Bulletin of the American Physical Society
2021 Annual Meeting of the APS Four Corners Section
Volume 66, Number 11
Friday–Saturday, October 8–9, 2021; Virtual; Mountain Daylight Time
Session K01: Physics of Biological Systems II |
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Chair: Alysia Marino, University of Colorado Boulder |
Saturday, October 9, 2021 1:00PM - 1:24PM |
K01.00001: Application, Assessment, and Development of Molecular Design Methods Invited Speaker: Dennis Della Corte Over millions of years, proteins have evolved to fulfill a plethora of life sustaining tasks. Even under physiological constraints, such as pH, temperature, and intracellular densities, they have adapted to accomplish specific tasks with high efficiency. Additionally, everything that defines a protein is encoded in its primary amino acid sequence, from its folded structure to its dynamical ensemble of states and the chemical universe that it can interact with. For decades humanity has sought to harness the power of proteins for new and important processes. While we have gained many important insights along the way, mankind still falls short of fully reproducing nature's remarkable ability to build custom nano machines. The de novo design of catalysts that mimic the affinity and specificity of natural enzymes remains one of the Holy Grails of chemistry. Despite decades of concerted effort, we are still unable to design catalysts as efficient as enzymes. However, imagine what we could accomplish if we had the skills to create proteins with high catalytic rates for crucial reactions, such as photosynthesis, plastic degradation, or nitrogen fixation! The Della Corte lab at BYU operates at the intersection of physics, biology, chemistry, chemical engineering, and computer science. It has the goal to learn the governing principles of molecular design and to apply these to solve world changing problems. This presentation will provide an overview of recent and current activities that leverage AI and physics based simulations to apply, assess, and develop molecular design methods at Della Corte lab at BYU. [Preview Abstract] |
Saturday, October 9, 2021 1:24PM - 1:36PM |
K01.00002: Nanopore with Self-aligned Transverse Tunneling Junction for DNA Detection and Sequencing Sanjana Mukherjee, Yuan Wang, Joshua Sadar, Ching-Wei Tsao, Quan Qing The integration of transverse electrodes with solid-state nanopore can open new opportunities for real-time detection and sequencing of DNA/RNA and other biomolecules, but the fabrication of such structure has been very challenging. We developed a new fabrication strategy to accurately produce solid-state nanopore device self-aligned with a pair of transverse metal tunneling junction, all integrated on a microfluidic chip. The nanopore and tunneling junction size is precisely regulated by electrochemical deposition method to selectively deposit or remove metal at the tip of the electrodes using an impedance based-feedback mechanism. With this design, we have demonstrated the first high yield (\textgreater 93{\%}) correlated detection of translocating DNAs from both the ionic channel and the tunneling junction with enriched event rate and have also observed events attributed to DNA bridging the transverse electrodes. In this talk, I will introduce the fabrication and characterization of the devices, and preliminary analysis of the signals obtained from translocating double strand DNAs. I will also discuss briefly on the optimization of electrochemical deposition parameters in the confined nanoscale device. [Preview Abstract] |
Saturday, October 9, 2021 1:36PM - 1:48PM |
K01.00003: Thermodynamic Analysis of Nanoparticles for the Treatment of Neurodegenerative Disease Seoyeon Choi, Richard Kyung Photodynamic therapy(PDT) is one of the most common treatments for AD. It utilizes photoirradiation to activate photosensitizers, which produce ROS to kill tumor cells. Moreover, as metal ion imbalance is found to be associated with Alzheimer’s Disease(AD), chelation therapy has been proposed. It makes use of chelators to capture and remove metal ions. This paper is focused on using the computer software Avogadro to find the stability and activity of nanoparticles used for PDT and chelation therapy through assessing their thermodynamic characteristics. As for chelators, metal-EDTA compounds and metal-DTPA compounds were compared. As for photosensitizers, porphyrins, chlorins, and phthalocyanines were analyzed. Optimized energy, dipole moment, and electrostatic potential map were used as the main criterion for analyzing thermodynamic characteristics. As a result, EDTA was found to have higher stability than DTPA. Cu-EDTA and Mg-EDTA were the most stabilized EDTA compounds, whereas Cu-DTPA was the most stabilized DTPA compound. Out of the porphyrin isomers, N-confused porphyrin and doubly N-confused porphyrin were found to be the most stable and reactive molecules. Also, chlorin and isobacteriochlorin were found to have better thermodynamic characteristics than bacteriochlorin. [Preview Abstract] |
Saturday, October 9, 2021 1:48PM - 2:00PM |
K01.00004: Effectiveness and Reliability of UVC Sterilization~For~Surface Pathogens:~Fluorescent~Tubes vs~LEDs Yash Soni, Kush Patel, Ashwin Suresh, Ajay Taduri, Shreyash Prakash, Nimith Gurijala, Vishesh Amin, Siddarth Jandhyala, Pranav Penmatcha, Aarush Thinakaran, Wesley Peng, Sri Swaminathan, Hemanth Yalahanka, Nicole Herbots The SARS-CoV-2 pandemic creates a need for safe, reliable, fast surfaced disinfection. UVC dissociates nucleic acid bonds in DNA and RNA of pathogens thereby killing them. Disinfection by UVC is fast and effective between 254-265 nm, and safer than 180-220 nm UVC which produces toxic ozone. UVC sources include fluorescent lamps and LEDs. Cost- and energy-effective UVC Fluorescent Lamps FL use toxic Hg vapor while solid state LEDs are compact and non-toxic. This work compares the power density PD stability and effectiveness of 254 nm UVC FL and 260-280 nm LEDs. A photodetector with a sampling area of 1 cm 2 probes PD, while 72 hrs incubation and Colony Forming Units (CFU) counting measures pathogen Kill Rate (KR). The PD of 3 identical FL and LED sources is measured 3 X for 60 s. every 10 s., a total 54 samplings. The PD measured mid- point on 10 cm long, 1 cm wide FL tubes varies by 30{\%} and increases by about 25{\%} over 60 s. PD measured on 3 sets of four 0.16 mm 2 LED vary by 12.5{\%} and show less than 1{\%} variation in 60 s. The KR of FUL and LED is 99.9 99{\%}. LEDs exhibit more reliable PD and KR. [Preview Abstract] |
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