BioPhysics
Throughout the past four weeks, I have listened to countless lectures and learned so much about Biology, Chemistry, and Physics. These lectures came up with two main conclusions: DNA is like a code (which is why we learned how to code in Python) and 'Everything that animals do, atoms do'. For my final project, I had to answer two questions and make a code showing how molecules conduct their random walks through space.
Programming: In this cluster, you have seen how DNA is used to create proteins which run all the processes in cells. Some would say that DNA is the software of life. Based on your knowledge of programming, evaluate that statement. In what sense is DNA like a software program? In what sense is it very different?
DNA is the code of life. DNA is made of three main things: phosphate, sugar, and nucleic acids. When these three things are put together, and the nucleic acids are lined up in different orders, they make life. A simple change of two bases can change black hair brown. Similarly, a small change in a code can change the output a system gives. For example, if I want to create a graph, and make the line red, if I change the line ‘r-’ to ‘k-’, the output I would receive is a black line. Both, DNA and software programs, depend on the littlest detail, and the output can be vastly different if one thing changes in either. On top of this, both DNA and software programs are a compilation of different things. DNA creates life, and it does that by creating a code which needs to be executed, making dozens of proteins, which make traits of a living organism. Software programs consist of functions and loops, and when the code is executed, a computer goes through every line, printing a single output according to what was programmed. While software programs and DNA have a lot in common, they do have one difference. DNA, while it is a code, has a physical output. DNA affects traits in organisms, which can be seen, felt, and heard. Software programs, on the other hand, give an intangible output. The output of a code is something that can be read and analyzed, but it has no effect on the physical world. The program is simply used to run apps on a phone, but a program cannot be seen in the real world.
Biophysics: Explain, in what sense, is the following statement true: ‘Everything that animals do, atoms do.’
‘Everything that animals do, atoms do.’ This is a statement that may seem confusing, but makes everything make sense. Animals do not have a purpose, their only reason to live is to exist. Animals walk around the world, finding a task, like an atom having a random walk. Atoms roam the air, finding other atoms, and trying to find something to do. In simulations, atoms try to find a specific spot in a room, but they walk around in circles until that is completed. Even once it finds the target, it simply walks around forever, finding the next target. So, atoms and animals are random walkers, simply finding a purpose which will change once they reach their previous goal.
Experiment: Changing the size of the target
Hypothesis: We both think that the target of the cell has a direct effect on the number of steps a walker takes. The larger the target is, the easier it will be for a walker to find it; however, the impact the size of the target carries will not lead to vastly different results unless we vastly change the size.
Data: The test for the size of the target was run 5 times. We have the default size (4x4) and 4 other sizes for the target: 1x1, 3x3, 7x7, and 10x10. The results below show the average number of steps each of the three walkers took after three trails (all tests are shown to the right).
Conclusion: All of these data points lead to one assumption: The larger the target, the less steps are needed. The random walkers need to find a specific spot in the box that takes up a small fraction of the space there, and it cannot see the target, so it must walk in random directions. When the target space is larger, the random walkers find it easier to get to the target because there is so much space in the room which is considered their destination. Therefore, as the target gets larger, covering up more space in the box, the cells need to take an average of less steps to reach the target.
