3.Pharmacometric models simulation using NONMEM, Berkeley Madonna and R.
Translational and Clinical Pharmacology 2017;25(3):125-133
In this tutorial, we introduce a differential equation simulation model for use in pharmacometrics involving NONMEM, Berkeley Madonna, and R. We report components of the simulation code and similarities/differences between software, rather than how to use each software. Depending on the purpose of the simulation, an appropriate tool can be selected for effective communication.
Computer Simulation
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Software
4.Thermal Problems and Methods in Invasive Microwave Coagulation Therapy.
Qun NAN ; Jianshu PENG ; Youjun LIU ; Yi ZENGON
Journal of Korean Society of Medical Informatics 2007;13(2):159-163
OBJECTIVE: To study some thermal problems in invasive microwave coagulation (IMC) therapy. METHODS: Temperature fields predicts, limitation and remedy methods of the Pennes bioheat transfer equation during the temperature distribution analyses and how to kill a large anomalistic tumor for only once were discussed. RESULTS: The coagulation area between the simulations and actual measured results showed good correspondence. Blood flow influenced the rise in temperature significantly. CONCLUSIONS: Thermal distribution with computer simulation in invasive microwave coagulation therapy is an accurate and reliable method.
Computer Simulation
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Microwaves*
5.Computational Medicine: Past, Present and Future.
Lan-Qing LYU ; Hong-Yan CUI ; Ming-Yi SHAO ; Yu FU ; Rui-Xia ZHAO ; Qiu-Ping CHEN
Chinese journal of integrative medicine 2022;28(5):453-462
Computational medicine is an emerging discipline that uses computer models and complex software to simulate the development and treatment of diseases. Advances in computer hardware and software technology, especially the development of algorithms and graphics processing units (GPUs), have led to the broader application of computers in the medical field. Computer vision based on mathematical biological modelling will revolutionize clinical research and diagnosis, and promote the innovative development of Chinese medicine, some biological models have begun to play a practical role in various types of research. This paper introduces the concepts and characteristics of computational medicine and then reviews the developmental history of the field, including Digital Human in Chinese medicine. Additionally, this study introduces research progress in computational medicine around the world, lists some specific clinical applications of computational medicine, discusses the key problems and limitations of the research and the development and application of computational medicine, and ultimately looks forward to the developmental prospects, especially in the field of computational Chinese medicine.
Algorithms
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Computer Simulation
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Humans
6.The use of tropical fruits for skills training in a neurosurgical boot camp
Juan Silvestre G. Pascual ; Kevin Ivan P. Chan ; Mary Angeline U. Hernandez ; Edroico B. Brillante ; Edmund John B. Cayanong ; Llex C. Soriano ; Gerardo D. Legaspi ; Kathleen Joy O. Khu
Philippine Journal of Surgical Specialties 2022;77(2):27-34
Objective:
Neurosurgical boot camps allow trainees to hone practical skills in a risk-free environment, but the models and simulators used are relatively costly. In developing countries like the Philippines, low-cost alternatives have to be devised. The authors aimed to demonstrate the feasibility of using local, readily available, and inexpensive tropical fruits as surrogate models for basic neurosurgical skills training during a neurosurgical boot camp.
Methods:
Locally available tropical fruits were used to teach basic neurosurgical skills to trainees. Coconut, pomelo, and watermelon were used as models for head clamp application, scalp and dural suturing, and ventriculostomy, respectively. Feedback was obtained from the participants after the boot camp.
Results:
All eight residents thought that the boot camp was useful in learning new skills, and that the fruit models served their purpose. The trainees favored the fruit models that catered to the skill sets required according to level of training. The use of tropical fruits in the boot camp also provided an informal atmosphere that was conducive to learning.
Conclusion
The novel use of tropical fruits as surrogate models in basic neurosurgical skills training was a feasible and affordable alternative in resource-limited settings, although the activity was perceived to be more useful to junior than to senior residents. The informal atmosphere generated by the use of the fruits contributed to an improved learning experience for the trainee.
Teaching
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Simulation Training
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7.Analysis of Driver-Passenger Relationship and Restoration of Accident Process Based on 3D Laser Scanning Technology.
Xue ZHANG ; Sheng Dong LI ; Yan Geng YU ; Fu ZHANG ; Chong Bin ZOU ; Zhi Liang ZOU ; Qi Feng MIAO ; Man Ting ZHANG ; Li Juan TANG ; Dong Ri LI
Journal of Forensic Medicine 2020;36(1):69-71
Objective To discuss the application of 3D laser scanner and computer technology in restoration of the accident scene and reconstruction of the accident process, as well as identification of the driver-passenger relationship. Methods The scene of a traffic accident, the accident vehicle and the vehicle of the same type as accident vehicle were scanned using 3D laser scanner. The accident scene, traces and accident vehicle were integrated using computer technology to restore the accident scene, and the accident process was reconstructed and analyzed by combining the characteristics of the body injuries. Results By restoring the accident scene and reconstructing the accident process with 3D laser scanner, it was determined that Wu was in the driving seat at the time of the accident. Conclusion It is more objective and scientific to use 3D laser scanning technology to restore the accident scene, reconstruct the accident process and analyze the moving track of the driver and passengers in the vehicle. It will help to improve the accuracy of forensic identification of road traffic accidents.
Accidents, Traffic
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Computer Simulation
9.Molecular dynamics simulation of force-regulated interaction between talin and Rap1b.
Zhe YU ; Yanru JI ; Wenhua HUANG ; Ying FANG ; Jianhua WU
Journal of Biomedical Engineering 2023;40(4):645-653
The binding of talin-F0 domain to ras-related protein 1b (Rap1b) plays an important role in the formation of thrombosis. However, since talin is a force-sensitive protein, it remains unclear whether and how force regulates the talin-F0/Rap1b interaction. To explore the effect of force on the binding affinity and the dynamics mechanisms of talin-F0/Rap1b, molecular dynamics simulation was used to observe and compare the changes in functional and conformational information of the complex under different forces. Our results showed that when the complex was subjected to tensile forces, there were at least two dissociation pathways with significantly different mechanical strengths. The key event determining the mechanical strength difference between the two pathways was whether the β4 sheet of the F0 domain was pulled away from the original β1-β4 parallel structure. As the force increased, the talin-F0/Rap1b interaction first strengthened and then weakened, exhibiting the signature of a transition from catch bonds to slip bonds. The mechanical load of 20 pN increased the interaction index of two residue pairs, ASP 54-ARG 41 and GLN 18-THR 65, which resulted in a significant increase in the affinity of the complex. This study predicts the regulatory mechanism of the talin-F0/Rap1b interaction by forces in the intracellular environment and provides novel ideas for the treatment of related diseases and drug development.
Molecular Dynamics Simulation
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Talin
10.Nucleobase-substituted ponatinib analogues: Molecular docking, short molecular dynamics, and drug-likeness profiling
Vince Lambert H. Padilla ; Glenn V. Alea
Philippine Journal of Health Research and Development 2024;28(2):56-66
Objectives:
This study aims to assess the drug-likeness and binding of nucleobase-substituted ponatinib analogues towards wild-type and T315I mutant BCR-ABL tyrosine kinases.
Methodology:
A total of 415 ponatinib analogues, encompassing single and combinatorial modifications on five parts of the drug
were generated, profiled in SwissADME, and subjected to molecular docking using AutoDock4. Complexes formed by the top
analogues then underwent a 100-ns molecular dynamics simulation with GROMACS.
Results:
Analogues featuring the replacement of the imidazo[1,2b]pyridazine with adenine and cytosine exhibited promising binding
free energies, attributed to the presence of primary amines that facilitate crucial hydrogen bond interactions in the hinge region.
RMSD, RMSF, and atomic distance analyses of the MD trajectories revealed that the six top analogues formed stable complexes in
their inactive DFG-out conformations. Changes in the MMPBSA and MMGBSA-calculated free energies were mainly driven by
changes in hydrogen bonds. Furthermore, drug-likeness predictions supported the formulation of most analogues for oral
administration.
Conclusion
Among the top analogues, VP10004 and VP81014 exhibited the most favorable binding free energies and interactions
with the target models, while VP10312 was identified as the most feasible candidate for synthesis.
Hydrogen Bonding
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Molecular Dynamics Simulation
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Molecular Docking Simulation