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PHYS 8990 Topic

Concepts in Computational Molecular Biophysics

Michael Bachmann

The understanding of biological processes is one of the most challenging tasks
modern interdisciplinary research has to tackle. Apart from the general interest
in the nature of cell processes, it is the enormous
impact of epidemic diseases that attracts scientists with biological, chemical,
medical, and physical background to combine efforts to solve the problems that
arise from malfunctions in the fine-tuned molecular interplay of cells and cell

Proteins are the most prominent examples of such molecules. They control almost
all relevant cell processes. The subtle, sensitive relationship between their
geometric structure and the associated biological function is the reason why
mutation, misfolding, and clustering can cause the breakdown of a complete cell
system. This is, e.g., the case in Alzheimer's disease, where the interaction of
neurons is disturbed by protein-mediated processes.

Why is this interesting for theoretical physics? The most exciting thing is that
a protein is a "no-no" in theory: It is too large to be treated by classical
mechanics, but it is large enough that a full quantum approach is possibly not
necessary (it is even too complex to try this). It is a "meso-scale" object, but
with individuality. Being a chain of linearly connected amino acids of different
types, this individuality is inevitably connected with the amino acid sequence,
which determines the biological function. Structurally, this "engraved disorder"
renders a protein and its function unique, but the associated "glassiness" makes
the understanding of the relationship between structure and function so
complicated. The identification of general principles is difficult. Proteins
live in an aqueous, thermal environment and thus require a statistical theory,
but being small, they lack the general assumption of an infinitely large
system (thermodynamic limit) in this theory. Therefore, their structural transitions -
although obvious and strong - are not phase transitions in the traditional
sense. These and many more reasons let proteins be interesting objects for
modern physics-based research, but also teach us that we have not yet found the
fundamental physical principles for the systems that control our well-being.

Since analytic theory is not applicable, sophisticated computer simulation
strategies are the only way out of the dilemma. The interested student will
learn how proteins are modeled and simulated and what intrinsic problems need to
be faced because of their individual nature.

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