432 Questions

any AI system is only as good as the training dataset used. An inevitable challenge will arise

in the not-​so-​distant future whereby AI outputs themselves will be accepted as sufficiently

gold-​standard for training new models. But if these AI outputs have not been subjected to

the rigorous experimental validation of the original training data, drift in output accuracy is

inevitable. So, revolutionary as AI is for big data processing, there needs to be checks and

balances in place.

9.7  SUMMARY POINTS

◾Systems biology coupled with biophysics enables significant scientific insight

through coupling cutting-​edge computation with experimental biophysics, often

in native biological systems.

◾Synthetic biology enables complex self-​assembled nanostructures to be fabricated

using biological material such as DNA, which have applications in nanomedicine

and basic biophysics investigations.

◾Biological circuits offer potential to design complex biocomputers inside living cells.

◾Biophysics developments have enabled miniaturization of biosensors to facilitate

lab-​on-​a-​chip technologies for improved personalized healthcare diagnostics and

treatment.

◾Biophysics can extend into the quantum world and into whole ecosystems.

QUESTIONS

9.1

The surface area of a light-​harvesting protein complex was estimated using AFM

imaging to be 350 nm². Sunlight of mean wavelength 530 nm and intensity equivalent

to 4 × 10²¹ photons m⁻² s⁻¹ was directed onto the surface of cyanobacteria containing

light-​harvesting complexes in their cell membranes, whose energy was coupled to the

pumping of protons across a cell membrane, with a steady-​state protonmotive force

of –​170 mV. To be an efficient energy transfer, one might expect that the effective

transfer time for transmembrane pumping of a single proton should be faster than

the typical rotational diffusion time of a protein complex in the membrane of a few

nanoseconds; otherwise, there could be energy dissipation away from the proton

pump. Explain with reasoning whether this is an efficient energy transfer.

9.2

With specific, quantitative reference to length scales, rates of diffusion, and

concentrations of nutrients, explain why a time-​sampling strategy is more sensible for

a bacterium than a space-​sampling mechanism for chemotaxis.

9.3

Discuss the biological, chemical, and biophysical challenges to efficiently deliver and

release a drug specifically to a given subcellular organelle that is caged inside a 3D

DNA nanostructure?

9.4

What do biologists mean by “robustness” in the context of a biological circuit? Using

an electrical circuit diagram approach, show how robustness can be achieved in prin­

ciple using feedback. How can oscillatory behavior arise in such robust systems?

9.5

What is a transcriptor? How can multiple transcriptors be coupled to generate a

bistable oscillator (i.e., an oscillating output in time between on and off states)?

9.6

If a particular single gene’s expression is in steady state in a spherical bacterial cell of

1 μm diameter such that there are a total of 50 repressor molecules in the cell, which

can each bind to the gene’s promoter with a probability of 10% s⁻¹, and the expressed

protein can directly activate its own expression at a rate of one molecule per second,

calculate the cellular concentration of the expressed protein in nM units stating any

assumptions you make.

9.7

How is Schrödinger’s famous quantum mechanical wave equation, which governs the

likelihood for finding an electron in a given region of space and time, related to the

probability distribution function of a single diffusing biological molecule? Discuss

the significance of this between the life and physical sciences.