FY 2022-2023

• B. Koyuncu and T. B. Le, Modeling shear stress distribution in ice-covered streams, Geological Society of London, Special Publications 540, SP540-2022-161 (2024).

• L. Akerkouch, H. Jasuja, K. Katti, D. Katti, and T. B. Le, The influence of fluid shear stress on bone and cancer cells proliferation and distribution, Annals of Biomedical Engineering 51, 1199 (2023).

• B. Koyuncu and T. B. Le, On the impacts of ice cover on flow profiles in a bend, Water Resources Research 58, e2021WR031742 (2022).

• B. Bakare, D. Motuba, and J. Szmerekovsky, Do corporate social responsibility ratings have any effect on traffic congestion?, Transportation Research Part A: Policy and Practice 165, 98 (2022).

• S. S. Graham, Z. P. Majdik, J. B. Barbour, and J. F. Rousseau, Associations between aggregate NLP-extracted conflicts of interest and adverse events by drug product, Studies in Health Technology and Informatics 290, 405 (2022).

• S. S. Graham, M. S. Karnes, J. T. Jensen, N. Sharma, J. B. Barbour, Z. P. Majdik, and J. F. Rousseau, Evidence for stratified conflicts of interest in research contexts: A methodological review, BMJ Open 12, e063501 (2022).

• P. T. Diem-Tran, T.-T. Ho, N.-V. Tuan, L.-Q. Bao, H. T. Phuong, T. T. G. Chau, H. T. B. Minh, C.-T. Nguyen, Z. Smanova, G. M. Casanola-Martin, B. Rasulev, H. Pham-The, and L. C. V. Cuong, Stability constant and potentiometric sensitivity of heavy metal–organic fluorescent compound complexes: QSPR models for prediction and design of novel coumarin-like ligands, Toxics 11, 595 (2023).

• A. Daghighi, G. M. Casanola-Martin, T. Timmerman,  D. Milenković, B. Lucic,  and B. Rasulev, In silico prediction of the toxicity of nitroaromatic compounds: Application of ensemble learning QSAR approach, Toxics 10, 746 (2022).

• S. Karabulut, B. Mansour, B. Rasulev, and J. W. Gauld, The hydrolysis rate of paraxonase-1 Q and R isoenzymes: An in silico study based on in vitro data, Molecules 27, 6780 (2022).

• Y. Zhuravskyi, K. Iduoku, M . Erickson, A. Karuth, D. Usmanov, G. Casanola-Martin, M. N. Sayfiyev, D. A. Ziyaev, Z. Smanova, and B. Rasulev, A quantitative structure-permittivity relationship analysis of a series of polymers, ChemRxiv, rn7s5 (2023).

• A. Tomić, M. Kovačić, H. Kusic, P. Karamanis, B. Rasulev, and A. L. Božić, Structural features promoting photocatalytic degradation of contaminants of emerging concern: Insights into degradation mechanism employing QSA/PR modeling, Molecules 28, 2443 (2023).

• K. Howlader and Lu Liu, Transfer learning pre-training dataset and fine-tuning effect analysis on cancer histopathology images, in 2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Las Vegas, NV, USA, 2022, pp. 3015-3022.

• R. Alenezi and S. A. Ludwig, Detecting pneumonia based on chest X-ray images using reinforcement learning, in IEEE Artificial Intelligence & Knowledge Engineering, Laguna Hills, CA, USA, 2022, pp. 67–73.

• K. Hoang, Defects and persistent luminescence in Eu-doped SrAl₂O₄, Physical Review Applied 19, 024060 (2023).

• Q. Yan, H. Xu, K. Hoang, X. Zhou, P. Kidkhunthod, P. Lightfoot, W. Yao, and Y. Tang, Na₂FeF₄ as a stable cathode material for Na-ion batteries, Applied Physics Letters 121, 143902 (2022).

• K. Hoang, Design of battery materials via defects and doping, in Computational Design of Battery Materials, edited by D. A. H. Hanaor (Springer, 2023).

• A. Karmacharya, D. Li, Y. Leng, G. Shi, Z. Liu, S. Yang, Y. Du, W. Dai, and S. Zhong, Targeting disease susceptibility genes in wheat through wide hybridization with maize expressing Cas9 and guide RNA, Mol. Plant-Microbe Interact. (2023).

• F. Manan, G. Shi, H. Gong, H. Hou, H. Khan, Y. Leng, C. Castell-Miller, S. Ali, J. D. Faris, S. Zhong, B. Steffenson, and Z. Liu, Prevalence and importance of the necrotrophic effector gene ToxA in Bipolaris sorokiniana populations collected from spring wheat and barley, Plant Disease 107, 2424 (2023).

• G. Shi, G. Kariyawasam, S. Liu, Y. Leng, S. Zhong, S. Ali, P. Moolhuijzen, C. S. Moffat, J. B. Rasmussen, T. L. Friesen, J. D. Faris, and Z. Liu, A conserved hypothetical gene is required but not sufficient for Ptr ToxC production in Pyrenophora tritici-repentis, Mol. Plant-Microbe Interact. 35, 336 (2022).

• S. Ghazanfari, A. Alesadi, Y. Liao, Y. Zhang, and W. Xia, Molecular insights into the temperature and pressure dependence of mechanical behavior and dynamics of Na-montmorillonite clay, Nanoscale Advances (2023).

• Y. Wang, S. Zhang, G. Freychet, Z. Li, K.-L. Chen, C.-T. Liu, Z. Cao, Y.-C. Chiu, W. Xia, and X. Gu, Highly deformable rigid glassy conjugated polymeric thin films, Advanced Functional Materials (2023).

• A. Ghasemi, Y. Liao, Z. Li, W. Xia, and X. Gu, Crystallization and melting of polymer chains on graphene and graphene oxide, Nanoscale 15, 12235 (2023).

• S. A. Tolba, W. Xia, Molecular insights into the hydration of zwitterionic polymers, Molecular Systems Design and Engineering 8, 1040 (2023).

• Y. Liao, Z. Li, L. Chen, A.B. Croll, and W. Xia, Crumpling defective graphene sheets, Nano Letters 23, 3637 (2023).

• Z. Cao, Z. Li, S. A. Tolba, G. T. Mason, M. Xiong, M. U. Ocheje, A. Alesadi, C. Do, K. Hu, T. Lei, S. Rondeau-Gagné, W. Xia, and X. Gu, Probing single-chain conformation and its impact on optoelectronic properties of donor-accepter conjugated polymers, Journal of Materials Chemistry A 11, 12928 (2023).

• H. Son, YD. M. Smith, Z. Li, T. Chang, W. Xia, and C. Davis, Particle alignment effects on mechanical properties of cellulose nanocrystal thin films, Materials Advances 4, 1053 (2023).

• W. M. A. Jayawardana, Y. Liao, Z. Li, W. Xia, and A. Croll, Crumpled kirigami, Soft Matter 19, 1081 (2023).

• X. Zheng, Y. Guo, J. Douglas, and W. Xia, Competing effects of cohesive energy and cross-link density on the segmental dynamics and mechanical properties of cross-linked polymers, Macromolecules 55, 9990 (2022).

• H. Zhao, J. Shanahan, S. Samson, Z. Li, G. Ma, N. Prine, L. Galuska, Y. Wang, W. Xia, W. You, and X. Gu, Manipulating conjugated polymer backbone dynamics through controlled thermal cleavage of alkyl side chains, Macromolecular Rapid Communications 43, 2200533 (2022).

• S. Gumber, O. Eniodunmo, S. Ivanov, S. Kilina, O. V. Prezhdo, D. Ghosh, and S. Tretiak, Hot carrier relaxation dynamics in non-stoichiometric cdse quantum dots: computational insights, Journal of Materials Chemistry A 11, 8256 (2023).

• B. Liu, X. Yang,  M. Jabed, S. Kilina,  Z. Yang,  and  W. Sun, Water-soluble dinuclear iridium(III) and ruthenium(II) bis-terdentate complexes: Photophysics and electrochemiluminescence, Dalton Transactions 51, 13858 (2022).

• A. Forde, L.  Lystrom, W. Sun, D. Kilin, and S. Kilina, Improving near-infrared emission of meso-aryldipyrrin indium(iii) complexes via annulation bridging: excited-state dynamics, J. Phys. Chem. Lett. 13, 9210 (2022).

• Y. Zheng, Y. Han, B. Weight, Z. Lin, B. Gifford, M. Zheng, D. Kilin, S. Kilina, S. Doorn, H. Htoon, and S. Tretiak, Photochemical spin-state control of binding configuration for tailoring organic color center emission in carbon nanotubes, Nature Com. 13, 4439 (2022).

FY 2021-2022

• T. B. Le, M. Usta, C. Aidun, A. Yoganathan, and F. Sotiropoulos, Computational methods for fluid-structure interaction simulation of heart valves in patient-specific left heart anatomies, Fluids 7, 94 (2022).

• L. Akerkouch and T. B. Le, A hybrid continuum-particle approach for fluid-structure interaction simulation of red blood cells in fluid flows, Fluids 6, 139 (2021).

• R. J. Jansen, M. Orr, W. R. Bamlet, and G. M. Petersen, A pilot study of blood-based methylation markers associated with pancreatic cancer, Frontiers in Genetics 13, 849839 (2022). 

• K. Rasuleva, S. Elamurugan, A. Bauer, M. Khan, Q. Wen, Z. Li, P. Steen, A. Guo, W. Xia, S. Mathew, R. Jansen, and D. Sun, Beta-sheet richness of the circulating tumor-derived extracellular vesicles for noninvasive pancreatic cancer screening, ACS Sensors 6, 4489-4498 (2021).

• Z. P. Majdik and J. Wynn, Building better machine learning models for rhetorical analyses: The use of rhetorical feature sets for training artificial neural network models, Technical Communication Quarterly 32, 63-78 (2023).

• K. Hoang, Rare-earth defects in GaN: A systematic investigation of the lanthanide series, Physical Review Materials 6, 044601 (2022). 

• K. Hoang, Rare-earth defects and defect-related luminescence in ZnS, Journal of Applied Physics 131, 015705 (2022).

• K. Hoang, C. Latouche, and S. Jobic, Why is it so difficult to realize Dy⁴⁺ in as-synthesized BaZrO₃? Journal of the American Ceramic Society 105, 4242-4249 (2022).

• W. J. S. Diniz, L. P. Reynolds, A. K. Ward, P. P. Borowicz, K. K. Sedivec, K. L. McCarthy, C. J. Kassetas, F. Baumgaertner, J. D. Kirsch, S. T. Dorsam, T. L. Neville, J. C. Forcherio, R. R. Scott, J. S. Caton, and C. R. Dahlen, Untangling the placentome gene network of beef heifers in early gestation, Genomics 114, 110274 (2022).

• W. J. S. Diniz, G. Bobe, J. Klopfestein, et al., Maternal selenium supplementation during different trimesters of pregnancy: Effects on neonatal calve muscle transcriptome, In: 12th International Symposium on Selenium in Biology and Medicine, Hawaii, USA (2022).

• W. J. S. Diniz, A. K. Ward, L. P. Reynolds, et al., PSVIII-22 Maternal vitamin and mineral supplementation affect fetal hepatic expression of genes underlying mineral homeostasis and lipid metabolism in early pregnancy, In: 2021 ASAS Midwest Section Meeting, USA (2021).

• W. J. S. Diniz, G. Bobe, J. J. Klopfenstein, Y. Gultekin, T. Z. Davis, A. K. Ward, and J. A. Hall, Supranutritional maternal organic selenium supplementation during different trimesters of pregnancy affects the muscle gene transcriptome of newborn beef calves in a time-dependent manner, Genes 12, 1844 (2021).

• M. S. Crouse, J. S. Caton, K. J. Claycombe-Larson, W. J. S. Diniz, A. K. Lindholm-Perry, L. P. Reynolds, C. R. Dahlen, P. P. Borowicz, and A. K. Ward, Epigenetic modifier supplementation improves mitochondrial respiration and growth rates and alters DNA methylation of bovine embryonic fibroblast cells cultured in divergent energy supply, Frontiers in Genetics 13, 812764 (2022).

• W. J. S. Diniz, M. S. Crouse, J. S. Caton, K. J. Claycombe-Larson, A. K. Lindholm-Perry, L. P. Reynolds, C. R. Dahlen, P. P. Borowicz, and A. K. Ward, DNA methylation dataset of bovine embryonic fibroblast cells treated with epigenetic modifiers and divergent energy supply, Data in Brief 42, 108074 (2022).

• M. A. Bari, P. Zheng, I. Vieira, H. Worral, S. Szwiec, Y. Ma, D. Main, C. Coyne, R. McGee, and N. Bandillo, Harnessing genetic diversity in the USDA pea germplasm collection through genomic prediction, Frontiers in Genetics 12, 707754 (2021).

• S. A. Atanda, J. Steffes, Y. Lan, M. A. Bari, J. Kim, M. Morales, J. Johnson, R. A. Saludares, H. Worral, L. Piche, A. Ross, M. A. Grusak, C. J. Coyne, R. J. McGee, J. Rao, and N. Bandillo, Multi-trait genomic prediction improves selection accuracy for enhancing seed mineral concentrations in pea (Pisum sativum L.), Plant Genome (2022).

• A. Bari, D. Fonseka, S. Stenger, H. Worral, L. Piche, S. Atanda, J. Kim, M. Morales, J. Johnson, R. Saludares, P. Flores, J. Pasche, and N. Bandillo, A greenhouse-based high-throughput phenotyping platform for identification and genetic dissection of resistance to Aphanomyces root rot in field pea, bioRxiv (2022).

• N. Bandillo, D. Jarquin, L. Posadas, A. Lorenz, and G. Graef, Genomic selection performs as effectively as phenotypic selection for increasing seed yield and leads to a rapid allele fixation in soybean, bioRxiv (2022).

• J. Roy, L. E. Mendoza, N. Bandillo, P. E. McClean, and R. Rahman, Genetic mapping and genomic prediction of sclerotinia stem rot resistance to rapeseed/canola (Brassica napus L.) at seedling stage, Theoretical and Applied Genetics 135, 2167-2184 (2022).

• B. Poudel, J. Mullins, K. D.  Puri, Y. Leng, A. Karmacharya, Y. Liu, J. Hegstad, X. Li, and S. Zhong, Molecular mapping of quantitative trait loci for Fusarium head blight resistance in the Brazilian spring wheat cultivar 'Surpresa', Frontiers in Plant Science 12, 778472 (2022).

• G. K. Kariyawasam, N. Wyatt, G. Shi, S. Liu, C. Yan, Y. Ma, S. Zhong, J. B. Rasmussen, P. Moolhuijzen, C. S. Moffat, T. L. Friesen, and Z. Liu, A genome-wide genetic linkage map and reference quality genome sequence for a new race in the wheat pathogen Pyrenophoratritici-repentis, Fungal Genetics and Biology 152, 103571 (2021).

• M. Wit, Y. Leng, Y. Du, M. Cegielko, E. Jablonska, W. Wakulinski, and S. Zhong, Genome sequence resources for the maize pathogen Fusarium temperatum isolated in Poland, Molecular Plant-Microbe Interactions 34, 214-217 (2021).

• S. V. Jaswandkar, K. S. Katti, and D. R. Katti, Molecular and structural basis of actin filament severing by ADF/cofilin, Computational and Structural Biotechnology Journal 20, 4157-4171 (2022).

• S. Kar, S. V. Jaswandkar, K. S. Katti, J. W. Kang, P. T. C. So, R. Paulmurugan, D. Liepmann, R. Venkatesan, and D. R. Katti, Label-free discrimination of tumorigenesis stages using in vitro prostate cancer bone metastasis model by Raman imaging, Scientific Reports 12, 8050 (2022).

• H. M. N. Faisal, K. S. Katti, and D. R. Katti, An insight into quartz mineral interactions with kerogen in Green River oil shale, International Journal of Coal Geology 238, 103729 (2021).

• H. M. N. Faisal, K. S. Katti, and D. R. Katti, Binding of SARS-COV-2 (COVID-19) and SARS-COV to human ACE2: Identifying binding sites and consequences on ACE2 stiffness, Chemical Physics 551, 111353 (2021).

• H. M. N. Faisal, K. S. Katti, and D. R. Katti, Differences in interactions within viral replication complexes of SARS-CoV-2 (COVID-19) and SARS-CoV coronaviruses control RNA replication ability, JOM 73, 1684-1695 (2021).

• H. M. N. Faisal, K. S. Katti, and D. R. Katti, Molecular mechanics of the swelling clay tactoid under compression, tension and shear, Applied Clay Science 200, 105908 (2021).

• S. V. Jaswandkar, H. M. N. Faisal, K. S. Katti, and D. R. Katti, Dissociation mechanisms of G-actin subunits govern deformation response of actin filament, Biomacromolecules 22, 907-917 (2021).

• K. S. Katti, H. Jasuja, S. Kar, and D. R. Katti, Nanostructured biomaterials for in vitro models of bone metastasis cancer, Current Opinion in Biomedical Engineering 17, 100254 (2021).

• M. D. S. Molla, D. R. Katti, and K. S. Katti, Mechanobiological evaluation of prostate cancer metastasis to bone using an in vitro prostate cancer testbed, Journal of Biomechanics 114, 110142 (2021).

• H. Jasuja, S. Kar, D. R. Katti, and K. S. Katti, Perfusion bioreactor enabled fluid-derived shear stress conditions for novel bone metastatic prostate cancer testbed, Biofabrication 13, 035004 (2021).

• J. Du, D. Katti, and H. Heinz, Multiscale experiments and modeling in biomaterials and biological materials, Part I, JOM 73, 1673-1675 (2021).

• J. Du, D. Katti, and H. Heinz, Multiscale experiments and modeling in biomaterials and biological materials, Part II, JOM 73, 2332-2334 (2021).

• A. B. Croll, Y. Liao, Z. Li, W. M. A. Jayawardana, T. Elder, and W. Xia, Sticky crumpled matter, Matter 5, 1792-1805 (2022).

• A. Alesadi, Z. Cao, Z. Li, S. Zhang, H. Zhao, X. Gu, and W. Xia, Machine learning prediction of glass transition temperature of conjugated polymers from chemical structure, Cell Reports Physical Science 3, 10091 (2022).

• S. Ghazanfari, H. M. N. Faisal, K. S. Katti, D. R. Katti, and W. Xia, A coarse-grained model for the mechanical behavior of Na-montmorillonite clay, Langmuir 38, 4859-4869 (2022).

• N. A. Miller, Z. Li, W. Xia, and C. S. Davis, Buckling mechanics modulus measurement of anisotropic cellulose nanocrystal thin films, ACS Applied Polymer Materials 4, 3045-3053 (2022).

• Y. Liao, Z. Li, W. Nie, and W. Xia, Effect of reconstructed vacancy defects on the crumpling behavior of graphene sheets, Forces in Mechanics 6, 100057 (2022).

• Z. Li, Y. Liao, Y. Zhang, Yida Zhang, and W. Xia, Microstructure and dynamics of nanocellulose films: Insights into the deformational behavior, Extreme Mechanics Letters 50, 101519 (2022).

• Y. Liao, Z. Li, S. Ghazanfari, F. Fatima, A. B. Croll, and W. Xia, Understanding the role of self-adhesion in crumpling behaviors of sheet macromolecules, Langmuir 37, 8627-8637 (2021).

• C. Bulathsinghalage and L. Liu, Transfer learning pre-training dataset effect analysis for breast cancer imaging, Proceedings of 14th International Conference on Bioinformatics and Computational Biology 83, 108-115 (2022).

• C. Bulathsinghalage and L. Liu, A heuristic strategy for multi-mapping reads to enhance Hi-C data, 2021 IEEE 21st International Conference on Bioinformatics and Bioengineering (BIBE), pp. 1-6 (2021).

• A. Karuth, A. Alesadi, A. Vashisth, W. Xia, and B. Rasulev, A reactive molecular dynamics study of hygrothermal degradation of crosslinked epoxy polymers, ACS Applied Polymer Materials 4, 4411-4423 (2022).

• G. P. J. Varghese, D. A. David, A. Karuth, F. M. J. Jabeen, P. M. S. Begum, J. J. George, B. Rasulev, and P. Raghavan, Experimental and simulation studies on nonwoven polypropylene-nitrile rubber blend: Recycling of medical face masks to an engineering product,  ACS Omega 7, 4791-4803 (2022). 

• N. Fjodorova, M. Novic, K. Venko, V. Drgan, B. Rasulev, M. T. Sacan, S. S. Erdem, G. Tugcu, A. P. Toropova, and A. A. Toropov, How fullerene derivatives (FDs) act on therapeutically important targets associated with diabetic diseases, Computational and Structural Biotechnology Journal 20, 913-924 (2022).