Meet the Enrique Gomez Lab.

Left to right (front): Melissa Aplan, Dan Ye, Wenlin Zhang, Brooke Kuei, Wei-Ting Ma, Sintu Rongpipi, Shreya Shetty

Left to right (back): Enrique Gomez, Alperen Ayhan, Josh Litofsky, Tyler Culp, Youngmin Lee, Timothy Castor, Renxuan Xie, Sean Nunez, Yuexiao Shen, Sang Yoo, Christopher Lyon

We have asked each member of Dr. Gomez’s lab to share a bit about themselves and their research. Here are their responses.

Dan Ye

I am working on characterization structure of different biological assemblies using synchrotron sources which involve a novel technique: Resonant Soft X-ray Scattering (RSoXS). This technique enhances the contrast between different components in a complex system by tuning X-ray energies to elemental absorption edges. Since the absorption spectra of each species are chemical specific, we can generate scattering contrast targeting specific chemical moieties. I have studied the structure of proteins in solution. Now I am moving forward to investigate the structure of virus particles using RSoXS to aid the design of vaccines. Another part of my project is to study the microscopic structure of plant cell walls to understand plant growth and the interactions between different components in the cell wall. This microscopic picture is going to facilitate the process of using biofuel as a major alternative energy source.

I am a member of Center for Lignocellulose Structure and Formation  (CLSF). I am working with Dr. Daniel Cosgrove and Dr. Sarah Kiemle from Penn State Biology Department to study the structure of plant cell walls. I am also collaborating with Dr. Susan Hafenstein and Lindsey Organtini from Penn State College of Medicine to study the structure of CVB3 viruses. I am also working very closely with Dr. Cheng Wang from Advanced Light Source in Lawrence Berkeley National Laboratory to explore the potential of RSoXS on characterizing biological materials.

Conference Presentations:

• Ye D., Le T. P., Cheng W., Zwart P. H., Gomez E. W. & Gomez E. D. Resonant soft X-ray scattering on protein solutions. American Physical Society’s Annual Meeting (2016).

Youngmin Lee

My research is regarding fully conjugated donor-acceptor block copolymers for organic photovoltaics.  These enable us to tune donor/acceptor interfaces and adopt the mesoscale structure within the active layer of organic photovoltaic devices.  The ability to control and modify the micro-phase separation of the block copolymer can offer a useful platform for understanding the relationship between chemical structure, nanoscale morphology, and photovoltaic device performance.  Furthermore, they may serve as model systems to study fundamental questions regarding optoelectronic properties and charge transfer.

Publications:

• Guo, Y. Lee, Y.-H. Lin, J. Strzalka, C. Wang, A. Hexemer, C. Jaye, D. A. Fischer, R. Verduzco, Q. Wang, E. D. Gomez, “Photovoltaic Performance of Block Copolymer Devices Is Independent of the Crystalline Texture in the Active Layer” Macromolecules, 2016, 49, 4599-4608
• Lee, E. D. Gomez, “Challenges and opportunities in the development of conjugated block copolymers for photovoltaics” Macromolecules, 2015, 48, 7385-7395
• C. Guo, F. I. Allen, Y. Lee, T. P. Le, C. Song, J. Ciston, A. M. Minor, E. Gomez, “Probing Local Electronic Transitions in Organic Semiconductors through Energy-Loss Spectrum Imaging in the Transmission Electron Microscope” Adv. Funct. Mater., 2015, 25, 6071-6076

Melissa Aplan

My project uses fully-conjugated block copolymers as model systems to examine current generation in organic solar cells. Despite tremendous advances in recent years, it is difficult to extract a set of design rules for higher performing devices as the mechanism for photocurrent generation is not fully understood. I synthesize block copolymers and then use absorbance and emission spectra of dilute solutions to quantify intramolecular charge transfer between the blocks. The same materials are incorporated as the active layer of organic solar cell devices, fabricated and measured in-house. I also characterize the solid-state solar cells using x-ray scattering techniques at the Advanced Light Source in Berkeley, CA. By following the properties of these carefully designed block copolymers from dilute solutions to solid-state devices, we can reveal unknown aspects of the current generation mechanism in organic solar cells.

I have presented my work at annual meetings of the American Physical Society, American Chemical Society, and Materials Research Society.

Tyler Culp

My research project focuses on using analytical characterization techniques such as transmission electron microscopy, soft X-ray scattering, and atomic force microscopy to study structure-property relationships in polyamide active layers used in thin film composite membranes for reverse osmosis and nanofiltration. Currently, I am using these techniques to obtain a 3D structure of the membrane to quantify functional group distributions present in the polymer.

I presented at the GRS and GRC conferences for membranes: materials and processes in New London, NH in August 2016. I’ll be presenting at the APS conference in New Orleans this March as well.

Wenlin Zhang

My research focuses on the computational design of semiflexible conjugated polymers. I use molecular simulations and analytical theories to predict various properties and behaviors of polymers, such as the persistence length and the nematic phase behaviors. Our overall work can help screen novel semiconducting polymers for high-performance electronic devices.

Publications:

• Zhang, W.; Gomez, E.D.; Milner, S.T., “Using surface-induced ordering to probe the isotropic-to-nematic transition for semiflexible polymers” Soft Matter, 2016, 12, 6141-6147.
• Kozuch, D.J.; Zhang, W.; Milner, S.T., “Predicting the Flory-Huggins χ parameter for polymers with stiffness mismatch from molecular dynamics simulations” Polymers, 2016, 8, 241.
• Zhang, W.; Gomez, E.D.; Milner, S.T., “Surface induced alignment for semiflexible polymers” Macromolecules, 2016, 49, 963-971.
• Zhang, W.; Gomez, E.D.; Milner, S.T., “Predicting nematic phases of semiflexible polymers” Macromolecules, 2015, 48, 1454-1462.
• Zhang, W.; Gomez, E.D.; Milner, S.T., “Predicting chain dimensions of semiflexible polymers from dihedral potentials” Macromolecules, 2014, 47, 6453-6461.

Sang Ha Yoo

My main research project is on finding structure-property relationships in thin film transistors fabricated via ZnO deposition. ZnO transistors have been of interest over amorphous Si transistors for their high charge mobility and single crystalline structure. ZnO exhibit semiconducting property since it is a compound of group 16 and 20 elements. However, only a little is known about the relationship between the single crystalline structure of ZnO transistors and their electronic property. My goal is to utilize various characterization tools to investigate the material properties of the semiconductor at the nanoscale and to further develop their electronic performance.

Sintu Rongpipi

My research project is using Resonant Soft X-Rays Scattering (RSOXS) to study Biological Assemblies. We propose to establish RSOXS as a standard characterization technique to investigate multicomponent biological assemblies like viral cells and plant cell walls. The project is co-advised by Dr. Esther Gomez as well.

Meet the Fichthorn Lab.

(Left to Right) Xiangyi Kong, Jenwarin Narukatpichai, Tonnam Balankura, Xin Qi, David Kalb, Dr. Kristen Fichthorn,
Alan Ng, Shih-Hsien Liu, Mert Yigit Sengul, Tianyu Yan, Zihao Chen

We have asked each member of our lab to share a bit about themselves. Learn more about our team’s research, publications, collaborations and hobbies.

Xiangyi Kong

My research is the computational study of nanoparticle self-assembly. Self-assembly can be a very powerful method to organize nanoparticles into the structures we desire. Theoretical studies can help us get a better understanding of this process and provide us with ideas of how to control it. Currently, I am constructing a coarse-grained model of the system of silica-coated Au nanowires assembled over a gold stripe and perform Monte-Carlo simulation of the assembly process. We expect that, beyond reproducing the experimental assembly pattern, this model can help predict new patterns of interest.

Tonnam Balankura

My research focuses on modeling the solution-phase synthesis of metal nanocrystals to understand their shape-control mechanism. Metal nanocrystals can form unique shapes such as nanocubes, nanowires and nanoplates. Although numerous syntheses can be found in the literature, the atomistic understanding of their shape-control mechanism remains elusive.

I use multi-scale modeling tools to advance our knowledge of the shape-control machinery and the interfacial phenomena involved in nanocrystal growth. Collaborating closely with Zhifeng Chen from Prof. Robert Rioux’s group, they bring my theoretical knowledge to life.

In my spare time, I enjoy dancing, cooking, eating and coding. I also participate in Penn State’s hip-hop dance club, “RAM Squad.” We are a group of friends that just can’t stop dancing! You can read more about my dance hobby on Her Campus, where I was featured as a campus celebrity.

Publications:

• Balankura T, Qi X, Zhou Y, Fichthorn KA. Predicting kinetic nanocrystal shapes through multi-scale theory and simulation: Polyvinylpyrrolidone-mediated growth of Ag nanocrystals. The Journal of Chemical Physics. 2016. http://scitation.aip.org/content/aip/journal/jcp/145/14/10.1063/1.4964297.
• Qi X, Balankura T, Zhou Y, Fichthorn KA. How Structure-Directing Agents Control Nanocrystal Shape: Polyvinylpyrrolidone-Mediated Growth of Ag Nanocubes. Nano letters. 2015. http://pubs.acs.org/doi/abs/10.1021/acs.nanolett.5b04204.

Conference Presentations:

• American Institute of Chemical Engineers Annual Meeting. San Francisco, CA. 2016. Kinetic Influence of Polyvinylpyrrolidone in the Shape-Control Mechanism of Ag Nanocrystal Synthesis.
• Materials Research Society Annual Meeting. Boston, MA. 2015. Molecular insights into how nanoparticles are grown into specific shapes.

Xin Qi

The goal of my project is to use molecular dynamic simulations to understand the mechanisms of shape-controlled nanocrystal growth, and ultimately to predict effective structure-directing agents before experimental testing. In my spare time, I love crafting and baking lovely, sweet treats.

Publications:

• How Structure-Directing Agents Control Nanocrystal Shape: Polyvinylpyrrolidone-Mediated Growth of Ag Nanocubes, Link: http://pubs.acs.org/doi/abs/10.1021/acs.nanolett.5b04204
• Obtaining the solid-liquid interfacial free energy via multi-scheme thermodynamic integration: Ag-ethylene glycol interfaces, Link: http://scitation.aip.org/content/aip/journal/jcp/145/19/10.1063/1.4967521

Conference Presentations:

• Gordon Conference, Crystal Growth and Assembly, University of New England, ME, Jul. 2015
• Material Research Society, Boston, MA, Dec. 2015
• AIChE Annual Meeting, San Fransisco, CA, Nov. 2016.

Shih-Hsien Liu

My research project is multiscale modeling [density-functional theory (DFT) and molecular dynamics (MD)] of the solution-phase syntheses of Au and Cu nanocrystal catalysts mediated by polyvinylpyrrolidone (PVP) and hexadecylamine (HDA) organic capping agents, respectively. This project aims at resolving structure-property relationships of PVP and HDA on Au and Cu surfaces respectively with DFT as well as MD to predict optimal parameters in the synthesis process.

I collaborated with Dr. Wissam Saidi, an Associate Professor of Mechanical Engineering and Materials Science at the University of Pittsburgh, to analyze electronic structures and the implicit solvent effect of PVP on Au surfaces.

In my free time, I jog and weight train to maintain my body strength and fitness. I also like photography, stargazing and enjoying the beautiful scenery of Happy Valley, Pennsylvania.

Publications:

• “Self-Assembled Monolayer Structures of Hexadecylamine on Cu Surfaces: Density-Functional Theory” Liu, S.-H.; Balankura, T.; Fichthorn, K. A. Physical Chemistry Chemical Physics 2016, 18 (48), 32753-32761.http://pubs.rsc.org/en/content/articlelanding/2016/cp/c6cp07030b
• “Synthesis of {111}-Faceted Au Nanocrystals Mediated by Polyvinylpyrrolidone: Insights from Density-Functional Theory and Molecular Dynamics” Liu, S.-H.; Saidi, W. A.; Zhou, Y.; Fichthorn, K. A. The Journal of Physical Chemistry C 2015, 119 (21), 11982-11990.http://pubs.acs.org/doi/abs/10.1021/acs.jpcc.5b01867

Conference Presentations:

• “PVP Facilitates {111}-Faceted Au Nanocrystals Formation: Insights from DFT and MD” TechConnect World Innovation Conference, Washington, D.C., Jun. 14-17, 2015.
• “Shape-Selective Synthesis of Au Nanoparticles: The Role of PVP” American Institute of Chemical Engineers Annual Meeting, San Francisco, CA, Nov. 3-8, 2013.
• “First-Principles Calculations of the Role of PVP in the Controlled Synthesis of Au Nanostructures” American Physical Society March Meeting, Baltimore, MD, Mar. 18-22, 2013.

Meet the Kumar lab.

(Left to Right) Megan Farell, Manish Kumar, Emilia Conte, Joachim Habel, Boya Xiong, Ben Schantz, Tingwei Ren, John Brezovec, Hasin Feroz, Yasin Al Fahham, Woochul Song, Henry Yen, Cory Jones

Allen Benjamin (Ben) Schantz

Our lab group works on creating biomimetic membranes, in which a chemically and mechanically stable block copolymer is the matrix and a transmembrane protein is the functional component. These membranes have application in water treatment, electricity generation, sensors, and medicine. I’ve done something of a variety of projects — examining the mechanism of the MOCP antimicrobial peptide (used to treat water in developing countries) using coarse-grained molecular dynamics simulations; developing a coarse-grained MD model for poly(1,2-butadiene)-poly(ethylene oxide), a polymer frequently used for creating biomimetic membranes; examining the mechanism of biomimetic membrane formation by dialysis, the method our group uses to synthesize these membranes, using small-angle neutron scattering; and attempting to form membranes from poly(ethylene oxide)-poly(propylene oxide), a cheap and biocompatible block copolymer.

The work on MOCP has been published in Langmuir and the neutron scattering work is in review by Macromolecules.

I’ve presented my work at the Gordon Research Seminar on Polymer Physics (2014), Penn State Graduate Research Symposium (2015), and American Physical Society March Meeting (2016).

My PB-PEO modeling and neutron scattering work has been a collaboration between the Kumar and Janna Maranas groups (I’m co-advised by these two professors), and I’ve worked with Dr. Paul Butler at the NIST Center for Neutron Research on the SANS project (he’s been a great resource, and is one of the corresponding authors on the upcoming paper).

Outside of research, my biggest hobby has been caving. I started by first year at PSU, and took over as club president a few years ago. I like being able to explore new places underground, get some exercise crawling and climbing around, and see an unusual side of nature.

Megan Farell

My research project is studying lipid bilayer formation on graphene, a 2D material. The aim of this work is to determine the structure of lipids on graphene, a highly hydrophobic substrate with appealing properties such as high surface area, high conductivity, and flexibility. The purpose of this project is to create a nanoscale, biocompatible platform for enzymatic fuel cells that can be used for diverse applications in the medical, energy, and environmental fields.

I was a supporting author for one of my labmates, Patrick Saboe, recently published paper on incorporating a membrane protein, Photosystem I, into a conductive polymer bilayer for enhanced photocurrent generation.

I will be attending the APS conference in March 2017.

I collaborate with Dr. Golbeck’s lab in the Biochemistry Department at Penn State and Dr. Robinson’s lab in the Material Science Department at Penn State.

My favorite restaurant is Sakura because I love sushi. My favorite hobby after work is shopping.

Boya Xiong

My research project is to understand the chemical/physical transformation of polymers used in hydraulic fracturing (“fracking”) under downhole conditions and its impact on subsequent membrane fouling during treatment. Ultra-high molecular weight (>million Dalton) polymers (guar gum and polyacrylamide) are the major ingredients used in fracking; however, their fate during fracking conditions and impact on membrane treatment has not been investigated. The size / structure of the initial and degraded (post-fracking) polymers governs their likelihood of being trapped in the small pore spaces in porous membranes. My work will significantly contribute to develop sustainable water management strategies and understand the unknown risks to water quality impacted by hydraulic fracturing activities. In addition, I also work on engineering a Moringa Oleifera seed modified sand filter for affordable point-of-use drinking water purification.


An initial study on membrane fouling by actual Marcellus shale wastewater has been published in Water Research. I have presented my work at ACS (2015 & 2016), NAMS (2015&2016), Gordon Research Seminar/Conference (2016), PennTech (2016). I have collaborated with Dr. Bill Burgos in Department of Environmental Engineering and Dr. Alexey Silakov from Department of Chemistry. My hobby after work is weightlifting.

Tyler Culp

My research project focuses on using analytical characterization techniques such as transmission electron microscopy, soft X-ray scattering and atomic force microscopy to study structure-property relationships in polyamide active layers used in thin film composite membranes for reverse osmosis and nanofiltration. Currently, I am using these techniques to obtain a 3D structure of the membrane in order to quantify functional group distributions present in the polymer.

I presented at the GRS and GRC conferences for membranes: materials and processes in New London, NH in August 2016. I’ll be presenting at the APS conference in New Orleans next March as well.

I am co-advised by Dr. Enrique Gomez in the chemical engineering department at Penn State and work in collaboration with the Dow Chemical Company. My favorite places to go out are probably Liberty or Local Whiskey.

Joachim Habel

My research project is about artificial biomimetic membranes. Biomimetic membranes should revolutionise water separation membrane technology, because they utilise a highly optimised water separation concept of nature. I’m trying to spincoat a polymeric thin layer that serves as a matrix for less stable cell components. Later artificial channels that mimic water separation membrane proteins of cells will be incorporated in that film. The film will be transferred on a porous membrane support to finally end up in an artificial biomimetic membrane. Without artificial channels, the polymeric layer is thought to get the support water and solute impermeable. With the channels, the polymeric layer is highly water permeable but impermeable to anything else.

This work was partly published in Yuexiao Shen’s PhD thesis and presented at the Gordon Research Conference & Seminar of Membranes: Materials and processes in summer 2016.

I collaborate with the group of Mihai Barboiu at the Institute des Membrane in Montpellier, France, who synthesize the artificial channels.
My favorite restaurant is The Corner Room. I like to explore music from all other the world, playing piano, writing short stories and swimming.

Tingwei Ren

My research project is membrane proteins based biomimetic membranes performance quantification and improvement. The major problem my research is trying to understanding what properties of biomimetic membrane will influence membrane protein incorporation, which will provide directions on developing functional biomimetic membranes with higher membrane protein compatibility.

This work has been presented at Biophysical Society Annual Meeting (2015), North American Membrane Society Annual Meeting (NAMS, 2016), Gordon Research Conference (GRC, 2016), it will also be presented in AICHE this coming November.

In Penn State, I collaborate with Professor Peter Butler’s group (Biomedical Engineering), Professor Costas Maranas group (Chemical Engineering). I also have collaborations with Professor Guillermo Bazan from UCSB.

I enjoyed reading detective fictions (the Tragedy of Y is my favorite book).

Hasin Maksura Feroz

I work with membrane protein characterization and ultrafiltration. My work focuses on making the first direct measurement of ion transport of light-driven chloride ion pump, halorohodopsin.

I have published one paper on the ultrafiltration of membrane proteins.

I have attended NAMS, BPS, Gordon research conference for membranes in 2013-2016. I worked with Prof. Andrew Zydney in chemical engineering and Prof. John Golbeck lab in BMB at Penn State. We also collaborate internationally with Prof Mike Blatt’s lab at University of Glasgow along with other schools in UK and USA as part of the MAGIC consortium (a BBSRC/NSF funded project).

I love Little Szechuan, because the food is spicy!

Woochul Song

My PhD research topic is developing artificial channel-based membranes for water purification. The major challenges include finding more optimized channel designs for selective water separation and developing fabrication process for channel-embedded two dimensional membranes.

I am first year PhD student who joined Prof. Kumar’s lab very recently and have no relevant progress at here. Rather than, I worked in research fields at interface between nanomaterials and biomedical sciences before joining Penn State in Fall 2016. At that time, I developed self-illuminating nanoparticles which can actively release anti-cancer drugs within tumorigenic environments.

I had several opportunities to present my works in domestic (South Korea) and international conferences, including MRS in Spring 2014 and Fall 2012 and The Korean Society for Biotechnology and Bioengineering Fall Meeting in 2013.

I collaborated with several research groups, including Dr. Cho’s research group (Seoul National University), Dr. Min’s group (Sogang University) and Dr. Ahn’s group (Korea Institute of Science and Technology). They are experts in biochemistry, nano colloids and organic chemistry respectively.
I often enjoy Five Guys burgers since I came to USA, it’s not been a while though. I’ve never experienced such like an awesome burger in my home country. I really like it!

Cory Jones

I just started with Kumar lab at the last week of October, and my project is on light driven ion transport membrane proteins: fundamental biophysics, biomedical applications and beyond. One of the areas we are looking into are methods to transport bicarbonate into plants for increased uptake of CO₂. Since I just started I have not published, presented, or collaborated yet. My favorite State College restaurant is probably the Corner Room, and my favorite hobby is Tae Kwon Do.

Meet the Dr. Zydney lab.

(Left to Right) Youngbin Baek, Ivan Manzano, Zhao Li, Andrew Zydney, Fatemeh Fallahianbijan, Mahsa Hadidi,
Parinaz Emami, Seyed Pouria Motevalian, Boya Xiong, Ying Li

Youngbin Baek (Post-doc)

My research is focused on the protein purification by ultrafiltration membrane. We are interested in evaluating the intermolecular interaction and its relationship with the membrane performance behavior and developing the models. I have presented my research at Gordon Research Conference in New London 2016 and would be presenting my work in AIChE meeting this year in San Francisco. My favorite equation would be Hagen-Poiseuille equation because it serves to predict a flux through the membrane.

Ying Li (Fifth year graduate student)

My research project is purification of plasmid DNA using ultrafiltration membranes. Plasmids are circular double-stranded extrachromosomal DNA that are produced by many bacteria – they can be used as vectors for delivering target genes in DNA therapeutics applications. It is particularly challenging to purify supercoiled plasmid DNA from other undesired isoforms using traditional separation methods such as chromatography. The objective of my research is to demonstrate the potential of UF membranes in purifying plasmid DNA – with focus on developing new strategies to enhance the selectivity between plasmid isoforms and reduce membrane fouling during the filtration process.

I have presented my work at AIChE, ACS, NAMS and Gordon Research Conference. This year I am fortunate to be selected as one of the finalists for MilliporeSigma Life Science Award and invited to present my research at their facility in Bedford, MA.

My favorite equation is Fick’s law(s). It’s a fundamental equation in mass transfer.

Ivan Manzano (Second year graduate student)

I am studying the use of ultrafiltration membranes for the purification of therapeutic grade RNA. These molecules are of special interest since the discovery of RNA interference and their potential use in the treatment of genetic disorders, cancer and other diseases. I have not published my ongoing research, but I have the sense that something will come out soon. I am looking forward to present my recent findings in the next AIChE meeting in San Francisco, CA this November.

I also conducted a research project with Colton Lagerman, a visiting student from The University of Kansas in collaboration with Dr. Salis. The project studied the influence of RNA structure in the transmission through narrow membrane pores.

My favorite equation is the resistance model, based on Darcy’s Law. This is a very helpful equation when studying membrane systems, with a simple experiment you can obtain a lot of information about the membrane integrity and any polarization effects.

Parinaz Emami (Second year graduate student)

My research is about ultrafiltration of pneumococcal polysaccharides and conjugate vaccines using membranes. In production procedure of conjugate polysaccharide vaccine, 98% of unreacted polysaccharides need to be separated due to quality purposes. Different membranes have been used for separation of the unreacted polysaccharide from conjugated ones. Our effort is to characterize the behavior of polysaccharides and conjugated polysaccharides during ultrafiltration in order to increase the yield of the process. By enhancing the efficiency of the separation process, the vaccine would be more accessible for worldwide use especially for developing countries.

Stagnant film model is one of my favorite equations since it has a broad application in explaining the bulk mass transfer in membrane base filtration systems. We can use this model to check the existence of concentration polarization phenomena in the system. This phenomenon occurs when there is a highly concentrated particle layer on the surface of the membrane which affects the performance of the membrane.

Zhao Li (Second year graduate student)

My research project is how to achieve continuous coupled precipitation-filtration process for the capture of recombinant proteins. This is a collaborative project with Dr. Todd Przybycien and his student Qin Gu at CMU. The achievement of the proposed research would provide a much lower cost for the initial purification in a fully continuous (steady-state) format, give much higher volume reduction and thus potentially lower cost for all subsequent steps than any of the currently used technologies for recombinant protein purification. This could essentially revolutionize downstream processing.

There are two major challenges that we need to address. First, it is of great importance to find precipitation conditions that not only give high yield and purity but also allow easy re-dissolution of an active protein product (without generation of denatured material or significant amounts of protein aggregates). Second, it is critical to find operation conditions that can permit processing the precipitate in a continuous manner using membrane filtration. These include achieving good separation between the precipitate and the impurities, getting high permeate flux (to minimize membrane area), and minimizing membrane fouling (to minimize membrane replacement).

My favorite equations are Filtration equation and Poiseuille’s law.

Meet the Salis Lab. Learn how we use biophysical models and methods to rationally predict and control the behavior of biological organisms.

(Left to Right) Grace Vezeau, Alex Reis, Sean Halper, Daniel Cetnar

Grace Vezeau

Current sensing technologies for diagnostic compounds, like human biomarkers or environmental pollutants, rely upon expensive and non-robust equipment. My research seeks to solve this problem by developing RNA-based biosensors. Certain RNA sequences, called aptamers, fold into specific shapes and bind strongly and specifically to target ligands. We can couple this sensing element to a measurable output, such as the expression of a fluorescent protein, by designing the RNA molecule to change shape upon ligand binding. The RNA molecule acts as a switch, where output is turned on when the ligand is present.

I presented my work on TNT-detecting biosensors at the Fall 2015 SynBERC retreat, and will be presenting a broader overview of RNA-based sensors at the Rustbelt RNA meeting this October.

My favorite (set of) equations are the Lotka-Volterra equations, two differential equations describing the population dynamics of predators and their prey. They are one of the first examples of using mathematics to successfully describe a biological phenomenon – a tradition we are carrying through today.

Alex Reis

Precise control over protein expression is required when engineering biological systems. My work is focused on developing sequence-to-function models of gene expression and regulation to allow programmable system behavior encoded at the DNA sequence level.

One of the most direct ways to encode the desired protein level in bacteria is to modify the ribosome binding site (RBS), a section of the protein’s mRNA that governs the rate at which the ribosome is recruited to initiate translation. The RBS Calculator is a thermodynamic equilibrium model used to predict relative protein level given an mRNA sequence (figure). Our group has steadily improved this model since 2009 (Salis et al., Nature Biotechnology), but we have identified subclasses of mRNA that fold slowly or incorrectly that are still poorly predicted. Inspired by these insights, I am building a non-equilibrium model of translation initiation that accounts for these RNA folding dynamics. To do this, I’ve accelerated an existing kinetic Monte Carlo method of RNA folding (FORTRAN) and will soon be building a Markov model to describe the transitions and interactions between an mRNA and the ribosome during translation initiation (Python).

I presented this work at the last Synberc retreat this past Spring at UC Berkeley. I’ll be giving a talk on this model comparison and analysis at AIChE this November in San Francisco (Bioengineering session).

As a side project, Sean, Phillip Clauer (undergrad), and I have also been working on the rational design of nonrepetitive sgRNAs for use in multiplex CRISPR/Cas9 applications. CRISPR is a powerful tool that now allows us to regulate and edit genes in a precise, targeted manner. One major shortcoming of this system is that you can only do one edit or gene knockdown at a time because you are limited by the expression of only one sgRNA. Our nonrepetitive sgRNAs will allow easy DNA synthesis and stable, robust expression of many sgRNAs. This will enable multiple simultaneous gene edits in genome engineering applications, multiple up- and down- regulations of genes in fundamental expression studies, and more complex logic than currently possible in synthetic genetic circuits.

On my mind a lot is the fluctuation theorem (restated as Crooks Fluctuation theorem) from statistical mechanics. The fluctuation theorem can give insights into the nonequilibrium behavior of biology (proteins, RNA, etc.) at the microscopic level. Stated in a general mathematical form below, as the time or system size increases, the forward time trajectory is exponentially more likely than the reverse, given that it produces entropy. In other words, there is always some nonzero probability that the entropy of an isolated system might spontaneously decrease. The second law of thermodynamics is a statistical one!

Sean Halper

In order to bring a desired biochemical product to market, companies and research groups often need to improve the titers of the pathway expressing their product of interest. However, the design-build-test cycle they use to maximize the productivity of pathways via the tuning of enzyme expression is too time-consuming and costly for pathways of sufficient size. My work with the Pathway Map Calculator uses de-dimensionalized kinetic models to model and predict the relationship between enzyme concentration and final product titer for a variety of pathways, while requiring less pathway variant data for large pathways than other methods.

I have presented my work at the Fall 2015 meeting of Synberc in Boston, MA and will be giving a presentation at AIChE this November in San Francisco.

My favorite equation is the semi-official formulation of Murphy’s Law, where Pm is the probability of a social or mechanical malfunction; Km is Murphy’s constant (1);  I, C, and U are the importance, complexity, and urgency associated with a given malfunction of frequency F on a base 10 subjective scale, respectively; and Fm is Murphy’s factor (approximately 0.01).

Daniel Cetnar

The use of natural products in medicine remains immensely important with active research occurring in anticancer, antibacterial, and antimicrobial drug development. Today, nearly 70% of all anti-infective drugs derive from natural products.

Interestingly, thousands of sequenced natural product gene clusters exist whose products have never been produced in appreciable quantities due to challenges in producing them in the native host. From sequence homology analysis, many of these natural products likely have useful properties, but have not been produced and confirmed. Discovering high-throughput methods to re-engineer sequenced gene clusters for efficient production in industrial bacterial strains remains immensely important for future drug development. My work aims to develop models and design rules to streamline gene cluster engineering for incorporation into the Operon Calculator. Currently, my work centers on understanding, quantifying, and modeling the structural basis of mRNA degradation to predict mRNA stability and design robust operons for reliable gene expression.

I presented my initial findings on mRNA degradation at the summer 2016 Synthetic Biology: Engineering, Evolution & Design (SEED) conference in Chicago, IL.

My favorite equation is the Hill equation because of its broad usefulness in describing biomolecular interactions. Many of the fundamental papers in Synthetic Biology make use of the Hill equation to describe genetic circuits and gene regulation.

On behalf of the ChE GSA, we would like to thank students from the Salis lab for putting together this awesome summary.

The ChE GSA started a new project in July, in which we will feature one of the research groups in our department monthly. Dr. Savage’s group courteously agreed to be our first group. Their profile can be found on our website. This month, our featured group is Dr. Michael Janik’s group.

We have asked the graduate students within Dr. Janik’s group questions related to their research and here are their responses.

Of course starting off with our ChE-style ice-breaker, what is your favorite equation of all time?

Ian McCrum: I would have to say HΨ=EΨ, the time-independent Schrödinger equation. It appears short and simple but provides a complete description of a time-independent quantum system.

Joel Bombile: Schrodinger equation is like Newton’s Law in classical mechanics. It predicts the future behavior of quantum mechanical systems by describing the time evolution of the associated wavefunctions. A system’s wavefunction gives a complete description its quantum state.

Gaurav Kumar: My favorite equation has to be HΨ=EΨ. It is so simple, yet complex and powerful. I make my supercomputers solve this equation every day.

Hauran He:  My favorite equation would be E=mc² because this equation serves to convert units of mass to units of energy and implies the possibility of converting energy into mass.

Monica Roy:  My favorite equation is the Bernoulli equation because it is a simple equation based on a fundamental scientific property of conservation of energy and it has lots of applications.

Let’s now talk about your research. From my understanding, Dr. Janik is very interested in advanced energy conversion technologies and catalysis. What is your project and what is the major problem that your project is trying to solve?

Gaurav Kumar:  The overarching theme of my research is the rational design of high-performance catalysts. A major problem in catalysis is the search for highly active and selective catalysts that maximize the yield of the desired product. My goal is to understand intrinsic and extrinsic factors affecting catalysis and use them to guide the design of high-yield stable catalysts, especially for C1 chemistry and biomass conversion.

Monica Roy:  My research is focused on trying to understand how methane reforming proceeds on lanthana-doped in ceria. We are interested in understanding dopant distribution, sulfur tolerance and coking resistance of the material so that we can make a good catalyst for methane reforming.

Joel Bombile: I use a mixed quantum and classical approach to model the electronic degrees of freedom of conjugated polymers, taking into account atomic coordinates changes. Motivated by their electronic and mechanical properties combined with low cost and ease of processing, conjugated polymers have found promising application as active elements in organic semiconductor devices. However, the low charge mobility, attributed to disorder in these materials compared to inorganic semiconductors have limited their widespread usage. Transport in conjugated polymers is poorly understood and this hampers the design and sustained development of new high-performance polymer semiconductors. An accurate description of electronic transport in these materials requires an effective account of the interaction between electronic and nuclear degrees of freedom. Coarse-graining is employed to allow access to larger length and time scales.

Hauran He: My research project is about designing a novel catalyst which can hydrogenate benzene or ethylene with high selectivity when they are co-fed into the same reactor. The major problem of this project would be finding a descriptor that can indicate the selectivity of hydrogenation reaction and test a large number of catalysts.

Ian McCrum: I use quantum mechanics to model electrochemical and electrocatalytic reactions that occur in batteries and fuel cells. My main focus is on understanding why electrolyte composition and pH have such a large effect on the rate of the hydrogen oxidation reaction, important for hydrogen fuel cells. If we can more fully understand the mechanism for this reaction, then we can design better, more active catalysts to produce lower cost and higher performing fuel cells.

Have you published your findings?

Gaurav Kumar: I have published two first author papers this year, and another paper is under review. My papers can be found here.

Ian McCrum: My most recent publication involved modeling hydrogen and hydroxide adsorption on stepped platinum electrode surfaces and examining the effect of alkali cations and pH (First principles simulations of cyclic voltammograms on stepped Pt(553) and Pt(533) electrode surfaces).

Joel Bombile: Please find my published work here. The tight binding model I proposed has the ability to replicate the broadening of the absorption spectrum of a dilute polymer by capturing the impact of dihedral fluctuations on the band structure of polythiophene.

Have you presented or will be presenting your work at any conferences in the near future?

Gaurav Kumar: I have presented posters at the North American Catalysis Society biennial meeting in Pittsburgh 2015, the AIChE annual meeting 2015, and the Gordon Research Conference (GRC) in Catalysis 2016. I also gave a talk at the AIChE meeting 2015, and would be presenting my work in AIChE meeting this year in San Fransisco.

Ian McCrum: Presentations I have given at conferences include the following:

– “Alkali cation effects on the hydrogen oxidation reaction in alkaline solutions” PCCS 2014 – Pittsburgh, PA.; AIChE 2014 – Atlanta, GA.
– “Effect of organic and alkali metal cations on the hydrogen oxidation reaction” ECS 2015 – Chicago, IL.
– “Effect of alkali metal cations on the hydrogen oxidation reaction” NACS NAM 2015 – Pittsburgh, PA.
– “Effects of pH and alkali cations on cyclic voltammograms and the HOR/HER” ECS 2016 – San Diego, CA.
– “Understanding how pH and alkali cations affect cyclic voltammograms and the hydrogen oxidation reaction on transition metal surfaces”
ACS 2016 – Philadelphia, PA; AIChE 2016 – San Francisco, CA

Joel Bombile: Our work has been presented at the Fall 2015 MRS meeting in Boston, MA, and at the 2016 Polymer Physics GRC in South Hadley, MA.

Thank you, members of Dr. Janik’s group, for taking the time to talk about their group.

The ChE GSA is starting a new monthly column that will feature one of the research groups in our department. Our first group is Dr. Phil Savage’s group.

(Top row, left to right) Jonathan Harcourt, Zach Berquist, Nate Kokinski, Phil Savage

(Bottom row, left to right) Xian Wu, Xueying Zhao, Jimeng Jiang, Lili Qian, James Sheehan

We have asked the graduate students within Dr. Savage’s group questions related to their research and here are some of their responses.

So let’s start off with a small ice-breaker ChE style, what is your favorite equation of all time?

Jimeng Jiang: My favorite equation is Fenske equation because Fenske is an alumni of Penn State!

James Sheehan: One of my favorite equations is the residual sum of squares due to its simplicity and robust use in optimization.

Xueying Zhao: My favorite equation is mass balance because it is an important equation in chemical reaction and we can derive other equations from it.

Jonathan Harcourt:  I don’t really have a favorite equation.  However, if I was forced to chose I would say the fundamental equation of thermodynamics, because it can be used to derive all of the other equations in classical thermodynamics.

Let’s talk more about your research. I understand that Dr. Savage’s research focuses on biofuels. What is your project and what is the major problem that your project is trying to solve?

James Sheehan: My current research focuses on the hydrothermal liquefaction (HTL) of proteins. HTL is a thermochemical process that uses water at elevated temperatures (200 – 400^oC) and pressures (10 MPa – 40 MPa) to transform biomass into biocrude-oil, a renewable fuel precursor. Biomass feedstocks are often rich in proteins and understanding their involvement in HTL is pertinent to producing high quality biocrude-oil. My research interests are identifying and modeling the reaction pathways involving proteins during HTL and their incorporation into biocrude-oil and recovery as valuable co-products such as amino acids or other nutrients.

Jimeng Jiang: My research project is ‘Demetallation of Biocrude from Hydrothermal Liquefaction of Microalgae’. Biofuels have the potential to be an alternative fuel of petroleum in the future. I am trying to remove the detrimental metals such as iron and sodium from algal crude oil to improve the quality of crude oil.

Xian Wu: Catalytic Fast HTL of Micro-algae. With the increasing demand for fuel, the limited amount of the fossil fuels may be a potential cause of an energy crisis. Micro-algae, which could be raised rapidly and harvested without consuming arable land, has shown its great potential to be processed into bio-crude, which is regenerable fuel. Without drying the harvested micro-algae, HTL fulfills the goal of converting the bio-feedstock into energy-condensed fuel. Recently, research proved that Fast HTL provided a higher yield of bio-crude than isothermal HTL. My project involves identifying catalysts that increase the quantity and quality of the bio-crude through Fast HTL of micro-algae and conducting kinetic analysis on the catalytic fast HTL. The final goal of the research is to formulate a realistic model that can predict the process of catalytic fast HTL of micro-algae.

Jonathan Harcourt: My research focuses on the effect of salt water on the process of HTL. One of the most promising potential biomass feedstocks is microalgae, because of its rapid growth rate.  Many of the fastest growing microalgae grow best in seawater. My research is investigating whether additional salts in seawater will affect the HTL process.  I will also do the same for catalytic HTL, since different components of seawater (i.e. Cl- ions) are known to poison many of the best catalysts for HTL.

Xueying Zhao: My research project is hydrothermal liquefaction of a microalga with a core-shell catalyst. The major problem that I’m trying to solve is about the deactivation of catalyst in the reaction. I’m trying to use the shell to isolate the catalytic core with algae.

Lili Qian: My research project is the hydrothermal liquefaction of sludge, aimed to produce biocrude oil using municipal sewage sludge. This research is trying to solve the sludge disposal problems, such as secondary pollutants caused by incineration and landfills. Also, waste biomass can be converted to biocrude oil to solve the energy shortage problems.

Dr. Savage’s group at Penn State is relatively young (started in 2014), but has the group been able to publish any papers? Additionally, have you attended or will you attend any conferences in the near future?

James Sheehan: This past spring, we published a journal article regarding the HTL of soy protein concentrate (Products and Kinetics for Isothermal Hydrothermal Liquefaction of Soy Protein Concentrate). This upcoming August, I will be presenting at the ACS Conference in Philadelphia, PA on HTL of proteins.

Thank you members of Dr. Savage’s group for taking the time to talk about their group.