Department of Chemistry and Biochemistry
Organic/Inorganic/Materials Seminar Series
O-I-M Faculty Introductions – Fall 2024
Friday, December 6, 2024
3:00 pm, WIL 110
Christopher Hendon
Assistant Professor
Chemistry and Biochemistry
Hendon Lab
Celeste Melamed
Assistant Professor – Fall 2025
Chemistry and Biochemistry
Department of Chemistry and Biochemistry
Physical Chemistry Seminar Series
Professor Andrew H. Marcus, University of Oregon
December 2, 2024 — 2:00pm
Tykeson 140
Title: Studies of local DNA structure and dynamics by nonlinear spectroscopy and single-molecule optical approaches
DNA contains the ‘genetic information’ that is encoded as specific DNA base sequences, and which is ‘read’ and ‘processed’ by proteins that interact with DNA at specific sites. The local conformations of DNA bases and sugar-phosphate backbones near single-stranded (ss) – double-stranded (ds) DNA junctions undergo thermally activated fluctuations (termed DNA ‘breathing’) within an unknown distribution of macrostates to permit the proper binding of proteins involved in core biochemical processes.
In this talk, I will discuss novel spectroscopic methods and analyses – both at the ensemble and single-molecule levels – to study structural and dynamic properties of exciton-coupled molecular dimer-labeled DNA constructs in which the dimer probes are inserted at key positions involved in protein-DNA complex assembly and function. The exciton-coupled dimer probes act as ‘sensors’ of the local conformations adopted by the DNA bases and backbones immediately adjacent to the probes. These methods can be used to study the biochemical mechanisms of protein-DNA recognition, complex assembly, and function in biological processes.
Department of Chemistry and Biochemistry
Organic/Inorganic/Materials Seminar Series
O-I-M Faculty Introductions – Fall 2024
Friday, November 8, 2024
3:00 pm, WIL 110
Carl Brozek
Assistant Professor
Chemistry and Biochemistry
Brozek Lab
Darren Johnson
Professor
Chemistry and Biochemistry
DW Johnson Lab
Amanda Cook-Sneathen
Assistant Professor
Chemistry and Biochemistry
Cook Lab
Department of Chemistry and Biochemistry
Physical Chemistry Seminar Series
Professor Teresa Rapp, University of Oregon
November 4, 2024 —2:00pm
Tykeson 140
Title: Photo-scissile Ruthenium Compounds for Tissue Engineering and Drug Delivery
Biology is complex. Any biological process we may wish to replicate, modulate, or direct exhibits complexity in both space and time. Spatial gradients of soluble proteins direct cell migration and proliferation. Cell populations must increase and decrease over various timescales. Any disruption to this order leads to a disordered state which is indicated in various diseases, chronic wounds, or tumorigenesis. If we wish to study these disordered systems, we need a platform that affords us control over biological events in both space and time.
Light offers both the researcher and clinician control over biological events in space and time. We leverage the uniquely powerful photochemistry of ruthenium polypyridyl compounds to trigger complex events in biological systems, from changing material environments to releasing drug cargoes on demand.
In this presentation I will discuss how we design and leverage ruthenium’s photochemistry and synthetic accessibility to produce the next generation of photodynamic biomaterials.
Department of Chemistry and Biochemistry
Physical Chemistry Seminar Series
Professor Dhiman Ray, University of Oregon
October 28th, 2024 —2:00pm
Tykeson 140
Title: Deep Learning Augmented Simulation of Biomolecules
Molecular dynamics (MD) simulations are used extensively to study the mechanisms of biological processes in atomistic resolution. Most physiological events, e.g. drug-target binding and protein folding, occur at beyond millisecond timescales. But, we can simulate only up to a few microseconds at an affordable computational cost. Enhanced sampling algorithms such as umbrella sampling, metadynamics, etc. can accelerate conformational sampling by applying external biasing potential. The accuracy and efficiency of these algorithms are sensitive to the choice of collective variable (CV), a low dimensional space along which the bias is applied. Intuitive CVs, e.g. distances, angles, etc. are often insufficient to adequately sample the conformational landscape.
Machine learning algorithms can play a key role in addressing these challenges. We demonstrated that collective variables constructed using deep neural networks with a generic and system-agnostic feature space provide accurate free energy surface for complex molecular systems e.g. protein folding and ligand binding. Using it in combination with the novel On-the-fly probability enhanced sampling (OPES) flooding algorithm, the kinetic properties can also be recovered. Integrating them with explainable artificial intelligence (XAI) methods such as surrogate models can help interpret mechanisms while further improving the sampling efficiency.
The Ray group works on the development and application of these algorithms to study complex biomolecular processes relevant to drug discovery, antibiotic resistance, and rational design of monoclonal antibodies.
Department of Chemistry and Biochemistry
Organic/Inorganic/Materials Seminar Series
O-I-M Faculty Introductions – Fall 2024
Friday, October 25, 2024
3:00 pm, WIL 110
Ramesh Jasti
Professor
Chemistry and Biochemistry
Jasti Lab
Romila Mascarenhas
Assistant Professor
Chemistry and Biochemistry
Research
Teresa Rapp
Assistant Professor
Chemistry and Biochemistry
Rapp Lab
Mike Pluth
Professor
Chemistry and Biochemistry
Pluth Lab
Department of Chemistry and Biochemistry
Organic/Inorganic/Materials Seminar Series
O-I-M Faculty Introductions – Fall 2024
Friday, October 18, 2024
3:00 pm, WIL 110
Victoria DeRose
Department Head, Professor
Chemistry and Biochemistry
DeRose Lab
Matthias Agne
Assistant Professor
Chemistry and Biochemistry
Gary Harlow
Research Assistant Professor
Chemistry and Biochemistry
Harlow Lab
Paul Kempler
Assistant Professor
Chemistry and Biochemistry
Kempler Lab
Department of Chemistry and Biochemistry
Physical Chemistry Seminar Series
Professor Julia Widom, University of Oregon
October 14th, 2024 —2:00pm
Tykeson 140
Title: Spectroscopic Studies of Nucleic Acid structure, Dynamics and Photophysics
RNA performs a diverse set of biological functions, many of which require it to fold into specific structures. Many techniques have been developed to study RNA folding, a number of which are based on fluorescence detection.
I will present work in which we used fluorescent analogues of the natural RNA bases to selectively probe the structures of different conformational subpopulations of RNA.
We investigated the photophysical properties of base analogues in different structural contexts using a combination of time-resolved fluorescence measurements and fluorescence-detected circular dichroism spectroscopy, which circumvents the ensemble averaging that typically limits the power of bulk spectroscopic methods such as CD.
Ensemble averaging can also be avoided by performing measurements on single molecules. I will present work in which we utilized single-molecule microscopy to investigate the ensemble of structures adopted by RNA
“switches”. These studies reveal how the 3D structure of RNA is impacted by intrinsic factors such as base sequence and extrinsic factors such as the
binding of small molecules.
As Teresa Rapp and Matthias Agne enter their second year as members of the Chemistry and Biochemistry Department’s research faculty, we thought we’d ask them for some thoughts and highlights from their first year at the University of Oregon. Here’s what they had to share ~
Teresa Rapp
What a whirlwind of a year it’s been! When I started at the U of O in September 2023, I was excited to jump into research and start mentoring and working with all the fabulous UO students! Little did I know I’d soon be managing over 12 trainees in my burgeoning research lab. Over the last 12 months we’ve converted 2/3rds of our lab space to a dark room with red light to build our light sensitive molecules, we’ve taken on two PhD students, a Master’s Intern, a Research Scientist, and 13 undergrads who have all made great progress towards their respective projects. I’m very proud of the group community we’ve built in our first year as a lab, and I look forward to all the years to come!
Matthias Agne
As we charge into our second year, I am so proud looking back at the team that has gotten us this far – and I cannot express enough thankfulness for the tremendous PhD rotation students, MS students and undergrads who gave so much of their time and energy to help build the lab and develop our capabilities. Our core team of 4 PhD students are currently tackling hard fundamental problems in energy materials research, from assessing vibrational dynamics in solids for better control of thermal and ionic transport to understanding thermodynamic driving forces for degradation in solid-state batteries, and more! They have taken huge initiative to develop these projects from concept to first results, and we anticipate a very productive year ahead. I would like to recognize the amazing support that I have received from my faculty colleagues and our administrative staff, which has made starting at the University of Oregon such a great experience. I look forward to continuing to grow our team at all academic levels and building collaborations here at UO and around the world!
