MICCoM PI Maria Chan has been awarded an Early Career award from the Department of Energy Basic Energy Sciences. Chans's awarded project is titled "Theory-informed Artificial Intelligence for Accelerating Materials Characterization," and aims to use a theory-informed artificial intelligence and machine learning framework to determine atomic positions in real-time from experimental characterization data. The project will be implemented in a user-friendly framework titled FANTASTX (Fully Automated Nanoscale To Atomistic Structure from Theory and eXperiment) will in turn enable and accelerate nanoscale materials understanding and design. Congratulations!
MICCoM PI Marco Govoni has been awarded an Early Career award from the Department of Energy Basic Energy Sciences Theoretical Condensed Matter Physics program. Govoni's awarded project is titled "Optical Control of Spin-polarization in Quantum Materials," and aims to enable the development of robust solid-state qubits as building blocks for applications in quantum sensing, quantum communication, and quantum computing. The project will use MICCoM's WEST code, of which Govoni is the leader, as well as a hierarchical modeling approach that harnesses artificial intelligence and quantum computing. Congratulations!
The paper from the groups of MICCoM researchers Giulia Galli, Francois Gygi, and Juan de Pablo, is titled "Dissociation of salts in water under pressure," and is published in Nature Communications. It was also featured by UChicago PME. The study employed newly developed coupling of Qbox and SSAGES to study the dissociation of NaCl in water at extreme conditions. The study identified two critical metastable states of the salt, and described their modification in the regime of water molecular dissociation, which can only be described properly by first-principles simulations.
Marco Govoni is participating in a 1-day workshop that aims at showcasing the landscape of container technologies and the concepts related to them targeting massively parallel calculations. Containers offer a way to package software applications and workflows to make them reproducible, shareable, and portable. The focus of this workshop, organized by UChicago’s Research Computing Center, is to facilitate the use of containers on HPC resources, providing examples of creating containerized MICCoM applications and using the singularity runtime to run native singularity images and make compatible the use of Docker containers.
Two MICCoM graduate students in the Pritzker School of Molecular Engineering (PME), were conferred doctoral degrees at UChicago's 533rd Convocation Ceremony. Dr. Ashley Guo and Dr. Jiyuan Li were both members of Juan de Pablo's research group. Guo's dissertation was titled Molecular Simulation of Biological Macromolecules: Aggregation, Ion Capture, and Sliding Dynamics. She worked on development of SSAGES and enhanced sampling methods within MICCoM, and is now a postdoctoral scholar at the Center for Soft Matter Research at New York University. Li's dissertation was titled Electrostatics and Hydrodynamics in Continuum-Scale Simulations: Numerical Approaches. He worked on SSAGES and COPSS within MICCoM, and is now a data scientist at Uber. Congratulations!
The class “Applied Scientific Computing in Molecular Engineering” taught by Marco Govoni at the University of Chicago aims at developing the next generation of computational scientists. This course provides hands-on practical training in scientific computing with a focus on applications to molecular engineering. The course provides: (i) training in core programming concepts and basics of good software development practices, (ii) advanced programming topics in CPU and GPU parallel programming and quantum computing, exploring their use through practical examples.
MICCoM has released two python packages for analysis of first principles simulations: PyCDFT, and PyZFS. PyCDFT computes diabatic states using constrained density functional theory, while PyZFS is used for the calculation of the zero-field splitting tensor, D, of molecules and solids. Both packages emphasize modular and object oriented design, and are compatible with various plane-wave DFT codes, including Qbox.
Pedro Amorim, a second year graduate student in Jonathan Whitmer's group, has been awarded a Outstanding Graduate Student Teaching Award by the University of Notre Dame. Presented annually, the award recognizes exceptional teaching in the classroom or in a teaching laboratory. Amorim is working on nonequilibrium sampling projects for the SSAGES code.
Jonathan Whitmer has been promoted to Associate Professor with tenure in the University of Notre Dame's Department of Chemical and Biomolecular Engineering, where he researches thermodynamics and statistical mechanics in soft materials. His group studies liquid crystals, polymer and polyelectrolyte phases, self-assembly, classical thermodynamics, and free energy methods. In MICCoM, Whitmer is the leader of SSAGES, which is a comprehensive suite of advanced methods for phase space sampling in quantum and classical molecular simulations.
MICCoM postdoc Nicholas Jackson has been appointed assistant professor in the Department of Chemistry at UIUC in Urbana, IL. His research focuses on computational soft materials, integrating molecular quantum mechanics, computational statistical mechanics, and machine learning to characterize the multiscale structure and function of soft materials with useful optoelectronic, bioelectronic, and sustainability applications. In MICCoM, Jackson has been working on machine learning for coarse-grained electronic structure as well as multiscale soft materials design. Jackson's professorship will begin in spring, 2021.
Graduate student Jiale Shi, a third year student in Chemical and Biomolecular Engineering at the University of Notre Dame, has passed PhD candidacy. Shi works on simulation of material properties in liquid crystals and solids using advanced sampling, as well as ab initio thermodynamics using the coupling of SSAGES and QBox. Graduate students Anne Leonhard and Shanghui Huang have also passed PhD candidacy in the departments of Chemical and Biomolecular Engineering and Chemistry. Both Leonhard and Huang work on development and application of the SSAGES code. Congratulations!
This month, MICCoM director Giulia Galli was elected to both the American Academy of Arts and Sciences (AAAS) and the National Academy of Sciences (NAS). Her research uses MICCoM-supported codes to understand, predict, and engineer material properties from first principles. “Giulia’s groundbreaking work in computational modelling of molecular behavior can help us address complex and pressing problems in areas such as renewable energy technology and quantum device engineering,” said Matthew Tirrell, dean of the Pritzker School of Molecular Engineering (PME).
MICCoM welcomes new postdoc Dr. Lan Huang! Huang joins MICCoM from the Department of Materials Science and Engineering at Texas A&M University. Huang is appointed at Argonne National Laboratory, where he will work various MICCoM software development projects.
The paper from the group of MICCoM researcher Giulia Galli, titled Molecular Polarizabilities as Fingerprints of Perturbations to Water By Ions and Confinement, has been published in the Journal of Chemical Physics. The work was featured by the journal and highlighted in AIP Scilight. It was also featured by Lawrence Livermore National Laboratory. The work was funded by the AMEWS Center, and uses MICCoM code Qbox.
MICCoM postdoc Sijia Dong has been appointed assistant professor in the Department of Chemistry and Chemical Biology at Northeastern University in Boston, MA. Her research focuses on first-principles-based and data-driven computational methods for complex molecular systems and materials. In MICCoM she has been working on machine learning techniques applied to electronic structure problems, for example the calculation of absorption spectra. Dong's professorship will begin in January, 2021.
Due to uncertainties and health concerns caused by the rapidly evolving COVID-19 situation, we are canceling the training event of MICCoM codes originally planned to be held at Argonne on March 30-31, 2020. We will be in touch with all participants in order to reschedule it online.
Nick Jackson, a Maria Goeppert Mayer Fellow at Argonne National Laboratory and visiting scientist in the group of Juan de Pablo, has been selected for multiple recent awards. They include the 2019 Maria Lastra Mentoring Award, 2019 MRS Postdoctoral Award, and the 2019 ACS PHYS Young Investigator Award. His current research concerns the development and application of computational algorithms for the multiscale design of soft materials.
MICCoM welcomes new postdoc Dr. Johnson Dhanasekaran! Dhanasekaran joins MICCoM from the Department of Mechanical and Aerospace Engineering at Cornell University, where he worked with Prof. Donald Koch. His dissertation was titled "Cloud packet model for drop-size evolution: Turbulence, gravity, non-continuum hydrodynamics, and Inertial-clustering." Dhanasekaran will work on the COPSS code.
Prof. Juan de Pablo has been selected for multiple recent awards and named lectureships. They include the Caltech Lacey Lectures (2020), Purdue Kelly Lecture (2020), Ohio State Lowrie Lectures (2020), Northwestern MAH Lectures (2019), NJIT Named Tomasino Award Lecture (2019), University of Nebraska-Lincoln NC3 Lecture (2019), University of Minnesota Neil Amundson Lecture (2019), and Arizona State Distinguished Lecturer (2019).
He Ma has been selected to be a Spring 2020 Research Intern at Google, where he will work on applying machine learning techniques to develop Density Functional Theory. He is a member of Giulia Galli's group, and works on MICCoM code development.
Giulia Galli delivered the Etter Memorial Lecture in Materials Chemistry at the University of Minnesota on Feb 4, 2020. Her talk was titled "Light-activated matter: from energy to quantum information science."
Giulia Galli has been awarded the Tommasoni-Chisesi prize by the University of Rome, La Sapienza, during a ceremony in Rome on January 31, 2020. The Tomassoni-Chisesi prize is an international prize intended to recognize outstanding achievements in physics.
Juan de Pablo was selected for the 2020 W. N. Lacey Lectureship at Caltech. He discussed the relationship between structure, activity, and motion in lyotropic liquid crystalline polymeric systems. His talks were titled "Soft matter design and characterization in the era of machine learning," and "Liquid Crystals - From Simple Self-Assembled Constructs, to Autonomous Materials."
MICCoM postdoc Michael Webb has been appointed assistant professor in the Department of Chemical and Biological Engineering at Princeton University in Princeton, NJ. His research focuses on computational study of novel soft materials for health and sustainability applications, with emphasis on predictive modeling frameworks to study aspects of charge-transport phenomena in polymeric media, stimuli-responsive behavior of biopolymer-based solutions/gels, and the interfacial physics/properties of polymer-composite materials. In MICCoM, Webb has been working on graph-based approaches for molecular coarse-graining as well as machine learning for soft materials applications. Webb's professorship will begin in spring, 2020.
Graduate students Mykyta Onizhuk and Yu Jin have advanced to PhD candidacy in the Department of Chemistry at University of Chicago. They are both in Giulia Galli's group, and work in part on MICCoM code development. Congratulations!
The project, “Advanced Materials Characterization with AI-informed Computation,” led by MICCoM PI Marco Govoni has been selected for the 2019-2020 Argonne Leadership Computing Facility Data Science Program (ADSP) at Argonne National Laboratory. ADSP connects leading researchers with ALCF scientists to push the state-of-the-art in machine learning, workflows, data analysis, and algorithmic development. The awarded project will aim to develop an AI-informed computational framework around the WEST and Qbox codes that integrates machine learning into existing workflows, thereby enabling the prediction of spectroscopic signatures of materials with fast turnaround.
MICCoM held an All-Hands meeting at Argonne National Laboratory on Nov. 4, 2019. All MICCoM PIs and participants met to discuss current work and future directions of the center. Presentations included talks on MICCoM software developments as well as applications of codes.
The Journal of Chemical Physics paper from the group of MICCoM researcher Francois Gygi, titled "Ensemble first-principles molecular dynamics simulations of water using the SCAN meta-GGA density functional," uses the SCAN density functional to study structural and electronic properties of water with robust statistics. The simulations include Raman and IR spectroscopy, showing consistently improved correspondance with experimental data at moderate computational cost. All simulation data generated in the study is available at http://www.quantum-simulation.org/reference/h2o/scan330/index.htm. The newly-implemented SCAN density functional is available in the newest version of the Qbox code.
Giulia Galli has been awarded the 2019 Feynman Theory Prize from the Foresight Institute, a think tank focused on molecular manufacturing. Every year, the Foresight Institute honors two researchers that make groundbreaking strides in nanotechnological development. She was recognized for significant contributions to the development of theoretical methods to simulate nanomaterials at the atomic level, with a focus on semiconductor nanoparticles and carbon-based systems. Galli received her award from Sir James Fraser Stoddart, 2016 Nobel Laureate in Chemistry, and Steve Burgess, president of the Foresight Institute, at an event in Evanston, IL., on September 30.
There are several open positions at MICCoM. We are looking for a postdoctoral candidate to perform research related to the development and experimental validation of computational models exploring new spin defects physics in optically active quantum systems. We are also hiring two software scientists for development and deployment of MICCoM codes and analysis codes for advanced sampling, molecular dynamics and electronic structure calculations. For more information, see our page on job opportunities.
AI technology is increasingly being used for everything from scanning the skies for supernovae to finding new drugs from millions of potential combinations and developing a deeper understanding of the complex phenomena underlying the Earth’s climate. In this story, Prof. Andrew Ferguson asks how using physical laws as inputs to artificial intelligence algorithms could accelerate discovery of new materials. Ferguson is also involved in the new UChicago Center for Data and Computing.
Qbox 1.68.0 (http://qboxcode.org) includes the SCAN meta-GGA density
WEST v4.0.0 (http://www.west-code.org/) has the following new features:
- Added client/server mode
- Added coupling to Qbox code (http://qboxcode.org)
- Added python3 interface
- Simplified the input format (now accepting both JSON and YAML formats)
- Expanded documentation
Qresp v1.2.0 (http://qresp.org/) has the following new features:
- Updated Curator UI
- Added Preview Functionality
- Added Share Functionality
- Changed configuration scheme
- Added sections into Qresp explorer
- Removed ssh connection and added Zenodo & HTTP connections
- New unit tests
Galli delivered the plenary lecture at the conference “Molecular and materials simulation at the turn of the decade: Celebrating 50 years of CECAM” in Lausanne, Switzerland. CECAM (Centre Européen de Calcul Atomique et Moléculaire) is the longest standing European Institute for the promotion of fundamental research on advanced computational methods and their application to science and technology. Galli's lecture was titled "Light-activated matter: from photo-electrochemical cells to optogenetics and quantum information systems." A video of the lecture is available here.
The Physical Review X paper from the group of MICCoM researcher Juan de Pablo, titled "Emergence of Radial Tree of Bend Stripes in Active Nematics," uses experiments and hydrodynamic simulations to study the emergence of bend stripes, which arise as spontaneous undulations of the director field in circularly aligned lyotropic liquid crystals doped with bacteria. These liquid crystals may find application in a variety of display technologies. The hydrodynamic simulations of liquid crystals were conducted with MICCoM software COPPS.
Wei Chen has been awarded the Kuck Computational Science & Engineering Scholarship at UIUC. The Kuck Scholarship is highly selective, supporting graduate students with research in hardware, software, architecture, or applications within the field of computational science and engineering. Wei Chen is a graduate student in Andrew Ferguson's group.
The US Department of Energy has announced a $32 million investment to accelerate the design of new materials through use of supercomputers. The funding supports the renewal of the Midwest Integrated Center for Computational Materials (MICCoM) as well as six other projects at national laboratories and universities. These projects will develop widely applicable open source software utilizing DOE’s current leadership class and future exascale computing facilities. Projects will provide software platforms and data for the design of new functional materials with a broad range of applications, including alternative and renewable energy, electronics, data storage and materials for quantum information science. The archived site from MICCoM's first four years may be found at: http://miccom-center.org/1
The University of Chicago announced a $100 million commitment from the Pritzker Foundation to support the new Pritzker School of Molecular Engineering, becoming the first university in the United States with a school dedicated to this emerging field. The new school builds on the success of efforts by the University and Argonne National Laboratory, which partnered in 2011 to establish the Institute for Molecular Engineering. MICCoM will work closely with the new school on research collaborations.
Dr. Govoni presented the highlight talk entitled “Qresp, a tool for curating, discovering and exploring reproducible scientific papers” at the Swiss Federal Institute of Technology Lausanne (EPFL). The keynote focused on outstanding problems (and proposed solutions) in sharing reproducible workflows in computational materials science. Qresp has previously been featured by UChicago News.
Prof. Galli gave the keynote address of the 2019 Nelson W. Taylor Lectureship in Materials Science and Engineering at Penn State University. Her talk was titled “Asking ‘why’ matters to predict the future,” and focused on insights and first principles predictions of material properties relevant to energy conversion processes and quantum information technologies.
The National Energy Research Scientific Computing (NERSC) center has awarded MICCoM codes WEST (Tier 1; PI: M. Govoni) and Qbox (Tier 2; PI: F. Gygi) early access and resources on the next-generation Perlmutter Architecture through the NERSC Exascale Science Application Program (NESAP). The new Perlmutter system will be built for NERSC at Lawrence Berkeley National Laboratory, and delivered in late 2020.
The Science Advances paper from the group of MICCoM researcher Juan de Pablo, titled "Electronic Structure at Coarse-Grained Resolutions from Supervised Machine Learning," uses artificial neural networks and coarse-graining to compute electronic structure across various conformations. The method finds application in the molecular engineering of organic, flexible electronics.
The U.S. Department of Energy (DOE) and Intel Corporation will build the first supercomputer with a performance of one exaFLOP in the United States. Auora will combine unprecedented processing power with the growing potential of artificial intelligence to help solve the world’s most important and complex scientific challenges. The announcement has been highlighted in UChicago News, the Chicago Tribune and the New York Times.
Galli was the recipient of the APS David Adler Lecturship Award in Materials Physics . She delivered a talk featuring several MICCoM codes, titled "Sorting through messy semiconductors with first principles calculations." She is pictured together with fellow APS prize recipients Julia Mundy (George E. Valley, Jr. Prize) and Claudia Felser (James C. McGroddy Prize for New Materials).
The Scientific Data paper by MICCoM researchers including Giulia Galli, Marco Govoni, and Juan de Pablo, is titled "Qresp, a tool for curating, discovering and exploring reproducible scientific papers." Qresp offers a distributed model for intuitive documentation of codes, curation of workflows, and publishing of computational data. It is the cornerstone of the MICCoM data effort. Qresp can be explored and downloaded at http://qresp.org. It was also featured as a MICCoM scientific highlight.
The Advanced Materials for Energy-Water Systems (AMEWS) Center is a new DOE Energy Frontier Research Center conducting research that enables the availability of clean water. MICCoM is collaborating closely with AMEWS in both expertise and codes to understand the fundamental behavior of water at surfaces with the development of applications in mind, including water disinfection and catalysts to degrade water pollutants.
The JACS paper by MICCoM researcher Jonathan Whitmer, titled "Role of Associative Charging in the Entropy–Energy Balance of Polyelectrolyte Complexes" uses the SSAGES suite to compute free energy profiles between polymer chains. The conclusions find application in molecular capture and release technology and layer-by-layer assembly of films. It was also featured as a MICCoM scientific highlight.
The annual Scientific Advisory Board meeting was held at Argonne National Laboratory. Members of the Scientific Advisory Board met with MICCoM PIs and participants to discuss current work and future directions of the center. Presentations included talks and posters on developments in software, validation strategies, and data infrastructure within the center.
The APS David Adler Lecturship Award in Materials Physics recognizes "outstanding contributors to the field of materials physics, noted for quality of research, review articles, and lecturing." Galli has been awarded "for the invention of methods, especially for the enhancement of ab initio molecular dynamics, to understand, predict, and engineer the electronic and structural properties of materials." She will receive the award at the 2019 APS March Meeting in Boston.
The MRS Materials Theory award recognizes "exceptional advances made by materials theory to the fundamental understanding of the structure and behavior of materials." Galli has been awarded for "the development of advanced first-principles simulation methods and their application to the understanding, prediction, and design of complex nanostructured materials." She will receive the award at the 2018 MRS Fall Meeting & Exhibit in Boston.
The Nature Nanotechnology paper by MICCoM researchers Giulia Galli and Dmitri Talapin, titled "Surface chemistry and buried interfaces in all-inorganic nanocrystalline solids" used the Qbox code to analyze nanoparticles capped with ligands for application in optoelectronic and photonic technologies.
Argonne has been chosen to lead a new Energy Frontier Research Center on the energy-water nexus. Argonne will partner with the University of Chicago and Northwestern University on the four-year project.
The PNAS paper, by Giulia Galli, titled "Ab initio spectroscopy and ionic conductivity of water under Earth mantle conditions" uses the Qbox code to analyze water at geophysically relevant conditions.
MICCoM has developed the open source software Qresp: “Curation and Exploration of Reproducible Scientific Papers” to facilitate the organization, annotation and exploration of data presented in scientific papers. Qresp may be used to both curate data presented in scientific papers or explore curated scientific papers.
The Sloan Research Fellowships promote fundamental research by early-career scientists, in recognition of distinguished performance and a unique potential to make substantial contributions to their field. Timothy Berkelbach's research focuses on electronic and optical properties of novel nanoscale materials.
The award recognizes those "who have made outstanding contributions which have had a major impact on advances in chemical science and industry and/or the chemical profession." Kanatzidis was selected to receive this award for his work defining the field of chalcogenide compounds (sulfides, selenides, and tellurides).
Nealey was recognized "for the development of directed self-assembly of block copolymers as an industrially significant process for nanolithography." His research often collaborates closely with computational efforts within MICCoM.
Whitmer was awarded the NSF's most prestigious award for early-career faculty for "Designing Colloidal Materials By Tilting the Free Energy Surface." The award supports the use of powerful computational modeling to develop a comprehensive picture of the clusters colloidal materials are likely to assemble into, and how specific aggregates may be achieved by modifying the structure and composition of colloidal particles.
Paper on Software Suite for Advanced General Ensemble Simulations (SSAGES) methodology and examples was published, from Juan de Pablo and Jonathan Whitmer research groups.
Paper published in PNAS Electrostatic confinement and manipulation of DNA molecules for genome analysis by Juan de Pablo and collaborators, highlights COPPS validation example.
Professor Juan de Pablo has received the APS Polymer Physics Prize, given annually by the American Physical Society (APS), "for his innovative models and algorithms for the simulation of macromolecular systems." This prize was established in 1960 with The Dow Chemical Company now serving as chief supporter. The prize recognizes outstanding accomplishment and excellence of contributions in polymer physics research. It consists of $10,000 and a certificate citing the contributions made by the recipient. For more information on the APS Polymer Physics Prize, please visit here.
The paper entitled "Parallel O(N) Stokes’ solver towards scalable Brownian dynamics of hydrodynamically interacting objects in general geometries" co-authored by X. Zhao, J. Li, X. Jiang, D. Karpeev, and Argonne researchers Heinonen and de Pablo, describes new, highly parallel algorithms (and the corresponding software) for calculation of hydrodynamic interactions in suspensions of nano-and micro-particles. The article has been chosen as a 2017 Editor's Choice article by The Journal of Chemical Physics. The new software is distributed as part of the COPSS suite by MICCoM.
A new series of topical workshops hosted by the editors of the Physical Review kicks off with materials design and discovery.
Monica Olvera de la Cruz has been awarded the 2017 Polymer Prize of the American Physical Society, “for outstanding contributions to the theoretical understanding of polymers, and the effects of electrostatic interactions on their structure and properties.”
A new Wiki space, hosted at the University of Chicago, is now accessible to all MICCoM members, allowing for smooth communications, exchange of ideas and circulation of knowledge within the Center.
A paper on "Reproducibility in density functional theory calculations of solids" appeared in Science, with François Gygi as co-author.
One of the three centers, MICCoM (Midwest Integrated Center for Computational Materials) is established at Argonne National Lab and is led by Prof. Giulia Galli. MICCoM's mission is to develop open-source advanced software tools to help the scientific community model, simulate and predict the fundamental properties and behavior of nanoscale and mesoscale materials for energy conversion technologies — including metastable materials assembled far from equilibrium conditions.