Monday, June 8, 2015

“Modeling in lakes”

Northeastern’s media people worked with Len Rubenstein, a very talented photographer/artist (, to make a picture of me for Northeastern’s “Making Tomorrow Happen” campaign (see link below). The idea of the picture (shown below) is to encapsulate my research, here modeling of urban water water quality to support swimming. It reminds me of when I was in graduate school working on a paper. I came up with a title that was something like “Modeling Arsenic Speciation in Lakes”. One of my collaborators told me that sounds like you are sitting in the lake with the laptop...

Wednesday, May 27, 2015

IAGLR Conference Report

I am at the IAGLR meeting in Burlington, Vermont. Yesterday, Neil made a presentation about his Lake Taihu model and on Friday I will talk about my Anabaena - nitrogen interaction model. Sahar is also here, learning about cyanobacteria in the Great Lakes for her neutral evolution model. As expected, there is a lot of talk about Lake Erie at this meeting. The lake is experiencing severe cyanobacteria blooms, which led to the shutdown of Toledo’s drinking water supply last summer. As a civil engineer, I think of this as an engineered system failing (of course the lake is natural, but we have “engineered” what we put into it). This happens in our field, a prominent example is the Tacoma Narrows Bridge, which dramatically collapsed the same year it opened. Following that failure, the structural engineering community figured out what they did wrong and changed how they design bridges. The environmental engineering community needs to engage in a similar effort now. Meeting web site:

Wednesday, May 20, 2015

Happy Birthday, Streeter and Phelps Equation

This year marks the 100th anniversary of the famous Streeter and Phelps water quality model. Unfortunately, despite incredible progress in the biological sciences, the biology in our operational water quality models has not changed much since then. In a vision paper, which just came out in ES&T (see link below), I critique the state of biology in our water quality models, and argue for updating it. I am happy that ES&T agreed to publish this paper and hope it will lead to some discussion about this important topic.
Link to paper:

Thursday, April 30, 2015

Lake Taihu Collaborators Visit

Last week we hosted Prof. Jackie Qin, Prof. Guangwei Zhu and Dr. Wei Li of the Chinese Academy of Sciences at Nanjing. We are working together on the Lake Taihu eutrophication project, which is now in its 3rd year. We had some very productive meetings talking about Taihu, and also some fun at the Beehive restaurant (see below).

Wednesday, April 22, 2015

UWM seminar visit

Last week I was at the University of Wisconsin at Milwaukee. This is a really nice place to visit, a beautiful town with a great waterfront to go for a run on. I had some very interesting discussions with researchers there. Specifically, I got to talk about the Anabaena - nitrogen interaction model we are developing. The model simulates individual cells with genes, transcripts, proteins and metabolites (see figure below). It exhibits some cool emergent behavior, like differentiating specialized N-fixing cells (heterocysts) as fixed N gets depleted. The model predicts several parameters, like nitrogenase (nifH) transcript levels and we are presently comparing the model to observations from laboratory experiments (see figure for an example, data are from Martı́n-Figueroa et al., FEBS Letters, 2000). The next step is to apply the model at the field scale. As I talk to people I always ask them if they have or know of any field data that we can use to compare the model to. The technology certainly exists, but there are only few published studies that show metatranscriptomics over time in surface waters, and none of them are really applicable to our model. So the data don’t seem to exist yet. This is an important milestone for me, because I have been working for the past 10 years to make our models catch up with observations. And now it seems we are actually ahead of them :)

Thursday, March 12, 2015

Aging in bacteria

I am please to announce the publication of our paper on aging in bacteria “From protein damage to cell aging to population fitness in E. coli: Insights from a multi-level agent-based model” in Ecological Modelling. This paper explores the fitness benefit of asymmetric damage partitioning (aging) in E. coli using an ABM. Specifically, we find that aging is beneficial, but the magnitude of the benefit is very small, so its probably a side-effect of some other process (see discussion in paper for more)We think this paper is an important contribution to understanding the role of aging in bacteria. In this post I want to do some mixing of art and science. In 2013 I attended the Congress of European Microbiologists (FEMS) in Leipzig, Germany. In his keynote address, Johan Leveau related the artwork of Ursus Wehrli (“The Art of Tidying Up”, to microbiology. I was really impressed by this and decided to apply that concept to our model to point to the role of spatial organization in aging of bacteria. 

Link to paper:

Thursday, January 1, 2015

New graduate student in my group

On Monday morning, Gunes and I welcomed a new member of our family: Mario Emre Ferdinand Hellweger. We are still a bit tired and overwhelmed, but very happy that everyone is healthy and to begin this new chapter in our lives. (This blog is for official research business only, so this guy has to be named a research assistant solely to indicate this fact.)