Three-Dimensional Computer Models of Biochemical Processes

This Laboratory Report uses computational biology and three-dimensional software applications to visualize biochemical processes. This strategy provides a more intuitive manner of explaining the actual microbiological concepts that one-dimensional or two-dimensional diagrams fail to represent successfully. Knowing what processes undergo in a chemical reaction by virtually observing them happen with fundamental physical properties can benefit a student’s educational pathway.

The simulation of molecular processes has been shown to bring extensive biological information for chemists, biologists, and computer scientists in a collaborative exchange of valuable information for each field. The implementation of computational biology has rightfully brought the attention of universities from all over the world. Dr. Dan Fu from the Liao Ning Petrochemical College in Fushun, China, states, “The 3D experiment simulation software uses computer software technology to simulate the traditional experiment operation process” (p.1).  This teaching method can be more cost-effective, safer, and less time-consuming for students whose focus involves physical, biological, or chemical real-life processes.

 It is an ambitious idea to say that by using computing software, there will be a more efficient way of teaching such convoluted concepts. However, if broken down correctly, a tool like this would allow students to look at the levels of cellular behavior in real time, how these interfere with each other, and what an intermolecular interaction in an organism would look like. In other words, we are talking about experimentation with concepts such as cell- division, proteins carrying nutrients and oxygen, and even entire human organs interacting with one another that can be visualized all inside a computer; something more or less like an actualized and innovative “virtual laboratory.” In short, it is a digital simulation of any chemical process that can be inspected at a molecular level.

This method has already been integrated into vocational colleges where the effects of 3D biological computing are bringing many significant advances in educational systems. Dr. Dan Fu states, “It has greatly improved the teaching effect and increased students’ interest in learning. At the same time, it provides a reliable guarantee for students to smoothly connect with internship positions and undertake work tasks, highlighting the characteristics of the information technology age”. (p. 1) It is important to note that this methodology is not attempting to replace real-life experiments with three-dimensional models but rather give students and scientists cumulative knowledge that can be obtained through safer and more ethical means. The idea of leaving away any traditional laboratory experimentation in STEM fields is not something that can be easily attainable. However, with this method, students and professionals will be more prepared and informed on what happens and how certain specific processes might look.

This is a system that is not only allowing students to have a better understanding of their course materials. This innovative tool allows scientists to model the interactions between the behavior of pathogens in the immune systems, for example. Allowing scientists to understand how diseases spread and how our bodies may fight back. The exchange of ideas and possible future outcomes, such as personalized medicine and even testing the effect of a drug on a virtual heart to understand its behavior and whether or not it is safe for our consumption, are other great uses given to 3D computer models of biochemical processes. Dr. Dan Fu proves this argument by providing the following visual of a possible Graphical User Interface. See Figures 1 and 2 below.

Figure 1. The interface of a 3D virtual simulation software Fu includes the name of the software, virtual space, virtual instruments, modules 1,2 and 3.  (p.2) 

Figure 2. Interface of learning and assessment Fu, D (p.2). It includes “ the button for entering the module of learning” and “The button for entering the module of assessment.”

 It is important to note that at this point, the author presents new information regarding other socioeconomic contents in addition to the literature search needed for a program of this sort. Dr. Dan Fu states that the virtual simulation software could also contain information such as the user’s employment situation. The characteristics of the specialty and the basic situation of students’ internship and employment are considered in the software. (p.3).  The purpose of having a record of said characteristics is uncertain. There is little mention of this or why this information is being collected other than the euphemism of creating a system where students can easily transition from colleges to internships and full-time employment. If the intentions of obtaining such data do not have any underlying purposes, then there are endless possibilities for what can be obtained from this practice. 

These three-dimensional visualization tools have been used in cutting-edge discoveries and breakthrough studies. One is Organoid Intelligence (OI), a new field that uses lab-grown brain organoids to mimic human cognitive processes and perform computational tasks. In a collaborative group of researchers, Dr. Thomas Hartung explains how using three-dimensional computer models in biochemical processes led to the articulated vision of using brain organoids for computational purposes. “This article synthesizes key information from three sources focused on using computational modeling to understand and predict biological processes. The sources explore mathematical frameworks for simulating biological systems, applying 3D software in experiments, and integrating various data types to construct multi-scale models, focusing on cardiac systems and drug development.” Through biochemical visualization, we are not only bringing future generations of scientists and engineers to a seamless and comprehensive training that will bring a new wave of discoveries. 

Based on the experimental findings, the integration of 3D simulation software demonstrated significant improvements in multiple aspects of the laboratory experience. Data indicated enhanced student proficiency in experimental protocols, with measurable procedural accuracy and safety compliance gains. See Figure 3 below.

Figure 3. Satisfaction rate of students for the software. Fu, D (p.4).

These results suggest that 3D simulation software is an effective pedagogical tool for chemical laboratory education, optimizing learning outcomes and operational efficiency. Further research is recommended to evaluate long-term retention rates and potential applications in advanced chemistry coursework, as well as more information about where all the data collected goes. Despite everything, the application is a big step for new pedagogical tools recently developed.

References

Block, G., & Goode, J. A. (2002, November 15). ‘In Silico’ Simulation of Biological Processes. Wiley Online Library. https://onlinelibrary-wiley-com.ccny-proxy1.libr.ccny.cuny.edu/doi/book/10.1002/0470857897 

Fu, D. (2023, October 3). Application of 3D Simulation Software in Chemical Experiments. IEEE xplore. https://www.ieee.org/ 

Smirnova, L., Caffo., Hartung, T., et Al Organoid Intelligence (OI): The New Frontier in biocomputing and intelligence-in-a-dish. Frontiers. https://www.frontiersin.org/journals/science/articles/10.3389/fsci.2023.1017235/full

https://dl-acm-org.ccny-proxy1.libr.ccny.cuny.edu/doi/abs/10.1145/563788.604453