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Chemistry Guest Seminars

A&P Seminars 2019

Analytical & Physical Seminars

W. Albert Noyes, Jr. Distinguished Visiting Lectureship

Thursday, October 24, 3:30pm - 4:30pm, NHB 1.720 jonas

Carrier dynamics in semiconductor quantum dots, from ballistic to thermodynamic

David Jonas


University of Colorado

Jonas Group

Current photovoltaic devices have a limit on how much energy can be collected from sunlight: photons with insufficient energy are not absorbed and photons with excess energy create excitons that thermalize before being collected. One way to increase this limit would be to convert the high-energy photons into more than one exciton each.  There is experimental evidence that multiple exciton generation can happen in semiconductor quantum dots, but the mechanism is unclear. A semiconductor quantum dot has a size large compared to lattice constants but small or comparable to the bulk Bohr exciton radius. In this situation, an excited electron is delocalized with respect to its parent atom but confined to the quantum dot. The same is true for the empty orbital left behind, which is called a hole. The electron and the hole together are termed an exciton.

When forming an exciton by optical excitation, any photon energy above the band gap, Eg, is distributed between the hole and the electron. This excess energy puts the electron and hole far from thermal equilibrium with the crystal, and potentially even with each other. The cooling of these "hot" carriers can occur by a variety of methods. Two methods of interest in quantum dot multiple exciton generation theories are phonon emission and impact ionization. In phonon emission, an exciton excites a vibration and scatters as a lower-energy exciton. In impact ionization an electron or hole loses excess energy by exciting another electron into the conduction band, thereby creating another exciton. Studies in the Jonas group include a variety of nonlinear spectroscopies in order to measure the timescales and importance of these mechanisms.

Publications (Group Site)

Author Metrics

h-index: 28  Total Publications:  63  Total Citations:  4105  (Web of Science, Sep. 2019)

Thursday, Sep. 26, 3:30pm - 4:30pm, NHB 1.720 prell

Solving the Problem of Polydispersity in Native Ion Mobility-Mass Spectrometry: Bacterial Pore-Forming Toxins and Beyond

Jim Prell

Assistant Professor

University of Oregon

Prell Labs

Abstract:  Native ion mobility-mass spectrometry (IM-MS) uses electrospray ionization from buffered, aqueous solutions to gently transfer biomolecular complexes into the gas phase, where their mass, size, composition, and high-order structure can often be rapidly, sensitively, and accurately determined. However, as instrument improvements have greatly increased the complexity, polydispersity, and heterogeneity of complexes that can be routinely detected, a major problem has arisen: how to make sense of the extremely congested IM-MS spectra that result from these diverse ion populations. The Prell Group has created signal processing tools to disentangle these spectra, using polydispersity as an advantage for characterizing native complexes via Fourier and Gábor Transform. In this talk, I describe application of these and other tools we have developed to characterize the structure of bacterial pore-forming toxin complexes and to provide a way around the dependence of native IM-MS on volatile salt buffers.

Publications (Group Site)

Publicatons (Google Scholar Citations)

Author Metrics

h-index: 24  Total Publications:  43  Total Citations:  1674  (Web of Science, Aug. 2019)

h-index: 24  Total Citations: 2102 (Google Scholar Citations, Aug. 2019)

Thursday, Sep. 19, 3:30pm - 4:30pm, NHB 1.720 afsar

Rapid Disease Diagnosis with Mass Spectrometry: Successes, Pitfalls and Challenges; A Personal Report

Arash Zarrine-Afsar

Assistant Professor, Medical Biophysics

University of Toronto


Dr. Zarrine-Afsar’s current research interests revolve around the development of novel molecular oncology methods as they relate to rapid pathology and tumour type or subtype characterization, with a special focus on neuro-oncology and pediatric brain cancers.  In particular, the utility of a hand held Picosecond InfraRed Laser (PIRL) desorption probe for rapid tumour type or subtype/subgroup identification based on real time, 10-second mass spectrometry (MS) analysis of the laser extracted tumour lipids and small molecule metabolites is being investigated. Current progress have made rapid determination of pediatric medulloblastoma (MB) subgroup affiliations on intrasurgical timescales possible with only 10-seconds of sampling and total analysis time, with a correct subgroup affiliation determination rate of ~98%, established over 100 independent banked ex vivo tumour tissues. A translational device development program based on the integration with surgical navigation platforms of the hand-held probe are being pursued that will lead to the novel concept of molecularly guided surgery based on spatially encoded mass spectrometry results for a personalized approach to MB resection that is aimed to reduce neurologic morbidity in low risk patients. The utility of the developed sampling probe that operates on the basis of Serially Mapping Ablated Residues from Tissue (SMART) is being expanded to other cancers through parallel developments of PIRL-MS signature libraries as well as real time, higher-order data and multivariate statistical analysis methods.  

Publications (UT Profile)

Author Metrics

h-index: 21  Total Publications:  237 Total Citations:  1529  (Web of Science, Aug. 2019)

Thursday, Sept. 5, 3:30pm - 4:30pm, NHB 1.720 fayer

Hydronium-Water Dynamics: Ultrafast Two Dimensional Infrared Chemical Exchange Spectroscopy

Michael Fayer

David Mulvane Ehrsam and Edward Curtis Franklin Professor of Chemistry

Stanford University

Fayer Lab


Two dimensional infrared (2D IR) spectroscopy is used to investigate the dynamics of water.  It is shown that a probe molecule, methylthiocyanate (MSCN), can be used to measure water hydrogen bond dynamics.  The efficacy of this molecule is the CN stretch’s ~30 ps lifetime, making possible measurements of relatively slow processes. In addition, MSCN has a well-defined spectrum even in concentrated HCl solutions.  First, MSCN is used to investigate dynamics of concentrated LiCl solutions.  Chemical exchange is observed that reveals the dynamics of the interchange of water and Li+ bonding to the CN nitrogen lone pair.  The time constants for Li+ replacing water and water replacing Li+ are obtained.  Then, concentrated HCl solutions are investigated.  The CN spectrum shows two bands, one with water H-bonded to the N lone pair and one with hydronium bonded to the lone pair. Again chemical exchange is observed, and the time constants for exchange of hydronium to water and vice versa are presented as a function of HCl concentration.  Two possible mechanism can describe the data: 1. the physical exchange of hydronium and water, as occurs for Li+ and water, and 2. proton hopping between hydronium and water, in which case only a proton moves.  Ab initio molecular dynamics simulations are used to determine the mechanism and other important aspects of the observables.  It is found that 80% of the observed dynamics are from proton hopping.  From the HCl concentration dependence in the experiments and the simulations it is possible extend the high HCl concentration measurements to the limit of infinite dilution to obtain the proton hopping rate. The measurement of the hopping rate determined from the direct chemical exchange experiments taken to infinite dilution coincides with the value inferred from mobility measurements.  An important result is that the hopping time is the same as the hydrogen bond rearrangement time in pure water.  It is argued that proton hopping is triggered by the concerted hydrogen bond rearrangement of many water molecule as obtained from 2D IR spectral diffusion measurements of pure water.  The water hydrogen bond rearrangement as the driving force for proton hopping is affirmed by the temperature dependence of pure water spectral diffusion compared to the temperature dependence of proton hopping times from mobility measurements.

Publications (Group Site)

Author Metrics

h-index: 81  Total Publications:  443  Total Citations:  22,580 (Web of Science, Jul. 2019)

Thursday, Aug. 22, 3:30pm - 4:30pm, NHB 1.720 raleigh

Action at the nanoscale: Single-molecule studies of protein dynamics

Gabriela Schlau-Cohen

Assistant Professor of Chemistry


Lab Web Page

Research in our group is inherently multidisciplinary; we combine tools from chemistry, optics, biology, and microscopy to develop new approaches to probe dynamics. We study dynamics in two classes of systems:  biological and bio-inspired light-harvesting systems that are of interest to solar energy research and biomass production; and bacterial and mammalian receptor proteins that are targets for human therapeutics. To explore these systems, we use ultrafast transient absorption spectroscopy, single-molecule fluorescence spectroscopy, and develop model membrane systems.

Publications (Group Site)

Publicatons (Google Scholar Citations)

Author Metrics

h-index: 16  Total Publications:  25  Total Citations:  1208 (Web of Science, Jul. 2019)

h-index: 17  Total Citations: 1628 (Google Scholar Citations, Jul. 2019)

Monday, May 13, 3:30-4:30pm, WEL 2.122clowers

Ion Beam Modulation Strategies to Maximize Throughput for Ion Mobility Spectrometry

Brian Clowers

Assistant Professor

Washington State University

Clowers Group

The core instruments designed and constructed in the Clowers Research Group are focused almost exclusively on the accurate measurement of gas-phase ion properties.  While stand alone ion mobility instruments are extremely useful in a field-based setting the combination of this technique with mass spectrometry provides a second dimension of analysis that is extremely powerful.  The research ion mobility instruments being constructed in our laboratory include both high (760 Torr) and low pressure (~4 Torr) instruments both capable of operating at a range of temperatures.

Publications (Group Site)

Publications (Google Scholar Citations)

Author Metrics

h-index:  25  Total Articles: 68  Total Citations:  2261  (Web of Science, Apr. 2019)

h-index: 30  Total Citations: 3330 (Google Scholar Citations, Apr. 2019)

Thursday, April 25, 3:30-5:00pm, WEL 2.122presse

Novel Mathematics to unravel intracellular life

Steve Pressé

Associate Professor

Arizona State University

Pressé Lab

At the single molecule level, experiments now follow the steps in the life's journey of a single protein; from its synthesis in a ribosome, to its activity in a complex dynamical environment, to its death by proteolysis. At the cellular level, experiments reveal with incredible detail how groups of proteins come together to regulate important events such as cell division. In an ideal world, experiments should not require much modeling to reveal physical insight -- the data should be self-evident. Yet biophysical data is noisy, complex and largely incomplete for a variety of reasons. This is especially true of data collected from live cells. On the theory side, we develop, adapt and use tools derived from statistics, statistical physics and stochastic processes, broadly defined, to understand living systems across multiple time and length scales. On this front, there are two main research directions in our group: 1) we develop methods to infer models from imaging and spectroscopy data in biophysics with a recent focus on Bayesian nonparametrics; 2) we are developing models to understand enzymatic and molecular motor efficiency. On the experimental front, we are exploring the role of hydrodynamics on the interaction of bacterial predators with their prey.

Publications (Group Site)

Publications (Google Scholar Citations)

Author Metrics

h-index:  12  Total Articles: 36  Total Citations:  614  (Web of Science, Apr. 2019)

h-index: 16  Total Citations: 928 (Google Scholar Citations, Apr. 2019)

Thursday, April 11, 3:30-4:30pm, WEL 2.122skinner

Anomalies in ambient and supercooled water: Is there a second critical point lurking nearby?

James Skinner

Crown Family Professor of Molecular Engineering

University of Chicago

Skinner Group

We are interested in the structure and dynamics of condensed phase systems, and in particular, in the theory of time-dependent phenomena in liquids. Experimentally, one important approach for determining the structure and dynamics of condensed matter involves linear and non-linear vibrational spectroscopy. Typically, such spectroscopy contains information about local molecular environments, whose extraction, however, usually requires theoretical models and their solutions. In order to accomplish this, we use ab initio calculations, molecular dynamics simulations, statistical mechanics, and basically any theoretical approach that will enable us to further our understanding. The systems we are working on include water, peptides and proteins, interfaces, membranes etc.

Publications (Group Site)

Publications (Google Scholar Citations)

Author Metrics

h-index:  66  Total Articles: 209  Total Citations:  12,746  (Web of Science, Mar. 2019)

h-index: 74  Total Citations: 15,714 (Google Scholar Citations, Mar. 2019)

Department Seminar

Wed. April 10, 11am-12noon, NHB 1.720xiang

Functional Oligonucleotides for Portable Diagnosis and "Smart" Therapeutics

Yu Xiang

Associate Professor

Tsinghua University

ResearchGate Profile

Publications (Google Scholar Citations)

Author Metrics

h-index: 32  Total Citations:  4829 (Google Scholar Citations, Mar. 2019)

Co-presented with the Dept. of Chemical Engineering

Thursday, March 28, 3:30-4:30pm, WEL 2.122sheldon

Nanomaterials and Light: New Opportunities in Energy Research

Matthew Sheldon

Assistant Professor

Texas A&M University

Sheldon Group

Our research considers fundamental questions of optical energy conversion relating to plasmonic and inorganic nanoscale materials. Our experiments are principally designed to identify and optimize unique nanoscale phenomena useful for solar energy conversion, as well as related opportunities at the intersection of nanophotonics and chemistry for broad application beyond the scope of solar energy.  The current world record solar cell operates at 44.4% power conversion efficiency. Thermodynamic analyses indicate that much higher efficiency is theoretically possible. Indeed, technical challenges, rather than laws of nature, limit current solar power convertors from achieving the maximum thermodynamic efficiency of 95%.

  • We explore how nanofabricated optoelectronic and plasmonic materials can provide systematic control of the thermodynamic parameters governing optical power conversion for optimization that can shape, confine, and interconvert the energy and entropy of a radiation field.
  • We employ optical and electrical characterization techniques with high spatial and energy resolution to probe optical excitation and relaxation mechanisms in nanostructured metals and semiconductors.

Publications (Group Page)

Author Metrics

h-index:  10  Total Articles:  18  Total Citations:  871  (Web of Science, Mar. 2019)

Thursday, March 14, 3:30-4:30pm, WEL 2.122bercovici

Microscale electrokinetics - from enhanced biochemical analysis to configurable flow patterns

Moran Bercovici

Associate Professor, Mechanical Engineering


Microfluidics Technology Laboratory

The unique physics of fluids at the microscale holds both challenges in the understating of basic physical phenomena and opportunities in leveraging these phenomena toward new technologies.  Our lab combines experimental, analytical, and computational tools to study microfluidic problems characterized by coupling between fluid mechanics, heat transfer, electric fields, chemical reactions, and biological processes.  We are currently interested in understanding basic mechanisms in electro-viscous-elastic interactions, thermocapillary, superhydrophobic surfaces, and in utilizing them to create new technologies for flow patterning, configurable microstructures, 3D printing, biosensing, and single cell analysis.

Publications (Microfluidics Technology Lab)

Author Metrics

h-index:  15  Total Articles:  46  Total Citations:  839  (Web of Science, Mar. 2019)

Thursday, February 28, 3:30-5:00pm, WEL 2.122grumstrup

Chemically- and Structurally- correlated Charge Carrier Transport in Disordered Materials

Erik Grumstrup

Assistant Professor

Montana State University

Group Page

Our research group utilizes nonlinear microscopy and ultrafast laser spectroscopy to interrogate and understand the optical, electronic, and chemical properties of materials important for advanced solar energy, catalytic, and electronics technologies. We are particularly interested in correlating macroscopic functionality with structural and compositional information on length scales between 10 nanometers and 10 microns. To this end, we use a variety of nonlinear microscopies, ab initio and semi-empirical theoretical methods, and ongoing technique development to advance understanding of how atomic and molecular scale interactions couple with mesoscopic interfaces and defects to determine overall material and device properties.

Publications (Group Site)

Author Metrics

h-index:  14  Total Articles:  28  Total Citations:  597  (Web of Science, Feb. 2019)

Thursday, February 21, 3:30-4:30pm, WEL 2.122burgard

Wastewater as a tool to understand community illicit drug consumption

Daniel Burgard

Professor ; Chair

University of Puget Sound

Faculty Profile

Dan is interested in environmental analyses and monitoring of air and water. Projects with Puget Sound students have included remote sensing measurements of in-use emissions from vehicles such as cars, trucks, school buses, transit buses, trains, and  boats (small personal vessels, commercial vessels and ocean-going vessels) both in the U.S. and internationally. Water analyses include quantifying trace levels of pharmaceuticals and illicit drugs in wastewater. 

Publications (Google Scholar Citations)


Author Metrics

h-index:  9  Total Articles:  16  Total Citations:  228  (Web of Science, Jan. 2019)

h-index: 10  Total Citations:  388 (Google Scholar Citations, Jan. 2019)

Noyes Lecture

Thursday, February 7, 3:30-4:30pm, WEL 2.122zare

Microdroplet Reactions: A New Frontier in Chemistry

Richard N. Zare

Marguerite Blake Wilbur Professor in Natural Science

Stanford University

Research Group Site

For summaries of the many research topics of the Zare Lab, see the ZareLab Guide.

Publications (Group Site)

Author Metrics

h-index:  111  Total Articles:  817  Total Citations:  49,142  (Web of Science, Jan. 2019)

Thursday, January 31, 3:30-5:00pm, WEL 2.122lewis

Materials by Design Principles in Artificial Photosynthesis: Discovery and Synergistic Integration of Light Absorbers, Electrocatalysts and Membranes for a Complete, Stable, Efficient, and Safe Solar Fuels Generator

Nathan S. Lewis

George L. Argyros Professor of Chemistry


Research Group Site

Our research spans from single materials to fully integrated, operational devices and focuses on solving present-day issues in energy and chemical sensing by controlling interactions between light, semiconductors, catalysts, and liquids.

Publications (Group Site)

Author Metrics

h-index:  86  Total Articles:  409  Total Citations:  36,577  (Web of Science, Jan. 2019)

Faculty Recruiting Seminar

Wednesday, January 16, 3:30-4:30pm, WEL 2.122xiang

Probing single molecules: from molecular electronics to multidimensional super-resolution microscopy

Limin Xiang

Postdoctoral Researcher

UC Berkeley

PhD 2016, Arizona State University

Ke Xu Group

The Xu group is an interdisciplinary lab that develops new physicochemical tools to interrogate biological, chemical, and materials systems at the nanoscale with extraordinary resolution, sensitivity, and functionality. To do so, we take a multidimensional approach that integrates advanced microscopy, spectroscopy, cell biology, and nanotechnology.

Publications (Google Scholar)

Author Metrics

h-index:  8  Total Citations:  265  (Google Scholar Citations, Dec. 2018)

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