Browsing by Subject "computer simulation"

Now showing 1 - 4 of 4
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    A Computational Study of the Mechanism for F1-ATPase Inhibition by the Epsilon Subunit
    (2013) Thomson, Karen J.; Pu, Jingzhi; Ge, Haibo; Sardar, Rajesh; Long, Eric C. (Eric Charles)
    The multi-protein complex of F0F1 ATP synthase has been of great interest in the fields of microbiology and biochemistry, due to the ubiquitous use of ATP as a biological energy source. Efforts to better understand this complex have been made through structural determination of segments based on NMR and crystallographic data. Some experiments have provided useful data, while others have brought up more questions, especially when structures and functions are compared between bacteria and species with chloroplasts or mitochondria. The epsilon subunit is thought to play a signi cant role in the regulation of ATP synthesis and hydrolysis, yet the exact pathway is unknown due to the experimental difficulty in obtaining data along the transition pathway. Given starting and end point protein crystal structures, the transition pathway of the epsilon subunit was examined through computer simulation.The purpose of this investigation is to determine the likelihood of one such proposed mechanism for the involvement of the epsilon subunit in ATP regulation in bacterial species such as E. coli.
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    Numerical Simulation of Dual-Fuel Compression-Ignition Engine in Part-Load Operating Condition With Double Injection
    (ASME, 2016-10) Jamali, Arash; Nalim, M. Razi; Mechanical Engineering, School of Engineering and Technology
    Natural gas substitution for diesel can result in significant reductions in pollutant emissions. In addition, with a high ignition temperature and relatively low reactivity, natural gas can enable promising approaches to combustion engine design. In particular, the combination of low-reactivity natural gas and high-reactivity diesel may allow for optimal operation as a reactivity-controlled compression ignition (RCCI) engine, which has potential for high efficiency and low emissions. In this computational study, a lean mixture of natural gas is ignited by direct injection of diesel fuel in part-load operating condition in a model of the heavy-duty CAT3401 diesel engine. A multi-dimensional simulation was performed using a finite-volume computational code for fuel spray and combustion processes in the Reynolds-averaged Navier-Stokes (RANS) framework. Adaptive mesh refinement (AMR) and multi-zone reaction modeling enables simulation in a reasonable time. The latter approach avoids expensive kinetic calculations in every computational cell, with considerable speedup. The model produces encouraging agreement between the simulation and experimental data. For reasonable accuracy and computation cost, a minimum cell size of 0.2 millimeters is suggested for the natural gas-diesel (NGD) dual-fuel engine. The results reveal that in part-load operating condition, much of the CH4, which is used as surrogate fuel for natural gas, cannot burn. The main goal of this research work is to assess the possibility to improve the performance of Caterpillar-3401 engine in NGD dual-fuel operation by in-cylinder modification strategies. The results reveal that among different strategies, double injection of diesel fuel with an early main injection can reduce the unburned hydrocarbon (UHC) emission significantly.
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    Revealing intrinsic changes of DNA induced by spore photoproduct lesion through computer simulation
    (Elsevier, 2023-05) Hege, Mellisa; Li, Lei; Pu, Jingzhi; Chemistry and Chemical Biology, School of Science
    In bacterial endospores, a cross-linked thymine dimer, 5-thyminyl-5,6-dihydrothymine, commonly referred to as the spore photoproduct (SP), is found as the dominant DNA photo lesion under UV radiation. During spore germination, SP is faithfully repaired by the spore photoproduct lyase (SPL) for normal DNA replication to resume. Despite this general mechanism, the exact way in which SP modifies the duplex DNA structure so that the damaged site can be recognized by SPL to initiate the repair process is still unclear. A previous X-ray crystallographic study, which used a reverse transcriptase as a DNA host template, captured a protein-bound duplex oligonucleotide containing two SP lesions; the study showed shortened hydrogen bonds between the AT base pairs involved in the lesions and widened minor grooves near the damaged sites. However, it remains to be determined whether the results accurately reflect the conformation of SP-containing DNA (SP-DNA) in its fully hydrated pre-repair form. To uncover the intrinsic changes in DNA conformation caused by SP lesions, we performed molecular dynamics (MD) simulations of SP-DNA duplexes in aqueous solution, using the nucleic acid portion of the previously determined crystal structure as a template. After MD relaxation, our simulated SP-DNAs showed weakened hydrogen bonds at the damaged sites compared to those in the undamaged DNA. Our analyses of the MD trajectories revealed a range of local and global structural distortions of DNA induced by SP. Specifically, the SP region displays a greater tendency to adopt an A-like-DNA conformation, and curvature analysis revealed an increase in the global bending compared to the canonical B-DNA. Although these SP-induced DNA conformational changes are relatively minor, they may provide a sufficient structural basis for SP to be recognized by SPL during the lesion repair process.
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    Toward Timely Data for Cancer Research: Assessment and Reengineering of the Cancer Reporting Process
    (JMIR Publications, 2018-03-01) Jabour, Abdulrahman M.; Dixon, Brian E.; Jones, Josette F.; Haggstrom, David A.; BioHealth Informatics, School of Informatics and Computing
    Background Cancer registries systematically collect cancer-related data to support cancer surveillance activities. However, cancer data are often unavailable for months to years after diagnosis, limiting its utility. Objective The objective of this study was to identify the barriers to rapid cancer reporting and identify ways to shorten the turnaround time. Methods Certified cancer registrars reporting to the Indiana State Department of Health cancer registry participated in a semistructured interview. Registrars were asked to describe the reporting process, estimate the duration of each step, and identify any barriers that may impact the reporting speed. Qualitative data analysis was performed with the intent of generating recommendations for workflow redesign. The existing and redesigned workflows were simulated for comparison. Results Barriers to rapid reporting included access to medical records from multiple facilities and the waiting period from diagnosis to treatment. The redesigned workflow focused on facilitating data sharing between registrars and applying a more efficient queuing technique while registrars await the delivery of treatment. The simulation results demonstrated that our recommendations to reduce the waiting period and share information could potentially improve the average reporting speed by 87 days. Conclusions Knowing the time elapsing at each step within the reporting process helps in prioritizing the needs and estimating the impact of future interventions. Where some previous studies focused on automating some of the cancer reporting activities, we anticipate much shorter reporting by leveraging health information technologies to target this waiting period.