NCASD Postdoc Gianmarc Grazioli, Lab PI Carter Butts, and Prof. Ioan Andricioaei from the UCI Chemistry Department have published new results showing how the performance of molecular dynamics simulations can be improved with a little help from machine learning. These results are contained in their forthcoming paper, “Automated Placement of Interfaces in Conformational Kinetics Calculations Using Machine Learning,” to appear in the Journal of Chemical Physics. Their new technique employs a machine learning approach known as a Support Vector Machine to automatically define high dimensional reaction coordinates for calculating chemical kinetics. This approach dramatically reduces the cost of studying the complex configurational changes of large biomolecules, such as proteins and DNA, as well as the cost of simulating high-dimensional systems such as those associated with complex chemical reactions. Understanding the complex motions of biomolecules and the kinetics of chemical reactions is essential not only for a deeper fundamental understanding of the molecular machinery that makes life possible, but also for such applications as the computational design of drug molecules and novel materials.
Lab PI Carter Butts has been elected to two offices in the American Sociological Association: the Section Council of the ASA Section on Methodology, and Chair-Elect of the ASA Section on Mathematical Sociology. Butts is currently serving a term on the Section Council of the ASA Section on Mathematical Sociology, and will transition from this office to the office of Chair in the coming year.
Sections of the ASA serve the sociological community by supporting research in specific fields of the discipline. The Section on Methodology supports work on novel techniques and practical advances in methods for the measurement and analysis of social phenomena, while the Section on Mathematical Sociology supports the development and use of mathematical, computational, and other formal approaches to the study of social systems. Research by NCASD lab members is frequently featured in conference activities by both sections, and we are pleased to have this opportunity to make further contributions to these important communities.
Lab Alumna Liana Landivar (Senior Researcher and Sociologist at the US Department of Labor) has released a new book, Mothers at Work: Who Opts Out? Landivar’s book examines a key question relating to the labor force participation of high-achieving American women: are mothers in managerial and professional occupations more likely to leave the labor force when they have children? Using four major government surveys, Mothers at Work offers a nationally representative account of mothers’ employment in 55 occupations and shows that women in managerial and professional occupations were the least likely to opt out but most likely to scale back by a few hours per week when they had children. By examining work-hour trends since 1970, this book shows that scaling back is taking place in a broader context of shorter work hours since the early 2000s across all groups of workers, including managers and professionals.
Landivar, who recently transitioned to the Department of Labor from the National Science Foundation, is an expert on gender and work, occupational trajectories, demography, and the STEM workforce. In addition to her appointment at the Department of Labor, Dr. Landivar holds an affiliation with the Maryland Population Research Center at the University of Maryland. Her work on the US labor force has been featured in White House and Congressional briefings, and has been covered widely in the media in outlets such as the Washington Post, the New York Times, Wall Street Journal, and Science.
Chitin, the polysaccharide-based material from which insects make their exoskeletons, is tough stuff – and digesting it is a tall order, especially for a plant. Nevertheless, some carnivorous plants, like the Cape Sundew, Drosera Capensis, are able to do just that. In a recent paper in Biochemica et Biophysica Acta, NCASD Lab PI Butts and members of the Martin Lab model the structures of 11 novel chitinases from D. Capensis, whose genome was published as part of the same collaborative effort this past year. Applying a combination of bioinformatics, molecular modeling, and techniques adapted from social network analysis, the team was able to predict the three-dimensional structure of each enzyme and gain insights into potential functional differences. Among the discoveries is a novel chitinase with two active domains that closely resembles a protein seen in microorganisms, but never before found in plants. These new enzymes can do more than bite bugs: chitin is also the essential component of fungal cell walls, and these molecules may hold promise for combating fungal growth on food or even fungal infections in humans. This work demonstrates the potential for fusing computational and data analytic techniques with biological know-how to quickly move from genomic “source code” to potentially valuable biomolecules.
The NCASD Lab is pleased to welcome Dr. Gianmarc Grazioli, who will be joining as a postdoctoral scholar as of spring quarter, 2017. Dr. Grazioli, who obtained his Ph.D. in the Andricioaei lab before a one-year stint in the Paesani lab at UCSD, brings with him a wealth of expertise in molecular modeling, particularly the use of modified potentials for importance sampling of trajectories in order to explore rare transitions. In his new position, Dr. Grazioli will contribute to the team’s work on modeling of protein aggregation, statistical methods for prediction of structural and functional properties of biological macromolecules, and the development of network analytic methods for the study of biological systems. A computational chemist by training, Grazioli adds to the lab’s diverse mix of disciplinary expertise (currently spanning sociology, statistics, electrical engineering, and computer science), and deepens the group’s bench in expertise related to simulation and sampling techniques.
CNRA Graduate Fellow and NCASD Lab Member Nolan Phillips has accepted a position as a postdoctoral scholar at Harvard University, starting in fall 2018. Phillips, who is completing his dissertation work on network comparison, model evaluation, and the dynamics of technology adoption by government agencies, will join the group of Professor Robert Sampson, where he will be working on an ambitious new project involving neighborhood ecology and community outcomes. This project is part of a broader interdisciplinary collaboration among researchers in the Boston area, including researchers at Harvard and Northeastern universities, to which Phillips will bring his experience with social network analysis, modeling, and the use of archival data.
Lab member Ben Gibson and co-author Burrel Vann won the 2016 ASA Methodology Section’s Clifford C. Clogg Award for the paper, “The Bootstrapped Robustness Assessment for Qualitative Comparative Analysis”.
Lab alumna Liana Landivar, formerly statistician at the US Department of the Census, has now accepted a position as survey statistician at the National Science Foundation. In her capacity at the Census, Landivar played a key role in managing the Census’s measurement and categorization of occupations – a complex task that supplies vital information on the health of the US economy and labor force for use by government, industry, and research entities. She was also active in helping to craft Federal guidelines for determining the occupations considered to be part of the science, technology, engineering, and mathematics (STEM) field. At NSF, Landivar will be leveraging her experience and expertise with occupations to help study the evolution of America’s science and technology labor force, including the changing demographics of workers in STEM fields. Her work there will provide insights to inform science and education policy, and to better assess occupational fields that are central to US competitiveness and economic growth.
NCASD lab members Butts and Zhang, in collaboration with Alfredo Freites and the Martin lab (UCI Chemistry and MB&B) are pleased to announce two forthcoming papers on the genome of the Cape sundew (Drosera Capensis), a widely cultivated carnivorous plant. The team’s sequencing of D. Capensis marks the first published genome in the family Caryophyllales, and the third carnivorous plant to be sequenced. In their forthcoming work, Butts, Martin, and colleagues identify and model a large number of novel proteases from the Capensis genome, identifying promising targets for biotechnological applications such as the preparation of samples for mass spectrometry or attacking bacterial biofilms on sensitive medical devices. The team has also identified a new “enzyme within an enzyme” with potential uses as an antifungal agent. In the spirit of UCI’s growing commitment to convergnce science, this research fuses state-of-the-art computational methods (including structure prediction, docking, and molecular dynamics), methods adapted from social network analysis, and traditional genomic and biophysical techniques to move from genomic “source code” to useful biomolecules in a fraction of the time and cost of conventional approaches. The team’s work is forthcoming at Proteins and the Computational and Structural Biotechnology Journal.
Lab alum Sean Fitzhugh, along with lab member Ben Gibson, lab alum Emma Spiro, and lab PI Carter Butts, have published their article “Spatio-temporal Filtering Techniques for the Detection of Disaster-related Communication” in an upcoming special issue of Social Science Research on big data. This paper develops a family of techniques for filtering large streams of communication across time and space in order to detect signals of hazard-related rumoring. They reliably detect signal of rumoring activity across a variety of disasters affecting a wide range of populations, from dense urban areas to sparse rural areas. The results highlight spatio-temporal variation of rumoring activity in response to impending and realized disasters. Additionally, they illustrate a case study of how message content varies across time and space during a disaster.
The article can be found online here.