ResearchFest

Tuesday, August 27, 2024

ORAL PRESENTATIONS:
Marvin D. Rausch Lectureship Award for Outstanding Oral Presentation (First place ): Nathanael Kuzio from Hardy Group (Hardy Group)
Paul Hatheway Terry Endowment Award as first-runner up (Second place): Jian Huang (Jianhan Chen Group)
William E. McEwen Scholarship Fund Award as a joint second-runner up (Joint Third):  Jeerapat Doungchawee (Vachet Group)
William E. McEwen Scholarship Fund Award as a joint second-runner up (Joint Third): Ranit Dutta  (Thayumanavan Group

MORNING POSTER SESSION:
Marvin D. Rausch Lectureship Award for Outstanding Poster Presentation (Joint First Place): Harini Nagaraj (Rotello Group) and Elizabeth Cote (Rotello group)
William E. McEwen Award for Outstanding Poster (Joint Second Place): Kanitin Khamnong (Vachet Group) and Elizaveta Shestoperova (Streiter Group)
William E. McEwen Award for Outstanding Poster (Joint Third Place): Priyanka Bhattacharyya (You Group) and Gaurav Singh (Metz Group)
Paul Hatheway Terry Endowment Award for Outstanding Poster (People's Choice): Nicholas Baker (DuChene Group)

AFTERNOON POSTER SESSION:
William E. McEwen Award for Outstanding Poster Presentation (First Place):  Amin Abek (Martin Group) 
William E. McEwen Award for Outstanding Poster (Second place):  Arnab Das (Metz Group)
William E. McEwen Award for Outstanding Poster (Third Place):  Jayashree Bhagabati (Thai Group)
Paul Hatheway Terry Endowment Award for Outstanding Poster (People’s Choice): Tracey Nelson (Walsh Group)

ALUMNI SERIES OUTSTANDING POSTER AWARD:
Overall Outstanding Poster: Zhaojie Zhang (DV Group)
Morning Outstanding Poster: Irina Sagarbarria (Hardy Group)
Afternoon Outstanding Poster: Emmanuel Rivera-Iglesias (Farkas Group)

Photo: Tim Gehan and DV

ResearchFest 2023 will feature keynote speaker Dr. Robert Herbst, student speakers, poster sessions, career panel lunch, vendor show, and BBQ social!

Student Speaker Abstracts

Accessing Metastable States with Shock Compression By: Kimberly Pereira The development of methods to enable the recovery of metastable high-pressure phasesto ambient conditions remains an outstanding challenge in materials science. One routethat remains unexplored is the use of shockwaves to rapidly decompress samples,analogous to the temperature quenching methods used to recover metastable high-temperature phases in steel processing. In our research, we use in situ X-ray diffraction toexplore the impact that dynamic compression and decompression has on the location ofphase boundaries in solid-state systems, with the goal of detecting and quantifying thekinetic effects that influence the phase transformations. We are specifically interested intransition metals, alloys, oxides, and carbides. Despite their structural simplicity, thesematerials remain poorly understood in terms of how they behave under extremeconditions. For example, there are significant differences between the phases observedunder static compression and the phases observed under dynamic compression to thesame conditions of pressure and temperature. Quantifying the crystal structure in thedynamic compression regime could inform fundamental understanding of atomicbonding, and could also offer insight into planetary processes such as those in our earth’sinterior. To reach these conditions and perform our experiments, we travel to some of thebrightest and most powerful light sources in the world including synchrotrons andXFELs, and collaborate with scientists at Lawrence Livermore National Laboratory andSLAC National Accelerator Laboratory. In this talk, I will present results from our studyinto elemental nickel under shock compression, where our exciting findings point to ahigher melting pressure and temperature than expected.

Finding the Common Thread: Factors that Impact Coulomb Interactions inDoped Organic Semiconductors By: Michael Lu-Díaz Conjugated polymers spearhead the field of organic electronics on multiple forefronts –flexible displays, health monitoring sensors, and photovoltaics. These polymers must beoxidized or reduced to create a charge carrier (polaron) that is balanced by the dopantcounterion — a process termed chemical doping. While necessary for electricalconductivity, this simple chemical process also produces complicated and unpredictablechanges; doping alters polymer microstructure, generates additional energetic disorder,and can create localized polarons. A lack of control over these parameters impedes furtherdevelopment. I will share a story of how we are reshaping our understanding of chargetransport in conductive polymers by controlling the polaron-counterion distance.Through experiments and numerical simulations, we proved that systems with differentstructural order and side chain composition exhibit different charge transport propertiesdepending on their polaron-counterion distance. We used a combination of doping-dedoping experiments, kinetic analyses, optical characterization, and X-ray scattering.Our results indicate that polymers with shorter polaron-counterion distances lead toincreased dopant-induced effects. Our work shows a need for an integrated moleculardesign that requires both low intrinsic polymer energetic disorder and extrinsic dopant-induced energetic disorder for efficient charge transport.

Towards Accurate Coarse-Grained Simulation of Protein Phase Separation: Rolesof Backbone Interactions and Residual Structures By: Yumeng Zhang Intrinsically disordered proteins (IDPs) frequently drive liquid-liquid phase separation(LLPS) processes that give rise to biomolecular condensates. These membranelesssubcellular compartments have been linked to myriad biological functions and variousdiseases including Alzheimer’s and amyotrophic lateral sclerosis. Working hand-in-handwith theory and experiment, molecular simulations have a central role to play in studyinghow sequence and structural features of IDPs modulate LLPS. For this, coarse-graining isgenerally required to access the length and time-scales of IDP phase separation. However,the widely-used Ca-only models treat IDPs as simple polymers and fail to capture theirpeptide nature. Here, we describe a hybrid resolution (HyRes) protein model withcoarse-grained side chains but an atomistic backbone for an accurate description of thebackbone and transient secondary structures in LLPS. We show that the GPU version ofHyRes is efficient enough for direct simulation of spontaneous phase separation of IDPs.Importantly, it is also accurate enough to capture the effect of single mutations on theLLPS propensity. Using two model systems, namely, GY-23 from pepHBP-1 and theconserved region (CR) from TDP-43, we further illustrate how HyRes simulations helpto elucidate the coupling between IDP conformational equilibrium and phase separation.These results suggest that the HyRes model provides an important new tool forunderstanding the molecular basis of IDP-driven LLPS in various biological processes.

Advanced DNA Probes for Imaging and Modulating Cell Membrane DynamicInteractions By: Ahsan Ausaf Ali The cell membrane is a complex and heterogenous structure composed chiefly of lipidsand proteins which dynamically interact with each other. These transient interactions arevery important in maintaining the integrity of the cell membrane and in the formation ofsignaling platforms which enable signal transduction and cell communication.Unfortunately, due to the fast nature of these interactions, our ability to visualize,quantify and precisely modulate them has been limited. We recently developed a probecalled the ‘DNA Zipper’ which may address these hurdles by predictably stabilizingtransient membrane interactions. Our DNA probe is anchored onto target membranelipids or proteins as a FRET pair and can reveal various biophysical properties of the livecell membranes. Since dysregulated membrane structures and interactions are known toplay critical roles in various diseases, this probe may also serve as a useful platform toidentify new drug molecules which may either induce or inhibit certain interactions.Therefore, we believe our DNA Zipper probe may have a broad range of applications toenhance our understanding of important cell membrane interactions and associated cellsignaling processes.

Tuesday, August 29, 2023

ORAL PRESENTATIONS:
Marvin D. Rausch Lectureship Award for Outstanding Oral Presentation (first place ): Michael Lu Diaz (DV Lab)
Paul Hatheway Terry Endowment Award as first-runner up (second place): Yumeng Zhang (Jianhan Chen Group)
William E. McEwen Scholarship Fund Award as a joint second-runner up (joint third): Ahsan Ausaf Ali (You Group)
William E. McEwen Scholarship Fund Award as a joint second-runner up (joint third): Kimberly Pereira (Walsh Group)

MORNING POSTER SESSION:
Marvin D. Rausch Lectureship Award for Outstanding Poster Presentation (First Place): Ruptanu Banerjee (Martin Group)
William E. McEwen Award for Outstanding Poster (Joint Second Place): Cristina-Maria Hirschbiegel (Rotello Group) & Jithu Krishna (Thai Group)
William E. McEwen Award for Outstanding Poster (Joint Third Place): Scott Thiel (Walsh Group)
Paul Hatheway Terry Endowment Award for Outstanding Poster (People's Choice): Nicholas Baker (DuChene Group)

AFTERNOON POSTER SESSION:
William E. McEwen Award for Outstanding Poster Presentation (Joint First Place): Daniil Ivanov (Kaltashov Group)
William E. McEwen Award for Outstanding Poster (Joint second place): Irina Sagarbarria (Hardy Group)
William E. McEwen Award for Outstanding Poster (Joint Third Place): Theo Prachyathipsakul (Thai Group)
Paul Hatheway Terry Endowment Award for Outstanding Poster (People’s Choice): Gaurav Mitra (Kittilstved group)

ResearchFest 2023 will feature keynote speaker Dr. Robert Herbst, student speakers, poster sessions, career panel lunch, vendor show, and BBQ social!

Student Speaker Abstracts

Accessing Metastable States with Shock Compression By: Kimberly Pereira The development of methods to enable the recovery of metastable high-pressure phasesto ambient conditions remains an outstanding challenge in materials science. One routethat remains unexplored is the use of shockwaves to rapidly decompress samples,analogous to the temperature quenching methods used to recover metastable high-temperature phases in steel processing. In our research, we use in situ X-ray diffraction toexplore the impact that dynamic compression and decompression has on the location ofphase boundaries in solid-state systems, with the goal of detecting and quantifying thekinetic effects that influence the phase transformations. We are specifically interested intransition metals, alloys, oxides, and carbides. Despite their structural simplicity, thesematerials remain poorly understood in terms of how they behave under extremeconditions. For example, there are significant differences between the phases observedunder static compression and the phases observed under dynamic compression to thesame conditions of pressure and temperature. Quantifying the crystal structure in thedynamic compression regime could inform fundamental understanding of atomicbonding, and could also offer insight into planetary processes such as those in our earth’sinterior. To reach these conditions and perform our experiments, we travel to some of thebrightest and most powerful light sources in the world including synchrotrons andXFELs, and collaborate with scientists at Lawrence Livermore National Laboratory andSLAC National Accelerator Laboratory. In this talk, I will present results from our studyinto elemental nickel under shock compression, where our exciting findings point to ahigher melting pressure and temperature than expected.

Finding the Common Thread: Factors that Impact Coulomb Interactions inDoped Organic Semiconductors By: Michael Lu-Díaz Conjugated polymers spearhead the field of organic electronics on multiple forefronts –flexible displays, health monitoring sensors, and photovoltaics. These polymers must beoxidized or reduced to create a charge carrier (polaron) that is balanced by the dopantcounterion — a process termed chemical doping. While necessary for electricalconductivity, this simple chemical process also produces complicated and unpredictablechanges; doping alters polymer microstructure, generates additional energetic disorder,and can create localized polarons. A lack of control over these parameters impedes furtherdevelopment. I will share a story of how we are reshaping our understanding of chargetransport in conductive polymers by controlling the polaron-counterion distance.Through experiments and numerical simulations, we proved that systems with differentstructural order and side chain composition exhibit different charge transport propertiesdepending on their polaron-counterion distance. We used a combination of doping-dedoping experiments, kinetic analyses, optical characterization, and X-ray scattering.Our results indicate that polymers with shorter polaron-counterion distances lead toincreased dopant-induced effects. Our work shows a need for an integrated moleculardesign that requires both low intrinsic polymer energetic disorder and extrinsic dopant-induced energetic disorder for efficient charge transport.

Towards Accurate Coarse-Grained Simulation of Protein Phase Separation: Rolesof Backbone Interactions and Residual Structures By: Yumeng Zhang Intrinsically disordered proteins (IDPs) frequently drive liquid-liquid phase separation(LLPS) processes that give rise to biomolecular condensates. These membranelesssubcellular compartments have been linked to myriad biological functions and variousdiseases including Alzheimer’s and amyotrophic lateral sclerosis. Working hand-in-handwith theory and experiment, molecular simulations have a central role to play in studyinghow sequence and structural features of IDPs modulate LLPS. For this, coarse-graining isgenerally required to access the length and time-scales of IDP phase separation. However,the widely-used Ca-only models treat IDPs as simple polymers and fail to capture theirpeptide nature. Here, we describe a hybrid resolution (HyRes) protein model withcoarse-grained side chains but an atomistic backbone for an accurate description of thebackbone and transient secondary structures in LLPS. We show that the GPU version ofHyRes is efficient enough for direct simulation of spontaneous phase separation of IDPs.Importantly, it is also accurate enough to capture the effect of single mutations on theLLPS propensity. Using two model systems, namely, GY-23 from pepHBP-1 and theconserved region (CR) from TDP-43, we further illustrate how HyRes simulations helpto elucidate the coupling between IDP conformational equilibrium and phase separation.These results suggest that the HyRes model provides an important new tool forunderstanding the molecular basis of IDP-driven LLPS in various biological processes.

Advanced DNA Probes for Imaging and Modulating Cell Membrane DynamicInteractions By: Ahsan Ausaf Ali The cell membrane is a complex and heterogenous structure composed chiefly of lipidsand proteins which dynamically interact with each other. These transient interactions arevery important in maintaining the integrity of the cell membrane and in the formation ofsignaling platforms which enable signal transduction and cell communication.Unfortunately, due to the fast nature of these interactions, our ability to visualize,quantify and precisely modulate them has been limited. We recently developed a probecalled the ‘DNA Zipper’ which may address these hurdles by predictably stabilizingtransient membrane interactions. Our DNA probe is anchored onto target membranelipids or proteins as a FRET pair and can reveal various biophysical properties of the livecell membranes. Since dysregulated membrane structures and interactions are known toplay critical roles in various diseases, this probe may also serve as a useful platform toidentify new drug molecules which may either induce or inhibit certain interactions.Therefore, we believe our DNA Zipper probe may have a broad range of applications toenhance our understanding of important cell membrane interactions and associated cellsignaling processes.