Hi Everyone:
Just a brief note today. Last month I was at Columbia U for a seminar visit. It was nice to see some old friends, including my PhD advisor Manu Lall. Earlier this month a group of faculty from Northeastern went over to CDM Smith (http://cdmsmith.com/) to learn about each others work and explore possibilities for collaborations. Its always good to get a reality check of what the “real” problems are faced by practicing engineers and scientists.
Now (Tuesday) I am off to Turkey, where I will be for a month on a mix of personal and business things. I will give a research seminar at Middle East Technical University [Orta Doğu Teknik Universitesi (ODTÜ) in Turkish], the top technical university in Turkey. After that I have quite a busy summer, including a workshop in Edinburgh, a meeting in Ann Arbor, the FEMS conference in Leipzig, and then to China for project meetings and an IWA conference. Here are some links for these:
http://www2.ph.ed.ac.uk/~rallen2/epsrcworkshop.html
http://www.mewe2013.org/
http://www2.kenes.com/fems2013/pages/home.aspx
http://dipcon.rcees.ac.cn/
Maybe we will meet in one of these places!
Güle Güle ("bye bye" in Turkish)
Ferdi
Sunday, May 12, 2013
Sunday, April 14, 2013
Capstone Final Presentations & Columbia Seminar & Freeman Lecture
Hi again,
It’s that time of year again... Capstones! Please join us for the 2013 Environmental Capstone student presentations. This year, the course is focusing on nonpoint source phosphorus inputs to the Charles River - one of the most important contemporary problems in the Boston area (and worldwide). Four Capstone teams have been working with communities (Boston, Brookline, Cambridge and Newton) and professional mentors (from CDM Smith, Kleinfelder, CRWA and MWH) to design site-specific, tailored solutions. Please join us and learn about the solutions they came up with. A flyer with more details is posted here: https://www.dropbox.com/s/jr1l77tusfp8thg/EnvCapstone2013.pdf
On April 26 I will be at Columbia University for a seminar visit. If you are in the area and interested in learning more about my work, please come. Here is the advertisement:
https://www.dropbox.com/s/u4ppxc9t0uvv9w4/Hellweger%204-26.pdf
Finally, I would like to invite you to the 2013 Freeman Lecture, which this year focuses on hurricane barrier design (motived by Hurricane Sandy). The details are below.
Best regards,
Ferdi
2013 John R. Freeman Lecture
Hurricane Storm Barrier Design and Operation
Presenters:
Lawrence J. Murphy, P.E.
CDM Smith/New York, NY
Michael Bachand, P.E.
USACE
Around the world numerous hurricane or storm surge barriers have been
constructed to protect areas deemed to be critical. With the recent impacts to the
Northeast United States from Hurricane Sandy and to a lesser extent Hurricane Irene
which made landfall a year earlier, concepts for providing flood protection to storm
prone areas have been a national focus. This lecture will present a concept design of
a barrier to protect a portion of Lower Manhattan, as well as provide information on
the operation of two storm barriers that currently exist in the northeast. Various
types of barricades utilized around the world and their effectiveness will also be
presented.
DATE: Thursday, April 18th, 2013
TIME: Reception: 6 p.m./ Lecture: 7 p.m.
LOCATION: MIT’s Tang Center (E51)
70 Memorial Drive
Cambridge, MA 02139
It’s that time of year again... Capstones! Please join us for the 2013 Environmental Capstone student presentations. This year, the course is focusing on nonpoint source phosphorus inputs to the Charles River - one of the most important contemporary problems in the Boston area (and worldwide). Four Capstone teams have been working with communities (Boston, Brookline, Cambridge and Newton) and professional mentors (from CDM Smith, Kleinfelder, CRWA and MWH) to design site-specific, tailored solutions. Please join us and learn about the solutions they came up with. A flyer with more details is posted here: https://www.dropbox.com/s/jr1l77tusfp8thg/EnvCapstone2013.pdf
On April 26 I will be at Columbia University for a seminar visit. If you are in the area and interested in learning more about my work, please come. Here is the advertisement:
https://www.dropbox.com/s/u4ppxc9t0uvv9w4/Hellweger%204-26.pdf
Finally, I would like to invite you to the 2013 Freeman Lecture, which this year focuses on hurricane barrier design (motived by Hurricane Sandy). The details are below.
Best regards,
Ferdi
2013 John R. Freeman Lecture
Hurricane Storm Barrier Design and Operation
Presenters:
Lawrence J. Murphy, P.E.
CDM Smith/New York, NY
Michael Bachand, P.E.
USACE
Around the world numerous hurricane or storm surge barriers have been
constructed to protect areas deemed to be critical. With the recent impacts to the
Northeast United States from Hurricane Sandy and to a lesser extent Hurricane Irene
which made landfall a year earlier, concepts for providing flood protection to storm
prone areas have been a national focus. This lecture will present a concept design of
a barrier to protect a portion of Lower Manhattan, as well as provide information on
the operation of two storm barriers that currently exist in the northeast. Various
types of barricades utilized around the world and their effectiveness will also be
presented.
DATE: Thursday, April 18th, 2013
TIME: Reception: 6 p.m./ Lecture: 7 p.m.
LOCATION: MIT’s Tang Center (E51)
70 Memorial Drive
Cambridge, MA 02139
Friday, March 15, 2013
DIMENSIONS Project Kick-Off
Hi Everyone:
Earlier this month I was in Morehead City at the UNC Institute of Marine Sciences for the kick-off meeting for our project on cyanobacteria in Lake Taihu (see my September 2012 post). It was a very productive visit. From a modeler’s perspective this project is exciting because it includes a lot of relevant and exciting observations not commonly available (e.g., ammonia regeneration, nifH gene expression, 14/15N isotope tracing, etc.). These will be a challenge to integrate in the model, but that is the fun part. It is also exciting to work on such an important problem, affecting the drinking water of millions of people. Here is a picture (from Paerl et al., 2011):
This project will keep us busy for a while!
Besides that, chairing a faculty search and teaching two classes is keeping me pretty busy this semester...
Best regards,
Ferdi
Earlier this month I was in Morehead City at the UNC Institute of Marine Sciences for the kick-off meeting for our project on cyanobacteria in Lake Taihu (see my September 2012 post). It was a very productive visit. From a modeler’s perspective this project is exciting because it includes a lot of relevant and exciting observations not commonly available (e.g., ammonia regeneration, nifH gene expression, 14/15N isotope tracing, etc.). These will be a challenge to integrate in the model, but that is the fun part. It is also exciting to work on such an important problem, affecting the drinking water of millions of people. Here is a picture (from Paerl et al., 2011):
This project will keep us busy for a while!
Besides that, chairing a faculty search and teaching two classes is keeping me pretty busy this semester...
Best regards,
Ferdi
Saturday, February 16, 2013
Bigelow Visit & ASLO Talk & Charles River Workshop
Hello Friends,
Last week I was at the Bigelow Lab (http://www.bigelow.org/) for a seminar. My visit was hosted by Ben Twining and Ramunas Stepanauskas. I really enjoyed the visit. One thing that stuck with me is the single cell genomics work Ramunas is doing. It turns out that cells of the same species (judged by 16S rRNA similarity) and from the same drop of water, typically (actually, apparently always) have different DNA. I always thought they would be the same, except for a rare mutation here and there. So are microbes as different as people? Have to do some more thinking about this... but - of course - as an individual-based modeler, I see a lot of opportunity for using IBMs here. “Single cell genomics is to metagenomics what individual-based modeling is to population-level modeling”?
Visit our presentations at ASLO! Neil Fredrick will present a talk entitled “EXPLORING MECHANISMS OF P CONTENT HETEROGENEITY IN CULTURED PHYTOPLANKTON USING AGENT-BASED MODELING” in session GS08A Plankton Ecology - Phytoplankton on Feb. 19. Here is a link: http://www.sgmeet.com/aslo/neworleans2013/viewabstract2.asp?AbstractID=10781
And John Berges will present “DIVERSE CAUSES OF CELL DEATH IN PHYTOPLANKTON IN SMALL FRESHWATER ECOSYSTEMS” in session SS79 Phytoplankton interactions in aquatic ecosystems. Here is a link:
http://www.sgmeet.com/aslo/neworleans2013/viewabstract2.asp?AbstractID=11365
We had our 3rd Charles River Water Quality Workshop last week, which was attended by 30 people. This is an annual event where we bring together people doing research on the river and share results in an informal setting. The agenda and presentation slides are available online here:
http://thecharles.org/2013WaterQualityWorkshopPresentations.html
Best regards,
Ferdi
Last week I was at the Bigelow Lab (http://www.bigelow.org/) for a seminar. My visit was hosted by Ben Twining and Ramunas Stepanauskas. I really enjoyed the visit. One thing that stuck with me is the single cell genomics work Ramunas is doing. It turns out that cells of the same species (judged by 16S rRNA similarity) and from the same drop of water, typically (actually, apparently always) have different DNA. I always thought they would be the same, except for a rare mutation here and there. So are microbes as different as people? Have to do some more thinking about this... but - of course - as an individual-based modeler, I see a lot of opportunity for using IBMs here. “Single cell genomics is to metagenomics what individual-based modeling is to population-level modeling”?
Visit our presentations at ASLO! Neil Fredrick will present a talk entitled “EXPLORING MECHANISMS OF P CONTENT HETEROGENEITY IN CULTURED PHYTOPLANKTON USING AGENT-BASED MODELING” in session GS08A Plankton Ecology - Phytoplankton on Feb. 19. Here is a link: http://www.sgmeet.com/aslo/neworleans2013/viewabstract2.asp?AbstractID=10781
And John Berges will present “DIVERSE CAUSES OF CELL DEATH IN PHYTOPLANKTON IN SMALL FRESHWATER ECOSYSTEMS” in session SS79 Phytoplankton interactions in aquatic ecosystems. Here is a link:
http://www.sgmeet.com/aslo/neworleans2013/viewabstract2.asp?AbstractID=11365
We had our 3rd Charles River Water Quality Workshop last week, which was attended by 30 people. This is an annual event where we bring together people doing research on the river and share results in an informal setting. The agenda and presentation slides are available online here:
http://thecharles.org/2013WaterQualityWorkshopPresentations.html
Best regards,
Ferdi
Friday, January 11, 2013
Happy New Year, Water Management on Steroids & Spring Semester Starts & Charles River Workshop
Hello Everyone:
First: Happy New Year!
Second: The news:
As mentioned in last month’s blog, I was in Israel as part of a delegation focusing on water technologies. The trip was very interesting and productive. I found water management in Israel quite fascinating. The country has experienced so many different phases including mostly dry land, water transfer/distribution, conservation, wastewater reuse and now desalination. One problem motivating the use of desalination is the concern over hormones in the wastewater (e.g., reduced sperm count and motility in males). Each of these phases are very strong, and I would characterize it as “water management on steroids”. I also had the opportunity to meet with other researchers at Technion, which may lead to some interesting collaborations. Here is a picture of me and my colleague, Auroop Ganguly at the Hadera Desalination Plant:
The Spring Semester is starting. I am teaching two classes. (1) The environmental section of the senior design capstone class. This year we are focusing on “community-scale solutions for reducing phosphorus inputs to the Charles River”. (2) The surface water quality modeling graduate class.
On behalf of the Charles River Conservancy (CRC) and the Civil & Environmental Engineering Department at Northeastern University (NU), I would like to invite you you to attend the Third Annual Charles River Water Quality Workshop on February 5, 2013 from 8 AM - Noon at NU. Charles River Water Quality Workshops were held in 2010 and 2011 and, similar to previous years, this workshop will focus on sharing water quality data gathered by a variety of skateholders, including US EPA Region 1, the Massachusetts Department of Public Health, and Charles River Watershed Association, and others during the 2012 season. Following the presentations, there will be time for a broader group discussion on work and experiences during 2012 and plans for the coming year.
Below is additional meeting information. Please RSVP by January 30th (see RSVP info below).
Location: Northeastern University Snell Library Room 90SL
Date and Time: February 5, 2013 | 8 AM - Noon
Directions: http://library.northeastern.edu/about/maps-and-directions
RSVP: Please RSVP by email to to patricia@thecharles.org. Be sure to include your name, title/position, organization, and phone number in your email.
Best regards,
Ferdi
First: Happy New Year!
Second: The news:
As mentioned in last month’s blog, I was in Israel as part of a delegation focusing on water technologies. The trip was very interesting and productive. I found water management in Israel quite fascinating. The country has experienced so many different phases including mostly dry land, water transfer/distribution, conservation, wastewater reuse and now desalination. One problem motivating the use of desalination is the concern over hormones in the wastewater (e.g., reduced sperm count and motility in males). Each of these phases are very strong, and I would characterize it as “water management on steroids”. I also had the opportunity to meet with other researchers at Technion, which may lead to some interesting collaborations. Here is a picture of me and my colleague, Auroop Ganguly at the Hadera Desalination Plant:
The Spring Semester is starting. I am teaching two classes. (1) The environmental section of the senior design capstone class. This year we are focusing on “community-scale solutions for reducing phosphorus inputs to the Charles River”. (2) The surface water quality modeling graduate class.
On behalf of the Charles River Conservancy (CRC) and the Civil & Environmental Engineering Department at Northeastern University (NU), I would like to invite you you to attend the Third Annual Charles River Water Quality Workshop on February 5, 2013 from 8 AM - Noon at NU. Charles River Water Quality Workshops were held in 2010 and 2011 and, similar to previous years, this workshop will focus on sharing water quality data gathered by a variety of skateholders, including US EPA Region 1, the Massachusetts Department of Public Health, and Charles River Watershed Association, and others during the 2012 season. Following the presentations, there will be time for a broader group discussion on work and experiences during 2012 and plans for the coming year.
Below is additional meeting information. Please RSVP by January 30th (see RSVP info below).
Location: Northeastern University Snell Library Room 90SL
Date and Time: February 5, 2013 | 8 AM - Noon
Directions: http://library.northeastern.edu/about/maps-and-directions
RSVP: Please RSVP by email to to patricia@thecharles.org. Be sure to include your name, title/position, organization, and phone number in your email.
Best regards,
Ferdi
Friday, December 14, 2012
Off to Israel & Geosyntec Seminar
Hi Everyone:
Ok, so I am off to Israel today. I am part of a delegation of about 50 people that are traveling as part of the “Massachusetts Water Innovation Mission to Israel”. We will visit some of the water infrastructure and meet with professionals and academics. I hope to learn more about water resources in this stressed region, and also make some connections for future research collaborations. If you want to learn more about this trip, you can read this article in Xconomy: http://goo.gl/ahpCZ.
I also presented a research seminar at Geosyntec Consultants, an environmental engineering and science company: http://www.geosyntec.com/UI/Default.aspx
I gave an overview of my research program and talked about a recent project looking at intraspecific nutrient heterogeneity. You can get my slides from here: https://www.dropbox.com/sh/81tv7ozuyu6a05x/oidkXVDlVg/2012/Geosyntec_Charles_Quota_Heterogeneity.pptx
Best regards,
Ferdi
Ok, so I am off to Israel today. I am part of a delegation of about 50 people that are traveling as part of the “Massachusetts Water Innovation Mission to Israel”. We will visit some of the water infrastructure and meet with professionals and academics. I hope to learn more about water resources in this stressed region, and also make some connections for future research collaborations. If you want to learn more about this trip, you can read this article in Xconomy: http://goo.gl/ahpCZ.
I also presented a research seminar at Geosyntec Consultants, an environmental engineering and science company: http://www.geosyntec.com/UI/Default.aspx
I gave an overview of my research program and talked about a recent project looking at intraspecific nutrient heterogeneity. You can get my slides from here: https://www.dropbox.com/sh/81tv7ozuyu6a05x/oidkXVDlVg/2012/Geosyntec_Charles_Quota_Heterogeneity.pptx
Best regards,
Ferdi
Thursday, November 15, 2012
New paper: 3rd in the “in silico series”
Hello People!
I am excited to announce the paper “Escherichia coli adapts to tetracycline resistance plasmid (pBR322) by mutating endogenous potassium transport: in silico hypothesis testing” to be published in FEMS Microbiology Ecology.http://onlinelibrary.wiley.com/doi/10.1111/1574-6941.12019/abstract
This is the third paper in my “in silico series”. The other two papers in the series are:
Carrying photosynthesis genes increases ecological fitness of cyanophage in silicohttp://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2009.01866.x/full
and
Resonating circadian clocks enhance fitness in cyanobacteria in silicohttp://www.sciencedirect.com/science/article/pii/S0304380010001602
Take a quick look at the model schematic in each paper (below). I think they nicely capture the spirit of the series. Specifically, all show cells with intracellular mechanisms (resolved down to the level of individual genes) [systems biology] and populations made up of individual cells [systems ecology]. This approach [systems bioecology] explicitly investigates the role of genes in the fitness of microbes.
Prochlorococcus model:
E. coli model:
For this paper, you may also like ...
… the source code:https://www.dropbox.com/sh/mgj7glkfgohljxg/9f73m3eldl
… the movie:http://youtu.be/Dt0-YEMtTiA
… the poster:https://www.dropbox.com/sh/81tv7ozuyu6a05x/7Vfkk1l2nS/2012/ISME_Tetracycline_Resistance.pdf
The fourth paper planned for the series is the yeast bet hedging one I am presently developing.
Do you have any interesting problems that can be investigated with this approach? I am always interested in talking and collaborating. Drop me a line!
Best regards,
Ferdi
I am excited to announce the paper “Escherichia coli adapts to tetracycline resistance plasmid (pBR322) by mutating endogenous potassium transport: in silico hypothesis testing” to be published in FEMS Microbiology Ecology.http://onlinelibrary.wiley.com/doi/10.1111/1574-6941.12019/abstract
This is the third paper in my “in silico series”. The other two papers in the series are:
Carrying photosynthesis genes increases ecological fitness of cyanophage in silicohttp://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2009.01866.x/full
and
Resonating circadian clocks enhance fitness in cyanobacteria in silicohttp://www.sciencedirect.com/science/article/pii/S0304380010001602
Take a quick look at the model schematic in each paper (below). I think they nicely capture the spirit of the series. Specifically, all show cells with intracellular mechanisms (resolved down to the level of individual genes) [systems biology] and populations made up of individual cells [systems ecology]. This approach [systems bioecology] explicitly investigates the role of genes in the fitness of microbes.
Prochlorococcus model:
Synechococcus model: 
E. coli model:
For this paper, you may also like ...
… the source code:https://www.dropbox.com/sh/mgj7glkfgohljxg/9f73m3eldl
… the movie:http://youtu.be/Dt0-YEMtTiA
… the poster:https://www.dropbox.com/sh/81tv7ozuyu6a05x/7Vfkk1l2nS/2012/ISME_Tetracycline_Resistance.pdf
The fourth paper planned for the series is the yeast bet hedging one I am presently developing.
Do you have any interesting problems that can be investigated with this approach? I am always interested in talking and collaborating. Drop me a line!
Best regards,
Ferdi
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