JavaScript is disabled. Please enable Javascript for full website functionality. To learn how to enable Javascript visit

The Connector - Spring 2023 Issue

Modeling the PhD Journey: Investigating the Stresses and Remedies

Saeed (left) and Raafat (right)

Pursuing a PhD is not for the faint of heart. At the same time academic research institutions are expanding graduate programs to improve their reputations and finances, there are fewer and fewer positions for professors. Successfully competing in the tight academic market depends on delivering excellent PhD research in, optimally, five years or less.

Anything that gets in the way of the PhD timeline causes stress. One of the most typical research-derailers is divergence, the distraction of a student away from their research focus.

Raafat M. Zaini, Assistant Professor of System Dynamics, Integrated Science and Technology Program, James Madison University and Saeed P. Langarudi, Associate Professor, Department of Geography, University of Bergen both experienced divergence as PhD students in Worcester Polytechnic Institute’s (WPI) System Dynamics program. “I planned to focus on innovation sustainability in research and development organizations,” Zaini said. “As I explored and read about that topic, I came upon the idea of organizational dissent and got excited. I thought, ‘Oh, maybe I’ll explore that! I’ll build a model!”

His excitement about organizational dissent faded when he presented his model idea to his advisor, Dr. Khalid Saeed. “He asked me what I was trying to do, and I didn’t have an answer,” says Zaini. “I was just excited about something new. It led to a horrible weekend. I felt a bit lost and worried about the time I had taken from my original topic. It was really stressful.”

Zaini had journaled about that experience and other aspects of his PhD journey. “To prepare for my research presentation, I reviewed my journal and noticed a pattern,” says Zaini. “There were points of divergence and then returning to the original with a different spin. I thought there might be a stock and flow thing going on.”

Zaini used Stella® to map out a model of his PhD journey. It includes three stocks: research ideas, collegial feedback, and knowledge, and demonstrates the sensitive dynamic relationships between them. New ideas, feedback, and knowledge can all cause the student to question, or diverge from, their initial intended focus. They can also help the student converge back to their research plan.

Stock and flow diagram of the PhD experience Stock and flow diagram of the PhD experience

“When Raafat shared his idea for a model of the PhD journey, I thought ‘Oh boy! I’ve had that experience too,’” says Langarudi. “I realized that the stresses Raafat and I felt were probably true for PhD students in other programs and around the world. I had never thought about it as a dynamic problem before.”

Together, Zaini and Langarudi continued to use Stella to build, refine, and validate a model of the PhD experience and to help users understand the causes of and remedies for divergence. “Raafat’s prototype model was based on his own experiences,” says Langarudi. “I made changes, through trial and error, to see if his formulations responded as expected. We wanted to be sure that the model reflected our own knowledge of the PhD journey but remained as simple as possible.”

While simple, the model has a built-in hierarchy that utilizes Stella’s module feature. “Modules allowed us to include complexity without showing it,” says Zaini. “When we need or want to, we can peek inside modules for deeper understanding of the model and its variables.”

The next step was to make sure that the model reflected a common PhD journey experience, not just their own. “We created a survey for PhD students,” says Zaini. “They chose graphics that best described elements of their PhD experience and answered written questions. We collected information on when their program began and finished, the number of thesis ideas they had along the way, and other quantitative and qualitative information that described their PhD journey.”

While survey answers further validated their assumptions about the PhD experience, Zaini and Raafat went further to test and understand the relationships between model variables. “We ran about 20,000 Monte Carlo simulations to account for uncertainty in the assumptions included in the model’s mathematical formulas,” says Langarudi. “We also tested which variable values were the most realistic.”

“Stella makes it very easy to run sensitivity analyses to test variable values which helped with the Monte Carlo simulations,” says Langarudi. “It’s also built for collaboration. Raafat and I could see and understand each other’s work.”

Having validated the model, Zaini and Langarudi focused on the impact of peer-to-peer sharing during the PhD process – the costs and benefits of presenting ideas to fellow students and faculty, and receiving and synthesizing feedback. “I started my PhD program in the Fall of 2011 and Saeed arrived in the Spring of 2012,” says Zaini. “At the time, we were the only two students in our program. We shared our ideas and work with professors. That’s stressful because you feel like their criticisms have to be implemented.”

Dr. Saeed described MIT’s brown bag lunch sharing sessions, organized by Peter Senge at that time, that gave students access to feedback from their own peers as well as professors. Using that example, Zaini and Langarudi founded WPI’s Collective Learning Meetings (CLM), a forum that continues to support PhD work there and at peer institutions.

“As founders of CLM, we wanted to understand the impact of peer-to-peer sharing,” says Zaini. “How did preparing for, leading, and getting feedback during sharing sessions help or hurt the graduate research process? Is there an optimal level of sharing? How does sharing interact with the number of ideas considered and knowledge acquisition? Is there a corrective mechanism to help a student move from stressful divergence to convergence with their intended research?”

“The most interesting insight from the model is that there isn’t a definitive way to use peer-to-peer sharing sessions to smooth divergence,” says Zaini. “There is a sweet spot between divergence and knowledge accumulation, but the most productive timing and frequency of sharing sessions will differ from student to student.”

“In general, if students share ideas too early, they risk extreme divergence,” says Zaini. “They haven’t thought through questions they should ask during sharing sessions or don’t have enough knowledge to react productively to feedback. If they wait too long to share, or don’t share often enough, they risk getting important feedback too late in the PhD process. Their research product suffers.”

The model does offer a mechanism for understanding the dynamics of the PhD process, which is useful for both PhD students and their advisors. Zaini points to the benefits of Stella’s storytelling features that allow users to understand all variables, their relationships, and their sensitivities. “I never show anyone an entire model,” says Zaini. “With storytelling, I open it piece by piece. Students and others follow a narrative to understand how the model is built. I can do that within Stella or create PowerPoint slides so that the story is portable.”

Zaini and Langarudi are now happily settling into professorships at their respective institutions. Despite the challenges of navigating the competitive academic market, they both feel they’ve landed where they should be.

“After graduation, I stayed at WPI as a post-doc and substituted for Dr. Saeed when he had to take a short leave,” says Zaini. “It was a heavy lift. I was also consulting at the time, but I developed a sense of teaching. I took a course on scientific teaching and learned how to develop lesson plans, how to be inclusive, and other important skills. When the opportunity opened at James Madison, where system dynamics is multi-disciplinary and matches my own education and career, it felt like the right fit.”

While Zaini had contemplated a career in industry, Langarudi was always aiming for academia. “I never had any doubts about my goal,” says Langarudi. “Earning a PhD is a big challenge. There are so many people and expectations to manage and, to fund my education, I worked almost full time as a consultant while conducting my own research.”

Langarudi credits his stubbornness and pragmatism for his systems dynamics successes and ability to secure a professorship. “I went to WPI to learn how to apply system dynamics to economic questions,” says Langarudi. “As I learned, I made models that did not work at all and were hard to start over. It taught me that being a perfectionist is a problem. You have to be pragmatic and think like an engineer to get the job done. The same is true for finding the right academic position. I made a pragmatic move to New Mexico to do post-doc work and build my portfolio which prepared me to grab the University of Bergen position.”

Now, Zaini and Langarudi are using their own experience and modeling insights to guide their work as research advisors. “I find that students are very worried about sharing,” says Zaini. “They wait too long because they’re afraid of criticism. I tell them that getting and receiving feedback are essential skills and critical for success.”

“Helping Raafat build this model certainly made me more cognizant of research as a dynamic process,” says Langarudi. “I find myself listening to students go on about new information and new ideas and think, ‘It’s probably time to ask them to stop exploring, synthesize data, and refocus.’”

Dr. Andrew S. Mount Uses Stella® to Research, Teach, and Test Product Ideas

Andrew Mount

Andrew S. Mount, PhD, founder, ConusCoat LLC, has spent his career asking hard questions. How do oyster shells regenerate? How fast will a virus spread and how many people will be infected? Will marine environments improve if boat hulls are sealed with non-toxic paints?

Mount has asked, and answered, those questions as a master’s student at College of Charleston, PhD candidate, research scientist, and college professor at Clemson University, and now as an innovative product developer and founder of ConusCoat LLC. Through those endeavors, he has used Stella to guide his and his students’ thinking to find and communicate new insights.

“Anyone can use Stella – you don’t have to be an engineer,” says Mount. “Stella’s graphical interface makes it easy for anyone to understand Systems Thinking and build models. Instead of worrying about calculus equations, users focus on the stocks and flows in a system, how they interact, and what those interactions yield. And, as research publications and other audiences increasingly require researchers and presenters to show their work, the isee Exchange™ has made it easier to post and share models.”

Research Question: How do oyster shells regenerate?

“Despite evidence to the contrary, marine biologists still believe that the regeneration of oyster shell material is an extracellular activity,” says Mount. In fact, through years of research and hypothesis testing, Mount discovered that the crystals that combine to form oyster shells are generated inside the animal’s cells.

That research began at the College of Charleston when Mount was earning a Master’s degree. “Lowell Seick, my mentor and thesis advisor, hypothesized that free amino acids secreted from oyster tissue into the fluid-filled space between the animal’s body and shell participated in nucleation,” says Mount. “Simply put, he thought the amino acids participated in calcium binding with carbonate to create crystals needed for shell building. He tasked me with finding those amino acids in the fluid.”

Through much trial and error and microscope-assisted searching, Mount did find free amino acids in the fluid he extracted from the space between the oyster shell and body. He built a model to demonstrate how the amino acids assisted the binding of calcium from outside the oyster’s cells to carbonate inside the cell to create new crystals.

Mount and Seick were pleased with the discovery but were presented with a new question. Dr. A.P. (Hap) Wheeler from Clemson University, a member of Mount’s thesis committee, asked if nucleation was impacted by the salinity, or salt content, of the fluid. “I realized I needed a way to run lots of experiments without running an actual experiment. That’s where Stella came in,” says Mount.

Using a Stella model allowed Mount to vary concentrations of protein, saline, and other fluid contents and look for nucleation. “It was a mathematical model and I used it to run about 70 experiments,” says Mount. “I was able to determine that the phosphoprotein didn’t nucleate anything. Instead, it sticks to calcium carbonate crystals, which helps new crystals attach to the existing shell.”

Now Mount understood the protein’s role in shell building, but where were the crystals coming from? “I came to the conclusion that nucleation wasn’t extracellular,” says Mount. “It was happening inside the cell. Unfortunately, with little to no research that concurs with mine, marine biologists have largely ignored my findings.”

They also seem to be ignoring reality. Ocean acidity levels have been rising, which would negatively impact extracellular nucleation. The environment outside the oyster’s body would be unfavorable. On the contrary, oyster populations are doing well.

Teaching Question: How fast will a pandemic spread and how many people will be infected?

“Teaching students to use Systems Thinking, as opposed to giving them a dusty book, has real value,” says Mount. “The model of professor as gatekeeper—students show up for a lecture, take notes, and then regurgitate for the exam—is really antiquated. We need to teach students to think, run data, and understand what’s happening.” Stella has been Mount’s classroom assistant for teaching students how to think and gain insights.

In 2003, almost 20 years before COVID-19 exploded into a global pandemic, Mount and his students modeled the Severe Acute Respiratory Syndrome (SARS) epidemic. The potentially catastrophic virus first appeared in Hong Kong and, like COVID-19, was highly contagious and could be fatal.

Hong Kong notified the World Health Organization (WHO) of the SARS outbreak in March 2003. Cases had been slowly building for several months and, as people travelled, other countries began reporting infections. WHO issued a global alert, and the world feared a pandemic.

“At the time, my senior biology seminar students were studying plagues,” says Mount. “When SARS hit the news, they became excited about modelling the outbreak to understand how fast the virus could spread and the number of people it could infect.”

The class took a mathematical ecology population-level deterministic approach to model building. Students focused on the number of susceptible people in a population and then applied the WHO’s reported rate of infection. Then they applied a recovery rate to the infected population.

Deterministic models assume average rates—in the case of SARS, average rates of infection— with no deviations across populations. Student SARS models considered infection rates across a global population without factoring in social, cultural, political, or other factors that would differentiate populations.

The class was divided into four-person groups that included a leader, a devil’s advocate who would question assumptions, a reporter, and a graphics person. Students who were experienced Stella users mentored peers who were new to modeling and the software. Each group built a model that simulated the population movement across susceptible, exposed, infective, and recovery states, or SEIR model. Models were driven by WHO data that reported the number of cases and mortalities every week.

WHO reports began in January and, by March, infection rates were growing. “The rate of infection or basic reproduction rate (R0) for SARS was 2.7, meaning that every person who contracted SARS would, on average, infect three others,” says Mount. “Any R0 over one indicates a pandemic. In calculating recovery, models applied WHO data that indicated 17% of infected people died.

“When students first ran their models they thought, ‘Oh no! The whole world will get SARS!” says Mount. In fact, as their models showed, SARS has a rapid onset, short peak, and rapid decline. That was because SARS' effective reproduction number declined as the population recovered.” In contrast, COVID-19 became a global crisis because while “COVID-19’s effective reproduction number also declined over time, the virus’ rate of mutation is incredibly high, with each successive variant having a higher R0.”

Graph of SARS data compared to Stella-generated graph 2003 SARS Epidemic in Hong Kong A. The outbreak (yellow) compared to Stella model (blue line) B. Stella diagram showing the S-E-I-R epidemiological model C. Effective reproduction rate (Re) is dependent on the number of recovered cases.

Product Innovation Question: Can an environmentally safe, biologic coating effectively replace the toxic, copper-based paint currently used to keep marine vessels clean of barnacles and other biofoulers?

Retired from teaching, Mount is now using Stella to develop an environmentally safe marine coating. From 2005 to 2018, he studied the cellular biology of barnacle biofouling supported by funding from the Office of Naval Research (ONR). ONR was looking for an alternative to the toxic copper paints that are currently used to keep vessel hulls free of barnacles. Now, Mount is translating that lab’s biofouling deterrence research into marketable anti-fouling technology.

“The grail is a clean hull that doesn’t have to be scraped and painted for 10 years,” says Mount. “We discovered that barnacles, oysters, bryozoans, and other biofoulers have specialized adrenergic cellular receptors. When disrupted by a conopeptide antagonist, which originates from secretory cells that line cone snail venom ducts, they won’t settle on a treated surface. The question was, could that biological deterrent replace toxic, copper-based paint.”

“In one year, a 30’ fishing boat coated with copper-based paint will leach over two pounds of copper into the ocean. Using a Stella model fitted to peer-reviewed data, we’ve been able to demonstrate a positive impact of replacing copper-based paint with an environmentally responsible coating. Just one gram of our biologic coating replaces 5.5 pounds of copper per gallon of antifouling paint.”

The modeled rate of copper release into the ocean is extremely precise, making it easy to predict toxicity effects for over 78 known marine species. Mount is finishing his manuscript and preparing to upload his model to the isee Exchange.

“The model will help the scientific and engineering communities communicate,” says Mount. “Accessible to anyone, even someone with no Stella experience, it will help potential investors through their due diligence process, provide a rationale for the resistant paint market to adopt a better solution, enable regulators and policy makers to craft better legislation and guidelines, and give consumers the information they need.”

Copper footprint of a 30 foot fishing boat Copper footprint of a 30-foot fishing boat. A. Published leaching data (blue) compared to Stella model (red) B. Stella model for copper epoxy antifouling paint. The model is within a 0.5% agreement of the actual leaching data at day 60 of the simulation.

On the Road

Yahoo! We are so excited to be attending this year’s ISDC in Chicago in person! Co-presidents Karim Chichakly and Bob Eberlein, lead software developer Billy Schoenberg, and customer service specialist Hilary Allen will all be there. Come see us at our booth or catch us on the run. Karim, Bob, Billy, and Steve Peterson will present Assemblies™: Lowering the Barriers to System Dynamics. Billy and Bob will present Measuring the change in behavior of a system with a single metric, and Billy will present Towards a fully coupled Integrated Climate Assessment Model: FRIDA Version 0.1. We can’t wait to catch up with many of you and meet others for the first time.

In September, Karim will be traveling to Madrid, Spain to attend the 21st Annual Latin American Conference on System Dynamics (CLADS) hosted at the Francisco University de Vitoria. This will be our first time attending in person since the pandemic and it will be great to reconnect with the Latin America Chapter.

Software Update

We continually strive to improve the Stella® experience with new, innovative features. Our 3.2 release saw the addition of Assemblies™, self-contained models that streamline the modeling process by serving as building blocks for other models. Our brand-new 3.4 release introduced the Assembly Exchange, a special section of the isee Exchange™ where users can share their custom assemblies and download others’ assemblies to their software. Other exciting additions include sliced graphs, which allow you to overlay values from different time periods to see how one period compares with another, a simplified calibration setup, an editor for non-apply-to-all graphicals, and more. For a complete list of new features, please check out our Feature Updates.

Tutorial Page Redesign

Over the past months, we have been adding many new tutorials and we realized our tutorial page layout was getting cumbersome. We have completely reorganized it. If you have not visited it yet, go take a look. We have organized the tutorials into categories to help you quickly find the one you need. If there are any topics you feel are missing, let us know. We will be happy to create them.

Three-Part Special Podcast Series

We recently released the first episode of our three-part special podcast series. We interviewed three educators that have dedicated much of their careers to incorporate System Dynamics into the K-12 curriculum. Learn how each was introduced to the field and how they have introduced dynamic modeling to the next generation. Our first podcast featuring Steve Peterson is currently available on our Webinars page. Stay tuned in the upcoming months when we release our second podcast featuring Diana Fisher, and our final podcast featuring Jon Darkow.

The South African Chapter System Dynamics Competition

The sixth annual South African Chapter of System Dynamics competition is off to a great start. This year’s competition has been reorganized to host three sessions to allow the competitors more time to engage and learn about dynamic modeling. It will focus on creating a sustainable fishing industry. The first session was held in April and participants worked to construct the Fish Banks simulation. The second, hosted in mid-June will focus on providing individual support for the participants to address their questions and struggles, enabling them to get a deep understanding of how to apply dynamic modeling concepts. The final session will allow the participants to share their work as well as any insights learned during the competition. Each session, judges will pick winners who demonstrate their understanding and skills. Session one’s winner was Alaize Dall'Orsoletta. Alaize demonstrated an operational threshold for ship selling, showed mastery of equations and models, and effectively used sensitivity analysis.

Updates to Evaluation and K-12 Site Licenses

We've made big changes to two of our popular license types!

We discontinued the former Trial license and replaced it with our new Evaluation license, a one-time 30-day license with all the functionality of our software, including the ability to save your work. This is a great license to see if Stella® works for your organization or project, to use in short courses or workshops, or just show off to your colleagues and friends. Using the Evaluation license also gives you 10% off a new license.

Starting March 1, 2023, we began offering free Stella Professional Online site licenses to K-12 schools. K-12 schools teach our future leaders, problem solvers, and creators, and we could not think of a better cause to support. We hope this will allow educators to incorporate dynamic modeling into their curriculum without worrying about budgets. To learn how you can gain access to a site license for your school, please contact

Partner Corner

Partner Corner introduces our consulting and training partners and shares their latest news.

Waters Center for Systems Thinking

The Waters Center for Systems Thinking has begun offering an introductory System Dynamics course for graduates of their Advanced Facilitator Credential program. Participants take a very hands-on approach to modeling using Stella Professional Online, which streamlines sharing and collaboration for the online course. It's been a real joy working with isee systems to make this opportunity possible.

The Advanced Facilitator program is an intensive one-year program that teaches facilitators and coaches how to integrate systems thinking into their practices, and is one of many outreach programs the Waters Center offers to promote and support systems thinking worldwide.

Impact Dynamics

Our game at Impact Dynamics is business performance transformation through strategic change programs. This means selling to, building credibility with, and earning the trust of the C-Suite. We have recently completed seven years’ doctorial research with the University of Bristol into the true source of, and solution to, change program failure. The fundamental reason for failure boils down to a causal decoupling between the five key disciplines engaged in transformation programs: strategy, investment, implementation, performance, and management of change.

Causal stories that narrate precise quantitative linkages between program deliverables, performance drivers, and stakeholder outcomes are the solution. To achieve this, our causal models must be completely transparent, totally credible, and sufficiently agile to enable real-time what-if analysis; C-Suites have very short attention. To this end, Systems Thinking provides the mindset, System Dynamics the tool, and Stella Architect the specific functionality. As Barry Richmond, founder of isee systems, quipped, “If performance is your aim, causation must be your game.”

Whole Systems Partnership

Whole Systems Partnership, our isee systems’ UK software reseller and Partner in the UK, have completed the transfer to an Employee Ownership Trust, which means that staff in the company now have a stake in the future success of the business. WSP have a wide range of experience in systems thinking and modeling and have been using iThink/Stella for 30 years. They’re currently developing ways of encouraging the spread and adoption of system dynamics across the health and care sector in the UK. This involves online model hosting, interoperability with data sources and business intelligence dashboards, as well as supporting the development of open-source modeling approaches and creative commons approaches. James Wright, Mark Gregson and Dr. Pauline Milne MBE have become the initial directors of the Trust. James said, “I have always enjoyed being part of the WSP team and to be part of the management team only makes me more excited for the future”.

The photo shows Peter Lacey and James Wright making it formal.

Lacey and Wright

Desta Research LLP

Over the last six months, DESTA has been using participatory systems thinking and modeling to model groundwater-agriculture-climate linkages in India, partnering with CINI, Sustain+ and ACWADAM. They developed SD models of village social-ecological systems consisting of the local aquifers and cropping practices for two locations through participatory modeling with the partners and took the models to rural agricultural communities via a STELLA interface. They carried out simulation exercises with the communities to test different groundwater conservation measures for their efficacy with the objective of developing groundwater conservation protocols. In parallel, they have been soliciting inputs from farmer federations across two geographies on how climate resilience and environmental sustainability can be enhanced through CINI’s Lakhpati Kisan Program. This is part of a longer-term engagement with CINI to bring a systems lens to their program’s Theory of Change, which is now expanding its boundary of concern to endogenize climate and environmental aspects while improving farmer incomes. To know more visit or get in touch at

Participatory modeling with Desta Participatory modeling with Desta

Pontifex Consulting

The past year included several client engagements that utilized the powerful interface features of Stella. Pontifex Consulting facilitated a six-month process for a team of civic leaders from across the Atlanta region: The Atlanta Regional Collaborative for Health Improvement (ARCHI). During the process, multiple Stella models were used to capture the collaborative’s assessment of important drivers of well-being (based on the ReThink Health framework of thriving). Small groups worked in separate rooms or remotely to discuss and evaluate several attributes. These were then aggregated into a Full Team view and discussed. The final session allowed teams to select customized initiatives and simulate potential impacts over the coming decade – in pursuit of high leverage interventions. The highly interactive process moved the group’s approach from addressing urgent needs (symptom-level) to focusing on more foundational issues (work upstream).

A simulation used in ARCHI A simulation used in ARCHI

Pontifex Consulting worked with Homer Consulting to develop a C-suite level learning lab. This lab helps organizational leadership understand challenges and solutions for developing effective emissions and carbon reduction strategies, in alignment with the Paris 2.0° C agreement trajectory.

Recent Posts

Fall 2022 Issue

The isee Exchange™ improves workforce planning for England's National Health System, interviews with 2022 Barry Richmond Scholarship winner Mariana M. Torres Arroyo and customer service representative Hilary Allen, new Stories of the Month, partner news, updates to software releases, and isee systems heads to Germany...

Fall 2021 Issue

A system dynamicist optimizes global-scale sustainability models, researchers use Stella® to manage the mental health toll of COVID-19, a Stella Users Network reminder, an isee COVID-19 update, the latest Stella and isee Exchange usage numbers, and isee systems returns to the virtual road...

Spring 2021 Issue

Stella® Architect facilitates online behavioral experiments, university students use Stella to analyze complex real-world problems, a new online training course, updates to software releases, and isee systems goes on the virtual road once again...

Phone: (603) 448-4990 Email:

   Monday - Friday: 9:00 am - 5:00 pm EDT | Saturday - Sunday: Closed
24 Hanover St, Ste 8A | Lebanon, NH 03766 | US

isee systems inc. holds trademarks registered in the U.S. Patent and Trademark Office for iThink®, Stella®, isee systems® and claims the following trademarks; isee NetSim™, isee Exchange™, Stella Live™, Causal Lens™, Stella Online™, Stella Professional Online™, and Assemblies™.

Terms of Use

© 2024. isee systems inc . All rights reserved.