Computer simulations: Doing science with computers

Outline

I. Introduction
Thesis statement: As computer simulations are an effective way to estimate the behavior of
different phenomena, different areas of research have been developed through computing:
computational physics, chemistry, and biology.
II. Body
A. Computational physics
1. Solid mechanics and dynamics.
a. Applied forces.
b. Motion, collision, and interaction.
2. Fluid dynamics.
a. Examples: Weather, pipelines, and aerodynamics.
3. Electromagnetism.
a. Electric and magnetic parameters and interactions of materials, circuits, and
electrical systems.
B. Computational chemistry
1. Molecular mechanics.
a. Atomic interactions and molecular docking.
2. Chemical/Molecular dynamics.
a. Evolution in time of particle and molecular systems.
C. Computational biology
1. Population growth.
a. Predator-prey interaction of two species of microorganisms (Curds, 1971).
2. Epidemics.
a. Spread of white pine blister rust in trees of a geographical area (McDonald,
1981).
3. Cancer biology.
a. Tumor cell growth with respect to nutrients (Ward & King, 1997).
III. Conclusion
There are several areas of computer science that make use of computer simulations to
understand phenomena of nature: computational physics, biology, and chemistry.

Introductory paragraph

There are several tools and methods available nowadays for the study of phenomena found in nature; for
instance, mathematical models and computer simulations. On the one hand, mathematical models help describe
a phenomenon over a set of variables, functions, and parameters, in order to establish a way to calculate and
predict that phenomenons behavior under diverse circumstances, environments, etc.; on the other hand,
computer simulations are a very convenient way to implement these models. Computer simulations are useful
since they assist automatizing and parametrizing high complexity problems, and helping visualize the produced
outcome effortlessly. Hence, as computer simulations effectively help estimate a set of results that represent a
phenomenons behavior, a broad variety of areas have been developed through computing; particularly,
computational physics, chemistry, and biology.
Body paragraph 1: Computational physics

The first area, computational physics, is the one concerned about everything that works, and can be explained, by
the laws of physics. Firstly, a good example of the kind of phenomena computational physics works is solid
mechanics and dynamics. This topic studies how solid systems behave according to different scenarios; to
illustrate, it is possible to simulate the way a solid of any specific geometry reacts or deforms, according to a set
of applied external forces on different points of it; or how solids in motion move, collide, interact, and affect each
other, according to their physical qualities. Secondly, fluid dynamics is another topic covered by this area. It is
possible to find many different sorts of computer simulations done regarding the phenomena involving the
dynamics of fluids; weather, pipelines, and aerodynamics are some examples of common simulated phenomena
of interest. Thirdly, there is also work done on electromagnetism; namely, everything related to the electric and
magnetic parameters and interactions of materials, circuits, and electrical systems.

Body paragraph 2: Computational chemistry

Although computational physics can also work on the molecular and atomic level, computational chemistry has a
deeper interest in analyzing chemical reactions and interactions, and calculating the structures and properties of
different molecules and solids. Computer simulations focused on this field work on two main topics: molecular
mechanics and chemical/molecular dynamics. The first topic, molecular mechanics, has to do with the study
atomic interactions and molecular docking; that is to say, it inspects how different couplings of compounds
behave, how they react, and how much energy they release. Equally important, the study of chemical/molecular
dynamics focuses on examining the evolution in time of the behavior of particle and molecular systems, making
use of both classic and quantum physics models.

Body paragraph 3: Computational biology

Finally, computational biology is the field that studies biological phenomena through different models and
techniques. This area covers a huge diversity of matters of interest, mostly because it can focus on different
levels: cellular, organic, systemic, genetic, behavioral, and social. Some common examples of the topics
computational biology covers through computer simulations are population growth, epidemics, and cancer
biology. Population growth is the study of the growth and reduction of different species (of any level) regarding
their interactions, environment, resources, and quantity. For instance, the study conducted by Curds (1971)
establishes a way to use computer simulations to determine and visualize the behavior of two microorganisms
that present a predator-prey interaction. Additionally, epidemics is another subject of interest, for the reason that
simulated models help determine how quickly an infectious disease spreads in some geographical area. An
example of this can be found in the academic work done by McDonald (1981); their study uses computer
simulations, which are developed in order to detect to what degree white pine blister rust spreads through time
in forests. Lastly, cancer biology is another important topic of computational biology, as it uses simulations of
predictive models to make it possible to visualize how tumor growth behaves under different circumstances.
Indeed, one case to mention is the piece of research of tumor growth from Ward and King (1997), where they
propose a mathematical model tested through computer simulations that show how fixed quantities of tumor
cells grow, reproduce, and die, with respect to a nutrient concentration in their environment.
Concluding paragraph

To conclude, there are several areas of computer science that make use of computer simulations to understand
phenomena of nature; these areas, namely, computational physics, biology, and chemistry, take advantage of
computer solutions in order to implement efficiently mathematical models of complex phenomena, and help give
researchers an insight or prediction of how these phenomena behave or evolve through time. Hence, there is a
great potential in the use of all these tools, methods, and models, to give a huge support in the advance of
science and research in several fields of interest. Lastly, it is important to highlight that obtaining good predictive
results of different phenomena not only depends on good implemented computer simulations, but also on the
proper comparison and validation of experts with real life data.

References

1. Curds, C. R. (1971). A computer-simulation study of predator-prey relationships in a single-stage continuous-

culture system. Water Research, 5(10), 793-812.

2. McDonald, G. I., Hoff, R. J., & Wykoff, W. R. (1981). Computer simulation of white pine blister rust epidemics.

3. Ward, J. P., & King, J. R. (1997). Mathematical modelling of avascular-tumour growth. Mathematical Medicine
and Biology: A Journal of the IMA, 14(1), 39-69.