM cells, as a first step they will interact with the cell surface α4β1 integrins and inhibit MM cell adhesion to the stroma, thereby preventing development of CAM-DR (Fig 1). In the second step, the chemotherapeutic agents will exert their synergistic cytotoxic effects after cellular uptake, as the nanoparticles will be designed to require a low pH environment such as the endocytic vesicles, to release active drugs. This way, the “smart” nanoparticles will act on the MM cells in a temporal fashion and prevent development of CAM-DR for improved patient outcome.

Contact: Associate Professor Basar Bilgicer, 205C McCourtney Hall, 574 631-1429,(bbilgicer@nd.edu)
Department of Chemical and Biomolecular Engineering

Microporous Membrane Reactors for Antibody Digestion and Characterization

Antibodies are the fastest growing class of therapeutic drugs. Due to the complex composition and biosynthesis of these drugs, quality control is vital to ensure that antibodies are effective and do not induce side effects such as an immune response. Mass spectrometry is the most powerful tool for antibody characterization, but it usually requires antibody digestion into smaller pieces that are amenable to characterization. This research aims to use membrane reactors to control antibody proteolysis and create a few large peptides that enable rapid detection of antibody modifications such as oxidation, phosphorylation, and glycosylation. Controlled digestion may also identify changes in protein conformation or the formation of disulfide bonds. The project will likely include immobilization of enzymes in membranes, performing digestion reactions and mass spectrometry, and interpreting mass spectrometry data.

Preferred disciplines:
The research is particularly appropriate for students in chemical engineering, chemistry, or biochemistry.
Contact: Professor Merlin Bruening, 140C McCourtney Hall, 574 631-3024 (mbruenin@nd.edu
Department of Chemical and Biomolecular Engineering

Nanostructured Polysulfone Polyelectrolyte Copolymer Membranes for Fuel Cells

Sulfonated polysulfone copolymers with controlled nanophase-separated morphology hold great potential
as alternatives to benchmark Nafion® for polyelectrolyte membrane fuel cells (PEMFCs), due to their much
better proton conductivity at low relative humidity (RH) levels and thermal stability. Previous research have
shown that long hydrophilic (ionic) sequences or high degree of sulfonation are needed to form wellconnected
proton conducting nanochannels that enables high proton conductivity at low RH. However, it invariably comes at the expense of high water uptake and excessive membrane swelling resulting in deterioration of the dimensional stability and mechanical robustness. This project aims to exploiting an innovative supramolecular strategy to address this water management challenge in PEM membranes via introducing triptycene-based building blocks into polymer backbones. It is expected that supramolecular interactions of chain threading and interlocking induced by triptycene units can effectively suppress water swelling while maintaining high water uptake, which is critical to provide high proton conductivity under low RH conditions. Specifically, both random and multiblock copolymers of systematically varied compositions will be developed in this project to investigate how supramolecular interactions of triptycene units govern the formation of proton-conducting nanochannels as well as proton transport properties. The project will start with the synthesis of triptycene diol monomer, which will be copolymerized with commercial sulfonated monomer to produce both random and multiblock copolymers. Comprehensive characterizations of the copolymers will be conducted to confirm the chemical structure (NMR ad FTIR) and access their thermal and mechanical properties (DSC, TGA, tensile test, etc.). Membrane fabrication and acidification will then follow to prepare free standing, defect-free films for water swelling measurement, morphology characterization (AFM, TEM) and proton conductivity measurements (Impedance spectroscopy).

Preferred disciplines: A student in materials science, chemical engineering, or chemistry is preferred, and having previous experience in a chemical laboratory would be helpful.

Contact: Assistant Professor Ruilan Guo, 205E McCourtney Hall, 574 631-3453 (rguo@nd.edu)
Department of Chemical and Biomolecular Engineering

Polymer Membranes with Tunable Microporosity for Gas Separations

Polymers with well-defined microporosity are highly desired for gas separation membranes, wherein high
microporosity enables fast gas transport while the finely tuned pore size regulates selective transport via
size sieving. Recently there have been markedly increasing research interests in developing microporous
polymers for gas separation membranes, such as polymers with intrinsic microporosity (PIMs). However,
the reportedly super high gas permeability of microporous polymers always accompanies with low selectivity, mainly due to the lack of precise control over pore size distribution in these polymers. Moreover, physical aging induced deterioration of permeability remains as one of the biggest challenges for microporous polymer membranes. This project will focus on constructing highly rigid ladder-like polymers using a shape-persistent building block based on pentiptycene-containing structural units. The novelty of this new type of microporous polymers lies in the truly intrinsic microporosity defined configurationally by the shape of the pentiptycene units, which offers unique opportunity to tailor the microcavity architecture in the membranes and simultaneously provide superior resistance towards physical aging by taking advantage of the rigid framework of pentiptycene moieties. The project will involve the synthesis of pentiptycene-based monomers with various bridgehead substituent groups, polymerization of tetrafunctional pentiptycene monomers with commercial comonomers, membrane fabrication/characterization, and pure-gas permeation tests.

Preferred disciplines: A student in materials science, chemical engineering, or chemistry is preferred, and having previous experience in a chemical laboratory would be helpful.

Assistant Professor Ruilan Guo, 205E McCourtney Hall, 574 631-3453 (rguo@nd.edu)
Department of Chemical and Biomolecular Engineering

Perovskite Photovoltaics

In recent years, nanomaterials have emerged as the new building blocks to construct light energy harvesting assemblies.1 Efforts are being made to design high efficiency organic metal halide hybrid structures that exhibit improved selectivity and efficiency towards light energy conversion.2-5 This project will evaluate the performance of solid state cesium lead halide perovskite solar cells. The summer research involves synthesis of semiconductor nanocrystals and dissolution processed thin perovskite films on various oxide films and construct solar cell. These cells will then be evaluated to establish their photovoltaic properties. The overall goal is to tune the photoresponse of the thin film solar cell through mixed halide composition and improve the solar conversion efficiencies.

Additional Resources:
1. Kamat, P.V., Quantum Dot Solar Cells. The Next Big Thing in Photovoltaics. J. Phys. Chem. Lett. 2013, 4, 908–918.

2. Christians, J.A., Fung, R., and Kamat, P.V., An Inorganic Hole Conductor for Organo-Lead Halide Perovskite Solar Cells. Improved Hole Conductivity with Copper Iodide. J. Am. Chem. Soc. 2014,136, 758–764.

3. Manser, J.S., Christians, J.A., and Kamat, P.V., Intriguing Optoelectronic Properties of Metal Halide Perovskites. Chem. Rev. 2016, 116, 12956–13008.

4. Christians, J.A., Miranda Herrera, P.A., and Kamat, P.V., Transformation of the Excited State and Photovoltaic Efficiency of CH3NH3PbI3 Perovskite upon Controlled Exposure to Humidified Air. J. Am. Chem. Soc. 2015, 137, 1530–1538.

5. Yoon, S.J., Draguta, S., Manser, J.S., Sharia, O., Schneider, W.F., Kuno, M., and Kamat, P.V., Tracking Iodide and Bromide Ion Segregation in Mixed Halide Lead Perovskites during Photoirradiation. ACS Energy Lett. 2016, 290-296.

Preferred disciplines: The expected and/or anticipated involvement of the REU student in the research. The student will involve preparation of perovskite films, spectroscopic and material characterization, solar cell fabrication and performance evaluation.

Preferred discipline(s), expertise, lab skills, etc. Chemistry/Physics Background at sophomore level.
Optional information such as limitations on schedule, preferred universities, etc. No preference

Contact: Professor Prashant V. Kamat, 235 Radiation Lab , 574 631-5411, (kamat.1@nd.edu)
Department of Chemical and Biomolecular Engineering

Nanostructure Assemblies for Sensing Application

Recent advances in the construction and characterization of graphene-semiconductor/
metal nanoparticle composites in our laboratory has allowed us to develop multi-functional materials for energy conversion and storage. These next-generation composite systems may possess the capability to integrate conversion and storage of solar energy, detection and selective destruction of trace environmental contaminants, or achieve single-substrate, multi-step heterogeneous catalysis. This research project will involve synthesis of graphene based assemblies for photocatalytic and photovoltaic conversion of light energy. The graphene oxidesemiconductor assemblies will be characterized by transmission electron microscopy and the excited state processes will be evaluated using time-resolved emission and absorption techniques. The goal is to optimize the performance of graphene based assembly and maximize the photoconversion efficiency.

1. Lightcap, I.V., Murphy, S., Schumer, T., and Kamat, P. V. Electron Hopping Through Single-to-Few Layer Graphene Oxide Films. Photocatalytically Activated Metal Nanoparticle Deposition. J. Phys. Chem. Lett. 2012, 3, 1453-1458.

2. Lightcap, I.V. and  Kamat, P.V. Graphitic Design: Prospects of Graphene-Based Nanocomposites for Solar Energy Conversion, Storage, and Sensing. Acc. Chem.Res. 2013, 46, 2235–2243.

3. Bridewell, V.L., Karwacki, C.J., and Kamat, P.V., Electrocatalytic Sensing with Reduced Graphene Oxide: Electron Shuttling between Redox Couples Anchored on a 2-D Surface. ACS Sensors 2016, 1, 1203-1207.

Preferred disciplines: The expected and/or anticipated involvement of the REU student in the research.
The student will involve preparation of graphene based semiconductor nanoassembly, spectroscopic and material characterization, and test the assemblies in sensing applications.

Preferred discipline(s), expertise, lab skills, etc. Chemistry/Physics Background at sophomore level.
Optional information such as limitations on schedule, preferred universities, etc. No preference

Contact: Professor Prashant V. Kamat, 235 Radiation Lab , 574 631-5411, (kamat.1@nd.edu)
Department of Chemical and Biomolecular Engineering

Fabrication of Solid State Batteries

Solid state batteries (SSB’s) may be a key enabler for electric vehicles. A solid electrolyte can overcome many shortcomings of present technology including offering wider electrochemical voltage ranges, better chemical compatibility, and improved safety. Progress is needed to overcome electrolyte limitations and provide more economical processing while still delivering sufficient energy density for automotive application.

ND researchers are developing ceramic materials (Li7La3Zr2O12) and low-cost processing methods to provide for high-power, solid-state, lithium-ion batteries for use in EVs. A key factor to drive down costs is the development of scalable, ceramic fabrication techniques.

The goal of this project is the chemical processing and sintering of nanosized electrolyte and electrode powders for development of composite electrode microstructures to yield high performance batteries. Liquid phase sintering of electrolytes has been developed to reduce required processing temperatures. Composite electrodes will be developed to permit co-sintering of electrode-electrolyte structures.

Student Involvement: Student will synthesize (chemical processing) and characterize (X-ray diffraction,
dilatometry) nano-sized powder of battery component materials (electrolytes, eletrodes). Slurries for tape casting will be prepared and sintered. Cast tapes will be characterized (impedance spectroscopy). Batteries will be fabricated from tapes (glove box work).

Preferred disciplines: Materials science, chemical engineering, chemistry

Contact: Professor Paul McGinn, 178 Fitzpatrick Hall, 574 631-6151 (pmcginn@nd.edu
Department of Chemical and Biomolecular Engineering

Elucidating Fundamental Transport Properties of Copolymer-derived Charge Mosaic Membranes

Nanoporous membranes based on self-assembled copolymer precursors are an emerging class of promising separation and purification devices, which will find application in water purification, pharmaceutical, and biofuel processing applications, due to the ability of researchers to control the nanostructure and chemistry of these multifunctional materials. To date, the most successful methodology for directing the assembly of nanostructured copolymer-based membranes has been the self-assembly and nonsolvent induced phase separation (SNIPS) procedure. This membrane fabrication protocol combines the thermodynamically driven selfassembly of copolymers in solution with the oft-used nonsolvent induced phase separation membrane fabrication technique. In addition to being facile and scalable, the versatility of the SNIPS process makes it an attractive membrane fabrication methodology. In particular, the membrane nanostructure and chemistry generated by the SNIPS process can be tuned by varying a number of engineering parameters. Recently, it was demonstrated that this flexibility could be exploited to generate charge-mosaic membranes based on the copolymer material platform. Charge mosaics contain both positively-charged and negatively-charged domains that traverse the thickness of the membrane. This structure enables both the cation and anion from a dissolved salt to permeate through the membrane without violating the macroscopic constraint of electroneutrality, and results in membranes that permeate dissolved salts more rapidly than solvent or neutral molecules. Unfortunately, the fundamental knowledge regarding how these membranes function is lagging. As such, the objective of this project is to identify the key material relationships that control the interplay between membrane nanostructure, functionality, and transport properties for charge mosaics membranes.

Student involvement: The student researcher will be asked to fabricate membranes using the SNIPS process, and elucidate how the nanoscale structure and chemistry of the membranes impact the observed
transport properties through experimental water flow and solute throughput tests.

Preferred disciplines: Chemical, Mechanical, and Environmental Engineers are well-suited to undertake this
research project.

Contact: Assistant Professor William Phillip, 205F McCourtney Hall, 574 631-2708 (wphillip@nd.edu
Department of Chemical and Biomolecular Engineering

Polymer Electrolytes for Advanced Rechargeable Batteries

The objective of the research is to investigate solid polymer electrolytes for use in lithium and/or magnesium rechargeable batteries. Such electrolytes have to potential for increase battery safety due to their lower volatility and higher thermal stability compared with commercial electrolytes. Current polymer electrolytes suffer from low ionic conductivities that result in low battery charge/discharge rates, which preclude their use in commercial devices.

This project will investigate the use of novel salts and/or additives in polymer electrolyte formulations.

Student Involvement: The REU student will prepare polymer electrolyte films and characterize the electrochemical and thermal properties of these films.

Preferred Disciplines: chemical engineering, not required, though greater levels of experience in a chemical laboratory are preferred.

Contact: Assistant Professor Jennifer.L.Schaefer, 205G McCourtney Hall, 574 631-5114 (Jennifer.L.Schaefer.43@nd.edu) Department of Chemical and Biomolecular Engineering

Dendrite Growth in Rechargeable Lithium Metal Batteries

Widespread commercialization of high energy density rechargeable lithium metal batteries has been
prevented for decades due to lithium dendrite growth. Lithium metal electrodeposits unevenly in many
conditions, leading to growth of lithium dendrites that can short‐circuit the battery and result in fire or
explosion. The parameters affecting lithium dendrite growth are still not well understood.
This project will investigate the effects of polymer electrolyte characteristics on dendrite nucleation

Student Involvement: The REU student will prepare polymer electrolyte films, fabricate lithium metal batteries,
and conduct short‐circuit testing.

Preferred Disciplines: Prior lab experience and a background in chemical engineering, chemistry, materials science, or a closely related field is preferred.

Contact: Assistant Professor Jennifer.L.Schaefer, 205G McCourtney Hall, 574 631-5114 (Jennifer.L.Schaefer.43@nd.edu) Department of Chemical and Biomolecular Engineering

Targeting Therapeutic Nanoparticles Through Supramolecular Affinity

We are motivated to advance the practice of therapeutic nanotechnology by capturing several of the
benefits of antibody targeting while avoiding some known complications. Antibodies are used for targeting
due to high affinity and biological tissue-specificity. There are, however, downsides to antibody use in
nanomedicine that could present issues in application moving forward: (i) Antibodies are fundamentally
opsonins, a bio-recognizable signal that promotes cell-mediated uptake and clearance of foreign particles
(e.g., viruses) by the reticuloendothelial system. Can we use alternative high-affinity targeting groups that
would not be subjected to active biological clearance? (ii) A typical therapeutic nanoparticle (diameter ~50-
100 nm) endowed with antibodies (hydrodynamic diameter of ~10 nm) would be expected to have its
surface properties and function altered by addition of this bulky appendage; furthermore, there is limited
area on the nanoparticle surface to attach such a large targeting group. Can we design targeting based on
minimal groups that have comparable affinity while limiting impact on the properties of the functional
nanoparticle? Using ultra-high affinity supramolecular interactions as a type of “molecular Velcro” our group
envisions a new therapeutic nanoparticle targeting axis built on minimal small molecule affinity motifs that
serve as drivers of localization, in lieu of large targeting antibodies, while at the same time not sacrificing
any affinity relative to an antibody-antigen interaction.

Student Involvement: An undergraduate working on this project will be expected to learn techniques for formulating synthetic nanoparticles to contain drugs and quantifying drug release using a combination of spectroscopy and chromatography. Additionally, this individual will be tasked with validating this mechanism for targeting in vitro through microscopy of fluorescent nanoparticles on cultured cells.

Preferred Disciplines: Disciplines related to Chemistry, Chemical Engineering, Materials Science, or Bioengineering are encouraged to apply. A minimum of some prior laboratory coursework is expected.

Contact: Assistant Professor Matthew Webber, 205B McCourtney Hall, 574 631-4246 (mwebber@nd.edu) Department of Chemical and Biomolecular Engineering

Engineering Responsive Peptide-based Drug Nanocarriers

We are motivated to improve therapeutic specificity of self-assembling drug nanocarriers by endowing
them with units that can promote a change in assembly state as a function of the presence of diseaserelevant
analytes and biomarkers. Typical nanocarriers for drug delivery demonstrate equilibrium-driven
release. This is inefficient at best, and at worst can result in the accumulation of drug off-target in the body
where it can elicit side-effects. Can we use disease-specific indicators to facilitate increased drug release
specifically at the site of disease, toward non-equilibrium, responsive drug delivery? Peptide self-assembly
affords one means to create nanostructures, and by virtue of these being based on non-covalent
interactions, the energy barrier that must be overcome in order to induce a change in assembly state is
modest relative to a system constructed covalently. Furthermore, peptide nanostructures can be designed
with control over shape, interfacial curvature, and aspect-ratio. Our objective in this project is thus to
incorporate analyte-sensing chemical units within a peptide backbone such that presence of the specific
analyte drives a change from an assembled peptide-based drug carrier to a disassembled monomeric form
accompanied by burst release of a drug.

Student Involvement: An undergraduate working on this project will be expected to learn techniques in solid-phase peptide synthesis, conduct routine characterization to study changes in material properties as a function of analyte concentration, and quantifying the loading and release of drugs from these nanostructures using a combination of spectroscopy and chromatography.

Preferred Disciplines: Disciplines related to Chemistry, Chemical Engineering, Materials Science, or Bioengineering are encouraged to apply. A minimum of some prior laboratory coursework is expected.

Contact: Assistant Professor Matthew Webber, 205B McCourtney Hall, 574 631-4246 (mwebber@nd.edu) Department of Chemical and Biomolecular Engineering

Effects of Acidity and Salinity on Polymer Drug-Delivery Complexes

Research description:
A host of interesting phenomena, both biological and technological, involve the complexation of charged
polymers; these may be long polymers with well-de ned secondary structure, such as proteins1, linear
polyelectrolytes, or multi-branched species2. A particularly interesting phenomenon within polyelectrolyte
solutions is coacervation3,4, a liquid{liquid phase separation where polymer-enriched liquid droplets are
formed within a dilute phase5. Coacervation is a puzzling process where two primarily aqueous phases become immiscible6. Aggregates (coacervates) formed in mixtures of oppositely charged polyelectrolytes are known as complex coacervates5,7,8. Coacervates occur in many natural systems9,10, and have found application in microencapsulation11,12 and extraction13 processes, as their ultra-low surface tension allows them to readily assimilate nanoparticles or drug payloads within aqueous suspension. Coacervation is intimately related to the process of layer-by-layer deposition, where films up to micrometers in thickness are built by iterative surface adsorption of polyelectrolytes. Such films are of interest as solid electrolytes in lightweight
batteries14,15, fuel-cell electrodes14,16, protective coatings16, and drug micro-encapsulation17.

This topic inspires REU projects involving characterization of coacervates through molecular dynamics
simulation. These are focused on the use of complex coacervates in the delivery of therapeutic compounds to
specific biological targets, as the highly charged, condensed environments they facilitate can act to stabilize
and protect molecular and macromolecular species.

1. Using a customized version of the LAMMPS open-source molecular simulation package,LAMMPS25
the student will examine the role of pH in the complexation of long polyions in the presence of added
salt. Of particular note are the connections between molecular structure and effective pKa in dilute
and concentrated solutions, as this quantity determines the useful phase window for coacervates as a
host material for drug delivery applications.

2. A second project involves the influence of the highly charged environment provided by a complex coacervate in stabilizing drugs|in particular protein based therapies|against deactivation and degradation.
the student will explicitly determine how these environments affect the pKa and native structure of
therapeutic compounds using coarse-grained and fully atomistic models.

Student Involvement:
It is preferable (but not required) for students interested in this project to have prior experience with writing
computer code (C++ preferred) and with scripting languages such as python and bash to facilitate running
computations on the Whitmer group cluster and CRC machines.

1. S. L. Perry, L. Leon, K. Q. Ho mann, et al. \Chirality-selected phase behavior in ionic polypeptide
complexes." Nature Communications, 6, 2015.

2. D. Priftis, X. Xia, K. O. Margossian, et al. \Ternary, tunable polyelectrolyte complex fluids driven by
complex coacervation." Macromolecules, 47(9):3076{3085, 2014.

3. S. L. Turgeon, C. Schmitt, and C. Sanchez. \Protein{polysaccharide complexes and coacervates." Curr.
Opin. Colloid Interface Sci., 12(4-5):166{178, 2007.

4. J. R. Nixon, A. H. Khalil, and J. E. Carless. \Phase relationships in the simple coacervating system
isoelectric gelatin : Ethanol : Water." J. Pharm. Pharmac., 18:409{416, 1966.

5. D. Priftis and M. Tirrell. \Phase behavior and complex coacervation of aqueous polypeptide solutions."
Soft Matter, 8(36):9396, 2012.

6. F. M. Menger and B. M. Sykes. \Anatomy of a coacervate." Langmuir, 14(15):4131{4137, 1998.

7. R. A. Riggleman, R. Kumar, and G. H. Fredrickson. \Investigation of the interfacial tension of complex
coacervates using eld-theoretic simulations." J. Chem. Phys., 136:024903, 2012.

8. C. G. de Kruif, F. Weinbreck, and R. de Vries. \Complex coacervation of proteins and anionic polysaccharides." Curr. Opin. Colloid Interface Sci., 9(5):340{349, 2004.

9. N. Pawar and H. B. Bohidar. \Statistical thermodynamics of liquid{liquid phase separation in ternary
systems during complex coacervation." Phys. Rev. E, 82(3):36107, 2010.

10. A. E. Smith, F. T. Bellware, and J. J. Silver. \Formation of nucleic acid coacervates by dehydration and
rehydration." Nature, 214(5092):1038{1040, 1967.

11. C. I. Onwulata. \Encapsulation of new active ingredients." Annu. Rev. Food. Sci. Technol., 3:183{202,

12. S. R. Bhatia, S. F. Khattak, and S. C. Roberts. \Polyelectrolytes for cell encapsulation." Curr. Opin.
Colloid Interface Sci., 10(1-2):45{51, 2005.

13. F.-J. Ruiz, S. Rubio, and D. Perez-Bendito. \Water-induced coacervation of alkyl carboxylic acide
reverse micelles: Phenomenon description and potential for the extraction of organic compounds." Anal.
Chem., 79:7473{7484, 2007.

14. J. L. Lutkenhaus and P. T. Hammond. \Electrochemically enabled polyelectrolyte multilayer devices:
from fuel cells to sensors." Soft Matter, 3(7):804, 2007.

15. D. M. DeLongchamp and P. T. Hammond. \Highly ion conductive poly(ethylene oxide)-based solid
polymer electrolytes from hydrogen bonding layer-by-layer assembly." Langmuir, 20(13):5403{11, 2004.

16. P. R. Van Tassel. \Polyelectrolyte adsorption and layer-by-layer assembly: Electrochemical control."
Curr. Opin. Colloid Interface Sci., 17(2):106{113, 2012.

17. D. B. Shenoy, A. A. Antipov, G. B. Sukhorukov, and H. Mohwald. \Layer-by-layer engineering of
biocompatible, decomposable core-shell structures." Biomacromol., 4(2):265{72, 2003.

18. M. E. Leunissen, C. G. Christova, A.-P. Hynninen, et al. \Ionic colloidal crystals of oppositely charged
particles." Nature, 437(7056):235{40, 2005.

19. G. A. Chapela, F. del Ro, and J. Alejandre. \Liquid-vapor phase diagram and surface properties in
oppositely charged colloids represented by a mixture of attractive and repulsive Yukawa potentials." J.
Chem. Phys., 138(5):054507, 2013.

20. K. Iwata, H. Okajima, S. Saha, and H.-o. Hamaguchi. \Local structure formation in alkyl-imidazoliumbased
ionic liquids as revealed by linear and nonlinear Raman spectroscopy." Acc. Chem. Res., 40:1174{1181, 2007.

21. H.Weingartner. \Understanding ionic liquids at the molecular level: Facts, problems, and controversies."
Angew. Chem. Int. Ed., 47:654{670, 2008.

22. J. Qin, D. Priftis, R. Farina, et al. \Interfacial tension of polyelectrolyte complex coacervate phases."
ACS Macro Letters, 3(6):565{568, 2014.

23. S. L. Perry and C. E. Sing. \Prism-based theory of complex coacervation: Excluded volume versus chain
correlation." Macromolecules, 2015.

24. Z. Ou and M. Muthukumar. \Entropy and enthalpy of polyelectrolyte complexation: Langevin dynamics
simulations." J. Chem. Phys., 124(15):154902, 2006.

25. S. Plimpton. \Fast parallel algorithms for short-range molecular dynamics." J. Comp. Phys., 117(1):1{19, 1995.

Contact: Associate Professor Jonathan Whitmer, 122A Cushing, 574 631-1417, (jwhitme1@nd.edu)
Department of Chemical and Biomolecular Engineering

Performance of Functional Metal–Organic Frameworks

Research description:
The beautiful and intricate geometries of metal{organic frameworks (MOFs),1 together with their impressive
capacities for energy storage, 2-5 carbon sequestration6,7 and catalysis8,9 inspire their study in equal amounts.
This array of applications is facilitated by the open structure of the MOF and the myriad choices of linking
molecules. In this project, we will examine the properties of some recently synthesized open structures,
including the ZnO2/pyridine carboxylate structures studied in the lab of Jason Hicks at Notre Dame.10
Of particular interest are the adsorption free energies and di usion constants for compounds within these
lattices, as they will influence operating conditions and capabilities of the MOF structure.

Student Involvement:
During the REU, the student will build molecular simulation models and learn techniques for statistically
characterizing the properties of crystal lattices, in addition to thermodynamic integration and manifold
reduction methods. The student will be expected to have some familiarity with writing computer codes,
preferably in C++. Beyond this, only general knowledge of physics and chemistry is required.

1. O'Kee e, Michael and Yaghi, Omar M., \Deconstructing the Crystal Structures of Metal-Organic Frame-
works and Related Materials into Their Underlying Nets." Chemical Reviews, 112, 675{702 (2012),

2. Yue, Hongyun, Shi, Zhenpu, Wang, Qiuxian, Cao, Zhaoxia, Dong, Hongyu, Qiao, Yun, Yin, Yan-
hong, and Yang, Shuting, \MOF-Derived Cobalt-Doped ZnO@C Composites as a High-Performance
Anode Material for Lithium-Ion Batteries." ACS Applied Materials & Interfaces, 6, 17067{17074 (2014),

3. Zhang, Guanhua, Hou, Sucheng, Zhang, Hang, Zeng, Wei, Yan, Feilong, Li, Cheng Chao, and Duan,
Huigao, \High-Performance and Ultra-Stable Lithium-Ion Batteries Based on MOF-Derived ZnO@ZnO
Quantum Dots/C CoreShell Nanorod Arrays on a Carbon Cloth Anode." Advanced Materials, 27, 2400{
2405 (2015), doi:10.1002/adma.201405222.

4. Li, Shun-Li and Xu, Qiang, \Metal-organic frameworks as platforms for clean energy." Energy Environ.
Sci., 6, 1656{1683 (2013), doi:10.1039/C3EE40507A.

5. Getman, Rachel B., Miller, Jacob H., Wang, Kenneth, and Snurr, Randall Q., \Metal Alkoxide Function-
alization in Metal-Organic Frameworks for Enhanced Ambient-Temperature Hydrogen Storage." Journal
of Physical Chemistry C, 115, 2066{2075 (2011), doi:10.1021/jp1094068.

6. Millward, Andrew R. and Yaghi, Omar M., \Metal{Organic Frameworks with Exceptionally High Ca-
pacity for Storage of Carbon Dioxide at Room Temperature." Journal of the American Chemical Society,
127, 17998{17999 (2005), doi:10.1021/ja0570032.

7. Wilmer, Christopher E., Farha, Omar K., Bae, Youn-Sang, Hupp, Joseph T., and Snurr, Randall Q.,
\Structure-property relationships of porous materials for carbon dioxide separation and capture." Energy
Environ. Sci., 5, 9849{9856 (2012), doi:10.1039/C2EE23201D.

8. Lee, JeongYong, Farha, Omar K., Roberts, John, Scheidt, Karl a, Nguyen, SonBinh T., and Hupp,
Joseph T., \Metal-organic framework materials as catalysts." Chemical Society Reviews, 38, 1450{1459
(2009), doi:10.1039/b807080f.

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Contact: Associate Professor Jonathan Whitmer, 122A Cushing, 574 631-1417, (jwhitme1@nd.edu)
Department of Chemical and Biomolecular Engineering

Predicting Material Elastic Responses from Molecular Simulations

Research description:
Elastic materials exhibit a restoring force which opposes applied stress, resulting from a perturbation away
from thermodynamic equilibrium. Materials may exhibit di erent types of elasticity depending on their
character.1 Each opposed deformation de nes an elastic modulus; liquid crystals may have three or more
elastic moduli characterizing their response to curvature deformations in their ordering eld;2 solids, both
crystalline and amorphous, also have several elastic moduli, such as the bulk modulus, shear modulus and
Young's modulus. Each of these moduli may be related to derivatives of the system's free energy relative
to a variable characterizing the extent of deformation. The Whitmer group has three potential projects
related to measurements of elastic properties in silico, which build on recent formalisms3-5 utilizing free
energy perturbation simulations to extract the elastic coecients of liquid crystals into the domain of two
dimensional membranes and three dimensional solids. We aim to characterize the typical elastic properties
of each phase, and validate our data against previous simulations and theoretical models.
In particular, the three projects are:

  • Application of free-energy perturbations to atomistic models of liquid crystals to predict elastic constants
    in silico
    , and contribute to development of a high throughput workflow for elastic property screening.
  •  The utilization of recently developed coarse-grained models of biological membranes to understand the enthalpic interactions and entropic packing alter the elastic behavior of a membrane. This project also seeks to demonstrate the e ectiveness of flat-histogram" methods6 relative to fluctuation methods in determining surface tension and elasticity of membranes.
  • Ionic liquid crystals, salt species which self-assemble into phases with charged and uncharged domains, have recently been of interest as novel battery electrolytes. Here we will examine the response behavior of self-assembled phases in the ionic liquid crystal [C16mim][PF6], to obtain structure-property relationships which will be useful in processing these materials.

During the summer REU, the student will work intensively on molecular simulation models and learn techniques of advanced sampling, in particular flat-histogram methods7 used for the measurement of free energies. The student will be expected to have some familiarity with writing computer codes, preferably in
C++. Beyond this, only general knowledge of physics and chemistry is required.

Preferred discipline(s), expertise, lab skills, etc.: Basic graphics and/or visualization knowledge, familiar
with programming in C/C++, OpenGL/GLSL/WebGL, or D3.js.

Contact: Associate Professor Jonathan Whitmer, 122A Cushing, 574 631-1417, (jwhitme1@nd.edu)
Department of Chemical and Biomolecular Engineering