Condensed Matter and Biophysics seminars
Condensed Matter seminars are held Tuesdays at 3:30 p.m. in Physics Research Building, room 245.
December 8, 2020
Dr. Kekenes-Huskey, Department of Cell & Molecular Physiology at Loyola University Chicago
Small molecule diffusion and reactions in complex environments
Molecular signaling is a multi-scale phenomenon that relies on the transport of substrates along chemical potential gradients and within crowded or confined spaces. Signaling occurs within biological environments including cellular compartments, cells and tissue, for which interactions between proteins, substrates, and the cellular environment impose significant temporal and spatial constraints on diffusion. These constraints can lead to markedly different dynamics in biological environments in contrast to a ‘well-mixed’ in vitro system. Yet quantifying the influence of atomistic- to micron-scale structural features of the solute and environment, including electrostatic interactions and friction, presents a considerable challenge to modeling and experimental inquiry. Recent mathematical and numerical developments are providing the foundation for multi-scale examination of diffusion-controlled processes and have yielded considerable insight into biological signaling. In this talk, I will present some of these methodologies, and their application to micron-scale diffusional anisotropy in an abiological system and a mock intercellular synapse.
November 17, 2020
Dr. Shengyi Sun, Center for Molecular Medicine and Genetics, Department of Biochemistry, Microbiology and Immunology, Wayne State University
Regulation of ER Homeostasis in Health and Disease
Accumulation of misfolded proteins in the ER underlies over 70 human diseases, although the underlying mechanism remains unclear. In eukaryotes, approximately 30% of all newly synthesized proteins undergo folding and maturation in the endoplasmic reticulum (ER) to reach a proper configuration. During this process, a significant fraction of nascent proteins may fail to fold properly, due to either an unwanted amino acid mutation or an error in the folding process. These proteins in the ER are recognized as misfolded and subsequently targeted to cytosolic proteasome for degradation by ER quality control system known as the ER-associated degradation (ERAD). ERAD mediates the recognition, retro-translocation, and ubiquitination of misfolded proteins (i.e. substrates) from the ER to cytosol for proteasomal degradation. Sel1L and Hrd1 protein complex represents the most conserved ERAD complex from yeast to humans. Our previous studies showed that Sel1L-Hrd1 ERAD is vital and multifaceted, as it mediates indispensable, homeostatic processes via turnover of specific substrates. However, our understanding of the physiological function and pathological importance of Sel1L-Hrd1 ERAD in metabolism remains limited. The goal of our research program is to gain a comprehensive understanding of the cellular and physiological functions of mammalian SEL1L-HRD1 ERAD, with a focus on inflammatory responses and iron metabolism.
Dr. Shengyi (Iris) Sun is an Assistant Professor at the Center for Molecular Medicine and Genetics and the Department of Biochemistry, Microbiology and Immunology at Wayne State University Medical School. She got her BS from the University of Hong Kong in 2009, majoring in biology, and PhD from Cornell University in Dr. Ling Qi’s laboratory in 2015, majoring in Biochemistry, Molecular and Cell Biology. She then went on to complete a postdoctoral fellowship with Drs. David Mangelsdorf and Steven Kliewer at UT Southwestern Medical Center. Her work has been published in Nat Cell Biol, Nat Immunol, PNAS, Gene & Development, Cell Reports, MBoC and etc. During her training, she was awarded with two prestigious fellowships, HHMI International Predoctoral Fellowship and Helen Hay Whitney Foundation Postdoctoral Fellowship. In July 2019, she started her independent career at Wayne State University.
Dr. Sun’s previous work in the Qi and Mangelsdorf-Kliewer labs elucidated the significance of mammalian ER-associated degradation (ERAD) and unfolded protein response (UPR), respectively, in various physiological and pathological contexts. She also studied the role of inflammation in β cell proliferation. In her own laboratory, she will continue delineating the physiological significance and molecular mechanism underlying ERAD machinery in health and disease, with a special focus on iron metabolism.
October 20, 2020
Sonali Gandhi, Department of Physics and Astronomy, Wayne State University
Fluorescence Cross-Correlation Spectroscopy (FCCS) to reveal the molecular mechanisms of lipolysis
The dynamics of lipids and proteins are crucial in the mechanisms of cellular functions. The interactions between proteins and lipids on the membrane surrounding lipid droplets regulates lipolysis and the digestion of triglycerides within the lipid droplet. In particular, we aim to develop novel methods for revealing the interactions between lipolysis-associated proteins, including adipose triglyceride lipase (ATGL), perilipin (PLIN), and alpha-beta hydrolase domain-containing protein 5 (ABHD5). In our current study, we apply fluorescence cross-correlation spectroscopy (FCCS) to study the interactions between these lipids and proteins. We use a super-continuum laser to excite the fluorescent proteins that diffuse through the diffraction-limited spot. The fluorescence emission is chromatically spread by a prism and collected by a sCMOS camera at 6 kHz. The intensity versus time of each color channel is extracted through a linear least-square fitting of each camera frame and temporally correlated. From the auto- and cross-correlation functions, we measure the diffusion rates and oligomerization of the proteins. To demonstrate the capabilities of our custom instrumentation, we use supported lipid bilayers (SLBs) to study the diffusion and cross-linking of membrane-bound cholera toxin subunit B. Our preliminary experiments show the hetero-oligomerization of ABHD5 and PNPLA3 on the ER of live COS7 cells. Our goal is to examine molecular-scale behaviors dependent on the phospholipid composition, PLIN associations, and protein concentrations in the presence of ligands. This study provides a further understanding of how lipolysis is regulated via protein interactions with the lipid membrane to regulate lipase activity.
Gobin Acharya, Department of Physics and Astronomy, Wayne State University
Revealing the microscopic dynamics of nanoconfined water and ethanol in graphene oxide
Water is the natural solvent as well as a major component of living beings which influences many biological activities. Ethanol is also an important fluid in chemical, biological and industrial processes. The purification of water and the separation of water and ethanol are important, but energy-intensive processes. Therefore, nanomaterials are being studied that may facilitate water and ethanol separation. One such material is graphene oxide (GO). When water and ethanol are confined in GO capillaries, their confinement can change the dynamic properties of the confined molecules. We utilized the momentum transfer (Q)-dependence of Quasi-Elastic Neutron Scattering (QENS) to reveal the dynamics and the almost isotropic behaviors of water and ethanol intercalated in GO at different temperatures. The microscopic dynamics of water and ethanol was probed and compared at different length and time scales and different temperatures by using several spectrometers. The results will be presented.
October 13, 2020
Dr. W. Vincent Liu, Department of Physics and Astronomy, University of Pittsburgh
Emerging order from real to imaginary time crystal
Quantum time crystal has been an intriguing many-body “time” state that has received much attention and debate since its early prediction. In this talk, first, I will construct a class of concrete “clean” Floquet models to answer the open question on the role of disorder and many-body localization. Second, by observing the equivalent role of the space and imaginary time in the path integral formalism, I will present the finding that hard-core bosons coupled to a thermal bath may exhibit the order of “imaginary spacetime crystal”
September 29, 2020
Dr. Heather A. Carlson, College of Pharmacy, University of Michigan
MixMD: Mapping Protein Surfaces to Discover Druggable Allosteric Sites
Cosolvent molecular dynamics (MD) simulations use small organic probe molecules to sample along a protein surface and identify binding "hotspots". The benefits of this approach are the protein can adapt to the presence of the cosolvents and the cosolvents must compete with water to interact with the protein. Accommodating protein flexibility and hydration effects are two leading challenges in structure-based drug discovery. Advances in cosolvent MD will be presented including applications to allosteric systems, prediction of bridging water molecules, identification of cryptic binding sites, and assessment of target druggability. Though these approaches are resource intensive, they have the promise of identifying previously unknown regulatory sites on proteins, which could significantly increase the number of drug targets available to treat a wide variety of medical disorders.
P Ghanakota, HA Carlson. Driving structure-based drug discovery through cosolvent molecular dynamics. J. Med. Chem. 2016, 59, 10383-10339.
P Ghanakota, HA Carlson. Moving beyond active-site detection: MixMD applied to allosteric systems. J. Phys. Chem. B 2016, 120, 8685-8695.
SE Graham, HA Carlson. Predicting displaceable water sites using mixed-solvent molecular dynamics. J. Chem. Info. Model. 2018, 58, 305-314.
RD Smith, HA Carlson. Identification of cryptic binding sites using MixMD with standard and accelerated molecular dynamics. J. Chem. Info. Model. 2020, in review.
Carlson received her B.S. (1991) in Mathematics, Chemistry, and Physics from North Central College in Naperville, IL. She received her M.S. (1992) and Ph.D. (1997) under the tutelage of Prof. William L. Jorgensen at Yale University. She received postdoctoral fellowships from the American Cancer Society and the Burroughs Wellcome Fund program, La Jolla Interfaces in Science, to study protein simulations and computational biology with Prof. J. Andrew McCammon at the University of California, San Diego.
Carlson began her academic career at the University of Michigan in 2000 as the John Gideon Searle Assistant Professor of Medicinal Chemistry. She was promoted in 2011 to Professor of Medicinal Chemistry (College of Pharmacy) and Chemistry (LSA) at the University of Michigan, Ann Arbor. She is also part of the Biophysics Program (LSA) and Bioinformatics Program (Med School). She has received two teaching awards, one chosen by her peers and one by the students. In 2002, Heather was named a Beckman Young Investigator. In 2006, she received an NSF CAREER Award and a Wiley International Journal of Quantum Chemistry Young Investigator Award. In 2008, she was chosen for the Corwin Hansch Award from the Cheminformatics and QSAR Society. She was chosen for the international honor of Novartis Chemistry Lecturer by Novartis Pharma AG for 2009-2010. In 2011, she was elected a Fellow of American Association for the Advancement of Science, Chemistry Division.
Her research broadly addresses computer modeling of protein-ligand interactions, from the basic biophysics of molecular recognition to applied inhibitor design. Funding from the NIH has allowed her to develop techniques for incorporating protein flexibility into drug discovery and methods for mapping protein surfaces to discover druggable allosteric and orthosteric binding sites. Funding from the Beckman Foundation, the NSF, and the NIH has allowed her to create Binding MOAD (Mother of All Databases), one of the largest collections of protein-ligand complexes with binding data. The latest enhancement to the database is the addition of cross-linked data showing potential polypharmacology events where ligands can bind to different proteins with similar binding sites. Polypharmacology can aide in drug repurposing and in identifying the causes of drug side effects.
September 22, 2020
Yuwen Mei, Department of Physics and Astronomy, Wayne State University
Traction Force Microscopy by Using Paramagnetic Particles
Mechanical cellular interactions heavily influence major cellular processes such as immune response, embryogenesis, angiogenesis, and metastasis. Most of these physiological processes are in direct relation to cell migration. Such biological function is responsible for positive responses in one’s body in aid of healing of wounds, or infamously, invasion of cancer cells through the connective tissues. To better understand these major physiological phenomena, it is critical to understand how these contractile motions are generated and quantification of traction forces is necessary. To measure these forces, Traction Force Microscopy is often employed, and fluorescent particles are embedded in the substrate as markers to track the forces being applied. However, such a setup has no control over marker positions and often introduces background noise, resulting in loss of spatial resolution. In addition, particle depth variations can result in underestimations in force estimations. Thus, we have improved our method of force detection by employing fluorescent paramagnetic nanoparticles. Under the influence of an external magnetic field, the paramagnetic nanoparticles readily form a single particle layer near the surface of the substrate. The inter-particle distance can be controlled by changing the magnitude of the magnetic field. We employ this method for biomechanical analysis of the pancreatic cancer cell line (PANC-1). With the background noise reduced significantly in the single-layer scheme, the image filtering process is simplified. Since the magnetic particles are in a much closer distance to the cells compared to the conventional methods, therefore reflects a more accurate force measurement.
Susheel Pangeni, Department of Physics and Astronomy, Wayne State University
Molecular-Scale Understanding of the Changes to Lipid Mobility Induced by Bilayer Curvature
Biological membranes have evolved tremendous complexity and versatility to perform processes that require the generation of membrane curvature. The interplay of bilayer curvature and mechanical properties are critical for diverse disease treatments and engineering applications. Molecular dynamics simulations provide both means of high-throughput testing of system parameters and revealing molecular-scale details of bilayer behavior. This work is guided by the hypothesis that the mechanical properties of lipids vary with bilayer topography to generates a force for molecular sorting and regulating lipid diffusion. The target is to study how membrane curvature and the molecular interactions between the lipids affect lipid behaviors. We used coarse-grained molecular dynamics (CGMD) models to reveal molecular resolution while enabling larger and longer simulations than all-atom simulations. We are exploring complex and challenging unsolved mechanisms in the cellular physics of trafficking and signaling. The effects of bilayer curvature on diffusion while mimicking of endocytic nano-mechanics is studied with the CGMD Martini model and compared to single-lipid tracking experiments.
September 15, 2020
Dr. Zhenfei Liu, Department of Chemistry, Wayne State University
Energy level alignment at molecule-substrate interfaces from first principles: Challenges and new developments
Molecule-substrate interfaces are ubiquitous in nanoscale functional materials and energy related applications. Characterizing the electronic structure at molecule-substrate interfaces, especially the energy level alignment between molecular frontier orbitals and the Fermi level of the substrate, is crucial for understanding interfacial charge dynamics. Density functional theory (DFT) has been successful in computing binding geometries and adsorption energies, but much less successful in predicting level alignments. This is because the latter depends on quasiparticle excitation energies, typically believed to be outside the reach of DFT. Many-body perturbation theory, such as the GW approach, provides a formal theoretical framework for quasiparticle energies, but the computational cost for typical interfaces is high. In this talk, I will introduce two methodological advancements for accurate and efficient calculations of level alignments at weakly coupled molecule-substrate interfaces: (1) an optimally tuned range-separated hybrid functional, taking into account the substrate screening effect via the image-charge model; and (2) a novel GW approach employing the additivity of the Kohn-Sham polarizability for the interface, which significantly reduces the computational cost compared to direct GW calculations.
2007 B.S. in chemistry, Peking University, China
2012 Ph.D. in theoretical chemistry (with Kieron Burke), University of California, Irvine
2012-2018 postdoc and then project scientist (with Jeff Neaton), Molecular Foundry, Lawrence Berkeley National Laboratory
Aug 2018 - assistant professor, Dept. of Chemistry, Wayne State University
2019 ACS Petroleum Research Fund Doctoral New Investigator Award
Shiva Pokhrel and Brendon Waters, Department of Physics & Astronomy, Wayne State University
Experimental and theoretical insights of percolation transition in nanoparticle composites
Abstract: Percolation, one of the standard models for disordered system, is a random probabilistic process which shows a phase transition. In this work, we investigate a flexible model system based on half-metallic spherocylindrical CrO2 nanoparticles, which can be gradually converted by annealing from metallic (CrO2) to insulating (Cr2O3) state. The composite samples with varying volume fraction were prepared by mixing Cr2O3 with CrO2. The percolation threshold and the power law scaling exponent near the threshold were identified experimentally by studying the changes in the electrical resistance of the pellets with different volume fractions. To more thoroughly investigate the microscopic origins of the observed trends in the bulk properties of the nanocomposite, a series of hard-particle simulations were conducted using the combination of Monte Carlo and mechanical contraction methods that can produce dense random packing of non-overlapped spherocylindrical particles. Using a scaling method to extrapolate to the infinite system-size limit, we determined several properties of critical behavior of the system and found them to be in good agreement with experimental results.
Arthur Bowman, Department of Physics & Astronomy, Wayne State University
High Mobility n-type PdSe2 Field Effect Transistors Enabled by Contact Engineering
Abstract: Two-dimensional (2D) semiconductors such as transition metal dichalcogenides (TMDs) have emerged as a promising candidate for post-silicon electronics. One such material of interest is palladium diselenide (PdSe2) because of its high electron mobility and excellent chemical stability. However, in spite of its relatively small bandgap, the performance of few-layer PdSe2 field-effect transistors (FETs) has been largely limited by the presence of a substantial Schottky barrier, which is likely due to Fermi-level pinning. In this work, we report the fabrication of high mobility n-type PdSe2 FETs, using a new method to significantly reduce the barrier height at the semiconductor/metal interface. As a result, we observed an order of magnitude reduction of contact resistance in comparison with conventional metal contacts. The effective mobility also improved from 133 cm^2 V^-1 s^-1 to ~ 256 cm^2 V^-1 s^-1 at room temperature, and from 260 cm^2 V^-1 s^-1 to ~ 670 cm^2 V^-1 s^-1 at 77 K. We believe the significantly improved device performance enabled by this novel contact engineering technique will enable further studies of the intrinsic properties of PdSe2 and other exciting new 2D material.
Professor Tao Huang, Department of Mathematics, Wayne State University
Analysis of Ericksen-Leslie system modeling hydrodynamic flow of nematic liquid crystals
Abstract: The Ericksen-Leslie model is a classic theory on modeling and analysis of the hydrodynamic flow of liquid crystals. In mathematical analysis, it is interesting to study the existence, uniqueness and partial regularity of global weak solutions, and the existence of singularities (defects) at finite time. In this talk, we will review our recent works related to these topics, especially for several simplified models.
Professor Robert Hovden, Department of Materials Science & Engineering, University of Michigan
Probing atomic structure across higher dimensions in 2D materials using sub-Angstrom electron beams
Abstract: Modern materials are designed atomic layer by atomic layer with architectural complexity extending into the third dimension. For charge ordered materials, dramatic electronic changes are associated with periodic lattice distortions that require higher dimensions to describe the crystal. Here I discuss how scanning / transmission electron microscopy can probe atomic structure across sub-Angstrom to micron length scales in both two, three, and higher dimensions for the hierarchical engineering and design of 2D materials.
In 2D-materials—such as graphene, MoS2, and TaS2—reduced dimensionality leads to unique properties that could transform future of electronic devices. Local atomic structure of 2D materials dictates local topology which greatly influences electronic properties and implementation in actual devices. Using a modern electron microscope we can count the atoms across grain boundaries, identify stacking structure, and locate individual defects and dopants. Concurrently, diffraction techniques provide an understanding of structure across billions of atoms at larger length scales. In combination, we obtain a complete description of the structure of 2D materials and correlate them with macroscopic properties.
For quantum materials with charge ordering, the crystal is described in higher dimensions by the addition a periodic lattice distortions (PLD). We show the persistence and restructuring of PLDs down to the ultrathin limit and across a metal-insulator phase transition using cryogenic scanning transmission electron microscopy. Using picometer precision, we unearth inhomogeneity in the charge order at room temperature, and emergent phase coherence at 93 K. Such local phase variations govern the long-range correlations of the charge-ordered state and locally change the periodicity of the modulations, resulting in wave vector shifts in reciprocal space. These atomically resolved observations underscore the importance of lattice coupling and phase inhomogeneity, and provide a microscopic explanation for putative "incommensurate" order.
Kraig Andrews, Department of Physics, Wayne State University
Improved Contacts and Device Performance in MoS2 Transistors using MoSe2 as an Interlayer
Abstract: We report a new contact engineering method to minimize the Schottky barrier height (SBH) of MoS2 field-effect transistors (FETs) by using MoSe2 as an interlayer. We demonstrate that the addition of an ultrathin MoSe2 interlayer between the MoS2 channel and Ti electrodes reduces the SBH at the contacts by a factor of 4 from ~ 100 meV to ~ 25 meV, contact resistivity by about 60 times from ~6×10−5Ω 𝑐𝑚2 to ~1×10−6Ω 𝑐𝑚2, and current transfer length by a factor of 6 from ~ 425 nm to ~ 70 nm. The drastic reduction of SBH can be attributed to the synergy of Fermi level pinning close to the conduction band edge of the MoSe2 interlayer and the conduction band offset between the MoSe2 interlayer and MoS2 channel. As a result, the two-terminal effective mobility also improves from ~ 30-40 cm2V-1s-1 to 50-60 cm2V-1s-1 at room temperature.
Dr. Arunima K. Singh, Assistant Professor, Arizona State University
Computational Study of Nanoscale Surfaces and Interfaces
Abstract: Surfaces and interfaces are at the heart of modern-day technology, playing a central role in a variety of fields including sensing, energy conversion, and nano-electronics. Recent advancements in ab-initio methods, materials informatics, and computing power present us with an exciting opportunity to predictively discover and design materials surfaces and interfaces. In this talk, through the example of two-dimensional materials, I will show how ab-initio simulations, combined with multi-scale modeling techniques and genetic algorithms can be used to computationally discover, synthesize, and functionalize nanostructured surfaces. I will show how such studies can be performed in a high throughput fashion to create databases of surfaces and their properties; drastically reducing the time needed to invent new materials for surface sensitive applications. In this light, I will show how we have identified scores of robust and synthesizable materials’ surfaces for photocatalysis.
Dr. Venkat Ganesan, Professor of Chemical Engineering, University of Texas at Austin
In Pursuit of Mechanically Strong, Conducting Polymer Electrolytes
Abstract: The design of polymer electrolytes often revolve around the goal of achieving simultaneously enhanced conductivities and mechanical strengths in the same material. Indeed, electrolytes possessing high conductivities but low mechanical strengths, exhibit undesirable features such as dendrite formation of the metallic lithium anode which leads to short circuit of the electrodes. Unfortunately however, factors that enhance the mechanical strength of a material often leads to a deterioration of the conductivity and vice versa. Hence, there is an outstanding interest in strategies which can simultaneous enhance both the conductivity and mechanical strength of the electrolyte material. In this talk, I will discuss some results emerging out of our research in using computational techniques to study three strategies which have been examined in this regard: (i) Addition of ceramic nanoparticles to the polymer electrolytes; (ii) Creating block copolymer versions of the polymeric electrolyte; (iii) Use of ionic liquids (either directly or in polymerized form) in the polymer electrolyte. In each case, a short overview of the new insights which emerged from computer simulations will be discussed.
Suzan Arslanturk, Computer Science, Wayne State University
Machine Learning Applications in Medicine and Biology
Abstract: Clinical datasets present unique opportunities for existing and emerging descriptive and predictive analytics methods and models. In this talk, I will first describe a novel data integration methodology to identify subtypes of cancer using multiple data types (mRNA, methylation, microRNA, copy number variation, somatic variants) that come from different platforms (microarray, sequencing, etc.). Next, I will focus on a machine learning methodology to better understand the human skeletal muscle cell atlas. In particular, developing long short-term memory (LSTM) units of a recurrent neural network (RNN) to be able to predict the time-dependent changes in the morphology of the skeletal muscle cells using Differential Expansion Microscopy (DiExM) and Expansion Microscopy (EM) images. Next, I will discuss motivations for the ongoing work in discovering resting state EEG networks in neonates.
September 11, 2018
Namita Shokeen (WSU)
Differential Dynamic Microscopy in soft matter research
Kraig Andrews (WSU)
Achieving Low-Resistance Ohmic Contacts to MoS2 and PdSe2 using Ultrathin Transition Metal Dichalcogenides as a Contact Interlayer
September 18, 2018
Xinxin Woodward (WSU)
Study of lipid sorting and dynamics at curvature sites
Yuwen Mei (WSU)
Study of Mechanobiology of Pancreatic Cancer Cells (PANC-1) by Traction Force Microscopy
September 25, 2018
Maxim Tsoi (University of Texas at Austin)
Voltage Controlled Antiferromagnetics for Spintronic Applications
October 9, 2018
Fengyuan Yang (Ohio State University)
FMR-Drive Pure Spin Transport in Metals and Magnetic Insulators
October 23, 2018
Tyler L. Cocker (Michigan State University)
Ultrafast Terahertz Microscopy: From Near Fields to Single Atoms
November 27, 2018
Precision Preclinical Imaging: Basic Science, Therapeutic Development, and Translation
Abstract: Biomedical engineers are used to working at the interface of multiple disciplines and acting as interpreters in order to enable rapid and impactful collaborative science across a broad spectrum of disciplines. Due to the characteristics embodied by imaging: fundamentals based in the physical sciences and engineering, the capability to be applied to a plethora of (patho) physiologies, and clinical application, imaging naturally attracts biomedical engineers.
Following a brief overview of several imaging modalities, the focus of this talk will be on preclinical magnetic resonance imaging (MRI), in particular, and how it can be used to further research in basic science, therapeutic development, and translation to the clinic. Examples discussed will primarily include the cardiovascular system. Complementary expertise that is requisite for the most successful imaging endeavors will also be highlighted (e.g. in silico methods, small animal models of the human condition, and rigorous pre- and post- statistical analysis). Emphasis will be placed on how highly-optimized preclinical imaging and thoughtful experimental design can result in unique and important conclusions that might only be gleaned by using such technology.
- Winter 2018
Fall 2017 and prior
View archive of fall 2017 and prior.