Department of Chemistry and Biochemistry
Physical Chemistry Seminar Series
Physical Chemistry Rotation Talks
Thursday, December 12, 2024
2:00pm in Pacific Hall, Room 30
Hosted by Julia Widom
SPEAKERS
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
Ben Bythell, Hazardous Materials Manager, Chemical Safety Officer
November 22, 2024
3:00 pm, WIL 110
Q & A Session to Follow
Hosted by the Chemistry and Biochemistry Department
Title: Hazardous Waste Determinations and New TSCA Legislation at University of Oregon
New federal TSCA legislation for dichloromethane/ methylene chloride (DCM) requires the University of Oregon and other research-use employers to generate a monitoring program to ensure employee safety. I shall discuss why the law has changed, how the monitoring program will help keep you safe, and what this means for your research and teaching.
Hazardous waste determinations are legally required to occur at the point of generation, i.e., by the lab generator. Most labs do a great job of labeling hazardous waste containers with an accurately filled-in tag. Each lab (PI-responsible) must document how hazardous waste determinations occur for each major process. i.e., with SOPS, SDSs, and chemical knowledge. Dr. Bythell will guide you and your students through completing this process using an online form (~ 2 minutes to complete). I will cover how this reduces lab (PI and institutional) liability, how often to fill in the form, and how to avoid unnecessary work/duplication. Dr. Bythell will audit each of these hazardous waste determination documents promptly and provide PIs, students, and staff copies to show legal compliance has occurred.
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.
