Condensed Matter and Biophysics seminars
Condensed Matter seminars are held Tuesdays at 3:30 p.m. in Physics Research Building, room 245.
Series archives
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Fall 2023
November 28, 2023
Joshua Veazey, Grand Valley State University, Grand Rapids, MI
A Single-Axis Tunneling Microscope for Undergraduate Labs
Abstract
We have developed a simplified alternative to the scanning tunneling microscope (STM) that restricts tip motion to one dimension: the z-axis tunneling microscope (ZTM) [1]. Here, the z-axis lies along the tip-sample separation. While no imaging is possible, students in advanced undergraduate labs can observe the exponential dependence on tunneling current with tip-sample gap and observe qualitative differences in the electronic density of states between metals, semimetals, and semiconductors. I will also discuss continued efforts to integrate control electronics and data acquisition into a fully open-access controller module. The ZTM is simpler and less costly to build than an STM, expanding access to a subset of STM experiments to reach more learners.
November 21, 2023
Suvranta Tripathy, University of Michigan-Dearborn, Dearborn, MI
Molecular Nano-Machines at Work
Abstract
Living systems possess unique mechanical and thermodynamic properties functioning far from thermal equilibrium. Nanometer-sized biological proteins, so-called molecular motors, or motor proteins, exert forces on cellular structures by the transduction of chemical energy from ATP hydrolysis to mechanical energy. These Nano-machines transport cargos to correct destinations within the cells at the appropriate times and facilitate critical cellular processes. Despite such importance, the regulation mechanisms of nano-motors in cells have not been fully explored. Our recent studies revealed a new way of transport regulation where membrane pH of cellular cargo such as phagosome can bias its directions of transport. Using optical tweezers in cells, we have quantified the force generation and tenacity of nano-motors at a single molecule level at a different pH level of the phagosomes. Our result provides deep insight into the cellular and molecular mechanisms of the phagocytosis process that is essential for the degradation of various pathogens.
November 7, 2023
Mrinomy Chini, Teerthanker Mahaveer University, India
Optoelectronic Applications of Rationally Synthesized Organic Semiconductors
Abstract
There has been a significant increase in the interest in organic optoelectronics over the last 20 years, owing to significant advancements in material design and purification, which have resulted in a significant increase in material performance. Organic materials are nowadays being widely used in optoelectronic devices like organic thin-film transistors, LEDs, solar cells, detectors, photorefractive devices, and so on. The low cost of these materials, as well as the potential of room-temperature deposition from solution on large-area and/or different substrates, are among the technological promises. This presentation briefly highlights the rationale behind organic semiconductors design and synthesis, and their applications in organic field effect transistors (OFETs), dye-sensitized solar cells (DSSCs), and electrochemical supercapacitors. OFETs help us to measure the n-type and p-type charge carrier mobilities of organic semiconductors. In the case of DSSCs, we have shown that the introduction of an efficient and precious platinum (Pt) free counter electrode made of nano-porous reduced graphene oxide (PG) and containing a PEDOT:PSS−PG composite on an FTO substrate, can be effectively employed as a counter electrode for DSSCs, owing to the demonstration of excellent I3− diffusion, remarkable photocatalytic activity, and better device performances along with desired stability. Hydrothermally reduced PGs and conducting polyaniline (PANI) nanofiber composites (PGs–PANI) have shown capacitive behavior superior to their individual PANI and PGs counterparts. This is due to the synergistic effect of PANI and PGs in improving the performance of supercapacitors.
October 24, 2023
Helen E. Durand, College of Engineering, Wayne State University
Investigating the Intersection of Automation Algorithms with Quantum Computation
Abstract
Next-generation manufacturing systems will have greater autonomy and efficiency due to advances in computers, control designs, and networking that enable more data to be utilized from throughout a plant and promote more optimal decision-making. Despite the significant advances in computing power over the last decades, many complex engineering problems remain time-consuming to solve on classical computing devices, such as computational fluid dynamics and finite element analysis models. This limits the complexity of models that can be considered when designing and evaluating control strategies, and raises the question of whether quantum computers could hold any benefits for reducing computation time for control-relevant problems in the future. The means for addressing this latter question is, however, non-obvious, so that initially exploring how control laws can be implemented on quantum computers may aid in providing direction toward answering the broader question. In this talk, we will discuss our results to date which probe the intersection of quantum computing with control, particularly focusing on control-theoretic considerations such as the conditions under which a controller implemented with the aid of a quantum computer might remain stabilizing for operation of a process, even in the presence of a non-deterministic quantum algorithm or noise in the physical device.
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Winter 2021
April 27, 2021
Dr. Indermeet Kohli, Henry Ford Health System, Detroit, MI
Ultraviolet C in Photodermatology
Abstract
In March 2020, the COVID-19 pandemic resulted in a critical shortage of personal protective equipment (PPE), particularly N95 filtering facepiece respirators, in hospitals throughout the United States and abroad. As such the ability to disinfect and reuse disposable N95 respirators was urgently needed. Ultraviolet C (particularly 254 nm) radiation is known for its germicidal effects. It inactivates microorganisms by causing DNA damage and preventing replication. This presentation will outline one center’s experience in applying the fundamental concepts of photomedicine directly to the global crisis at hand, providing timely solutions to critical problems including shortages of PPE during this pandemic.
April 20, 2021
Dr. Michael Page, Air Force Research Lab, Wright-Patterson Air Force Base, OH
High Frequency Acousto-Magnetic Electronics
Abstract
Modern warfare will take place in environments in which a complex and hostile electromagnetic spectrum exists. Rather than the permissive environments of the past, warfighters will have to operate in a contested EM spectrum facing near-pear technology absent the advantage of vastly superior capabilities. Disruptive advancements in RF/microwave technologies will be required to maintain our warfighter technology advantage. One particularly promising avenue of exploration for novel high frequency devices lies within the field of strain mediated multiferroics. While multiferroics has a rich history of advancement, currently, the field has largely been limited to the study of how static changes in one order parameter affect the dynamics of another. As an alternative approach, my work focuses on the exploration of phonon/magnon interactions in multiferroic heterostructures. In particular, we seek to understand the interconversion between high frequency strain in piezoelectrics and dynamic magnetic properties in an adjacent magnetic material. These explorations are enabling new understanding of the dynamics of interactions between various multiferroic ordered states resulting in advances in materials, characterization methods, and device design in multiferroic heterostructures.
Specifically, I will discuss my work in Acoustically Driven Ferromagnetic Resonance (ADFMR) and a variety of interesting results both from a fundamental science aspect as well as with an eye towards applications, such as compact RF isolators. In support of these devices and for other efforts, I will also describe our progress in growing exceptionally high quality epitaxial magnetic films such as yttrium iron garnet and spinel ferrites. Finally, I will discuss the suite of characterization tools we have developed for high-frequency and high resolution imaging of magnetic and acoustic dynamics such as scanned nitrogen vacancy center magnetometry, Brillouin light scattering, and acoustic wave imaging.
April 13, 2021
Prof. Alexey Kolmogorov, Binghamton University, SUNY, Department of Physics
Development of neural network-based interatomic potentials for acceleration of structure prediction
Abstract
Interatomic models based on neural networks (NNs) have emerged as attractive alternatives to traditional potentials. Being general and flexible learning machines, NNs can be tuned to describe diverse atomic environments with near ab initio accuracy. In an effort to automate the construction of NN models for multielement systems, we have developed a systematic data generation protocol to sample relevant parts of configuration space and a stratified training scheme to fit models sequentially from the bottom up: first for unaries, then for binaries, and so on. This approach implemented in our MAISE package has allowed us to generate a library of practical NNs for several metals and alloys. Practical use of such NN interatomic models in structure prediction has demonstrated that they are efficient enough to accelerate ab initio global structure searches by orders of magnitude and reliable enough to identify overlooked stable materials [1].
[1] S. Hajinazar, A. Thorn, E.D. Sandoval, S. Kharabadze, A.N. Kolmogorov, Comput. Phys. Commun. 259, 107679 (2020).
March 30, 2021
Dr. Hsun-Jen (Ben) Chu, NOVA research Inc.
From exfoliation to stacking: The interfaces, strain, and defects of 2D materials
Abstract
Van der Waals layered materials, such as transition metal dichalcogenides (TMDs), are an exciting class of layered materials with weakly bonded interlayers which enables one to create so-called van der Waals heterostructures (vdWH). Although the vdWH exhibits many fruitful exciting novel properties through interlayer coupling, the interface contamination in vdWH remains a major obstacle to achieve those properties. To clearly observe the intrinsic properties, such as defect density of monolayer TMDs (electrical), interlayer exciton in vdWH (optical), or atomic reconstruction in vdWH (mechanical), the clean interfaces are in urgent needs. In our research, we first introduced a unique AFM technic so-called “nano-squeegee” for crating clean interfaces in vdWH which paves the way for investigating intrinsic electrical, optical, and mechanical properties of the TMD vdWH.
Based on the clean interfaces in the vdWH enabled by the “nano-squeegee”, we could quantitively investigate the PL quality of the Monolayer TMD and correlated it with the defect density of the Monolayer TMDs. By using conductive AFM, we could measure the local electrical conductance which presumably indicates the defects sites on the TMD monolayer. The higher defect density of the TMD leads to lower PL emission or quantum yield. Another promising attribute of vdWH is control over the twist angle between layers, which leads to the formation of Interlayer exciton (ILE) when forming a type II band alignment heterostructure. With hBN encapsulation and a relative rotational angle close to 60 degrees, well pronounced ILE emission is observed at room temperature and further splits into two distinct peaks (ILE1 and ILE2) at low temp. Furthermore, we demonstrate that the ILE emission peaks have opposite circular polarizations when excited by circularly polarized light. Ab initio calculations provide an explanation of this unique and potentially useful property and indicate that it is a result of the indirect character of both transitions. We further investigate the atomic structure arrangement of TMDs by TEM and reveal that the heterostructure indeed reconstructs under a small twist angle ( ≤ 1°) between the TMDs in the commensurate system. With a small twist angle, periodic domains form with commensurate stacking within the domain. On the other hand, a rigid moiré structure is also observed by TEM when a larger twist angle (≥ 3°) is applied. This finding provides a significant departure from the current rigid-lattice moiré theory in such a system which only considered the constituent layers as rigid lattices and has not allowed for atomic-level reconstruction. These results may also provide fundamental insights into the mechanical and optical behavior of this exciting class of semiconductor heterostructure.
March 23, 2021
Dr. Vinayak Bhat, International Research Centre MagTop, Institute of Physics, Polish Academy of Sciences,
Direct Observation of Magnon Modes in Kagome Artificial Spin Ice with Topological Defects
Abstract
Kagome artificial spin ice (KASI) is a network of Ising type nanobars on a kagome lattice. We investigate spin dynamics of a KASI consisting of Ni81Fe19 nanomagnets arranged on an interconnected kagome lattice using broadband ferromagnetic resonance (FMR), magnetic force microscopy (MFM), micro-focus Brillouin light scattering (BLS) microscopy and X-ray photoemission electron microscopy (XPEEM). Micro-focus BLS performed on magnetically disordered states exhibit a series of magnon resonances which depend on topological defect configurations. We experimentally reconfigure microstates in ASI using a 2D vector field protocol and apply microwave-assisted switching to intentionally trigger reversal. Our work is key for the creation of avalanches inside the kagome ASI and reprogrammable magnonics based on ASIs.
Acknowledgement: The research was supported by the Swiss National Science Foundation via Grant No. 163016. V.S. Bhat acknowledges support from the foundation for Polish Science through the IRA Programme financed by EU within SG OP Programme.
February 16, 2021
Joseph Packizer, Wayne State University
Crystalline Anisotropic Topological Superconductivity in Planar Josephson Junctions
Abstract
We theoretically investigate the crystalline anisotropy of topological phase transitions in phase-controlled planar Josephson junctions (JJs) subject to spin-orbit coupling and in-plane magnetic fields. It is shown how topological superconductivity (TS) is affected by the interplay between the magnetic field and the orientation of the junction with respect to its crystallographic axes. This interplay can be used to electrically tune between BDI and D symmetry classes in a controlled fashion and thereby optimize the stability and localization of Majorana bound states in planar Josephson junctions. Our findings can be used as a guide for achieving the most favorable conditions when engineering TS in planar JJs and can be particularly relevant for setups containing non-collinear junctions which have been proposed for performing braiding operations on multiple Majorana pairs.
Siphiwo R. Dlamini, Wayne State University
Designing Quantum States in Two-Dimensional Systems by Reconfiguring Local Magnetic Proximity Fields
Abstract
We theoretically investigate the crystalline anisotropy of topological phase transitions in phase-controlled planar Josephson junctions (JJs) subject to spin-orbit coupling and in-plane magnetic fields. It is shown how topological superconductivity (TS) is affected by the interplay between the magnetic field and the orientation of the junction with respect to its crystallographic axes. This interplay can be used to electrically tune between BDI and D symmetry classes in a controlled fashion and thereby optimize the stability and localization of Majorana bound states in planar Josephson junctions. Our findings can be used as a guide for achieving the most favorable conditions when engineering TS in planar JJs and can be particularly relevant for setups containing non-collinear junctions which have been proposed for performing braiding operations on multiple Majorana pairs
January 26, 2021
Dr. Rezvan Shahoei, University of Illinois at Urbana Champaign
Computational Modeling and Simulation of Ligand-Gated Ion Channels
Abstract
Pentameric ligand-gated ion channels, from bacteria to the brain, convert chemical signals into electric signals. In this talk, I will present the results from two projects in which molecular dynamics (MD) simulations and MD-based methods are utilized to study two members of this protein superfamily and their interactions with small molecules. The first project focuses on menthol binding to the most abundant nicotinic acetylcholine receptor in the brain. In the second project, MD simulations are used to determine the functional states of experimentally-derived models of the human α1 glycine receptor.
January 19, 2021
Dr. Moynul Hasan, Jagannath University
Mechanism of Initial Stage of Pore Formation by Antimicrobial Peptide Magainin 2
Abstract
Antimicrobial peptides (AMPs) are a diverse class of naturally occurring molecules that are produced as a first line of defense by all multicellular organisms and can fight against bacteria, yeasts, fungi, viruses and even cancer cells. Magainin 2, which is isolated from the skin of frogs, is a representative AMP. Magainin 2, forms pores in lipid membranes and induces membrane permeation of the cellular contents. Although this permeation is likely the main cause of its bactericidal activity, the mechanism of pore formation remains poorly understood. Recent data suggest that binding of magainin 2 (at initial stage) to the outer monolayer of lipid bilayer induces tension or stretching in the inner monolayer that plays an important role in pore formation. To confirm the mechanism of magainin 2-induced pore formation at initial stage, I prepared asymmetrically packed giant unilameller vesicles, GUVs (diameter > 10 m), where inner monolayer is highly packed (less stretched) than outer one. Then the interaction of magainin 2 with these GUVs were investigated by single GUV method.
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Fall 2020
December 8, 2020
Dr. Kekenes-Huskey, Department of Cell & Molecular Physiology at Loyola University Chicago
Small molecule diffusion and reactions in complex environments
Abstract
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
Abstract
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.
Bio
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
Abstract
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
Abstract
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
Abstract
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
Abstract
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.
References
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.Bio
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
Abstract
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
Abstract
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
Abstract
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.
Bio
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 -
Winter 2020
February 25
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.
February 11
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.
January 28
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.
January 21
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.
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Fall 2019
October 1
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.
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Winter 2019
April 16
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.
April 9
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.
March 26
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.
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Fall 2018
September 11, 2018
Namita Shokeen, Wayne State University
Differential Dynamic Microscopy in soft matter research
Kraig Andrews, Wayne State University
Achieving Low-Resistance Ohmic Contacts to MoS2 and PdSe2 using Ultrathin Transition Metal Dichalcogenides as a Contact Interlayer
September 18, 2018
Xinxin Woodward, Wayne State University
Study of lipid sorting and dynamics at curvature sites
Yuwen Mei, Wayne State University
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
Joan Greve
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
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Fall 2017 and prior
View archive of fall 2017 and prior.