Dr. Brian Munsky announces book launch

Brian Munsky (Asst. Prof., CBE) is excited to announce the recent publication of “Quantitative Biology – Theory, Computational Methods, and Models.”  The textbook culminates 12 years’ experience teaching quantitative modeling of biological processes at the annual q-bio Summer School by editors Brian Munsky, William S. Hlavacek (Los Alamos National Laboratory) and Lev S. Tsimring (UC San Diego). The book was driven by a young and enthusiastic community of former q-bio Summer School students and lecturers, who contributed thirty chapters covering basic theoretical concepts, descriptions of modern computing methods, and detailed examples of quantitative biological investigations. The textbook includes contributions by members of the US National Academy of Science (Prof. Herbert Levine, Rice University) and the National Academies of Science Institute of Medicine (Prof. Michael Savageau, UC Davis) as well as two chapters authored by CSU students Zachary Fox (Ph.D student, SBME), Lisa Weber (Ph.D Student, CBE), and William Raymond (2017 B.S. Grad, CBE/BIOM). The 728-page B&W textbook has been published by MIT Press, and is available for online purchase.”

More information available at MIT press: https://mitpress.mit.edu/books/quantitative-biology

The book is also available for purchase on Amazon and Barnes & Noble.

2017 Annual q-Bio Summer School Held at CSU

Participants in the q-bio Summer School at Colorado State University pose for group photo, June 5, 2017.

This past summer, CSU hosted the 11th Annual q-bio Summer School in the Suzanne and Walter Scott, Jr. Bioengineering Building. The two-and-a-half week qbSS enrichment program was attended by more than 100 participants, including 33 competitively-selected visiting graduate students and postdocs who represented top universities from all over the world.

Quantitative biology, or q-bio, is an emerging interdisciplinary field that encompasses many different approaches to modeling, understanding, predicting, and manipulating biological processes. Since its launch in 2007, the purpose of the q-bio Summer School is to provide comprehensive scientific training and career advancement opportunities to students who wish to explore this growing field of scientific inquiry.

The thriving qbSS program was brought to Colorado in 2015 by CBE Professor Brian Munsky, who organized the event and secured sponsorships to subsidize student and lecturer travel. Professor Munsky has participated in qbSS since its inception, and has been a lead organizer since 2010, when he was the Richard P. Feynman Distinguished Postdoctoral Fellow in Theory and Computing at the Los Alamos National Laboratory. “The quality of students, faculty, and mentors at the qbSS has improved every year since 2007, and we have become the world’s premier training program for quantitative methods in biology,” said Professor Munsky, “Holding this program in Fort Collins helps to cement CSU’s role as a leader in this rapidly expanding field.”

The 12-day experience involved more than 110 different lectures, poster sessions, student talks, discussion panels, and mentored-course projects. Of the 26 lecturers that participated, four lecturers were qbSS alumni, and 17 institutions were represented. The program was led by faculty members from CSU and collaborating institutions, as well as multi-level industry experts.

The main topics of the 2017’s qbSS program included cell signaling, cancer dynamics, single-cell gene regulation, and computational synthetic biology. The three main CSU organizers were Professors Brian Munsky (CBE), Ashok Prasad (CBE) and Patrick Shipman (MATH).  Professor Munsky lectured on topics related to single-cell gene regulation while Drs. Prasad and Shipman lectured on topics related to computational synthetic biology, including dynamical systems biology, limit cycles, and oscillations. Both Drs. Prasad and Shipman have participated in qbSS since 2015.

The program offered general seminars for both q-Bio students and the general public. Moreover, theme-specific breakout sessions were offered to registered students, and the program also offered eight different career discussion panels. Panelists included CSU Vice Provost for Faculty Affairs Dan Bush, President of the CSU Postdoc Association Mario Oyola, and dozens more ranging from postdocs to senior university administrators.

Participants in the q-bio Summer School at Colorado State University participate in a breakout session lecture, June 5, 2017.

Students who were polled on their qbSS experience agreed that the broad range of topics and flexibility of the program were accommodating. “The organizers created an extremely welcoming environment that set the stage for the whole course. As for the lectures, almost everyone was useful and interesting, and they were appropriately spaced out. It was also great having some free time to hang out with the other students and explore Fort Collins!” mentioned an anonymous student participant.

“This summer school will have a significant impact as I have learned an enormous amount. Having the broad introduction has given me appreciation of the field of q-Bio and the chance to conduct a project that represents my interest. It’s a topic that is critical today and in the future,” said another anonymous student participant.

Drawing upon qbSS’s success, Prof. Munsky and collaborators Dr. Lev Tsimring (UCSD) and Dr. William S. Hlavacek (LANL) have just completed editing for a q-Bio textbook to cover material related to the qbSS program.  This textbook will include 30 chapters contributed by 75 authors, most of whom are former qbSS students and lecturers. This community-written book is scheduled to be published by MIT Press in 2018, and is expected to be adopted for use in q-Bio classes around the world.

“q-Bio has created and nurtured an enthusiastic and highly successful community of interdisciplinary scientists at the interface of mathematics, computation and biology. The qbSS program is helping to transform bioscience as we know it, and its impact will be felt for many decades to come,” added Professor Munsky.

qbSS’s 400+ alumni are now among the nation’s top young faculty and researchers in the integrated fields of quantitative biology, many of whom are developing and conducting q-Bio research and teaching programs. With such impactful results, Dr. Munsky is inspired to secure sponsors to ensure the future of the program. “We hope qbSS can continue to provide young scientists and engineers with the skills and resources to solve tomorrow’s most pressing bioscience and biomedical challenges.”

For more information on q-Bio and the qbSS program, visit http://q-bio.org/wp/.

Dr. Kipper’s Lab Works to Revolutionize Tissue Regeneration in Injured Patients

Electrospun chitosan nanofibers on mouse bone taken at 1000x magnification, that SBME Graduate Student, Raimundo Romero used as part of his research.

Dr. Matthew Kipper’s lab is currently incorporating electrospinning in their research for biomedical applications. His work was recognized and funded by the Musculoskeletal Transplant Foundation in 2011, and he continues to make strides with this research.

SBME Graduate Student, Raimundo Romero is currently working on replicating native bone tissue structure to enhance bone graft healing in injured patients. “In our lab, we use electrospinning as a way to create materials that can be used to deliver therapeutic proteins and stem cells for tissue regeneration. By delivering the right signals to the injured tissue, we can enhance the tissue healing response to heal injuries to tissues that may not otherwise heal by themselves,” Romero said.

The electrospinning technique is being used because of its ability to manufacture materials with microscopic dimensions and large surface areas for an array of unique applications. More specifically, electrospinning creates nanofibers, or ultra-thin fibers, in various configurations. Electrospinning uses an electrical field to draw a charged polymer solution from a syringe, which is then deposited on a grounded collector.

Romero became one of Dr. Kipper’s graduate students during his first year of graduate school. “I rotated through Dr. Kipper’s lab. I found his blend of biomaterial and tissue engineering research areas fascinating,” he said.

In addition to this project, Dr. Kipper and ME professor, Dr. Ketul Popat, recently involved two CBE undergraduate senior design teams for the advancement of other electrospinning applications.  One team worked to optimize the process of electrospinning Demineralized Bone Matrix onto a mat for the creation of scaffolds for cell growth, and another team designed a new process for the production of engineered tissues.

Electrospinning apparatus used in Dr. Kipper’s Lab.

Romero is optimistic for the future of this revolutionary research, “Eventual clinical translation of the tissue engineering materials produced in our lab is the ultimate goal. To that end, we plan to further investigate our materials and optimize the directed tissue healing response.”

New CBE Exchange Program with Zhejiang University to Launch Soon

Professors David Dandy, Christie Peebles, and Ken Reardon touring a 3-D printing laboratory at Zhejiang University.

CBE is bringing the world closer together through complementary research and education initiatives. For the past 18 months, department head, Dr. David Dandy, and Professor Kenneth Reardon have led the development of a collaboration with the College of Chemical and Biological Engineering at Zhejiang University in Hangzhou, China, located about an hour from Shanghai.

Undergraduate and graduate students at both universities will have the opportunity to explore their research interests through a new lens while gaining international exposure. The exchange program will highlight specific areas of research, including biotechnology, and polymer science and engineering.

This collaboration started at the faculty level. “We as a department have been thinking about what makes sense for our students and professors,” said Dr. Reardon. “This will hopefully lead to university-level relationships so other CSU departments can benefit from this partnership, too.”

A former CBE Ph.D. student who is now on the faculty at Zhejiang University helped Dr. Reardon become aware of the possibilities of a research collaboration. After several meetings with Zhejiang counterparts, the program specifics are nearing completion and exchanges will begin in 2018.

Professor Ken Reardon listening to a question from a student after his presentation on meta-proteomics at Zhejiang University.

“We look forward to how this relationship will enhance the educational experience of all students involved, and benefit the quality of research taking place at both universities,” said Dr. Reardon.

CBE’s ChemE Car Looks Forward to Nationals after Placing 3rd at Rocky Mountain Regional Conference

ChemE Car team members accepting their 3rd place trophy at the regional competition in North Dakota.

CSU’s ChemE Car team has had a long history of success at CSU, and its most recent design is no exception.

The team consists of 24 students, including 12 active members. Most are CBE students, however, electrical and mechanical engineering students have contributed in the past. They are always looking to diversify their team with members from all engineering disciplines.

Placing third at the Rocky Mountain Regional Conference qualifies them to compete at the national competition this fall in Minneapolis, Minn., where they placed ninth last year.

“We are very excited about the opportunity to compete and learn from other schools. The competition is always great and we get to see very innovative ideas on display. We are confident in our car and our team’s ability to be ready for the competition,” said ChemE Car president, Zach Schafer.

Annually, teams from colleges all over the country participate in the national competition. Criteria is based on distance driven with a specified water load, and the car must be both powered and stopped by a chemical reaction.

Currently, the team is developing two cars – one for the national competition this fall, and another for the regional competition next spring. One of the cars is powered by a hydrogen field cell and stopped by the reaction between magnesium and hydrochloric acid. The plan for the additional car is to power it with thermoelectric generators and stop it with the decomposition of hydrogen peroxide.

We wish our ChemE Car team the best of luck at the national competition this fall!


CBE 2017 Senior Design Project Recap

Students (L to R): Joe Dennis, Fatima Altimimi, Andy Farquhae, Chase Hunrer, Meena Rezai


This project explored the commercial feasibility of the production of monoclonal antibodies (mAb) using transgenic tobacco plants (Nicotiana benthamiana). Protein production is typically done with mammalian cells or bacteria, so using plants in a new approach; and comparing the two methods was their goal. Specifically, the students conducted a techno-economic analysis on both the upstream and downstream processes and examined key differences between the methods. They also described the advantages of using transgenic tobacco and detailed additional safety considerations of the process. In addition, process flow diagrams for the upstream and downstream processes were thoroughly modeled using SuperPro Designer software.


Students (L to R): Sarah LaBonde, Attie Pennybaker, Emilie Asbury, Cassie Schucker

ELECTROSPINNING OF DEMINERALIZED BONE MATRIX – Mentored by CBE & ME Faculty, Drs. Matthew Kipper and Ketul Popat

The purpose of this project was to optimize the process of electrospinning Demineralized Bone Matrix onto a mat for the creation of scaffolds for cell growth. A scaffold composed of biological polymers such as DBM, as opposed to synthetic polymers would improve the compatibility, making it more stable for use in the medical field.  Electrospinning is the process in which a polymer is dissolved in a solvent, the solvent and polymer are ejected into an electric field, the solvent evaporates, and the polymer is collected on a plate. The DBM used in this project was allograft bone without inorganic material, creating a natural alternative to synthetic polymers. Once the group successfully optimized the process, they investigated the cell growth capabilities of the electrospun scaffolds. Potential uses of this scaffold could be seen in a patient with tissue damage; offering a quicker and more natural recovery.


Students (L to R): Abdulkarim Altwaijiri, Logan Weshinskey, Brandon Herre, Brandon Eagan, Ismail Al-Helal


A chemical called R134a, previously used as a refrigerant in automobiles and home/industrial AC units, was notorious for producing harmful emissions, so, this group designed a their own chemical process to create HFC-1234yf, a more environmentally-friendly refrigerant. HFC-1234yf is patented by Du Pont, however, along with creating this chemical, the group decided to dive into the economical logistics behind its manufacturing process. An analysis was performed to determine the feasibility of creating a process plant from scratch. Using capital investment and return on investment, the selling price for the refrigerant was calculated and compared against Du Pont’s price to determine if it could compete. It was concluded that the price of the reactants was the major driving force for the cost of manufacturing and that even with having a high price of reactants, HFC-1234yf could still be produced more inexpensively than the selling price of it. The group concluded that the Du Pont process is highly profitab


Students (L to R): Ian Minck, Abdullah Bagais, Abdullah Saifaddin, Tyler Calvino, (Osama Albayti, not pictured)


A major portion of this group’s project was to complete a technoeconomic analysis of a Vinyl Chloride Monomer (VCM) production plant versus an existing U.S. patent. The plant uses a method of converting ethylene and chlorine to di-chloroethane, which is then broken down to VCM under high temperatures. In the technical analysis this group performed, a Process Flow Diagram (FPD) was developed and a cost analysis was created. An additional minor part of the project was to design a polymerization unit to convert VCM to PVC using a current U.S. patent.  Both processes resulted in a very favorable Return on Investment.


Students (L to R): Patrick Rolseth, Lamia Dawahre, Sara Alhababi, Mitch Maloof, Dana Kuglin


This group’s project, in support of NREL’s Co-optima initiative, focused on the continuous extraction of volatile fatty acids produced by a bacteria Clostridium butyricum from lignocellulosic hydrolysate, which is a stream fed to bacteria so that it can convert fermentable sugars to butanol and other VFA’s. The ability to remove VFA’s from an aqueous solution, in an economically feasible manner, is of high interest, as these VFA’s act as precursors to biofuels. Extraction and purification of these acids from the fermentation broth can be fed into further ketonization steps to produce biofuels. This group’s design goals focused on membrane extraction through a TOPO, a complex solvent, and kerosene mixture to continuously remove VFA’s produced during fermentation. A TOPO-acid complex is formed and then further distilled to convert VFA’s into a pure vapor form. The use of an immobilized cell reactor is also introduced within their design to optimize the proceeding extraction.


Students (L to R): Bryant Hiraki, Eli Mcpherson, Stacey Zintgraff, Cassidy Wright, Aidan Ceney, Anthony Roulier

MONOCLONAL PRODUCTION IN TOBACCO – Project Inspired by the Center for Disease Control and Prevention; Mentored by CBE Faculty, Dr. Christine Peebles

This group’s plant-based pharmaceutical senior design project sought to advance the promising technology of recombinant proteins transient expression in tobacco plants for biopharmaceutical manufacturing. The target, provided by the Center for Disease Control and Prevention, was a therapeutic antibody protein for Japanese Encephalitis Virus, a virus prevalent in Asia. The application would be a neutralizing therapy administered intravenously to a person infected with the virus. The group closely considered methods that scaled well to ease the transition from lab bench to pilot plant and eventually full scale manufacturing. Their work was divided into three subgroups: upstream, downstream, and quality control. Anthony Roulier and Eli McPherson, of the upstream team,  confronted the technical challenges of strain optimization and genetic cloning of the various organisms used. Cassidy Wright and Aiden Ceney, of the downstream team, developed effective methods for tobacco genetic transformation and purification of the antibody. Quality control was composed of Bryant Hiraki and Stacey Zintrgraff, and tasked with understanding the biochemistry of antibodies that enabled proper analysis and confirmation of function. The year-long project was successful in transforming tobacco and purifying the protein for future work in animal studies with the CDC Fort Collins campus.


Students (L to R): Neal Sullivan, Justin Walton (not pictured Nicholas Kennedy)


This team partnered with Carestream to reduce the bromide concentration found in wastewater effluent. This is a priority for Carestream, the former medical division of Kodak, because of its detrimental affect on the reproduction of water flea species Ceriodaphnia dubia. Ceriodaphnia dubia is often used as an indicator species when testing toxicity levels in wastewater treatment plant effluent streams. The team tested two different methods for bromide removal. The first tested three types of powdered activated carbon, and the second tested a polystyrene ion-exchange resin called Amberlite IRA 910. Various approaches to sample jar tests were performed by the team in order to test the effectiveness of each method while also attempting to better understand how to integrate the bromide removal mechanism into Carestream’s current wastewater treatment process. While the activated carbon testing was not effective, the polystyrene resin has shown promising results for bromide removal in Carestream’s frequently changing wastewater effluent.


Students (L to R): Jonathan Haskins, Andrew Hodge, Grace Hyde, Audrey Einhellig


This group spent the semester working with Dr. Snow’s lab on a protein called CJ, grown in genetically engineered E. Coli bacteria. When crystallized, the protein has great potential for a wide variety of uses, such as in pharmaceuticals. To date, Dr. Snow’s team has been working on a small laboratory scale. This project’s goal was to design a working process for CJ purification and crystallization on a larger scale. The project was intended to both lay the groundwork for Dr. Snow to eventually scale up operations, and to find out if CJ production is profitable. The design included three different process possibilities for comparison, with an economic analysis for each.


Students (L to R): Addison Cheek, Catherine Mercy, John Travers, Brisco Arechederra


This group worked with AstraZeneca, a global biopharmaceutical company which manufactures monoclonal antibody products utilizing cell culture processes. The group evaluated options to add HTST (high temperature, short time) media treatment capability in a new manufacturing facility, to mitigate the risk of viral contamination of mammalian cultures. If a viral contamination of a culture occurs, the required decontamination efforts significantly impact manufacturing operations and reduce AstraZeneca’s ability to deliver vital medicines to patients. The culture process requires treatment of four types of media and one glucose solution that all must be sterilized in the system. Their project provides the design, sizing and throughput, and cost analysis for two automated HTST systems for media treatment as well as a cleaning process for the equipment used. The group hopes to see this design implemented in the manufacturing facility in the near future.


Students (L to R): Yiqi Xie, Tori Beckwith, Cameron Connell, Janel Abbott

ELECTROSPINNING OF DECELLULARIZED ADIPOSE TISSUE – Mentored by CBE & ME Faculty, Drs. Matthew Kipper and Ketul Popat

This project, under the guidance of Dr. Matthew Kipper of CBE and Dr. Ketul Popat of ME, designed a new process for the production of engineered tissues. The engineered tissue consists of stable, nanostructured fibers made of decellularized adipose tissue (DAT). The process for production of these new engineered tissues involves processing adipose tissue in a suitable solvent condition by electrospinning to form fibers with tissue in a suitable solvent condition. The resulting fiber material will serve as a  for cell and tissue culture. Since they are composed of biologically-derived material, the group expects that DAT nanofibers will have improved performance when compared with synthetic polymer-derived scaffolds, currently on the market. They a variety of parameters, i.e. supply voltage, solvent, and solution supply rate, to control the scaffold formation and optimize the DAT nanofiber diameter.


Students (L to R): Jake Denney, Matt Pinkham (not pictured Zack Dwyer, Zach Heuer, Dillon Jarrell)   

DESIGN OF NOVEL SMALL MOLECULE INHIBITORS OF ZIKA NS5 METHYLTRANSFERASE – Mentored by Veterinary Medicine and Biomedical Sciences Faculty, Dr. Mark Brown

This team worked to computationally design a vaccination for the 2016 global outbreak of the Zika Virus. The group dived into the effects of NS5 Methyltransferase, a nonstructural protein encoded by the RNA genome of Zika that accelerates two methylations of the RNA structure, which are essential for the virus’s survival. With that information at hand, the group computationally built a set of small molecule inhibitors that constrained the binding of the RNS structure to the protein, preventing methylation of Zika. Future work in this endeavor will include the synthesis and assessment of the drug, and in vitro and in vivo screens.


Students (L to R): Grant Henke, Angelo Zito, Macall Hock, Sara Al-Harthy, Jordan Waite

CARBON DIOXIDE MEMBRANE SEPARATION FROM FLUE GAS – Mentored by CBE Faculty, Drs. T. Gordon Smith and Travis Bailey

This team’s project explored a method of removing carbon dioxide from the flue gas of a coal powered plant for the purpose of capturing and storing carbon dioxide to reduce fossil fuel emissions into the atmosphere. In the past, various technologies have been proposed to accomplish this goal. This group researched the feasibility of using ionic membranes to see if there was room for improvement. The team used the Aspen Plus process design program to simulate the separation of carbon dioxide and nitrogen. A variety of ionic membranes were investigated. The team came up with an improved process which included revisions to the original membrane thickness and pressure for optimal membrane performance.  An economic study suggests that this could be a realistic way to reduce fossil fuel emissions if a carbon credit of $50 per ton was available.



Get to Know the AIChE Student Chapter

AIChE Student Chapter at the Regional Conference in North Dakota.

Whether it’s networking, gaining industry perspective, community involvement, or having fun with fellow students, the student chapter of the American Associate for Chemical Engineers’ at CSU offers real-world CBE experiences.

“AIChE is a great way for chemical engineers of any year to get involved on campus and for students to learn about opportunities in their field,” said Sarah Igli, president of AIChE, CSU.

There are opportunities at every level of involvement. Igli encourages all CBE students to join at the national level to receive access to the AIChE publications, library, career resources, and safety certification tools. At the student chapter level, students can attend bi-weekly meetings showcasing industry speakers from the oil and gas, pharmaceutical, and research sectors, among others. Socials and brewery tours are also hosted for students to get to know each other in a relaxed environment.

AIChE students volunteering at a STEM fair at Timnath, Colo.

Joining AIChe’s student chapter is also a way to get involved on campus and in the community. The chapter participates in CSU’s RamRide, which is a volunteer program providing a free, safe, non-judgmental ride home for all CSU students. Students also do demonstrations, and create games and workshops for local K-12 schools to motivate young students in STEM subjects.

AIChE students bond on a tour of Fiesty’s Distillery.

In addition, AIChE students can attend regional and national conferences which include unique career workshops and industry presentations at locations across the country.

For those students with leadership qualities, there are opportunities to run for office positions, too, which is what Igli did. “Being president of AIChE has helped me to learn to manage my time better because I am going to school full time, working a part time job, and planning meetings and events for AIChE. It has also given me the chance to hear what the students want out of a student organization and how I can improve it for future students.”