Bulletin of the American Physical Society
APS March Meeting 2021
Volume 66, Number 1
Monday–Friday, March 15–19, 2021; Virtual; Time Zone: Central Daylight Time, USA
Session B36: Undergraduate Research III: Biophysics and Related SystemsLive Undergrad Friendly
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Sponsoring Units: APS/SPS Chair: Midhat Farooq, American Physical Society |
Monday, March 15, 2021 11:30AM - 11:42AM Live |
B36.00001: 3D Computational Approach to Morphological Brain Abnormalities in Autism Shannon Brindle, Rasha Makkia Autism spectrum disorder (ASD) is an idiopathic neuro-developmental disorder that develops in early childhood. The prevalence is extreme as 1 in 54 children aged 8 years in the United States have an autism diagnosis. Early diagnosis is correlated with optimized patient outcome due to expeditious therapy [1]. Thus, research is needed to understand morphological brain abnormalities during development. Physicians lack a diagnostic model for ASD and rely on patients' behaviors, thus there remains a need for a computational human brain model from imaging sets to address morphological abnormalities in brains of ASD patients [2]. The model would provide the medical community with a prototype to aid in ASD diagnoses. The implications of this research are significant as it offers a novel diagnostic tool for an elusive disorder. A computational model offers a promise for enhanced early diagnosis and future research on treatment solutions. |
Monday, March 15, 2021 11:42AM - 11:54AM Live |
B36.00002: Improvements to Positron Emission Tomography Sensitivity via Double-Ended Readout Christopher Layden, Karol Lang, Kyle Klein Positron emission tomography (PET) is a powerful, noninvasive nuclear imaging technique used extensively for identifying cancer and brain disease. The sensitivities of clinical PET scanners have improved considerably in recent years, at pace with advancements in scintillator and photodetector technologies. In particular, significant improvements have been made in the coincidence resolving time (CRT or “time resolution”) of PET scanners, resulting in tighter event localization and thus better signal-to-noise ratios. However, optimization of time resolution conventionally requires short scintillator crystals, which allow more gamma rays to escape, diminishing the overall sensitivity. An alternative but clinically unrealized technique for achieving excellent time resolution is the coupling of a second photodetector to the front face of long scintillator crystals. Through Monte Carlo simulations, we indicate that a PET scanner employing this technique may reach a CRT below 200 ps, far outperforming current state-of-the-art scanners. |
Monday, March 15, 2021 11:54AM - 12:06PM Live |
B36.00003: Using Consensus Docking to Improve the Effectiveness of Molecular Docking Programs Brenden Stark, Connor Morris, Dennis Della Corte Molecular docking programs are widely used in modeling protein-ligand interactions during drug discovery. These programs computationally predict the binding pose and affinity for the interaction and can rate ligand conformations using a scoring function, but they can at times produce inaccurate predictions. One method to improve the use of these programs is consensus docking. Consensus docking evaluates protein-ligand binding using multiple docking programs and/or scoring functions to provide a more accurate prediction of the complex. This presentation will provide an overview of the different forms of consensus docking, giving the benefits as well as the drawbacks to this approach. We will also compare the effectiveness of these methods to a traditional molecular docking approach and present areas we have identified for the potential improvement of consensus docking. |
Monday, March 15, 2021 12:06PM - 12:18PM Live |
B36.00004: Nested Sampling for Exploration of Protein Fitness Landscapes Bryce Johnson, Alexander Golinski, Sandhya Appiah, Diya Saha, Stefano Martiniani Recent advances in machine learning offer predictive methods to determine protein developability metrics (related to expression, solubility, and stability) from sequence alone, thus enabling a more efficient search of developable protein mutants to be screened experimentally. One such approach utilizes high throughput measurements to learn relevant amino acid properties and their interactions to predict developability with increased accuracy. However, even for a small protein scaffolds such as Gp2, a random search can parse at most O(10-8) of all possible protein variants. Here, we overcome this difficulty by using nested sampling (NS), a Monte Carlo scheme for Bayesian parameter estimation and model selection, also commonly utilized in statistical thermodynamics to efficiently explore energy landscapes with many competing minima. We employ NS to explore the fitness landscape inferred by the machine learning model. Our analysis includes a non-linear dimensionality reduction (UMAP) of protein properties for high developability sequences identified by the algorithm, density of states estimation, and a unique topographical analysis of the fitness landscape. A simple parallelization algorithm for NS to speed up convergence and runtime for high number of sequences is also discussed. |
Monday, March 15, 2021 12:18PM - 12:30PM Live |
B36.00005: Real time control of a period doubling bifurcation in frog hearts. Molly Halprin, Conner J Herndon, Flavio Fenton Arrhythmia, irregular heartbeats caused by disorganized firing of impulses, is the largest contributor to heart disease, the leading cause of death in the US and other industrialized countries. T-wave alternans (TWA) are a promising electrocardiogram index of ventricular arrhythmic susceptibility that involves measuring beat-to-beat variation in electrocardiogram T-waves (which correspond to ventricular repolarization). It has been shown that TWA is originated by a period doubling bifurcation when cardiac tissue is paced at fast constant cycle lengths. The bifurcation can be explained theoretically via linear stability analysis of a physiological adaptation function that can be calculated experimentally. In this study, we measure the adaptation function and use this theory to test a real time control method, that has been tested with numerical models, in the frog hearts. In this talk I will describe the theory behind the bifurcation, the real time control method and system we have developed for it as well as experimental results. With this work we aim to provide insight into future technologies for arrhythmia prevention in humans. |
Monday, March 15, 2021 12:30PM - 12:42PM Live |
B36.00006: Probing Nano-Bio Interaction using Raman Spectroscopy Jessica Fink, Bishwajite Karmakar, Kartik Ghosh With the COVID-19 pandemic, bio-nanotechnology has taken an increased role in the fight against the virus. A virus is made of proteins and RNA/DNA. Therefore, if the chemical bonds in RNA/DNA can be broken, then the virus can diminish. Nanoparticles of ZnO, CuO and NaCl have shown anti-bacterial properties based on studies using these molecules to disinfect surgical masks and gowns. They may have the ability to be an anti-viral disinfectant. Little is known about nanotechnology’s anti-viral properties, and this research project seeks the interaction between inorganic nanomaterials with RNA and DNA. Raman spectroscopy has been used to probe the nature of the chemical bonds of the individual biomolecules such as adenine, one of the four nucleotide bases of DNA. It will be interesting to see how the nature of bonding in adenine changes when it interacts with the inorganic nanomaterials ZnO, CuO, and NaCl. This data will help understand the nano-bio interaction at the molecular level. The comparison of adenine and nanomaterials incubated adenine should show if the chemical bonds in the biomolecule did indeed alter. The expected result is the bonds will alter and how the bonds alter is one aspect of this project. |
Monday, March 15, 2021 12:42PM - 12:54PM Live |
B36.00007: Imaging of Soft Matter Particulate Systems in Aqueous Solutions by Scanning Electron Microscopy Richard Sent, Petru Stefan Fodor, Kiril Streletzky When using a scanning electron microscope (SEM) to image soft-matter systems, the imaging dose is limited due to the potential radiation damage to the sample. This limits the signal-to-noise ratio making it challenging to distinguish regions with similar contrast from each other. In our case study, while taking a SEM video of polymeric microgels diffusing in a suspension of ionic liquid, the microgels did not contrast significantly with the surrounding ionic liquid. The noise also made it challenging to visually identify single microgels. Additionally, manual tracking of particles can be a laborious process. A three-stage program was developed to optimize this process. First, in order to improve the visibility of the particles, the program enhances the contrast by squaring intensity values, reduces noise with a series of filters, and converts each video frame to black and white image data using thresholding. A new video is reconstructed from the edited frames. Secondly, once particle visibility is improved, a custom machine learning model is used to automatically identify the xy position of every particle. This model is trained using thousands of positive and negative images. Lastly, the program automates the analysis of the data. |
Monday, March 15, 2021 12:54PM - 1:06PM Live |
B36.00008: Form and Locomotion of Magnetically Driven Soft Robots in Sediment Beds Trinh Huynh, Julien Chopin, Arshad Kudrolli We study the shape and locomotion of a soft robot with a magnet head and elastic tail in fluid-saturated granular media driven by an oscillating magnetic field. Our studies are motivated by soft robot designs based on biomimetic principles which organisms exploit in response to the surrounding environment and stimuli. The applied oscillating field, magnetic field strength, and filament tail length, along with the sediment volume fraction and depth are control variables, in our study. Exploiting refractive index matching of the grains, we measure the shape and speed of the robot over time. A transition from reciprocal to anguilliform body is observed because of subtle balance of drag, propulsion, and elastic restoring forces. We will discuss the impact of the change of gait on the nonlinear increase of swimming speed observed with driving frequency. |
Monday, March 15, 2021 1:06PM - 1:18PM Live |
B36.00009: Putting a New Spin on the Flight of Jabillo Seeds Aman Desai, Jessie Ribera, Dwight Whitaker Our presentation describes the explosive seed dispersal of the Hura crepitans fruit. Through high-speed video analysis of an exploding fruit, we observe that the seeds fly with backspin as opposed to topspin, which was previously assumed. Backspin orients seeds to minimize drag during flight since it is stable against gyroscopic precession, and this consequently increases dispersal distance. The seeds’ range is estimated by using results from the seeds of Ruellia ciliatiflora, which are similarly shaped but approximately 10 times smaller than those of Hura crepitans. We note that the effects of lowering drag on the range are more pronounced at higher speeds. We also see that the effect of launch height on the range of the seeds becomes less consequential at higher launch speeds. Our model - developed using the combination of high-speed video analysis of Hura crepitans seeds and results from seeds of Ruellia ciliatiflora - predicts dispersal distances similar to those in a previous study of Hura crepitans seeds. |
Monday, March 15, 2021 1:18PM - 1:30PM Live |
B36.00010: Magnetic Particle Motion Through High Viscous Fluids Influenced by a Magnetic Field River Gassen, Kathrin Spendier
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Monday, March 15, 2021 1:30PM - 1:42PM Live |
B36.00011: Analysis of a Self-Propelled Particle Model for Understanding Flocking Transition in Sperm Paul Yanka, Jelani L Lyles, Devonne N Rattigan, Ojan Damavandi, Daniel Sussman, M. Lisa Manning, Chih-Kuan Tung Self-propelled particle (SPP) models have been used to derive useful knowledge in active matter systems for more than two decades. When the self-propelled velocities tend to align, there can be a flocking transition in certain regions of parameter space. The goal of our SPP model is to help us understand and predict our experimental observations of flocking in bull sperm. Here, we present preliminary results from our simulations. When we analyze simulations with a quadratic repulsion potential and no alignment, the mean squared displacement (MSD) scales linearly with time to show a purely diffusive motion, as expected. When alignment is introduced, we observe flocking behavior, where the MSD scales quadratically with time, as expected for a flock of particles moving together in a fixed direction. Future work will focus on whether distributions of self-propelled velocities and persistence times can help explain the statistics of flocking (including cluster size distributions) seen in our experiments. |
Monday, March 15, 2021 1:42PM - 1:54PM Live |
B36.00012: Surface plasmon resonance response of Au-Al thin films and their potential for use in gas, water, and biological sensors Molly Kate Kreider, Abdul Qadeer Rehan, Robert Malcolm Kent, Mariama Rebello Surface plasmon resonance (SPR)-based sensors take advantage of the SPR response of certain metals to identify minor changes in the index of refraction of the sensing medium, most often to detect the presence/concentration of some other substance. Owing to the small scale of these changes, sensors rely on materials, such as Au, whose SPR response is both well-defined, with a small full width at half maximum (FWHM) and large peak height, and highly sensitive to smalll changes. In this work, we calculate the sensitivity to a change in the index of refraction of the sensing material, FWHM, and peak height of the SPR responses of four different thicknesses of various AuAl alloyed thin films, including pure ones, fabricated through the co-sputtering method. We analyze these three metrics for three different sensing media, air, water, and a biological environment, for both fixed incident wavelength and fixed incident angle. This analysis yielded that Au0.85Al0.15 was most comparable to Au, having a higher sensitivity and similar FWHM/peak height for each sensing medium and sensor type. For a fixed incident angle, while all alloys had larger FWHMs, they outperformed the pure materials in terms of sensitivity for all three sensing media. |
Monday, March 15, 2021 1:54PM - 2:06PM On Demand |
B36.00013: Lens-less Imaging Through Incoherent Illumination Zuhad Nisar, Mohammad Saqib, Anwar Hussain The lens-less technique will be evaluated to obtain high resolution images. LED followed by a USAF resolution chart as a mask, sample and detector respectively in a column. The sample info collected by the detector directly without any objective lens. Drawbacks of the lens-less microscopy i.e. twin image and signal to noise ratio will be addressed properly to obtain high resolution image. The sample information will be encoded by the mask at sensor plane during reconstruction process. To retrieve the sample information from captured raw images corresponding to LED illumination, the backward propagation model is applied. According to this model, each image is backward propagated to the sample plane with updating their amplitude. The field is then propagated to the mask plane with the updating free space propagation factor and finally the updated version of sample is obtained using stochastic gradient descent method. Three types of masks will be used phase, amplitude and combination of both with random distribution. The reconstruction process of the sample information will help to reconstruct not only the amplitude but the phase of the sample as well. The application of such type of technique is most commonly in biomedical engineering for infection diagnostic purpose. |
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