Upcoming Seminars & Events

Professor Mona Minkara
Department of Bioengineering
Northeastern University
Abstract

Unlocking the Secrets of Breath and Defense: Surfactant Proteins’ Role in Lung Health and Fighting Disease

In this talk, we explore the impact of Surfactant Proteins B (SP- B) and D (SP-D) on pulmonary function and immune defense, using computational techniques. Our findings highlight the dynamic structural properties of SP-B, essential for breathing. We employed homology modeling based on the crystallized Mini B structure and the saposin family of proteins to develop a computational model of SP-B. Molecular dynamics simulations were then employed on both open and closed states of SP-B in hydrophilic and hydrophobic environments, simulating conditions found within the alveoli. Our research provides insight into SP-B’s conformational stability and interactions under various alveolar conditions, elucidating its adaptation to different environments and enhancing our knowledge of its structure-function relationships and impact on breathing. Additionally, we investigated SP-D’s antiviral mechanisms against Influenza A, revealing how its double mutant variant (Asp325Ala and Arg343Val) exhibits improved antiviral efficacy. We used full-atomistic molecular dynamics simulations with microsecond trajectories to explore the molecular mechanism of these mutations on SP-D’s ability to bind the viral glycan trimannose as a model. This work deepens our understanding of surfactant protein dynamics and suggests new avenues for therapeutic development against pulmonary diseases and viral infections.

Mona Minkara

Dr. Minkara’s research uses a variety of methods from computational chemistry that she has employed throughout her academic career. While pursuing her BA in Chemistry at Wellesley College, Dr. Minkara worked with Dr. Mala Radhankrishnan, where she used computational methods to explore the binding of drugs to HIV-1 Reverse Transcriptase. After completing her BA in 2009, Dr. Minkara spent a year conducting research at Wellesley under a Howard Hughes Medical Institute Research Grant. In 2010, she began her graduate studies at the University of Florida supported by a National Science Foundation Graduate Research Fellowship. Under her co- advisors, Dr. Kenneth M. Merz Jr. and Dr. Erik Deumens, she focused on using molecular dynamics simulations to design a new inhibitor for Helicobacter pylori urease, an enzyme that helps bacteria survive in the stomach, and in 2015, she received her PhD in Chemistry. She then joined Dr. J. Ilja Siepmann’s lab as a post-doc at the University of Minnesota Twin Cities Chemical Theory Center. In this role, Dr. Minkara used Monte Carlo simulations to explore the interfacial properties of surfactants, the surface tension of water, and the miscibility gap of supercritical fluids.

Hosted by Professor Ilja Siepmann

Professor Mona Minkara
Department of Bioengineering
Northeastern University
Abstract

Building the COMBINE Lab: Breaking Barriers as a Blind Chemist

In this talk, Mona Minkara, an assistant professor of Bioengineering at Northeastern University, shares the story behind building the Minkara Computational Modeling for BioInterface Engineering (COMBINE) Laboratory. As a blind chemist, Mona faced challenges and overcame internalized ableism to see her blindness as an asset in the lab’s work. She emphasizes the importance of combining diverse perspectives in science to solve new problems and advocates for disability inclusion in STEM. Her story challenges us to reflect on our biases and recognize the importance of creating inclusive spaces and striving for equitable opportunities for all. 

Throughout her academic journey, Mona navigated the complexities of securing the necessary accommodations for her education and selecting a graduate school that offered the support she needed. Her mentors played a significant role in helping her overcome internalized ableism and see her blindness as an unseen advantage. This perspective has been a driving force in her work. Mona’s story asks us to reflect on how we can work together to break down barriers, and acknowledges there are still barriers to break – we still need to make the results of scientific research and its literature accessible to all people.

Mona Minkara

Dr. Minkara’s research uses a variety of methods from computational chemistry that she has employed throughout her academic career. While pursuing her BA in Chemistry at Wellesley College, Dr. Minkara worked with Dr. Mala Radhankrishnan, where she used computational methods to explore the binding of drugs to HIV-1 Reverse Transcriptase. After completing her BA in 2009, Dr. Minkara spent a year conducting research at Wellesley under a Howard Hughes Medical Institute Research Grant. In 2010, she began her graduate studies at the University of Florida supported by a National Science Foundation Graduate Research Fellowship. Under her co- advisors, Dr. Kenneth M. Merz Jr. and Dr. Erik Deumens, she focused on using molecular dynamics simulations to design a new inhibitor for Helicobacter pylori urease, an enzyme that helps bacteria survive in the stomach, and in 2015, she received her PhD in Chemistry. She then joined Dr. J. Ilja Siepmann’s lab as a post-doc at the University of Minnesota Twin Cities Chemical Theory Center. In this role, Dr. Minkara used Monte Carlo simulations to explore the interfacial properties of surfactants, the surface tension of water, and the miscibility gap of supercritical fluids.

Hosted by Professor Alexander Umanzor

Professor Alexander Spokoyny
Department of Chemistry
University of California, Los Angeles
Abstract

Organometallic Strategies for Modifying Biomolecules

Over the past decade, we and others have been engaged in developing a toolbox of organometallic reagents that can transfer complex functional groups onto biomolecules. This talk will describe some historical perspectives, reagent design considerations, and state-of-the-art chemistry that was discovered and developed in our laboratories. Specifically, I will highlight how this recent emergence of organometallic chemistry for the modification of biomolecular nanostructures has begun to rewrite the long-standing assumption among practitioners that small-molecule organometallics are fundamentally incompatible with biological systems. As research progresses, many of the challenges associated with applying organometallic chemistry in this context are being reassessed. Looking to the future, the growing utility of the organometallic transformations we and others have been developing will likely make them more ubiquitous in the construction and modification of biomolecular nanostructures. As such, I will also highlight several key emerging opportunities in this area of research.

Alexander Spokoyny

Professor Alexander Spokoyny is a professor and chair of the Chemistry and Biochemistry Department at UCLA and a faculty member of the California NanoSystems Institute (CNSI). He received his Ph.D. degree from Northwestern University in inorganic chemistry in 2011 and conducted a post-doctoral stint at MIT in chemical biology. His group’s research focuses on fundamental synthetic chemistry challenges that can be further applied to address pressing problems in biology, medicine, and materials science. Over his career, he has co-authored more than 100 research manuscripts and received numerous national and international awards, including being named a 2024 Fellow of the Royal Society of Chemistry (FRSC), receiving the 2020 Camille Dreyfus Teacher-Scholar Award, the 2019 National Science Foundation CAREER Award, the 2018 Cottrell Scholar from the Research Corporation for Science Advancement, the 2017 Alfred P. Sloan Fellowship in Chemistry, the 2017 NIH/NIGMS Maximizing Investigators’ Research Award (MIRA), the 2016 Chemical and Engineering News (C&EN) Talented 12, the 2016 3M Non-Tenured Faculty Award, the 2013 Grand Poster Prize from the American Peptide Society, the 2012 International Union of Pure and Applied Chemistry (IUPAC) Prize for Young Chemists, and the 2011 American Chemical Society Inorganic Young Investigator Award. His research has been highlighted by the popular press, including Science, Nature, C&EN, Cell Press, RSC, and other news outlets. At UCLA, Spokoyny has also been engaged in efforts to broaden scientific literacy among non-STEM undergraduates and students incarcerated at state prison facilities. For his efforts, he has received the 2021 UCLA Distinguished Teaching Award and the 2022 UCLA Community Service and Praxis (DEI) Award.

Hosted by Professor Ian Tonks

Professor Robert S. Paton
Department of Chemistry
Colorado State University
Abstract

Data-driven predictions of organic reactivity and selectivity

Quantum chemical models of reaction mechanism and selectivity provide a powerful tool to explain the outcome of laboratory experiments. However, since many reactions involve several steps and multiple conformers, the computational expense of QM approaches often prevent their application to predict reaction outcomes more broadly. Surrogate machine-learning models with quantum chemical accuracy at a fraction of the computational cost are set to transform the accessibility of computational predictions of reactivity and selectivity. I will discuss machine learning efforts utilizing knowledge and data from QM studies to generate surrogate models for the large-scale prediction of various atomic and molecular properties. We have developed graph neural networks to predict computational and experimental observables such as spin density, chemical shift, thermochemistry and reactivity. In this talk I discuss the performance of these models in high-throughput predictions of reactivity and selectivity of heteroaromatics and in goal- directed molecular optimization of stable organic radicals, along with strategies to improve model transferability.

Robert Paton

Dr. Robert Paton is a Professor of Chemistry and the inaugural holder of the Marshall Fixman and Branka Ladanyi Professorship at Colorado State University. Research in the Paton group is focused on the development and application of computational tools to accelerate chemical discovery. Paton has received the Harrison-Meldola Medal of the Royal Society of Chemistry (RSC), an Outstanding Junior Faculty Award from the ACS Computers in Chemistry Division, the Silver Jubilee Prize of the Molecular Graphics and Modeling Society and is a Fellow of the RSC. The Paton group enjoy collaborative research and are members of the NSF Center for Computer- Assisted Synthesis (C-CAS), the NSF Molecular Maker Lab Institute (MMLI), and the Center for Sustainable Photoredox Catalysis.

Hosted by Suman Bhaumik

Psychological Safety: FROM Understanding & Embracing TO Action

Shari L. Robinson will return to the Department of Chemistry to dive deeper into the topic of psychological safety. This is a follow-up talk to Shari's January 2024 presentation, Understanding and embracing an environment of psychological safety.

Shari L. Robinson joined the University of Minnesota as the inaugural DEI Director for CCAPS (College of Continuing and Professional Studies) in April 2023. She comes to us after moving to the Twin Cities in 2020 and after a 2-year faculty appointment at the University of St. Thomas. Shari is a social worker and a linguistic anthropologist by training with over two decades of experience as a faculty member developing and teaching social work courses and professional development trainings on aging, anti-Blackness, anti-racism, queer/trans studies, race, social justice and whiteness, as well as cultural anthropology courses at many colleges and universities across Michigan, Massachusetts, and now Minnesota. Prior to her career in higher education, Shari had over a decade of professional and clinical practice experience working solely with older adults. In her spare, but rare time, Shari enjoys spending time with her many house plants and fish tanks; reading all things Afro-futurism and YA literature which features Black girl mermaids; watching Star Trek runs; cooking (and eating!) all types of food; walking around the many Minnesota lakes, as well as enjoying the rich cultural scene in the Twin Cities and traveling to warm places with her spouse, Jackie.