Wenhao Sun

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We are interested in resolving outstanding fundamental scientific problems that impede the computational materials design process. Our group uses high-throughput density functional theory, applied thermodynamics, and materials informatics to deepen our fundamental understanding of synthesis-structure-property relationships, while exploring new chemical spaces for functional technological materials. These research interests are driven by the practical goal of the U.S. Materials Genome Initiative to accelerate materials discovery, but whose resolution requires basic fundamental research in synthesis science, inorganic chemistry, and materials thermodynamics.

Ronald Gary Larson

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Larson’s research has been in the area of “Complex Fluids,” which include polymers, colloids, surfactant-containing fluids, liquid crystals, and biological macromolecules such as DNA, proteins, and lipid membranes. He has also contributed extensively to fluid mechanics, including microfluidics, and transport modeling. He has also has carried out research over the past 16 years in the area of molecular simulations for biomedical applications. The work has involved determining the structure and dynamics of lipid membranes, trans-membrane peptides, anti-microbial peptides, the conformation and functioning of ion channels, interactions of excipients with drugs for drug delivery, interactions of peptides with proteins including MHC molecules, resulting in more than 50 publications in these areas, and in the training of several Ph.D. students and postdocs. Many of these studies involve heavy use of computer simulations and methods of statistical analysis of simulations, including umbrella sampling, forward flux sampling, and metadynamics, which involve statistical weighting of results. He also has been engaged in analysis of percolation processes on lattices, including application to disease propagation.

Alpha helical peptide bridging lipid bilayer in molecular dynamics simulations of “hydrophobic mismatch.”

Kenichi Kuroda

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Synthetic polymers have been used as a molecular platform to develop host-defense antimicrobial peptide (AMP) mimics toward the development of “polymer antibiotics” which are effective in killing drug-resistant bacteria. Our research has been centered on the AMP-mimetic design and chemical optimization strategies as well as the biological and biophysical implications of AMP mimicry by synthetic polymers. The AMP-mimetic polymers showed broad-spectrum activity, rapid bactericidal activity, and low propensity for resistance development in bacteria, which represent the hallmarks of AMPs. The polymers form amphipathic conformations capable of membrane disruption upon binding to bacterial membrane, which recapitulates the folding of alpha-helical AMPs. We propose a new perception that AMP-mimetic polymers are an inherently bioactive platform as whole molecules, which mimic more than the side chain functionalities of AMPs. The chemical and structural diversity of polymers will expand the possibilities for new antimicrobial materials including macromolecules and molecular assemblies with tailored activity. This type of synthetic polymers is cost-effective, suitable for large-scale production, and tunable for diverse applications, providing great potential for the development of versatile platforms that can be used as direct therapeutics or attached on surfaces.

Veera Sundararaghavan

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Veera Sundararaghavan is a Professor of Aerospace Engineering at the University of Michigan – Ann Arbor and the director of Multiscale Structural Simulations Laboratory. His research is on multi-length scale computational techniques for modelling and design of aerospace materials with a focus on microstructural mechanics (crystal plasticity, homogenization) and molecular simulation. He is particularly interested in new computational techniques that can revolutionize the way we compute in materials science: machine learning and quantum computing algorithms. He has made important contributions in the area of integrated computational materials engineering (ICME) including reduced order representations for microstructure-process-property relationships, Markov random fields approach for microstructure reconstruction, and parallel, multiscale algorithms for optimizing deformation, fatigue, failure and oxidation response in polycrystalline alloys, high temperature ceramic matrix composites and energetic composites. Methods of choice for data science include deep Boltzmann machines, undirected graph models (Markov random fields) and Support vector machines.

An illustration of the hybrid Quantum-Classical computation technique: Quantum Annealer is used as a Boltzmann sampler while the gradient optimization is carried out using classical computation

Dominika Zgid

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Our work is interdisciplinary in nature and we connect three fields, chemistry, physics and materials science. Our goal is to develop theoretical tools that give access to directly experimentally relevant quantities. We develop and apply codes that describe two types of electronic motion (i) weakly correlated electrons originating from the delocalized “wave-like” s- and p-orbitals responsible for many electron correlation effects in molecules and solids that do not contain transition metal atoms (ii) strongly correlated electrons residing in the d- and f-orbitals that remain localized and behave “particle-like” responsible for many very interesting effects in the molecules containing d- and f-electrons (transition metal nano-particles used in catalysis, nano-devices with Kondo resonances and molecules of biological significance – active centers of metalloproteins). The mutual coupling of these two types of electronic motion is challenging to describe and currently only a few theories can properly account for both types of electronic correlation effects simultaneously.

Available research projects in the group involve (1) working on a new theory that is able to treat weakly and strongly correlated electrons in molecules with multiple transition metal centers with applications to molecular magnets and active centers of enzymes (2) developing a theory for weakly correlated electrons that is able to produce reliable values of band gaps in semiconductors and heterostructures used in solar cells industry (3) applying the QM/QM embedding theories developed in our group to catalysis on transition metal-oxide surfaces and (4) applying the embedding formalism to molecular conductance problems in order to include correlation effects.

Lei Chen

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Lei Chen’s group focus on applying data science tools to advanced manufacturing. Chen’s research expertise and interests are to integrate the physics-based computational and experimental methods and data-driven approaches, to exploit the fundamental phenomena emerged in advanced manufacturing and to establish the design protocol for optimizing the materials and process parameters of as-fabricated parts for quality control. Current research can be summarized by:
1 One of significant challenges in additive manufacturing (AM) is the presence of heterogeneous sources of uncertainty involved in the complex layer-wise processes under non-equilibrium conditions that lead to variability in the microstructure and properties of as-built components. Consequently, it is extremely challenging to repeat the manufacturing of a high-quality product in mass production, and current practice usually reverts to trial-and-error techniques that are very time-consuming and costly. This research aims to develop an uncertainty quantification framework by bringing together physical modeling, machine-learning (ML), and experiments.
2 Computational microstructure optimization of piezocomposites involves iterative searches to achieve the desired combination of properties demanded by a selected application. Traditional analytical-based optimization methods suffer from the searching efficiency and result optimality due to high dimensionality of microstructure space, complicated electrical and mechanical coupling and non-uniqueness of solutions. Moreover, AM process inherently poses several manufacturing constraints e.g., the minimum feature size and the porosity in the piezoelectric ceramics as well as at the ceramics-polymer interface. It is challenging to include such manufacturing constraints since they are not explicitly available. This research aims to develop a novel data-driven framework for microstructure optimization of AM piezoelectric composites by leveraging extensive physics-based simulation data as well as limited amount of measurement data from AM process.
3 Lithium (Li) and other alkali metals (e.g., sodium and potassium) are very attractive electrode candidates for the next-generation rechargeable batteries that promise several times higher energy density at lower cost. However, Li-dendrite formation severely limits the commercialization of Li-metal batteries, either because dendrite pieces lose electrical contact with the rest of the Li-electrode or because growing dendrites can penetrate the separator and lead to short circuits. This research aims to develop a computational model to accelerate the design of dendrite-free Li-metal batteries.

9.9.2020 MIDAS Faculty Research Pitch Video.

Blueprint for the research: data-driven modelling of additive manufacturing. Stereolithography-based and laser melting-based additive manufacturing processes are used to fabricate the powder-based piezoelectric ceramics and metals respectively, with controllable complex microstructures and/or architectures to tune material properties. Physics-based numerical simulations are performed in an “in-house” multiscale computational framework, which includes macroscopic finite-element based manufacturing process modelling, mesoscopic phase-field modelling of microstructure evolution and design, and first principles/CALPHAD calculation of thermodynamics and kinetics. Data-driven approaches include machine learning and uncertainty quantification with surrogate models, such as polynomial chaos expansion, Gaussian process, radial basis functions, etc.

Bryan R. Goldsmith

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Bryan R. Goldsmith, PhD, is Assistant Professor in the department of Chemical Engineering within the College of Engineering at the University of Michigan, Ann Arbor.

Prof. Goldsmith’s research group utilizes first-principles modeling (e.g., density-functional theory and wave function based methods), molecular simulation, and data analytics tools (e.g., compressed sensing, kernel ridge regression, and subgroup discovery) to extract insights of catalysts and materials for sustainable chemical and energy production and to help create a platform for their design. For example, the group has exploited subgroup discovery as a data-mining approach to help find interpretable local patterns, correlations, and descriptors of a target property in materials-science data.  They also have been using compressed sensing techniques to find physically meaningful models that predict the properties of perovskite (ABX3) compounds.

Prof. Goldsmith’s areas of research encompass energy research, materials science, nanotechnology, physics, and catalysis.

A computational prediction for a group of gold nanoclusters (global model) could miss patterns unique to nonplaner clusters (subgroup 1) or planar clusters (subgroup 2).

A computational prediction for a group of gold nanoclusters (global model) could miss patterns unique to nonplaner clusters (subgroup 1) or planar clusters (subgroup 2).

 

Nils G. Walter

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Nils G. Walter, PhD, is the Francis S. Collins Collegiate Professor of Chemistry, Biophysics and Biological Chemistry, College of Literature, Science, and the Arts and Professor of Biological Chemistry, Medical School, at the University of Michigan, Ann Arbor.

Nature and Nanotechnology likewise employ nanoscale machines that self-assemble into structures of complex architecture and functionality.  Fluorescence microscopy offers a non-invasive tool to probe and ultimately dissect and control these nanoassemblies in real-time.  In particular, single molecule fluorescence resonance energy transfer (smFRET) allows us to measure distances at the 2-8 nm scale, whereas complementary super-resolution localization techniques based on Gaussian fitting of imaged point spread functions (PSFs) measure distances in the 10 nm and longer range.  In terms of Big Data Analysis, we have developed a method for the intracellular single molecule, high-resolution localization and counting (iSHiRLoC) of microRNAs (miRNAs), a large group of gene silencers with profound roles in our body, from stem cell development to cancer.  Microinjected, singly-fluorophore labeled, functional miRNAs are tracked at super-resolution within individual diffusing particles.  Observed mobility and mRNA dependent assembly changes suggest the existence of two kinetically distinct assembly processes.  We are currently feeding these data into a single molecule systems biology pipeline to bring into focus the unifying molecular mechanism of such a ubiquitous gene regulatory pathway.  In addition, we are using cluster analysis of smFRET time traces to show that large RNA processing machines such as single spliceosomes – responsible for the accurate removal of all intervening sequences (introns) in pre-messenger RNAs – are working as biased Brownian ratchet machines.  On the opposite end of the application spectrum, we utilize smFRET and super-resolution fluorescence microscopy to monitor enhanced enzyme cascades and nanorobots engineered to self-assemble and function on DNA origami.

Artistic depiction of the SiMREPS platform we are building for the direct single molecule counting of miRNA biomarkers in crude biofluids (Johnson-Buck, A. et al. Kinetic fingerprinting to identify and count single nucleic acids. Nat Biotechnol 33, 730-732 (2015)).

Artistic depiction of the SiMREPS platform we are building for the direct single molecule counting of miRNA biomarkers in crude biofluids (Johnson-Buck, A. et al. Kinetic fingerprinting to identify and count single nucleic acids. Nat Biotechnol 33, 730-732 (2015)).

Jie Shen

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One of my research interests is in the digital diagnosis of material damage based on sensors, computational science and numerical analysis with large-scale 3D computed tomography data: (1) Establishment of a multi-resolution transformation rule of material defects. (2) Design of an accurate digital diagnosis method for material damage. (3) Reconstruction of defects in material domains from X-ray CT data . (4) Parallel computation of materials damage. My team also conducted a series of studies for improving the quality of large-scale laser scanning data in reverse engineering and industrial inspection: (1) Detection and removal of non-isolated Outlier Data Clusters (2) Accurate correction of surface data noise of polygonal meshes (3) Denoising of two-dimensional geometric discontinuities.

Another research focus is on the information fusion of large-scale data from autonomous driving. Our research is funded by China Natural Science Foundation with focus on (1) laser-based perception in degraded visual environment, (2) 3D pattern recognition with dynamic, incomplete, noisy point clouds, (3) real-time image processing algorithms in degraded visual environment, and (4) brain-computer interface to predict the state of drivers.

Processing and Analysis of 3D Large-Scale Engineering Data

Processing and Analysis of 3D Large-Scale Engineering Data

Emanuel Gull

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Professor Gull works in the general area of computational condensed matter physics with a focus on the study of correlated electronic systems in and out of equilibrium. He is an expert on Monte Carlo methods for quantum systems and one of the developers of the diagrammatic ‘continuous-time’ quantum Monte Carlo methods. His recent work includes the study of the Hubbard model using large cluster dynamical mean field methods, the development of vertex function methods for optical (Raman and optical conductivity) probes, and the development of bold line diagrammatic algorithms for quantum impurities out of equilibrium. Professor Gull is involved in the development of open source computer programs for strongly correlated systems.

Quantum impurities are small confined quantum systems coupled to wide leads. An externally applied time-dependent magnetic field induces a change in the population of spins on the impurity, leading to time-dependent switching behavior. The system's equations of motion are determined by a many-body quantum field theory and solved using a diagrammatic Monte Carlo approach. The computations were performed at Columbia University and the University of Michigan.

Quantum impurities are small confined quantum systems coupled to wide leads. An externally applied time-dependent magnetic field induces a change in the population of spins on the impurity, leading to time-dependent switching behavior. The system’s equations of motion are determined by a many-body quantum field theory and solved using a diagrammatic Monte Carlo approach. The computations were performed at Columbia University and the University of Michigan.