Bulletin of the American Physical Society
Four Corners Section 2022 Meeting
Volume 67, Number 14
Friday–Saturday, October 14–15, 2022; Albuquerque, New Mexico
Session J05: Biophysics and Soft Condensed Matter II |
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Chair: Keith Lidke, The University of New Mexico Room: UNM PAIS 2540 |
Saturday, October 15, 2022 8:30AM - 8:42AM |
J05.00001: A Look at Information Loss in Diffraction-Limited Data Compression Matthew T Hogan, Michael Vershinin In the last twenty years, advances in new microscopy techniques have made it possible to examine the location of a single molecule with nanometer-scale precision and reconstruct the world of biology from the level of a single molecule to the story of a cell (and potentially an entire organism). Professionals in biophysics rely on precise measurements to make accurate claims, especially for diffraction-limited particles of interest, as the slightest variation in the data could alter the analysis. Most institutions are rapidly moving towards open data policies where data must be archived and made available at publication time. In addition, data retention policies are now commonplace. For TB-scale data sets, these requirements become cost-prohibitive, so practical archival of data files necessitates their compression. Until now, little research has been done on the feasibility of scientific data compression and whether the relevant information is accurately preserved therein. We examined the fidelity of four modern codecs in their ability to preserve positional data in synthetically generated images. Our results suggest that 80% compression is attainable for single images, although pixel-locking effects may prove challenging to overcome. |
Saturday, October 15, 2022 8:42AM - 8:54AM |
J05.00002: Characterization of Light-Activated Microswimmers for Controllable Motion John A Castaneda, John G Gibbs, Jennifer S Martinez The active movements of flocks of birds and schools of fish occurs due to individual moving organisms altering their velocities based upon the behavior of their nearest neighbors. These collective “active matter” behaviors also exist at the micron and nanometer scale. For example, “microswimmers” convert chemical energy into motion on a length-scale comparable to biological prokaryotic cells. An example of our artificial, nonbiological microswimmers is a catalytic Janus particle that has surface-asymmetry with specific physico-chemical properties at different locations upon the particle. I will focus on controlling the morphology of these microswimmers which may allow one to engineer light-activated, self-propelled microswimmers with controlled characterization. My goal is to investigate the solid/liquid interface of microswimmers in order to engineer collective motion and responsive assembly as a function of multiple external fields and variables. I propose that it is possible to engineer photoactive microswimmers for desired motion directly from a photocatalyst, magnetic materials and combing these microswimmers with other nanoscale structures through; Physical Vapor Deposition (PVD) and Glancing Angle Deposition (GLAD) with electron beam and thermal evaporating systems. Furthermore these ideas proposed ideas allow for the creation of microswimmers that exhibit controllable collective motion and behavior. |
Saturday, October 15, 2022 8:54AM - 9:06AM |
J05.00003: Automated Analysis of Conformational Flexibility in Small Molecules Using SAMPL7 Physical Properties Challenge Datasets from Alchemical Free Energy Simulations with MDPOW Cade Duckworth, SHUJIE FAN, Alia Lescoulie, Bogdan I Iorga, Oliver Beckstein Analysis of conformational flexibility is essential in identifying differences in solute-solvent and electrostatic interactions of small molecules. MDPOW (https://github.com/Becksteinlab/MDPOW), a python package, automates calculation of water-solvent partition coefficients from free energy perturbation (FEP) simulations, but subsequent analysis requiring user selection of each atom group poses a problem when sampling the entire conformational space, so there is a need to automate the process of obtaining relevant atom groups and their dihedral angles. Our extension of MDPOW automatically obtains dihedral atom groups from each molecule’s simulation ensemble and the kernel density estimation (KDE) of their dihedral angle frequencies, comparing across solvents and intermolecular interactions. Testing was done on large datasets from MDPOW generated for the SAMPL7 physical properties challenge, including simulation data that returned log Pow estimates within a minimum precision level of 0.1 log units for AMBER/GAFF force fields. This development provides an automated workflow for sampling the whole conformational space of small molecules. Future adaptation for additional observables (bond length, hydrogen bonding) and implementation of Random Forest classification for measuring convergence will result in complete automation of physical properties analysis across libraries of small molecules, promising useful applications in screening for potential drug candidates. |
Saturday, October 15, 2022 9:06AM - 9:18AM |
J05.00004: A Novel, Hand-Held, Fast, Small Volume Blood Diagnotstics Device to Correlate Biomarkers with Mild Cognitive Impairment and Alzheimer's Disease Jason Mayo, Jennifer Wong, Sean Stanek, Haley Ellis Nearly 44 million people worldwide suffer from Alzheimer’s Disease (AD), a progressive, neurodegenerative disease that destroys critical brain functions. AD has become the 6th leading cause of US deaths and is one of the most expensive conditions to care for, costing ~ $300 M/year. Diagnosing AD early on and monitoring is key to slow AD’s progression. Early detection during the Mild Cognitive Impairment (MCI) phase is critical as drug treatments and cognitive therapy are then more effective. AD diagnostic methods are limited. They include first self-reporting or reporting by those close to the patient. This is often inefficient and delays treatment past the critical phase of MCI. AD can be confirmed by spinal tap and complex brain imaging. Recently, blood methylglyoxal (MGO) levels were found to correlate significantly with AD1 and in patients who develop MCI leading to AD2. This makes MGO a potential biomarker for early diagnosis of MCI when it is a precursor to AD. Hence, the present work aims to prototype a novel, hand-held, fast, inexpensive, and accurate Small Volume Blood Diagnostics (SVBD) device, Alz-BioSs™, to test for the presence MCI via MGO levels and help monitor the impact of treatments on a regular basis. Alz-BioSs™ aims to help diagnose and then monitor MCI and AD during the MCI precursor phase to provide patients a greater chance for effective treatments. Alz-BioSs™ measures MGO in blood plasma by collecting a 0.5 mL blood drop into a single-use microfluidic chip for rapid, passive separation of plasma from blood. Extracted 0.2-0.3 mL plasma reacts then into an adjacent chip coated with bio-reagent o-phenylenediamine (OPD) and gold nanoparticles (AuNP). The resulting colorimetric reaction is detected via a miniature optical cage system (OCS) using LEDs and photodetectors to quantify MGO levels via photo-absorption, akin to some handheld blood glucose monitor used for diabetes monitoring. |
Saturday, October 15, 2022 9:18AM - 9:30AM |
J05.00005: Extended X-ray Absorption Fine Structure Calibrated Hemoglobin-Bound Iron Fraction via Blood Thin Films Rapidly Solidified From 100µL Drops Arjun Sekar, Rianna N Rane, Aarush Thinakaran, Ashwin Suresh, Pranav Penmatcha, Jordan Bischoff, Karen L Kavanagh, Nicole Herbots Measuring the fraction of Iron bound to Hemoglobin in whole blood can detect anemia. But state-of-the-art Blood diagnostics via High Performance Liquid Chromatography (HPLC) use large blood volumes (8-10 mL) leading to Hospital Acquired Anemia in 74% of patients. |
Saturday, October 15, 2022 9:30AM - 9:42AM |
J05.00006: Particle Processing: Recent Developments Implementing DEM Simulations Leo E Silbert, Ishan Srivastava, Joseph M Monti, Gary S Grest, Jeremy B Lechman The handling, transport, and packing of granular materials has broad relevance, |
Saturday, October 15, 2022 9:42AM - 9:54AM |
J05.00007: Coarse-Grained LAMMPS Simulations of Supercoiled DNA Cayson J Hamilton Through modeling we can visualize and understand how DNA is folded and stored within bacterial cells. Prokaryotic DNA is compacted almost 1000 fold and is highly organized, this conformation having a direct impact on gene expression in cells. DNA-binding proteins known as NAPs bind to DNA and create a highly dense, supercoiled structure that allows the lengthy bacterial DNA to both fit in the small cellular space as well as unwind and separate when it comes time for replication. We have performed coarse-grained simulations modeling varying amounts and kinds of NAPs binding to helical DNA, demonstrating their influence on its spatial organization and density. These visual representations shed light on the underlying factors behind transcription and replication. Understanding the compaction process might eventually help medicine to target DNA replication and suggest new strategies for designing antibiotics. |
Saturday, October 15, 2022 9:54AM - 10:06AM |
J05.00008: Nanoporous membranes transport phenomenon: Experiments match Simulations Shriram Elangovan, Vishal Nandigana Nanoporous membranes and 2D materials based Graphene, MoS2 nanoporous membranes transport is well matched with theory and experiments for the first time. We use a dynamical oscillator model derived thoroughly from Poisson-Nernst-Planck-Navier-Stokes model and Langevin dynamics model that match the experiments of I-V characteristics with the theoretical model. The theoretical model was found to match with the experiments for varying concentrations of ionic electrolyte, pH, solvent gels, pore diameter and pore thickness. The theory matched the experiments results of linear I-V characteristics and nonlinear I-V characteristics observed both in thick and ultrathin 2D nanoporous membranes when the ionic electrolyte concentration, pH is varied for the same designed pore diameters. The ion-ion interactions, ion-wall interactions, ion-water interactions, electric field induced nanoporous entrance/exit polarization on ionic electrolyte results in the desired I-V characteristics when the electric field is driven from the bulk reservoir of dimensions greater than few centimeters. Nanoporous membranes experiments match with theoretical model show many applications in water desalination, DNA sequencing, bio-applications, ionic separation and power generator renewable energy applications. |
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