Engineering Commons^™

Polymer-Based Microfluidic Device For On-Chip Counter-Diffusive Crystallization And In Situ X-Ray Crystallography At Room Temperature, Sarthak Saha, Can Özden, Alfred Samkutty, Silvia Russi, Aina Cohen, Margaret M. Stratton, Sarah L. Perry

Chemical Engineering Faculty Publication Series

Proteins are long chains of amino acid residues that perform a myriad of functions in living organisms, including enzymatic reactions, signalling, and maintaining structural integrity. Protein function is determined directly by the protein structure. X-ray crystallography is the primary technique for determining the 3D structure of proteins, and facilitates understanding the effects of protein structure on function. The first step towards structure determination is crystallizing the protein of interest. We have developed a centrifugally-actuated microfluidic device that incorporates the fluid handling and metering necessary for protein crystallization. Liquid handling takes advantage of surface forces to control fluid flow and enable …

Anaerobic Digestion: Awareness, Implementation, And Simulation, Kieran Tay, Nicholas Sbalbi, Michael Forozis, Flo Sabatini

Student Showcase

Anaerobic digestion (AD) is the process in which organic matter is fermented in an oxygen-deprived environment to produce renewable biogas. Our project is multi-faceted, with the overall goal of raising public awareness of AD as a transitional energy source. To that end, our group has named itself Undergraduates Raising Awareness for Anaerobic Digestion (URAAD). We are approaching this goal on three fronts, including (i) a website, (ii) a physical lab-scale digester, and (iii) a computer simulation of anaerobic digestion.

The first component, the website, was developed with the aim of serving as a resource for the public. It includes educational …

100th Anniversary Of Macromolecular Science Viewpoint: Opportunities In The Physics Of Sequence-Defined Polymers, Sarah L. Perry, Charles E. Sing

Chemical Engineering Faculty Publication Series

Polymer science has been driven by ever-increasing molecular complexity, as polymer synthesis expands an already-vast palette of chemical and architectural parameter space. Copolymers represent a key example, where simple homopolymers have given rise to random, alternating, gradient, and block copolymers. Polymer physics has provided the insight needed to explore this monomer sequence parameter space. The future of polymer science, however, must contend with further increases in monomer precision, as this class of macromolecules moves ever closer to the sequence-monodisperse polymers that are the workhorses of biology. The advent of sequence-defined polymers gives rise to opportunities for material design, with increasing …

Designing Electrostatic Interactions Via Polyelectrolyte Monomer Sequence, Tyler K. Lytle, Li-Wei Chang, Natalia Markiewicz, Sarah L. Perry, Charles E. Sing

Chemical Engineering Faculty Publication Series

Charged polymers are ubiquitous in biological systems because electrostatic interactions can drive complicated structure formation and respond to environmental parameters such as ionic strength and pH. In these systems, function emerges from sophisticated molecular design; for example, intrinsically disordered proteins leverage specific sequences of monomeric charges to control the formation and function of intracellular compartments known as membraneless organelles. The role of a charged monomer sequence in dictating the strength of electrostatic interactions remains poorly understood despite extensive evidence that sequence is a powerful tool biology uses to tune soft materials. In this article, we use a combination of theory, …

Design Rules For Encapsulating Proteins Into Complex Coacervates, Whitney Blocher Mctigue, Sarah L. Perry

Chemical Engineering Faculty Publication Series

We investigated the encapsulation of the model proteins bovine serum albumin (BSA), human hemoglobin (Hb), and hen egg white lysozyme (HEWL) into two-polymer complex coacervates as a function of polymer and solution conditions. Electrostatic parameters such as pH, protein net charge, salt concentration, and polymer charge density can be used to modulate protein uptake. While the use of a two-polymer coacervation system enables the encapsulation of weakly charged proteins that would otherwise require chemical modification to facilitate electrostatic complexation, we observed significantly higher uptake for proteins whose structure includes a cluster of like-charged residues on the protein surface. In addition …

Control Of Thiol-Maleimide Reaction Kinetics In Peg Hydrogel Networks, Lauren E. Jansen, Lenny J. Negrón-Piñeiro, Sualyneth Galarza, Shelly Peyton

Chemical Engineering Faculty Publication Series

Michael-type addition reactions are widely used to polymerize biocompatible hydrogels. The thiol-maleimide modality achieves the highest macromer coupling efficiency of the reported Michael-type pairs, but the resulting hydrogel networks are heterogeneous, because polymerization is faster than the individual components can be manually mixed. The reactivity of the thiol dictates the overall reaction speed, which can be slowed in organic solvents and acidic buffers. Since these modifications also reduce the biocompatibility of resulting hydrogels, we investigated a series of biocompatible buff­ers and crosslinkers to decelerate gelation while maintaining high cell viability. We found that lowering the polymer weight percentage (wt%), buffer …

Anomalously Diffusing And Persistently Migrating Cells In 2d And 3d Culture Environments, Igor D. Luzhansky, Alyssa D. Schwartz, Joshua D. Cohen, John P. Macmunn, Lauren E. Barney, Lauren Jansen, Shelly Peyton

Chemical Engineering Faculty Publication Series

Appropriately chosen descriptive models of cell migration in biomaterials will allow researchers to characterize and ultimately predict the movement of cells in engineered systems for a variety of applications in tissue engineering. The persistent random walk (PRW) model accurately describes cell migration on two-dimensional (2D) substrates. However, this model inherently cannot describe subdiffusive cell movement, i.e. migration paths in which the root mean square displacement increases more slowly than the square root of the time interval. Subdiffusivity is a common characteristic of cells moving in confined environments, such as three-dimensional (3D) porous scaffolds, hydrogel networks, and in vivo tissues. We …

A Graphene-Based Microfluidic Platform For Electrocrystallization And In Situ X-Ray Diffraction, Shuo Sui, Yuxi Wang, Christos Dimitrakopoulos, Sarah L. Perry

Chemical Engineering Faculty Publication Series

Here, we describe a novel microfluidic platform for use in electrocrystallization experiments. The device incorporates ultra-thin graphene-based films as electrodes and as X-ray transparent windows to enable in situ X-ray diffraction analysis. Furthermore, large-area graphene films serve as a gas barrier, creating a stable sample environment over time. We characterize different methods for fabricating graphene electrodes, and validate the electrical capabilities of our device through the use of methyl viologen, a redox-sensitive dye. Proof-of-concept electrocrystallization experiments using an internal electric field at constant potential were performed using hen egg-white lysozyme (HEWL) as a model system. We observed faster nucleation and …

Complementary, Semi-Automated Methods For Creating Multi-Dimensional, Peg-Based Biomaterials, Elizabeth A. Brooks, Lauren E. Jansen, Maria F. Gencoglu, Annali M. Yurkevicz, Shelly Peyton

Chemical Engineering Faculty Publication Series

Tunable biomaterials that mimic selected features of the extracellular matrix (ECM), such as its stiffness, protein composition, and dimensionality, are increasingly popular for studying how cells sense and respond to ECM cues. In the field, there exists a significant trade-off for how complex and how well these biomaterials represent the in vivo microenvironment, versus how easy they are to make and how adaptable they are to automated fabrication techniques. To address this need to integrate more complex biomaterials design with high-throughput screening approaches, we present several methods to fabricate synthetic biomaterials in 96-well plates and demonstrate that they can be …

Zwitterionic Peg-Pc Hydrogels Modulate The Foreign Body Response In A Modulus-Dependent Manner, Lauren Jansen, Luke D. Amer, Esther Y-T Chen, Thuy V. Nguyen, Leila S. Saleh, Todd Emrick, Wendy F. Liu, Stephanie J. Bryant, Shelly Peyton

Chemical Engineering Faculty Publication Series

Reducing the foreign body response (FBR) to implanted biomaterials will enhance their performance in tissue engineering. Poly(ethylene glycol) (PEG) hydrogels are increasingly popular for this application due to their low cost, ease of use, and the ability to tune their compliance via molecular weight and crosslinking densities. PEG hydrogels can elicit chronic inflammation in vivo, but recent evidence has suggested that extremely hydrophilic, zwitterionic materials and particles can evade the immune system. To combine the advantages of PEG-based hydrogels with the hydrophilicity of zwitterions, we synthesized hydrogels with co-monomers PEG and the zwitterion phosphorylcholine (PC). Recent evidence suggests that …

Rheological Characterization Of Liquid-To-Solid Transitions In Bulk Polyelectrolyte Complexes, Yalin Liu, Brian Momani, H. Henning Winter, Sarah L. Perry

Chemical Engineering Faculty Publication Series

Polyelectrolyte complexation has long been known to result in both liquid and solid complexes. However, the exact nature of the liquid-to-solid transition remains an open question. We have used rheology to explain this phenomenon for the model system of poly(4-styrenesulfonic acid, sodium salt) (PSS) and poly(diallyldimethyl ammonium chloride) (PDADMAC) in the presence of potassium bromide (KBr). The use of a time-salt superposition allows for a detailed analysis of changes in the linear viscoelastic response for both liquid complex coacervates and solid polyelectrolyte complexes as a function of salt concentration, and facilitates unambiguous determination of the mechanism for this phase transition. …

The Effect Of Comb Architecture On Complex Coacervation, Brandon M. Johnston, Cameron W. Johnston, Rachel A. Letteri, Tyler K. Lytle, Charles E. Sing, Todd Emrick, Sarah L. Perry

Chemical Engineering Faculty Publication Series

Complex coacervation is a widely utilized technique for effecting phase separation, though predictive understanding of molecular-level details remains underdeveloped. Here, we couple coarse-grained Monte Carlo simulations with experimental efforts using a polypeptide-based model system to investigate how a comb-like architecture affects complex coacervation and coacervate stability. Specifically, the phase separation behavior of linear polycation-linear polyanion pairs was compared to that of comb polycation-linear polyanion and comb polycation-comb polyanion pairs. The comb architecture was found to mitigate cooperative interactions between oppositely charged polymers, as no discernible phase separation was observed for comb-comb pairs and complex coacervation of linear-linear pairs yielded stable …

A Student-Created, Open Access, Living Textbook, Sualyneth Galarza, Sarah L. Perry, Shelly Peyton

Chemical Engineering Faculty Publication Series

Textbooks are expensive, updated infrequently, and rarely used effectively by students. We discuss here a way for students to create the textbook for the course, helping them feel ownership over the course material. This Wiki-based, student-created textbook is online free for use, widely accessible by all, and editable during the course of and as topics evolve. This type of textbook format is particularly well suited to upper-level electives on topics that are rapidly emerging. We have nucleated a student created textbook here, fully online and open access, for two upper elective courses in chemical engineering. Wikis offer an easy-to-learn platform …

Microfluidics: From Crystallization To Serial Time-Resolved Crystallography, Shuo Sui, Sarah L. Perry

Chemical Engineering Faculty Publication Series

Capturing protein structural dynamics in real-time has tremendous potential in elucidating biological functions and providing information for structure-based drug design. While time-resolved structure determination has long been considered inaccessible for a vast majority of protein targets, serial methods for crystallography have remarkable potential in facilitating such analyses. Here, we review the impact of microfluidic technologies on protein crystal growth and X-ray diffraction analysis. In particular, we focus on applications of microfluidics for use in serial crystallography experiments for the time-resolved determination of protein structural dynamics.

Sequence And Entropy-Based Control Of Complex Coacervates, Li-Wei Chang, Tyler K. Lytle, Mithun Radhakrishna, Joel J. Madinya, Jon Vélez, Charles E. Sing, Sarah L. Perry

Chemical Engineering Faculty Publication Series

Biomacromolecules rely on the precise placement of monomers to encode information for structure, function, and physiology. Efforts to emulate this complexity via the synthetic control of chemical sequence in polymers are finding success; however, there is little understanding of how to translate monomer sequence to physical material properties. Here we establish design rules for implementing this sequence-control in materials known as complex coacervates. These materials are formed by the associative phase separation of oppositely charged polyelectrolytes into polyelectrolyte dense (coacervate) and polyelectrolyte dilute (supernatant) phases. We demonstrate that patterns of charges can profoundly affect the charge–charge associations that drive this …

Strain-Stiffening Gels Based On Latent Crosslinking, Yen H. Tran, Matthew J. Rasmuson, Todd Emrick, John Klier, Shelly Peyton

Chemical Engineering Faculty Publication Series

Gels are an increasingly important class of soft materials with applications ranging from regenerative medicine to commodity materials. A major drawback of gels is their relative mechanical weakness, which worsens further under strain. We report a new class of responsive gels with latent crosslinking moieties that exhibit strain-stiffening behavior. This property results from the lability of disulfides, initially isolated in a protected state, then activated to crosslink on-demand. The active thiol groups are induced to form inter-chain crosslinks when subjected to mechanical compression, resulting in a gel that strengthens under strain. Molecular shielding design elements regulate the strain-sensitivity and spontaneous …

The Predictive Link Between Matrix And Metastasis, Lauren E. Barney, Lauren Jansen, S. R. Polio, Sualyneth Galarza, Maureen E. Lynch, Shelly Peyton

Chemical Engineering Faculty Publication Series

Cancer spread (metastasis) is responsible for 90% of cancer-related fatalities. Informing patient treatment to prevent metastasis, or kill all cancer cells in a patient's body before it becomes metastatic is extremely powerful. However, aggressive treatment for all non-metastatic patients is detrimental, both for quality of life concerns, and the risk of kidney or liver-related toxicity. Knowing when and where a patient has metastatic risk could revolutionize patient treatment and care. In this review, we attempt to summarize the key work of engineers and quantitative biologists in developing strategies and model systems to predict metastasis, with a particular focus on cell …

Complex Coacervate-Based Materials For Biomedicine, Sarah L. Perry, Whitney C. Blocher

Chemical Engineering Faculty Publication Series

There has been increasing interest in complex coacervates for deriving and trans- porting biomaterials. Complex coacervates are a dense, polyelectrolyte-rich liq- uid that results from the electrostatic complexation of oppositely charged macroions. Coacervates have long been used as a strategy for encapsulation, par- ticularly in food and personal care products. More recent efforts have focused on the utility of this class of materials for the encapsulation of small molecules, pro- teins, RNA, DNA, and other biomaterials for applications ranging from sensing to biomedicine. Furthermore, coacervate-related materials have found utility in other areas of biomedicine, including cartilage mimics, tissue culture scaffolds, …

Linear Viscoelasticity Of Complex Coacervates, Yalin Liu, H. Henning Winter, Sarah L. Perry

Chemical Engineering Faculty Publication Series

Rheology is a powerful method for materials characterization that can provide detailed information about the self-assembly, structure, and intermolecular interactions present in a material. Here, we review the use of linear viscoelastic measurements for the rheological characterization of complex coacervate-based materials. Complex coacervation is an electrostatically and entropically-driven associative liquid-liquid phase separation phenomenon that can result in the formation of bulk liquid phases, or the self-assembly of hierarchical, microphase separated materials. We discuss the need to link thermodynamic studies of coacervation phase behavior with characterization of material dynamics, and provide parallel examples of how parameters such as charge stoichiometry, ionic …

Graphene-Based Microfluidics For Serial Crystallography, Shuo Sui, Yuxi Wang, Kristopher W. Kolewe, Vukica Srajer, Robert Henning, Jessica D. Schiffman, Christos Dimitrakopoulos, Sarah L. Perry

Chemical Engineering Faculty Publication Series

Microfluidic strategies to enable the growth and subsequent serial crystallographic analysis of micro-crystals have the potential to facilitate both structural characterization and dynamic structural studies of protein targets that have been resistant to single-crystal strategies. However, adapting microfluidic crystallization platforms for micro-crystallography requires a dramatic decrease in the overall device thickness. We report a robust strategy for the straightforward incorporation of single-layer graphene into ultra-thin microfluidic devices. This architecture allows for a total material thickness of only ∼1 μm, facilitating on-chip X-ray diffraction analysis while creating a sample environment that is stable against significant water loss over several weeks. We …

Metabolic Modeling Of A Chronic Wound Biofilm Consortium Predicts Spatial Partitioning Of Bacterial Species, Poonam Phalak, Jin Chen, Ross P. Carlson, Michael A. Henson

Chemical Engineering Faculty Publication Series

Background

Chronic wounds are often colonized by consortia comprised of different bacterial species growing as biofilms on a complex mixture of wound exudate. Bacteria growing in biofilms exhibit phenotypes distinct from planktonic growth, often rendering the application of antibacterial compounds ineffective. Computational modeling represents a complementary tool to experimentation for generating fundamental knowledge and developing more effective treatment strategies for chronic wound biofilm consortia.

Results

We developed spatiotemporal models to investigate the multispecies metabolism of a biofilm consortium comprised of two common chronic wound isolates: the aerobe Pseudomonas aeruginosa and the facultative anaerobe Staphylococcus aureus. By combining genome-scale metabolic …

Polyelectrolyte-Functionalized Nanofiber Mats Control The Collection And Inactivation Of Escherichia Coli, Katrina A. Rieger, Michael Porter, Jessica D. Schiffman

Chemical Engineering Faculty Publication Series

Quantifying the effect that nanofiber mat chemistry and hydrophilicity have on microorganism collection and inactivation is critical in biomedical applications. In this study, the collection and inactivation of Escherichia coli K12 was examined using cellulose nanofiber mats that were surface-functionalized using three polyelectrolytes: poly (acrylic acid) (PAA), chitosan (CS), and polydiallyldimethylammonium chloride (pDADMAC). The polyelectrolyte functionalized nanofiber mats retained the cylindrical morphology and average fiber diameter (~0.84 µm) of the underlying cellulose nanofibers. X-ray photoelectron spectroscopy (XPS) and contact angle measurements confirmed the presence of polycations or polyanions on the surface of the nanofiber mats. Both the control cellulose and …

Where To Buy Materials For The Activities, Morton Sternheim

Nanotechnology Teacher Summer Institutes

Sources for some of the less common materials used in the activities.

Seeing At The Nanoscale: New Microscopies For The Life Sciences, Jennifer Ross

Nanotechnology Teacher Summer Institutes

Visualizing single modules with fluorescence microscopy

Mechanics Of Intact Bone Marrow, Lauren Jansen, Nathan P. Birch, Jessica D. Schiffman, Alfred J. Crosby, Shelly Peyton

Chemical Engineering Faculty Publication Series

The current knowledge of bone marrow mechanics is limited to its viscous properties, neglecting the elastic contribution of the extracellular matrix. To get a more complete view of the mechanics of marrow, we characterized intact yellow porcine bone marrow using three different, but complementary techniques: rheology, indentation, and cavitation. Our analysis shows that bone marrow is elastic, and has a large amount of intra- and inter-sample heterogeneity, with an effective Young’s modulus ranging from 0.25-24.7 kPa at physiological temperature. Each testing method was consistent across matched tissue samples, and each provided unique benefits depending on user needs. We recommend bulk …

Green Materials Science And Engineering Reduces Biofouling: Approaches For Medical And Membrane-Based Technology, Kerianne M. Dobosz, Kristopher W. Kolewe, Jessica D. Schiffman

Chemical Engineering Faculty Publication Series

Numerous engineered and natural environments suffer deleterious effects from biofouling and/or biofilm formation. For instance, bacterial contamination on biomedical devices pose serious health concerns. In membrane-based technologies, such as desalination and wastewater reuse, biofouling decreases membrane lifetime, and increases the energy required to produce clean water. Traditionally, approaches have combatted bacteria using bactericidal agents. However, due to globalization, a decline in antibiotic discovery, and the widespread resistance of microbes to many commercial antibiotics and metallic nanoparticles, new materials, and approaches to reduce biofilm formation are needed. In this mini-review, we cover the recent strategies that have been explored to combat …

Prism-Based Theory Of Complex Coacervation: Excluded Volume Versus Chain Correlation, Sarah L. Perry, Charles E. Sing

Chemical Engineering Faculty Publication Series

Aqueous solutions of oppositely charged polyelectrolytes can undergo liquid–liquid phase separation into materials known as complex coacervates. These coacervates have been a subject of intense experimental and theoretical interest. Efforts to provide a physical description of complex coacervates have led to a number of theories that qualitatively (and sometimes quantitatively) agree with experimental data. However, this agreement often occurs in a degeneracy of models with profoundly different starting assumptions and different levels of sophistication. Theoretical difficulties in these systems are similar to those in most polyelectrolyte systems where charged species are highly correlated. These highly correlated systems can be described …

A Cell–Ecm Screening Method To Predict Breast Cancer Metastasis, Lauren E. Barney, E. C. Dandley, Lauren Jansen, Nicholas G. Reich, A. M. Mercurio, Shelly Peyton

Chemical Engineering Faculty Publication Series

Breast cancer preferentially spreads to the bone, brain, liver, and lung. The clinical patterns of this tissue-specific spread (tropism) cannot be explained by blood flow alone, yet our understanding of what mediates tropism to these physically and chemically diverse tissues is limited. While the micro- environment has been recognized as a critical factor in governing metastatic colonization, the role of the extracellular matrix (ECM) in mediating tropism has not been thoroughly explored. We created a simple biomaterial platform with systematic control over the ECM protein density and composition to determine if integrin binding governs how metastatic cells differentiate between secondary …

Smooth Muscle Stiffness Sensitivity Is Driven By Soluble And Insoluble Ecm Chemistry, William G. Herrick, Shruti Rattan, Thuy V. Nguyen, Michael S. Grunwald, Christopher W. Barney, Alfred J. Crosby, Shelly Peyton

Chemical Engineering Faculty Publication Series

Smooth muscle cell (SMC) invasion into plaques and subsequent proliferation is a major factor in the progression of atherosclerosis. During disease progression, SMCs experience major changes in their microenvironment, such as what integrin-binding sites are exposed, the portfolio of soluble factors available, and the elasticity and modulus of the surrounding vessel wall. We have developed a hydrogel biomaterial platform to examine the combined effect of these changes on SMC phenotype. We were particularly interested in how the chemical microenvironment affected the ability of SMCs to sense and respond to modulus. To our surprise, we observed that integrin binding and soluble …

Background And Available Potential Energy In Numerical Simulations Of A Boussinesq Fluid, Shreyas S. Panse

Masters Theses 1911 - February 2014

In flows with stable density stratification, a portion of the gravitational potential energy is available for conversion to kinetic energy. The remainder is not and is called “background potential energy”. The partition of potential energy is analogous to the classical division of energy due to motion into its kinetic and internal components. Computing background and available potential energies is important for understanding stratified flows. In many numerical simulations, though, the Boussinesq approximations to the Navier-Stokes equations are employed. These approximations are not consistent with conservation of energy. In this thesis we re-derive the governing equations for a buoyancy driven fluid …