Physical Sciences and Mathematics Commons^™

Nanopore Guided Regional Assembly, Eleni Adam, Desh Ranjan, Harold Riethman

College of Sciences Posters

The telomeres are the “caps” of the chromosomes and their vital role is to protect them. Possible telomere dysfunction caused by telomere rearrangements can be fatal for the cell and result in age-related diseases, including cancer. The telomeres and subtelomeres are regions that are hard to investigate. The current technology cannot provide their complete sequence, instead the DNA is given in multiple pieces. Current methods of assembling the pieces of these regions are not accurate enough due to the region’s high variability and complex repeated patterns. We propose a hybrid assembly method, the NPGREAT, which utilizes two of the latest …

Combine Cryo-Em Density Map And Residue Contact For Protein Structure Prediction: A Case Study, Maytha Alshammari, Jing He

College of Sciences Posters

Although atomic structures have been determined directly from cryo-EM density maps with high resolutions, current structure determination methods for medium resolution (5 to 10 Å) cryo-EM maps are limited by the availability of structure templates. Secondary structure traces are lines detected from a cryo-EM density map for α-helices and β-strands of a protein. A topology of secondary structures defines the mapping between a set of sequence segments in 1D and a set of traces of secondary structures in 3D. In order to enhance the accuracy in ranking secondary structure topologies, we propose a method that combines three sources of information …

End-To-End Physics Event Generator, Yasir Alanazi, N. Sato, Tianbo Liu, W. Melnitchouk, Michelle P. Kuchera, Evan Pritchard, Michael Robertson, Ryan Strauss, Luisa Velasco, Yaohang Li

College of Sciences Posters

We apply generative adversarial network (GAN) technology to build an event generator that simulates particle production in electron-proton scattering that is free of theoretical assumptions about underlying particle dynamics. The difficulty of efficiently training a GAN event simulator lies in learning the complicated pat- terns of the distributions of the particles physical properties. We develop a GAN that selects a set of transformed features from particle momenta that can be generated easily by the generator, and uses these to produce a set of augmented features that improve the sensitivity of the discriminator. The new Feature-Augmented and Transformed GAN (FAT-GAN) is …

Examining Arctic Melt Pond Dynamics Via High Resolution Satellite Imagery, Austin Abbott, Victoria Hill

College of Sciences Posters

The Arctic Ocean is a rapidly changing environment, and a key observational system for monitoring climate change. The Arctic is going under a rapid transition from thicker, multi-year ice, to thinner first-year ice, that may have many potential consequences. As first year Arctic sea ice begins to retreat in the spring and early summer, melting snow and ice form ponds on the surface- “melt ponds”. These melt ponds increase light transmission to the water column, resulting in warming and increased primary production under the ice. Recent advances in high resolution satellite imagery now allow us to monitor the development and …

Design, Commissioning And Preliminary Results Of A Magnetic Field Scanning System For Superconducting Radiofrequency Cavities, Ishwari Parajuli, Jeffrey Nice, Gianluigi Ciovati, William Clemens, Jean Delayen, Alex Gurevich

College of Sciences Posters

Superconducting radiofrequency (SRF) cavities are one of the building blocks of modern particle accelerators. Such cavities are typically made of bulk niobium, operate at liquid helium temperature (2 - 4 K) and have some of the highest quality factors found in Nature. One of the leading source of residual losses, which limits the quality factor in SRF cavities, is trapped magnetic flux from either residual ambient magnetic field or thermoelectric currents. The flux trapping mechanism depends on different niobium surface preparations and cool-down conditions. Suitable diagnostic tools are not yet available to study the effects of such conditions on magnetic …

Nb3Sn Coating Of Complex Srf Cavity Structures, Jayendrika Tiskumara, Uttar Pudasaini, Grigory Eremeev, Charlie Reece, Jean Delayen

College of Sciences Posters

In the modern SRF research, Thin films coated niobium cavities are used for the low cost and increased quality factor. Among the potential thin film materials applied on the niobium, performances demonstrated by the Nb3Sn cavities makes this material attractive for SRF accelerator applications giving higher critical temperature and higher accelerating gradients. While the majority of research efforts are currently focused on the development of elliptical single-cell and multi-cell cavities, the potential of this material is evident to other cavity types, which may have complex geometries. We are working towards the development of Nb₃Sn-coated Half-wave resonator and twin …

Direct Visualization Of 3-Dimensional Force And Energy Map Of A Single Molecular Switch, Abeykoon Mudiyanselage Shashika Darshani Wijerathna, Zaw Myo Win, K. Z. Latt, Yang Li, A. T. Ngo, L. Curtiss, R. Zhang, S. W. Hla, Y. Zhang

College of Sciences Posters

Mechanical properties of molecules adsorbed on materials surfaces are increasingly vital for the applications of molecular thin films. Here, we conduct a fundamental research to induce conformational change mechanically on a single molecule and quantify the driving force needed for such molecular shape switch via a low temperature (~ 5K) Scanning Tunneling Microscope (STM) and Qplus Atomic Force Microscope (Q+AFM). Our measurement maps a three-dimensional landscape for mechanical potential and force at single molecule level with high spatial resolution in all three dimensions of a few angstrom (10^-10 m).

Molecule TBrPP-Co (a cobalt porphyrin) deposited on an atomically clean …

The Magnetic Field Penetration Measurement Of Thin Film And Multilayered Superconductors For Srf Cavities, Iresha Harshani Senevirathne, Jean Delayen

College of Sciences Posters

Radio Frequency (RF) Cavities are used in particle accelerators and they are typically formed from or coated with superconducting materials. High purity niobium is the material of choice for SRF cavities and niobium cavities operate at their theoretical field limits. SRF researchers have begun a significant R&D effort to develop alternative materials to continue to keep up with the demands of new accelerator facilities. To achieve high performance with high accelerating gradient, cavity material should have an ability to persist in superconducting state under high magnetic field without magnetic flux penetration through the cavity wall. Therefore, the magnetic field at …

Npgreat: Hybrid Assembly Of Human Subtelomeres With The Use Of Nanopore And Linked-Read Datasets, Eleni Adam, Desh Ranjan, Harold Riethman

College of Sciences Posters

The telomeres are vitally important regions that are located at the tips of the chromosomes. Their dysfunction, caused by length shortening can lead to senescent cells, which in turn cause age-related diseases, including cancer. The subtelomeres, located next to the telomeres, possess the critical role of regulating the adjacent telomere lengths. Even after many years of research, human subtelomeres have proven to be very hard to assemble due to their morphology. In order to overcome these problems, the hybrid assembly method we develop utilizes two of the latest available types of data, which complement each other: Linked-Reads and ultralong Nanopore …

D-Vine Copula Model For Dependent Binary Data, Huihui Lin, N. Rao Chaganty

College of Sciences Posters

High-dimensional dependent binary data are prevalent in a wide range of scientific disciplines. A popular method for analyzing such data is the Multivariate Probit (MP) model. But the MP model sometimes fails even within a feasible range of binary correlations, because the underlying correlation matrix of the latent variables may not be positive definite. In this research, we proposed pair copula models, assuming the dependence between the binary variables is first order autoregressive (AR(1))or equicorrelated structure. Also, when Archimediean copula is used, most paper converted Kendall Tau to corresponding copula parameter, there is no explicit function of Pearson’s correlation coefficient …

Sulfur Dioxide From The Atmospheric Chemistry Experiment Satellite, Doug Cameron

College of Sciences Posters

The version 4.0 dataset from the Atmospheric Chemistry Experiment – Fourier Transform Spectrometer (ACE-FTS) on SCISAT, released in March of 2019, has sulfur dioxide (SO₂) volume mixing ratio (VMR) profiles as a routine data product. From this dataset, global SO₂ distributions between the altitudes of 10.5 km and 23.5 km are analyzed. The global distribution of all SO₂ VMR data by altitude is broken down into 30° and 5° latitude zones. Seasonality of the global SO₂ distribution is explored. Volcanic SO₂ plumes are isolated in the dataset and compared with extinction data from the …

Cylindrical Similarity Measurement For Helices In Medium-Resolution Cryo-Electron Microscopy Density Maps, Salim Sazzed, Peter Scheible, Maytha Alshammari, Willy Wriggers, Jing He

College of Sciences Posters

Cryo-electron microscopy (cryo-EM) density maps at medium resolution (5-10 Å) reveal secondary structural features such as α-helices and β-sheets, but they lack the side chains details that would enable a direct structure determination. Among the more than 800 entries in the Electron Microscopy Data Bank (EMDB) of medium-resolution density maps that are associated with atomic models, a wide variety of similarities can be observed between maps and models. To validate such atomic models and to classify structural features, a local similarity criterion, the F1 score, is proposed and evaluated in this study. The F1 score is theoretically normalized to a …