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Physical Biology of the Cell

Rob Phillips, Jane Kondev, Julie Theriot

Chapter 18

Light and Life - all with Video Answers

Educators


Chapter Questions

02:53

Problem 1

Energy of the hydrogen atom
The goal here is to make a crude order-of-magnitude estimate of the size of an atom by examining the "competition" between the electrostatic potential between the proton in the nucleus of the atom and the electron, on the one hand, and the kinetic energy cost of confinement, on the other. To do this, write a total energy of a toy model of a hydrogen atom as a function of the parameter $a$ that is of the form
$$E_{\text {tot }}(a)=E_{\text {kinetic energy }}(a)+E_{\text {electrostatic }}(a)$$
The kinetic-energy contribution can be estimated by using the Heisenberg uncertainty principle as was done in the chapter, and you should rederive it and explain how it scales with $a$. Then, write the interaction energy between the proton and the electron to obtain $E_{\text {electrostatic }}(a) .$ Next minimize with respect to the unknown atomic size $a$ and find an expression for the size of the atom as a function of key parameters such as $\hbar, m,$ and $e .$ How does your resulting expression compare with the Bohr radius?

Sana Riaz
Sana Riaz
Numerade Educator
04:46

Problem 2

Toy model of tunneling
In Figure $18.56,$ we show a simple model of electron tunneling through a finite barrier. Compute the transmission coefficient, the ratio between the incoming and outgoing amplitudes, for an incoming wave of energy $E$ and a barrier of height $V>E$

Sana Riaz
Sana Riaz
Numerade Educator
02:49

Problem 3

Approximate calculation of the energies for the finite potential well
For a deep but finite potential well, the wave functions corresponding to the lowest energy levels are well approximated by the simple, sinusoidal wave functions obtained in the case of an infinite well (see Figure 18.11 ). Therefore, a simple approximation for the energy spectrum of a particle in a finite well can be obtained by computing the expectation value of its Hamiltonian in the energy eigenstates for the infinite-well case. Here, we test the validity of this approximation by direct comparison with the exact energy spectrum computed in the chapter.
(a) Compute the normalized energy eigenfunctions $\psi_{n}(x)$ for a particle in an infinite-well potential of width $a$ by solving the Schrödinger equation, Equation 18.11 , with the boundary condition given by Equation $18.13,$ and imposing the normalization condition $\int_{0}^{a} \psi_{n}(x)^{*} \psi_{n}(x) \mathrm{d} x=1$
(b) Compute the approximate values of the dimensionless energies for a particle in a finite well, $\tilde{x}_{n}=-\tilde{E}_{n} / V_{0},$ where $\tilde{E}_{n}=\left\langle\psi_{n}|\hat{H}| \psi_{n}\right\rangle,$ using the wave functions $\psi_{n}$ from (a) and the Hamiltonian for the particle in a finite well described in the chapter. Express your result for $\tilde{x}_{n}$ in terms of the dimensionless parameter $\alpha$ defined in Equation 18.30
(c) Following the strategy outlined in the Computational Exploration on p. $733,$ compute the exact values of dimensionless energies $x_{n}$ for $n=1,2,3,4$ by solving Equation 18.32 for $\alpha$ that corresponds to a finite well with $V_{0}=10 \mathrm{eV}$ and $a=1 \mathrm{nm} .$ Compare these values with those obtained in (b) and comment on the validity of the approximation.

Sana Riaz
Sana Riaz
Numerade Educator
02:38

Problem 4

Proton-motive force
(a) Use Equation 18.61 to make an estimate of the contribution of the $\mathrm{H}^{+}$ concentration gradient to the proton-motive force in a cell. The typical pH difference is roughly 1 (about 7.7 inside and 7.0 outside).
(b) It takes about four protons to make one ATP from ADP. If the free energy needed is in the range $20-23 k_{\mathrm{B}} T,$ how large must $V$ be in order to generate an ATP assuming that the energy of the proton-motive force can be harvested with $100 \%$ efficiency? Recall that the definition of 1 eV $\approx 160 \mathrm{zJ} \approx 40 \mathrm{k}_{\mathrm{B}} T$ is the energy gained by moving a charge of one electron through a potential difference of one volt. (Problem courtesy of Daniel Fisher.)

Sana Riaz
Sana Riaz
Numerade Educator
04:02

Problem 5

Electron tunneling
In this problem, the reader is asked to flesh out all of the details appearing in the appendix (Section 18.5 ). In particular, derive Equation 18.131 and compute what this implies about the tunneling rate.

Sana Riaz
Sana Riaz
Numerade Educator
03:30

Problem 6

Seeing the North star
Polaris has been known to generations of northern hemisphere navigators as a tool for finding latitude by simple geometrical measurements with a sextant. How much light actually reaches our eyes from a star like Polaris? Given that the luminosity of Polaris is roughly 2000 times that of the sun $(1000 \mathrm{W} / \mathrm{m}^{2} at the Earth)$ and that it is at a \right. distance of 430 light years from Earth, work out the power output of Polaris, the number of photons crossing the pupil of your eye each second coming from this famous star and the mean spacing between these photons. What is the mean rate of arrival of photons to a single cone cell?

Sana Riaz
Sana Riaz
Numerade Educator
04:33

Problem 7

Eyes and the diffraction limit
(a) A point source emits an electric field that can be thought of as the real part of $\psi=(A / r) \mathrm{e}^{\mathrm{i}(\omega t-\mathbf{k} \cdot \mathbf{r})},$ where $\mathbf{r}$ is a vector
pointing away from the source and $r=|\mathbf{r}| . \omega$ is the frequency and $\mathbf{k}=k \hat{\mathbf{r}}$ is the wave vector, which points in the radial direction. Notice that the amplitude $A / r$ decreases as we move away from the source. Show that if we look at the field at a distance $Z$ that is far away from the source, the incoming light can be thought of as a plane wave. This means that the phase is given by $\omega t-k Z$ everywhere on that plane.
(b) We now imagine an aperture as a series of tiny point sources, each serving to emit radiation as dictated by Huygens' principle. Write the field due to each point source on the plane located at a distance $Z$ and position $r$ on the $x$ -axis as shown in Figure $18.39(\mathrm{C}) .$ Do this as a function of the position of the source within the aperture given by $R$ and $\phi .$ Once again, use the approximation that the screen is very far away from the aperture in order to simplify your expressions.
(c) Add up the contribution of all point sources by integrating over the expression you obtained in (b). You will get a result in terms of Bessel functions. Calculate the intensity of the field at the screen by computing $I=\psi \times \psi^{*}$
(d) For reasonable parameters, make a plot of the intensity profile on the screen using software such as Mathematica or Matlab. Find the first zero in intensity and relate it to the expression for the resolution limit given in Equation 18.69 What does this mean in terms of the human resolution limit? If you have two objects at about $1 \mathrm{m}$ from you, what is the minimum separation between them such that you can still resolve them as separate?

Sana Riaz
Sana Riaz
Numerade Educator
01:46

Problem 8

Resolution of fossil insect eyes
Estimate the angular resolution of the insects whose fossil eyes are shown in Figure $18.57(\mathrm{A})$

Rabeya Zahid
Rabeya Zahid
Numerade Educator
03:54

Problem 9

MWC model for signal transduction in the eye
Throughout the book, we have argued that the treatment of ligand-gated ion channels is a fascinating problem in statistical mechanics and that the Monod-Wyman-Changeux $(\mathrm{MWC})$ model provides a great response to that challenge. Here, we explore this model in the context of cyclic-nucleotide-gated channels that are gated by cGMP.
(a) Write down an MWC model for the ligand-gated channel and calculate the probability of the channel being open as a function of the ligand concentration. Construct separate versions of this model by considering channels with 1,2,3 and 4 binding sites.
(b) For each version of the model, compare the resulting curve to the data shown in Figure 18.58 for the bovine retinal CNG channel. In order to do this, perform a "fit by eye." It might be useful to understand how each model behaves in the limits $L \rightarrow 0, L \rightarrow+\infty,$ where $L$ is the concentration of $\mathrm{cGMP}$, and how the sharpness of the curve is affected by the choice of the various model parameters. What do you conclude about the number of binding sites for cGMP in this channel?

Sana Riaz
Sana Riaz
Numerade Educator
05:00

Problem 10

Waiting time distributions
One informative way of analyzing the frequency of events is illustrated in Figure $18.47(\mathrm{C})$. Here, the cumulative probability of events is obtained by measuring how many events have occurred if we wait a time $t .$ This cumulative probability is fit to the equation $n=N\left[1-\mathrm{e}^{-t / \tau}\right],$ where $N$ is the total number of events. Show that his functional form is precisely what is expected for a process characterized by the waiting time distribution $p(t)=\mathrm{e}^{-t / \tau}$

Sana Riaz
Sana Riaz
Numerade Educator
02:44

Problem 11

Statistics of photon detection in the eye
Using the Poisson distribution, generate the curves in Figure $18.48(\mathrm{B})$

Rabeya Zahid
Rabeya Zahid
Numerade Educator