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Full-Text Articles in Physical Sciences and Mathematics
Triphlapan: Predicting Hla Molecules Binding Peptides Based On Triple Coding Matrix And Transfer Learning, Meng Wang, Chuqi Lei, Jianxin Wang, Yaohang Li, Min Li
Triphlapan: Predicting Hla Molecules Binding Peptides Based On Triple Coding Matrix And Transfer Learning, Meng Wang, Chuqi Lei, Jianxin Wang, Yaohang Li, Min Li
Computer Science Faculty Publications
Human leukocyte antigen (HLA) recognizes foreign threats and triggers immune responses by presenting peptides to T cells. Computationally modeling the binding patterns between peptide and HLA is very important for the development of tumor vaccines. However, it is still a big challenge to accurately predict HLA molecules binding peptides. In this paper, we develop a new model TripHLApan for predicting HLA molecules binding peptides by integrating triple coding matrix, BiGRU + Attention models, and transfer learning strategy. We have found the main interaction site regions between HLA molecules and peptides, as well as the correlation between HLA encoding and binding …
Comparison Of Experimental And Theoretical Electron-Impact-Ionization Triple-Differential Cross Sections For Ethane, Esam Ali, Kate Nixon, Andrw Murray, Chuangang Ning, James Colgan, Don H. Madison
Comparison Of Experimental And Theoretical Electron-Impact-Ionization Triple-Differential Cross Sections For Ethane, Esam Ali, Kate Nixon, Andrw Murray, Chuangang Ning, James Colgan, Don H. Madison
Physics Faculty Research & Creative Works
We have recently examined electron-impact ionization of molecules that have one large atom at the center, surrounded by H nuclei (H2O, NH3, CH4). All of these molecules have ten electrons; however, they vary in their molecular symmetry. We found that the triple-differential cross sections (TDCSs) for the highest occupied molecular orbitals (HOMOs) were similar, as was the character of the HOMO orbitals which had a p-type "peanut" shape. In this work, we examine ethane (C2H6) which is a molecule that has two large atoms surrounded by H nuclei, so that …
Interference Effects For Intermediate Energy Electron-Impact Ionization Of H₂ And N₂ Molecules, Zehra Nur Ozer, Hari Chaluvadi, Don H. Madison, Mevlut Dogan
Interference Effects For Intermediate Energy Electron-Impact Ionization Of H₂ And N₂ Molecules, Zehra Nur Ozer, Hari Chaluvadi, Don H. Madison, Mevlut Dogan
Physics Faculty Research & Creative Works
We have studied electron impact ionization of H2 and N2 molecules at intermediate energies to look for possible two center interference effects experimentally and theoretically. Here we report a study of the interference factor I for 250 eV electron-impact ionization. The experimental measurements are performed using a crossed-beam-type electron-electron coincidence spectrometer and theoretical calculations are obtained using the Molecular Three Body Distorted Wave Approximation (M3DW). We found that the I-factor demonstrated strong evidence for two-center interference effects for both H2 and N2. We also found that the I-factor is more sensitive to projectile angular scans …
Theoretical Triple-Differential Cross Sections Of A Methane Molecule By A Proper-Average Method, Hari Chaluvadi, C. G. Ning, Don H. Madison
Theoretical Triple-Differential Cross Sections Of A Methane Molecule By A Proper-Average Method, Hari Chaluvadi, C. G. Ning, Don H. Madison
Physics Faculty Research & Creative Works
For the last few years, our group has calculated cross sections for electron-impact ionization of molecules using the molecular three-body distorted-wave approximation coupled with the orientation-averaged molecular orbital (OAMO) approximation. This approximation was very successful for calculating ionization cross sections for hydrogen molecules and to a lesser extent nitrogen molecules. Recently we used the approximation to calculate single ionization cross sections for the 1t2 state of methane (CH4) and we found major discrepancies with the experimental data. Here we investigate the validity of the OAMO approximation by calculating cross sections that have been properly averaged over all …
A Theoretical Model Of Multi-Agent Quantum Computing, F. Matthew Mihelic
A Theoretical Model Of Multi-Agent Quantum Computing, F. Matthew Mihelic
Faculty Publications
The best design for practical quantum computing is one that emulates the multi-agent quantum logic function of natural biological systems. Such systems are theorized to be based upon a quantum gate formed by a nucleic acid Szilard engine (NASE) that converts Shannon entropy of encountered molecules into useful work of nucleic acid geometric reconfiguration. This theoretical mechanism is logically and thermodynamically reversible in this special case because it is literally constructed out of the (nucleic acid) information necessary for its function, thereby allowing the nucleic acid Szilard engine to function reversibly because, since the information by which it functions exists …