Researchers develop Bluetooth powered “virtual virus” to track COVID-19’s spread

April 2nd, 2021News, Research

A virtual virus spread between smartphones could help track disease transmissions in real-time Throughout the country we have seen states lifting social-distancing measures and spring breakers crowding the beaches of Miami. What is the effect that this will have on the global pandemic? With current technologies we will have to wait until it’s too late to find out. To address this challenge, researchers developed a new scientific machine learning module that could provide real-time monitoring of COVID-19 transmission through a digital “virus” which spreads between smartphones via Bluetooth. Raj Dandekar, a PhD candidate in the MIT Department of Civil and [...]


A virtual virus spread between smartphones could help track disease transmissions in real-time

Throughout the country we have seen states lifting social-distancing measures and spring breakers crowding the beaches of Miami. What is the effect that this will have on the global pandemic? With current technologies we will have to wait until it’s too late to find out. To address this challenge, researchers developed a new scientific machine learning module that could provide real-time monitoring of COVID-19 transmission through a digital “virus” which spreads between smartphones via Bluetooth.

Raj Dandekar, a PhD candidate in the MIT Department of Civil and Environmental Engineering and Christopher Rackauckas, an instructor in the Department of Mathematics along with researchers from a number of universities are tackling the challenge of mitigating disease spread to save lives with their research project, called Safe Blues.

“Safe Blues, was developed to better understand how epidemics spread among the population, says Raj Dandekar, co-author in the research. “One of the biggest challenges in managing the coronavirus pandemic has been a lack of real-time data. The data of a patient being infected and recorded as positive can be one or two weeks.”

This time delay in having real-time data hinders the ability of public health officials to monitor the current situation to predict future viral spread and governments from initiating regulatory measures to control outbreaks.

Population behavior is also changing rapidly due to pandemic fatigue and states lifting social distancing measures and mask mandates, all challenges that becomes harder for public health and government officials to observe, model, and predict where new infections might occur.

In the Safe Blues methodology, virus-like tokens are spread between mobile devices via Bluetooth, similarly to how a biological virus spreads between people. By studying how this virtual virus evolves, we can gain real-time insights into how COVID-19 is spreading through the population.

“This method could be potentially really useful because the virus moves through social networks, says Christopher Rackauckas, Applied Mathematics Instructor in the MIT Department of Mathematics. “The network connection through people’s phones is where you can start to understand the social network effects and then start to observe in real-time where people are interacting with one another and the potential clusters in certain regions.”

Safe Blues uses digital tokens (strands) that are passed between other mobile phones that come in proximity with the virtual virus only when certain data criteria are met, such as length of time and distance. “It mimics the behavior of how a biological virus spreads between people, but in a harmless and traceable way using a machine learning supported epidemiological model,” says Dandekar.

“Safe Blues is not about predicting who’s infected, it’s about predicting population statistics and when infections are going to rise to better predict what type of measures are going to be effective,” added Rackauckas.

The application has the potential to empower policy decision-making for future epidemics to save lives and minimize the economic and social effects around the world.

The researchers have developed Safe Blues into a prototype in the form of an app on Android devices, similar to existing contact tracing apps. They are in the initial stages of launching a campus wide experimental trial at the University of Auckland City Campus.

The research on the model framework is published in Patterns Cell Press journal. Safe Blues is in its early stages and being piloted for efficacy at the University of Auckland. More information about the novel approach is available on the Safe Blues website at safeblues.org

Safe Blues Bluetooth Technology

[Left] Safe Blues Concept Illustration shows individuals of the population with Safe Blues-enabled devices take part in spreading Safe Blues strands. SARS-CoV-2-infected individuals are in red and others are in green. The Safe Blues system operates independently of the health status of individuals. [Right] The Android App for the campus planned experiment

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Josephine Carstensen receives NSF CAREER award for outstanding research and education

March 25th, 2021News

The National Science Foundation (NSF) selected an MIT School of Engineering professor, who is developing new methods for sustainable design, to receive its most prestigious award for junior faculty members. Josephine Carstensen, an assistant professor in the Department of Civil and Environmental Engineering (CEE) received the 2021 Faculty Early Career Development (CAREER) Award, which supports promising early career faculty members who exemplify and serve as academic role models in research and education. The award will allow her to investigate improved structural design methods that could shift the paradigm of design and manufacturing into a single unified process. A five-year, $560,000 [...]

The National Science Foundation (NSF) selected an MIT School of Engineering professor, who is developing new methods for sustainable design, to receive its most prestigious award for junior faculty members.

Josephine Carstensen, an assistant professor in the Department of Civil and Environmental Engineering (CEE) received the 2021 Faculty Early Career Development (CAREER) Award, which supports promising early career faculty members who exemplify and serve as academic role models in research and education. The award will allow her to investigate improved structural design methods that could shift the paradigm of design and manufacturing into a single unified process.

A five-year, $560,000 grant will support her project “Integrated Design and Digital Fabrication using Topology Optimization and Material Extrusion 3D Printing.” Topology optimization is a design technique that generates new, high performing design solutions and considered a powerful design approach for Additive Manufacturing (AM). However, topology-optimized designs must be prepared by the design engineer to facilitate the production, a process that results in performance loss of the final product. Carstensen’s research aims to eliminate the pre-production process so designs are print ready. The integration of design and manufacture investigated in this project will ease the process used by design engineers and improve the performance of fabricated products.

“Carstensen’s work could have broad societal impact in many diverse fields from the sustainable design of civil structures, aerospace and automotive components, sports and other protective equipment to novel lightweight materials, and biomedical implants,” says Ali Jadbabaie, head of the MIT Department of Civil and Environmental Engineering. “I am delighted that the NSF has chosen her to receive this much-deserved CAREER Award, indicating the impact of her work at this early stage and its alignment with our department’s research on bold sustainable solutions across scales.”

Additionally, the grant will support an integrated educational program that will stimulate interest in the future of engineering design, especially among students who do not typically engage with science, technology, engineering and math (STEM). This includes the creation of K-12 STEM-based outreach initiatives for middle school art class through the MIT Edgerton Center, and courses and research engagements for undergraduate students of engineering, computer science and graduate engineering students.

“I am honored and grateful to receive the NSF CAREER award,” says Carstensen. “I’m excited for the opportunity to further integrate manufacturing and design into becoming one process and to inspire and train the next generation of design engineers to creatively approach design problems while considering manufacturing aspects of design.”

Carstensen’s laboratory top + ad is developing new rigorous methods and algorithms that can improve structural design. The group leverages new manufacturing possibilities to make structures lighter, faster, safer and is re-examining the traditional approach to structural design on scales ranging from high-rise buildings to small porous materials.

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Ralph M. Parsons Laboratory Spring 2021 Seminars Fridays 12 -1 pm, Zoom

Environmental Science Seminar Series Feb 12 – Ludmila Aristilde, Northwestern University. Host: Plata Molecular insights on organic carbon cycling dynamics in bacterial cells, soil pores, and river processes Feb 26 – Amy Hrdina, MIT. Host: Kroll The Parallel Fate and Transformation of Toxins in the Body and in the Atmosphere Mar 5 – Ramunas Stepanauskas, Bigelow Laboratory. Host: Chisholm Group With trillions of microbes out there, which one do you choose? Mar 12 – Anthony Walker, Oak Ridge National Laboratory. Host: Des Marais Quantitative cat herding: Integrating the evidence for a terrestrial carbon sink caused by increasing atmospheric CO2 Mar [...]

Environmental Science Seminar Series

Feb 12 – Ludmila Aristilde, Northwestern University. Host: Plata
Molecular insights on organic carbon cycling dynamics in bacterial cells, soil pores, and river processes

Feb 26 – Amy Hrdina, MIT. Host: Kroll
The Parallel Fate and Transformation of Toxins in the Body and in the Atmosphere

Mar 5 – Ramunas Stepanauskas, Bigelow Laboratory. Host: Chisholm Group
With trillions of microbes out there, which one do you choose?

Mar 12 – Anthony Walker, Oak Ridge National Laboratory. Host: Des Marais
Quantitative cat herding: Integrating the evidence for a terrestrial carbon sink caused by increasing atmospheric CO2

Mar 19 – Seppe Kuehn, The University of Chicago. Host: Cordero
The structure-function problem in denitrifying bacterial communities

Mar 26 – Holly Michael, University of Delaware. Host: Harvey
Is offshore fresh groundwater a resource for the future? Exploring hydrogeologic connections through the continental shelf

Apr 2 – Amy Mueller, Northeastern University. Host: Hemond
Role of multisensors and data science in optimizing operation of environmental infrastructure

Apr 9 – Maureen Coleman, The University of Chicago. Hosts: Des Marais & Chisholm
Not just bigger: the Laurentian Great Lakes as a unique microbial ecosystem

Apr 16 – Naomi Levine, University of Southern California. Host: Chisholm
Small but mighty – marine microbial dynamics and the impact on global carbon cycling

Apr 23 – Rachel O’Brien, The College of William & Mary. Host: Kroll
Photolysis of chromophores in atmospheric organic compounds: chemical transformations and photo bleaching

Apr 30 – Adam Subhas, Woods Hole Oceanographic Institution. Host: Plata
The Marine CaCO3 Cycle and its Role in CO2 Neutralization

Organized by David Des Marais and Desiree Plata. Contact  lumidi@mit.edu

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3Q with Lydia Bourouiba: How has our knowledge of the coronavirus changed since last spring

January 9th, 2021MIT Civil and Environmental Engineering

Lydia Bourouiba is an Associate Professor in the Department of Civil and Environmental Engineering at MIT, where she directs The Fluid Dynamics of Disease Transmission Laboratory. Her research and contributions in 2020 led to a newer understanding of respiratory emission dynamics and had implications for mask and respiratory design, social distancing recommendations, and other public health interventions during and after the COVID-19 pandemic. Professor Bourouiba sat down to share insights gained from her research over the past year. Q. How has our knowledge of the virus changed since last spring and what has that meant for your work? A. Many [...]


Lydia Bourouiba is an Associate Professor in the Department of Civil and Environmental Engineering at MIT, where she directs The Fluid Dynamics of Disease Transmission Laboratory. Her research and contributions in 2020 led to a newer understanding of respiratory emission dynamics and had implications for mask and respiratory design, social distancing recommendations, and other public health interventions during and after the COVID-19 pandemic. Professor Bourouiba sat down to share insights gained from her research over the past year.

Q. How has our knowledge of the virus changed since last spring and what has that meant for your work?

A. Many things changed, and some didn’t. Most of the changes we have seen in terms of our knowledge are, in part, related to the pathology and the reaction of the immune system — how the virus interacts with the body is one of the keys for patient treatment.  Another aspect is the ability to develop vaccines currently being deployed. Compared to historical precedent, this was done in a very short timescale of one year. Even with the massive effort it took to do that, we’re not really going to see the level of deployment that we would want to see for probably another year. The last important piece we have learned relates to knowledge about transmission; we now know that SARS-CoV-2 is definitely not just transmitted via large drops over short distances as was originally claimed. There is a very important component of transmission that occurs through inhalation of what remains in the air after a cough or sneeze and there are a number of questions remaining about that and the environmental conditions that promote or inhibit such routes of transmission and how much certain locations or indoor spaces enhance such routes of transmission versus others. We know that the airborne route definitely contributes significantly to transmission, but we still need more information to understand precisely how and what biophysical mechanisms are at play. So, we learned a lot but there is a lot that we still need to learn if we are serious about improving future prevention and mitigation of the spread of this pathogen.

Q. People are now being vaccinated but it will be some time before society is safe enough to return to normal. With the winter months still ahead, how can people avoid spreading coronavirus in indoor spaces with poor ventilation?

A. We still have a long road ahead of us before the vaccine covers the percentage of the population that we need in order to prevent further spread and stop the pandemic. In the meantime, indoor spaces that are poorly ventilated are a major issue and improving those situations should be of the highest priority. This could require making full infrastructure upgrades if the means are sufficient to do so, but if not, there are low-cost ways to improve natural ventilation and localized filtration systems that are more affordable. Steps should also be taken to minimize the number of individuals that occupy such indoor spaces, making sure that those who are vulnerable are not in contact with others that are highly and actively connected and interacting with many others regularly. So, essentially applying high standards of control and mitigation with respect to occupancy, face covering, air and surface hygiene, and distancing remain critical. Wearing high-grade masks is also an option for individuals that are at particularly high risk. Finally, it will be important to enable full and sufficiently homogeneous air changes in rooms with poor ventilation by opening the windows and ensuring adequate patterns of air circulation at regular intervals, even in the winter.

Q. Is there anything we can learn from this experience to avoid future outbreaks causing such global problems?

A. First, we shouldn’t repeat the pattern of past epidemics or pandemics in which within a year a resolution of the COVID-19 crisis we would see a return to completely ignoring the issue of infectious diseases and risks of epidemics and pandemics of respiratory infectious diseases in particular. We must ensure that there is more investment in monitoring and prevention in addition to massive efforts in developing vaccines. We need to think more holistically. It’s not just about vaccine development because as you can see, even with a historic level of resources, coordination, and some of the biggest pharmaceutical companies of the world coming together, we still need at least two years in the best-case scenario before an emerging pathogen that causes a serious pandemic can be tackled with a vaccine. In one sense, we were lucky with SARS-CoV-2 because another virus could have transmitted just as easily but with a much higher death rate. We are currently experiencing a bad-case scenario, but it’s not the worst-case scenario and we know that these pathogens will keep emerging. We need a strong mobilization system for early detection information-sharing worldwide so that the very early cases for such new emerging pathogens are identified and information is centralized and can be used quickly. But we also need a chain connected to that, ensuring proper investment in prevention before we even know what the pathogen can really do and to ensure that a system is in place to minimize the risk of worst-case scenarios triggered by high-frequency transmission settings that we know can occur. That’s something that I think we really need to think about from a societal standpoint, and which would have a big impact in terms of not having entire areas of the economy shut down before a vaccine is deployed, if it becomes available. Such holistic investments in early detection and prevention of transmission would have a big return on investment because the economy would simply be much more resilient, even when facing new pathogen threats.

One other piece that is really important to touch on is the need for fundamental research; often it is not obvious early on what will become important when a crisis hits. It is thus critical to fund research that sometimes does not necessarily look ready for immediate application. The type of research I do and have started years prior to this pandemic was not particularly popular in terms of funding but ultimately a lot of the insights we gained were helpful in guiding key policies and implementing mitigation strategies. So, the importance of investment in fundamental science and early vision, even when it’s not immediately applicable is critical to also keep in mind because when we face new challenges, it is often the insights from such research become or drive part of the solutions.

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Looking beyond luxury: MIT researchers eye silk as a powerful tool in the fight against climate change and global food sustainability

December 2nd, 2020Uncategorized

According to the United Nations, the world has seen a rapid, seven-fold increase to the global population, leading to an important question in our quest to address human impact on climate change: how can we continue to feed everyone without devastating our natural resources? In the United States alone, the U.S. Department of Agriculture estimates that about 13.7 million households experienced food insecurity in 2019. Benedetto Marelli, a professor of Civil and Environmental Engineering at MIT, is willing to bet on an unusual source to help tackle these challenges around food insecurity and sustainability: silk. “We are wasting 30 to [...]


According to the United Nations, the world has seen a rapid, seven-fold increase to the global population, leading to an important question in our quest to address human impact on climate change: how can we continue to feed everyone without devastating our natural resources? In the United States alone, the U.S. Department of Agriculture estimates that about 13.7 million households experienced food insecurity in 2019. Benedetto Marelli, a professor of Civil and Environmental Engineering at MIT, is willing to bet on an unusual source to help tackle these challenges around food insecurity and sustainability: silk.

“We are wasting 30 to 40 percent of the food we are producing which means we are wasting 25 percent of the freshwater that the entire world consumes. Food waste is the third CO2 generator in the world behind China and the United States, so it has a big impact.” says Marelli. “On top of that, we are wasting food that can feed 1.6 billion people while 800 million people suffer from food insecurity – in the U.S. almost 10 percent of the population.”

Marelli studies the properties of silk to understand how the material can be optimized to improve the way food is packaged and stored in the hope of reducing waste. He is the cofounder Mori, Inc – previously Cambridge Crops – a company working to design silk-based products to extend the shelf life of perishable food, such as meat and produce . Marelli also recently unveiled a sensor using silk microneedles, designed to identify consumers when a product has gone bad, reducing the need for guessing that can lead to products being thrown out before they’ve spoiled.

Silk is a versatile natural byproduct harvested from silkworms made for their cocoons. Humans have coveted the material’s luxurious textile properties for centuries, but it only recently has silk has garnered interest as a preservative. Since silk is nontoxic to humans, it can be packaged with or even placed into food consumed by humans, but more importantly, like with a silkworm in a cocoon, silk actually works to keep pathogens out, protecting food from disease-causing microbes.

“Silk acts like a barrier for microbial spoilage, when you think about the cocoon, that’s what it does – it protects the silkworm from the environment,” says Marelli. “One of the problems we face is not only food security but food safety, especially food that has pathogens inside. Right now, you have several thousands of people in the United States die each year from food borne pathogens.”

In addition to the potential direct benefit for U.S. and global consumers, Marelli envisions silk as a cash crop that farmers can tap into for a regular source of income, while also helping to reduce the amount of food wasted each year. Because of the extremely short stage of the silkworm – 28 days from egg hatched to cocooning – harvesting the silk would allow farmers to count on a consistent monthly wage. Additionally, the mulberry tree that silkworms prefer for the environment to make their cocoons are relatively low-maintenance and do not require a lot of additional resources to grow, provided the right climate conditions.

“It is important to find solutions that can minimize the amount of inputs that we’re putting in agriculture and food production. At the moment we are using too much fertilizer, pesticides, too much water, so we need to be able to develop new agricultural practices, and inform the growers who are already doing a lot of work to modernize themselves,” says Marelli. “We need to provide them with simple tools which help them minimize the amount of inputs, which is also good for them because their costs decrease.”

Reducing our reliance on crops that require huge investments of resources to grow them isn’t just good for farmers living in traditional areas either  it opens up a new realm of opportunity where and when crops can be grown, which would shift the paradigm in how we currently think about farming in general. New techniques such as vertical farming and other alternative farming methods are becoming more common, charting a path forward for shifting production from land to cities as we move towards soilless agriculture. But for Marelli, sustainability is key metric to consider in any forward-thinking agricultural process, and this mindset continues to inform his approach to design and refine his silk technologies.

“When it comes to regenerating silk to make coatings, that is where we need to be sure that the process, we develop can be made sustainable at scale, not just in the lab,” says Marelli. “No matter what, sustainability needs to be part of the process.”

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Projecting climate change impact on malaria transmission in Africa

November 30th, 2020Uncategorized

For Elfatih Eltahir, malaria symptoms always began the same way: chills that eventually gave way to high fever, a pounding headache, and nausea that persisted until this cycle finally broke days later. First encountered at a young age and again throughout his college years, Eltahir, now a Professor of Civil and Environmental Engineering at MIT, only had about two weeks until symptoms would return to sideline him again. “This pattern became my norm to the extent that I stopped checking with doctors first, and often chose to go directly to the nearest lab to check for evidence of malaria in [...]


For Elfatih Eltahir, malaria symptoms always began the same way: chills that eventually gave way to high fever, a pounding headache, and nausea that persisted until this cycle finally broke days later. First encountered at a young age and again throughout his college years, Eltahir, now a Professor of Civil and Environmental Engineering at MIT, only had about two weeks until symptoms would return to sideline him again.

“This pattern became my norm to the extent that I stopped checking with doctors first, and often chose to go directly to the nearest lab to check for evidence of malaria in my blood,” says Eltahir. “From there, I would stop by a pharmacy to buy chloroquine injections and bring them home to my sister who is a doctor, to ask her for help performing the injections.”

Growing up in Africa and attending university in Khartoum, capital of Sudan, malaria was a shadow that loomed large over everyday life like most cities in that region. This formative early life experience ultimately shaped Eltahir’s decision to study the environmental determinants of malaria for much of his career. In his new book, Projecting the Impacts of Climate Change on Malaria Transmission in Africa, Eltahir combines his personal experience contracting and treating the disease with his work, using it as an example to better understand the nexus of climate change, health, and poverty in Africa.

“Using rigorous field research and advanced disease transmission modeling, we were able to understand how climate change will impact this disease, which is one of the major public health challenges in Africa, and we were able to identify which regions of the continent are going to be more impacted by the hazards from increased transmission of malaria,” says Eltahir. “When you think of disease impact, you have to think socioeconomic status too – poverty.”

The book, coauthored by former graduate students in Eltahir’s Research Group: Arne Bomblies, now Assistant Professor of Civil and Environmental Engineering at the University of Vermont, and Teresa K. Yamana, an associate research scientist at Columbia University, and Noriko Endo, Product Manager at Biobot Analytics, summarizes the results of their research, representing the culmination of nearly two decades of work. Mosquitoes carrying malaria thrive in wet, warm temperature that is not too hot. Using custom made computer models, Eltahir’s group predicted that in Western Africa, climate change may keep environmental potential for malaria transmission the same or slightly hurt mosquito populations as temperatures rise. But in parts of Eastern Africa where the climate is more temperate, impacts of climate change could lead to a rise in the ideal conditions for mosquitoes carrying the disease.

“Bands of warmer temperature are likely to creep up into the highlands of Ethiopia, pushing it into the sweet spot for mosquito breeding,” says Eltahir, who predicts that low-income residents of the area will be disproportionately affected by the disease. “Now, when people think of the main challenge of our times, which is climate change, there is more interest in the nexus of climate change, health and poverty. This is a big topic now, but something we started looking at fifteen years ago.”

For Eltahir, it is important not only for scientists to talk about the global effects of climate change, but also to illustrate how people will see those changes occur at regional and local scales, and most importantly, what concrete steps can be taken to mitigate the harmful effects of climate change.

“The main reason for writing this book, and doing the research, is to inform society of these impacts, and hopefully that would motivate effective adaption policies to climate change.”

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