News

Jan 20
0

New powerful computational framework will help understand aggressive behaviors of cancer cells

By | Feature, Research

Cancer is an illness caused by an uncontrolled division of transformed cells, which can originate in almost  any organ of the body.  Cancer is not a single disease, even when it arises in the same site of the body. Tremendous variability exists in progression of disease and response to therapy among different persons with the same general type of cancer, such as breast cancer. Even at the level of a single person, cancer cells show tremendous heterogeneity within a single tumor and among a primary tumor and metastases. This heterogeneity causes drug resistance and fatal disease. The prevailing dogma is that heterogeneity among cancer cells arises randomly, generating greedy individual cancer cells that compete for growth factors and optimal environments. The rare “winners” in this competition survive and metastasize. However, tumors consistently maintain heterogeneous subpopulations of cancer cells, some of which appear less able to grow and spread. This observation prompted Gary and Kathy Luker, cancer cell biologists at the University of Michigan, to hypothesize that cancer cells may actually collaborate under some circumstances to cause disease and not just compete. The idea that single, heterogeneous cancer cells work collectively within a constrained range of variability to drive population-level outputs in tumor progression is a ground-breaking concept that may revolutionize how we approach cancer biology and therapy.

The team is using innovative approaches to extract and merge data streams from models that generate heterogeneous cell behaviors

...cancer cell biologists have teamed up with computational scientists and experts in artificial intelligence to focus the power of these fields on understanding and overcoming heterogeneity in cancer.

To understand causes of single-cell heterogeneity in cancer and conditions that motivate cancer cells to collaborate, an interdisciplinary team of scientists at UM formulated an entirely new conceptual approach to this challenging problem. The cancer cell biologists have teamed up with computational scientists and experts in artificial intelligence to focus the power of these fields on understanding and overcoming heterogeneity in cancer. Building on large, single-cell data sets unique to the team, they will combine inverse reinforcement learning, an artificial intelligence method typically applied to discover motivations for human behaviors, with computational models inferred on the basis of the physics and chemistry of cell signaling and migration. They have proposed an entirely new conceptual approach combining single cell data, physics-based modeling and artificial intelligence to single-cell heterogeneity and intercellular interactions. By discovering  testable molecular processes underlying “decision-making” by single cells and their “motivations” for acting competitively or collaboratively, this research blazes a new path to understand and treat cancer. Their high-risk, high-reward approach to understand how each cell in a population processes information and translates that to action driving cancer progression, has attracted an award of $1 million dollars by the Keck Foundation. 

The team includes Gary Luker (Radiology, Microbiology and Immunology; Biomedical Engineering), and Kathryn Luker (Radiology), who are leading the experimental studies of cell signaling and migration; Jennifer Linderman (Chemical Engineering; Biomedical Engineering); and Krishna Garikipati (Mechanical Engineering; Mathematics), who are leading the machine learning and modeling side of the project. Nikola Banovic (Electrical Engineering and Computer Science) and Xun Huan (Mechanical Engineering) are using artificial intelligence approaches to discover decision-making policies and rewards for cancer cells, working with the rest of the investigators to incorporate experimental data and physics/chemistry-based models into their approaches.

The Keck Foundation research program seeks to benefit humanity by supporting projects in medical research, science and engineering. This project combines all of these research areas to tackle cancer in a new way. The idea for this project originated in the 2020 MICDE faculty workshop in AI for Physically based Bio-medicine Workshop. The workshop brought together an interdisciplinary group of faculty members to discuss ways to advance artificial intelligence and machine learning methods for biomedical problems. After seeding the idea, a subset of these researchers were awarded an MICDE catalyst grant and a MIDAS PODS grant. These funds were used to establish the proof of concept and to generate preliminary results. 

Computational science is becoming increasingly indispensable in many areas of biomedical science. While the current proposal focuses on cancer, this innovative computational framework represents a transformative leap with widespread applications in multiple other biomedical, physical, and social sciences. MICDE supports innovative and interdisciplinary projects aiming to advance the current paradigms.

Portraits of Kathryn Luker, Gary Luker, Krishna Garikipati, Jennifer Linderman, Nikola Banovic and Xun Huan

Project’s principal investigators (left to right): Kathryn Luker (Radiology), Gary Luker (Radiology, Microbiology and Immonology, and Biomedical Engineering), Krishna Garikipati (Mechanical Engineering, and Mathematics), Jennifer Linderman (Chemical Engineering, and Mathematics), Nikola Banovic (Electrical Engineering and Computer Science) and Xun Huan (Mechanical Engineering).

Sep 24
0

“Get non-Real”: Department of Energy grant funds novel research in High-Performance Algorithms at U-M

By | Feature, Research

“Preparing for the future means that we must continue to invest in the development of next-generation algorithms for scientific computing,”

Barbara Helland, Associate Director for Advanced Scientific Computing Research, DOE Office of Science
Source: www.energy.gov/science/articles/department-energy-invests-28-million-novel-research-high-performance-algorithms

New research from the University of Michigan will help revolutionize the data processing pipeline with state-of-the-art algorithms to optimize the collection and processing of any kind of data. Algorithms available now are built for real data, meaning real numbers, however, most of the data we see on the internet is non-real, like discrete data, or categorical. This project is part of a $2.8 million grant from the Department of Energy on algorithms research, which is the backbone of predictive modeling and simulation. The research will enable DOE to set new frontiers in physics, chemistry, biology, and other domains. 

“Preparing for the future means that we must continue to invest in the development of next-generation algorithms for scientific computing,” said Barbara Helland, Associate Director for Advanced Scientific Computing Research, DOE Office of Science. “Foundational research in algorithms is essential for ensuring their efficiency and reliability in meeting the emerging scientific needs of the DOE and the United States.”

The U-M project, led by associate professor Laura Balzano and assistant professor Hessam Mahdavifar, both of electrical engineering and computer science, is one of six chosen by DOE to cover several topics at the leading-edge of algorithms research. According to the DOE, researchers will explore algorithms for analyzing data from biology, energy storage, and other applications. They will develop fast and efficient algorithms as building blocks for tackling increasingly large data analysis problems from scientific measurements, simulations, and experiments. Projects will also address challenges in solving large-scale computational fluid dynamics and related problems.

Laura Balzano and Hessam Mahdavifar portraits

Laura Balzano, associate professor of electrical engineering and computer science (left); Hessam Mahdavifar assistant professor of electrical engineering and computer science (right)

Balzano and Mahdavifar, both Michigan Institute for Computational Discovery and Engineering (MICDE) affiliated faculty members, will use a $300,000 portion of the overall grant to study randomized sketching and compression for high-dimensional non-real-valued data with low-dimensional structures.

“Randomized sketching and subsampling algorithms are revolutionizing the data processing pipeline by allowing significant compression of redundant information,” said Balzano. “Sketches work well because scientific data are generally highly redundant in nature, often following a perturbed low-dimensional structure. Hence, low-rank models and sketching that preserves those model structures are ubiquitous in many machine learning and signal processing applications.” 

Even though a lot of the data used and processed in scientific and technological applications are best modeled mathematically as discrete, categorical or ordinal data, most state-of-the art randomized sketching algorithms focus on real-valued data. To add to this, in practical applications, treating high-dimensional data can be challenging in terms of computational and memory demands. Thus, the proposed project will significantly expand the applicability of randomized sketching.

“A key to data-driven modeling is to carefully reformulate the computational and data analysis challenges and take full advantage of the underlying mathematical structure that is often common across application areas,” said Krishna Garikipati, MICDE director and professor of mechanical engineering and mathematics.”This research and the work that Laura and Hessam are doing is critically important to the advancement of computational discovery.”

Aug 20
0

MICDE catalyst grant leads to new NSF funding to study cascade “ecohydromics” in the Amazonian headwater system

By | Feature, News, Research

The Amazon Basin cycles more water through streamflow and evaporation than any other contiguous forest in the world, and transpiration by trees is a critical part of this cycle. Understanding how plant roots, stems, and leaves interact with soil water to regulate forest transpiration across landscapes is a critical knowledge gap, especially as climate changes. Professor Valeriy Ivanov, from the Department of Civil and Environmental Engineering at U-M, is the lead investigator in a newly NSF funded project that links diverse disciplines – plant ecophysiology, ecology, and hydrology – and will build a unique modeling framework to characterize landscape variation in physiological and hydrological processes in the Amazon Basin. The framework will integrate a wide array of field observations with detailed watershed modeling for hypothesis testing. The team includes Tyeen Taylor, research fellow also from the Civil and Environmental Engineering Department at U-M, and many collaborators in the U.S. at the University of Arizona, University of West Virginia, University of Nebraska, as well as Brazilian researchers at the Federal University of Eastern Para, and Federal University of Amazonas, National Institute for Amazonian Research, and Eastern Amazon Agricultural Agency. Detailed, physical models of ecophysiology and above- and below-ground hydrology will be informed by observations of leaf physiology, tree morphological traits, soil moisture, groundwater, and streamflow. Data and models will be integrated employing novel tools in probabilistic learning and uncertainty quantification. The computational framework tools to be used in this project were developed in part with the support from MICDE Catalyst grant program for the 2018 project “Urban Flood Modeling at “Human Action” Scale: Harnessing the Power of Reduced-Order Approaches and Uncertainty Quantification” led by Prof. Ivanov. 

Given (a) a mechanistic model M (e.g., a stomatal conductance model), (b) one can treat its inputs 𝛏 (e.g., parameters) as random variables. These inputs are sampled and model simulations are carried out. Using (c) PCEs, we construct a surrogate model that best approximates the model output – left-hand-side of (c). The surrogate is then evaluated with Monte Carlo simulations and used for (d) parameter inference. (d.1) is the flow of outputs from the surrogate model into a likelihood function L (D | 𝛏) to compare the surrogate model output and observed data D. This inference produces the posterior distribution for 𝛏. This pdf can then be sent back to the surrogate in (d.2) to reduce the uncertainty in the inputs and to obtain pdf for a quantity of interest (e).

“The reduced-ordered modeling approach developed during the MICDE Catalyst grant project is a key element of the new project,” said Prof. Ivanov, “the MICDE seed funding has allowed us to build a general framework that is applicable to a wide range of computational applications in earth-system science, and thus made our project proposal more competitive”.

The MICDE Catalyst Grants program funds projects that have the potential to catalyze and reorient the directions of their research fields by developing and harnessing powerful paradigms of computational science. This new NSF project is an example of the reach of the program.

Read more.

Aug 16
0

We welcome 20 students to the 2021-22 class of MICDE graduate fellows

By | Feature, News

MICDE is proud to announce the recipients of the 2021 MICDE graduate fellowships. The fellows’ research projects involve the use and advancement of scientific computing techniques and practices. “This year, MICDE awarded fellowships in a wide array of disciplines ranging from chemistry to biostatistics and interdisciplinary mathematics to applied physics,” said Krishna Garikipati, MICDE director and professor of mechanical engineering and mathematics. “Engineering is also well represented with fellows focused on disciplines such as aerospace, biomedical, civil and environmental, climate and space, industrial and operations, materials science, mechanical, and naval architecture and marine engineering.”

For the past seven years, MICDE has awarded fellowships to over 135 graduate students from our large community of computational scientists. “I am so excited and honored to be a part of the MICDE Fellowship program. My research interest is in an interdisciplinary field between healthcare and data science. This fellowship symbolizes my core value for career development as a data scientist in healthcare,” said 2021 MICDE Fellowship recipient Hyeon Joo, Ph.D. pre-candidate in health infrastructure and learning systems and scientific computing. The MICDE graduate student top-off fellowship provides students with a stipend to use for supplies, technology, and other materials that will further their graduate education and research. Among other things, awards have helped many to travel to conferences and meetings around the world to share the rich and diverse research in computational science being carried out at U-M.

Yifu An, Climate and Space Sciences Engineering
Andre Antoine, Applied Physics
Shreyas Bhat, Industrial and Operations Engineering
Erin Burrell, Mechanical Engineering and Scientific Computing
Alanah Cardenas-O’Toole, Climate and Space Sciences Engineering
Brian Chen, Applied and Interdisciplinary Mathematics
Xinyu Fei, Industrial and Operations Engineering and Scientific Computing
Nicholas Galioto, Aerospace Engineering
Vishwas Goel, Materials Science and Engineering and Scientific Computing
Min-Chun Han, Civil and Environmental Engineering
Dalia Hassan, Chemistry and Scientific Computing
Alexander Hrabski, Naval Architecture and Marine Engineering and Scientific Computing
Javiera Jilberto Vallejos, Biomedical Engineering and Scientific Computing
Hyeon Joo, Learning Health Sciences and Scientific Computing
Timothy Jugovic, Chemistry and Scientific Computing
Ismael Mendoza, Physics and Scientific Computing
Aagnik (Nick) Pant, Applied Physics and Scientific Computing
Hardik Patil, Civil and Environmental Engineering
Amanda Wang, Materials Science and Engineering
Wenbo Wu, Biostatistics and Scientific Computing

Learn more about the fellows and the MICDE Fellowship program

Jul 16
0

2021-2022 Catalyst Grant awardees continue to forge new fronts in computational science

By | Feature, News, Research

The Michigan Institute for Computational Discovery and Engineering (MICDE) announced the awardees of the 2021-2022 round of Catalyst Grants. Since 2017 MICDE Catalyst Grants program has funded a wide spectrum of cutting-edge research, this year focusing on AI for physically-based biomedicine, quantum computing, convergence of natural hazards with economic dislocation, and computational integration across scales and disciplines in biology. The five projects awarded in this round represent these new frontiers of computational research spearheaded by the Institute through its initiatives.

Prof. Shravan Veerapaneni (Mathematics) is working on advancing quantum algorithm research. His team will develop a Variational Quantum Monte Carlo algorithm that can potentially be applied to a wide range of linear algebraic tasks, like QR and Singular Value Decomposition (SVD). 

Profs. Salar Fattahi (Industrial and Operations Engineering) and Arvind Rao (Computational Medicine and Bioinformatics, Biostatistics) are revisiting existing theoretically powerful maximum-likelihood estimation mathematical methods to identify areas of weakness and strengthen them for use in biomedical, largely genomic, applications.

Profs. Gary Luker (Microbiology and Immunology), Nikola Banovic (Electrical Engineering and Computer Science), Xun Huan (Mechanical Engineering), Jennifer Linderman (Biomedical Engineering and Chemical Engineering), and Kathryn Luker (Radiology), will develop a physics/chemistry-aware inverse reinforcement learning (IRL) computational framework that will support the understanding single-cell and cooperative decision-making that drive tumor growth, metastasis, and recurrence.

Profs. Seth Guikema (Civil and Environmental Engineering and Industrial and Operations Engineering) and Jeremy Bricker (Civil and Environmental Engineering) will develop an integrated computational modeling approach to studying equity and resilience during natural hazard events, specifically estimating what essential services are the main constraints on individuals returning to a more normal life post-hazard, and assess inequities in resilience to coastal flooding events. 

Prof. Jesse Capecelatro (Mechanical Engineering and Aerospace Engineering) and Alberto Figueroa (Biomedical Engineering and Vascular Surgery), will develop a versatile, physics-driven, computationally efficient, and massively parallel numerical framework to simulate the interaction between fluids and biological particles in patient-specific vasculature geometries. This framework will enable next-generation computer-aided diagnostics.

“This year’s cohort of MICDE Catalyst Grants range from quantum computing for engineering science, AI for the physics of cancer, and computational advances in hazards engineering, through mathematical advances in data science, and bioengineering,” said MICDE Director Krishna Garikpati, a professor of mathematics and mechanical engineering. “These projects represent new frontiers of computational research spearheaded by MICDE through its initiatives.”

Learn more about MICDE’s Catalyst Grant program and funded projects here.

“This year’s cohort of MICDE Catalyst Grants … represent new frontiers of computational research spearheaded by MICDE through its initiatives.”

Krishna Garikipati
Director, MICDE

Jun 09
0

Job Opening: Modeling, Simulation and Optimization of Energy Systems Research Engineer

By | Feature, SC2 jobs

The Bosch Research and Technology Center in Sunnyvale, CA seeks to hire an outstanding research engineer to develop novel hybrid multiscale, cross-domain modeling, simulation, and optimization tools for Bosch products. This engineer would join a team of PhDs with a variety of competences including high fidelity CFD-based multiphysics modeling, adjoint-based optimization, high performance computing and model-based state estimation and controls. The team focuses on design and optimization of residential and transportation technology targeting high energy efficiency and reduced emissions, including fuel cells, electric vehicle components, and heating systems.

Read more.

May 14
0

miRcore is looking for group leaders to guide high school students in performing computational biomedical research

By | Feature, SC2 jobs

miRcore, a 501(c)(3) non-profit org., is looking for group leaders to guide groups of high school students in performing computational biomedical research. Group leaders will be paired with a younger co-lead. During our remote camps, students will finish a research project within about one week, while learning and applying new tools every day. Group leaders will be expected to assist and support these students.

2017 miRcore GIDAS Biotechnology Summer Camp participants

Ideal group leaders are:
1) Graduate or college students (professionals with PhDs welcome)
2) Experienced (or interested) in computational biomedical research
3) Have a passion to inspire young minds
4) Able to commit to a specific camp

Camps run June-August, and leaders will be compensated with $450 per camp session.
Group leaders usually describe the experience as fun, meaningful, an opportunity to learn new research skills, and reigniting their passion for science.

Learn more and apply here: https://forms.gle/6oD9cDqULebxarCE7

Dec 03
0

University of Michigan’s Ph.D. in Scientific Computing: A history of supporting research through education

By | Educational, Feature

#Computationalscience everywhere!

Left side, 2167 configuration console for the IBM/System 360 Model 67-2 (duplex) at the University of Michigan, c. 1969 [Picture by Scott Gerstenberger – Scott Gerstenberger, Public Domain]

The University of Michigan’s joint Ph.D. program in Scientific Computing recently achieved a record enrollment of 137 students. Between 2015, when 15 students were enrolled -mainly from the Colleges of Engineering and Literature, Science and the Arts- and today, the program has witnessed an explosive growth of interest on the part of U-M students. The program now has students enrolled from over 30 departments spanning 8 different schools and colleges, and more than 130 students have graduated in the last 31 years, including 17 students to-date in 2020.

This popularity is emblematic of the dominant role that computation plays in the world today. With the breakneck pace at which new hardware and software architectures are being developed, the boom in simulation-based research in a growing number of disciplines, and the initiatives in data and computational sciences implemented at U-M in the last few years, including the establishment of the Michigan Institute for Computational Discovery & Engineering, and the Michigan Institute for Data Science (MIDAS), it may seem only natural that scientific computing should attract this level of interest. However, like all exceptionally successful undertakings, it owes a great deal to its past. We reached back more than three decades to piece together the history of the Ph.D. in Scientific Computing at U-M.

The broader history of computational science and high performance computing at the University of Michigan is rich and extensive. U-M has been at the forefront of Cyberinfrastructure research for many decades, marked by the acquisition of U-M’s first virtual memory computer in 1967, an IBM 360/67, one of the first computers of its kind in the world. This milestone was followed by many others, including further hardware acquisitions and establishment of new units to support advanced research computing. An important early step was taken in 1985 when the College of Engineering established the Laboratory for Scientific Computation (LaSC). LaSC’s goal was to foster and promote the use of scientific computation in research and instruction at U-M. During those years, several reports from national study committees established computational science as the third pillar of scientific methodology, along with theory and experimentation. Faculty members of LaSC, who were at the forefront of driving these trends  recognized that any initiative in this field needed to include a robust student training program. 

left: Prof. Kenneth Powell (Aerospace Engineering), director of the Ph.D. in Scientific Computing program since 2005; right: Prof. William Martin (Nuclear Eng. and Rad. Sciences), director of the program from 1989 to 2004.

Prominent at that time in LaSC were Prof. William “Bill” Martin (Nuclear Engineering and Radiological Sciences – NERS), the laboratory’s director, Prof. John Boyd (Atmospheric, Oceanic and Space Sciences), the laboratory’s associate director, and Prof. Edward Larsen (NERS), who was hired as part of the College of Engineering’s initiative to move aggressively in the area of scientific computing. Together, they designed a graduate academic program with the goal of giving students a more comprehensive training in numerical analysis and computer science than is typically possible within standard disciplinary programs housed within individual departments and schools. The fundamental idea was that, to excel in computational science and engineering, one must have a thorough understanding of the mathematical and physical problems to be solved, expertise in  the methodologies and algorithms, and a foundation in computer science to be able to apply this arsenal of techniques on modern computer platforms. The need for a thorough understanding of the physical problems led directly to the requirement that students had to be enrolled in a traditional Rackham degree program (i.e., a home department), while the need for mathematical underpinning and knowledge of algorithms and computer science topics led to the requirements for courses in numerical analysis, parallel algorithms, and related topics. The PhD in Scientific Computing program was approved by the State of Michigan in 1988, and enrolled its first students in 1989. This was well in advance of a wider recognition of the centrality of computation in academia and industry. It is true today, as it was in 1988, that students can apply to the PhD in Scientific Computing program from any Rackham-recognized PhD program at the UM. This unique and flexible administrative structure has enabled the rapid growth experienced in recent years as scientific computing has become an indispensable tool in many fields of academic endeavor. 

Prof. Quentin Stout, director of the Center for Parallel Computing 1992-2001 [Picture source: NASA Insights 1998]

The oversight of the degree program has evolved over the years as administrative structures around scientific computing have shifted. Regardless of its administrative home, the program has always been organized under the Rackham School of Graduate Studies. Originally, the College of Engineering had oversight of the program, with Prof. Martin appointed as director, and with guidance from the LaSC Education Committee. This setup continued through the merger of LaSC and the Center for Parallel Computing1 into the Center for Advanced Computing in 2001. In 2005, Prof. Kenneth Powell (Aerospace Engineering) was named director of the program succeeding Prof. Martin, and has continued in the role since. In 2008, the Office of Research Cyberinfrastructure (ORCI) was established, and the oversight of the program changed to the U-M Office of Research. In 2013, when ORCI was re-named as Advanced Research Computing, and the Michigan Institute for Computational Discovery & Engineering (MICDE) was born, oversight was transferred to MICDE.

Since its inception, the program has been described as intended for students who will make intensive use of large-scale computation, computational methods or algorithms in their doctoral studies. Although the requirements and goals of the program have not  changed in 31 years, the research applications, the algorithms and methodologies, and the computer platforms have been in constant evolution. Naturally, the courses offered in support of the program have followed closely. In 1989 the core research areas behind the program were computational fluid dynamics, advanced computer architectures, and particle transport, with the majority of the students coming from engineering, and mathematics. Still, students working in areas where computation was less recognized, such as AIDS transmission or social research projects, also were enrolled. Over the next two decades, the tremendous increase in simulation-based research by the faculty in engineering and physical sciences added many other focus areas, including material science, astronomy, and high energy physics, to name just a few. This growth added a new driver as data-intensive research gained importance in those fields. 

Prof. Suzanne Weekes, Associate Dean of Undergraduate Studies, ad interim, and Professor of Mathematical Sciences at Worcester Polytechnic Institute (U-M 1995, Mathematics and Scientific Computing) [Picture source: SIAM News Sept. 2020]

Several faculty members have had an important role shaping the program, by offering fundamental courses and providing mentorship. Notably, Prof. Quentin Stout, from Computer Science and Engineering, has had a prominent role in the program. He was the founding director of the Center for Parallel Computing, which  provided the basis for subsequent units in this sphere at U-M. He also developed, and has been teaching, Parallel Computing since 1985, innovating its curriculum to remain at the cutting edge of the current techniques, important aspects of which have been based on his own research. Other foundational courses, such as the Department of Mathematics’ Numerical Methods for Scientific Computing I & II and Numerical Linear Algebra have been offered for more than 30 years. More recently the Department of Physics course, Computational Physics, and the College of Engineering course, Methods and Practice of Scientific Computing, along with an array of courses in machine learning, have played prominent roles in transforming the curriculum in scientific computing as research in these areas has likewise redefined the field.

Unsurprisingly, the Ph.D. in Scientific Computing has produced many exceptional alumni. The first student graduated from the program in 1992, and notably for its time, two of the first four graduates were women, when gender imbalance was barely recognized. A majority of the program graduates went on to  positions in academia or the National Laboratories, with the rest working in varied fields in industry or government. Some of these outstanding alumni include Suzanne Weekes, U-M 1995 (Mathematics and Scientific Computing), currently Associate Dean of Undergraduate Studies, ad interim, and Professor of Mathematical Sciences at Worcester Polytechnic Institute. Prof. Weekes has recently been named SIAM executive director, and will start her new role on January 1, 2021.  Another alumna, Rona Oran, U-M 2014 (Space Science and Scientific Computing), is a computational plasma physicist at MIT and a member of the NASA team that is designing and planning a mission to the metal asteroid Psyche to be launched in 2020.

The current goal of the program is still founded on the original idea of strengthening the students’ foundations in methodology and computer science. The leadership of the program strives to bring computational science to more research fields, but importantly, aims to do so by enhancing diversity in the field. An important marker of U-M’s success on this front came in  2018 in the form of the Henry Luce Foundation’s award to the University of two Claire Boothe Luce Ph.D. fellowships for women to enroll in the Ph.D. in Scientific Computing. The program is committed to pursuing other such opportunities and creating an environment where students of all backgrounds and identities feel welcome and thrive.

1 In 1992 U-M was awarded a major equipment grant by the National Science Foundation to create a testbed of parallel computing architectures. The Center for Parallel Computing was established to operate the facility. The center installed and operated several different parallel computers over the years, including KSR-1, KSR-2, Convex Exemplar, SGI PowerChallenge, IBM SP2, and AMD and Apple clusters.

Oct 08
1

Reducing lung cancer mortality through modeling and simulations

By | Feature, Research

Lung cancer remains the leading cause of cancer related mortality in the US, and globally, accounting for 1.8 million deaths annually. Many of these deaths are preventable by the implementation of prevention strategies, including tobacco control policies and lung cancer screening recommendations, and by improvements in lung cancer treatment.  In the US, these policies have generally been implemented based on the analysis and outcomes of the population as a whole, although data analyses have shown that smoking and lung cancer rates, and access to healthcare and interventions, vary significantly by education, income, and race/ethnicity.

The Cancer Intervention and Surveillance Modeling Network (CISNET) Lung Working Group (LWG), led by Rafael Meza, associate professor of Epidemiology from the School of Public Health and MICDE member, has been awarded a new $8.5M grant to investigate the synergistic impacts of tobacco control policies, lung cancer screening and treatment interventions in the US and in middle-income nations. For the past 15 years, the CISNET LWG has contributed to the development of US national strategies for reducing the lung cancer burden by quantifying, through modeling and simulation, the impact of tobacco control on smoking, lung cancer, and overall mortality, as well as the population benefits and harms of lung cancer screening. This new grant will allow the group to expand their work to consider the impact of treatment improvements, including targeted therapies and immunotherapies,  and the synergies between treatment and prevention interventions. It also will enable the researchers to continue their work in addressing smoking and lung cancer disparities. The consortium uses a comparative modeling approach, where multiple, but distinct, models use the same data inputs, and aim to answer a common question with different approaches. This allows the group to assess the strengths and weaknesses of the different models, and aid the decision making process.

Established in 2000, CISNET is a consortium of NCI-sponsored investigators who use modeling and simulation to improve their understanding of cancer control interventions in prevention, screening, and treatment and their effects on population trends in incidence and mortality. CISNET is committed to bringing the most sophisticated evidence-based planning tools to population health and public policy. These models have been used to guide public health research and priorities, and have aided the development of optimal cancer control strategies. Besides lung cancer, CISNET also includes breast, colon, cervical esophageal and prostate cancer groups. 

Jun 04
0

Modeling the transmission of infectious aerosols

By | Feature, Research

Inhalation of micron-sized droplets represents the dominant transmission mechanism for influenza and rhinovirus, and recent research shows that it is likely also the case for the novel coronavirus.  Increasing evidence suggests that the transmission of infectious aerosols is more complex than previously thought. Coughing, sneezing and even talking yield a gaseous flow field near the infected person that is dynamic and turbulent in nature. Existing models commonly employed in simulations of aerosol transmission attempt to represent the effect of turbulence using random walk models that are often phenomenological in nature, employing adjustable parameters and inherently assuming the turbulent fluctuations ‘felt’ by a droplet do not depend upon direction. To design physics-informed guidelines to minimize the spread of this virus, improved predictive modeling capabilities for effectively tracking the aerosol paths are needed. Dr. Aaron M. Lattanzi and Prof. Jesse Capecelatro, from Mechanical Engineering and MICDE are tackling this problem by focusing on mathematical modeling of aerosol dispersion. They derived analytical solutions for the mean-squared-displacement resulting from systems of stochastic differential equations. A key element of their methodology is that the solution connects stochastic theory inputs to statistics present in high-fidelity simulations or experiments, providing a framework for developing improved models.

Simple simulation of aerosol dispersion from a single-point source. The grey, cone-like surface is the approximation using Force Langevin (FL) theory and the colored particles are from integration of Newton’s equations with stochastic drag forces.

Prof. Capecelatro’s research group develops physics-based models and numerical algorithms to leverage supercomputers for prediction and optimization of the complex flows relevant to energy and the environment. The main focus of their research involves developing robust and scalable numerical tools to investigate the multiphysics and multiscale phenomena under various flow conditions, like those that they study here. They recently submitted their findings to the Journal of Fluid Mechanics, and are continuing to work on this problem hoping it will help understand the transmission of COVID-19 and therefore help optimize current guidelines.