Physics of Life (2022) / Chapter Skim
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From page 40... ...
Specific Recommendation: Federal agencies and private foundations should establish programs for the support of international students in U.S. PhD programs, in biological physics and more generally.
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Chapter 10 explores the human dimensions of science, focusing on international engagement and equality of opportunity. Many of the issues are immediately relevant to biological physics, but also much more general, and need to be addressed across science as a whole.
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policy toward international students and scientists are being driven by concerns about national and economic security. Conclusion: The open exchange of people and ideas is critical to the health of biological physics, physics, and the scientific enterprise generally.
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Although the experience of each group is unique, one can find related problems for all of the underrepresented groups in the biological physics community. Parallel to the role of Historically Black Colleges and Universities (HBCUs)
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There is a sense, however, that biological physics has a special role to play in welcoming a broader community. Conclusion: The biological physics community has a special opportunity to reach broader audiences, leveraging human fascination with the living world to create entrance points to physics for a more diverse population of students and for the general public.
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, although it is more precise to say that evolution has selected organisms that achieve effective solutions to these problems. One of the central problems in biological physics is to turn qualitative notions of function into precise physical concepts.
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efficient energy theoretical ideas on conversion; nanoscale thermodynamics and linear and rotary motors. information on small scales and away from equilibrium.
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Parts of this understanding now are well established, providing a solid foundation for exploration of quantum effects in other biologi cal processes. From a historical perspective, the emergence of this understanding straddles the emergence of biological physics as a part of physics, and thus some of the crucial insights are seen now as part of mainstream biology, or perhaps part of biophysics as a biological science.
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More generally, photosynthetic organisms contain many more chlorophyll molecules than those involved directly in the chemical reactions driven by light, leading to the picture of a large "antenna" composed of many chlo rophylls, absorbing light and funneling energy to a "reaction center" that contains only a handful of these molecules. The problem of energy transfer in the photosynthetic antenna would recapture the attention of the physics community in the 21st century, with the first direct evidence that the process involves quantum mechanical coherence.
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These results are in marked contrast to typical chemical reactions, where rates are exponentially sensitive to temperature changes, following the Arrhenius law. This is a sign that quantum mechanical effects are important, and through the 1970s and 1980s, the biological physics community reached a relatively complete under standing of this.
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In large molecules such as the photosynthetic reaction center, there is a mix of high frequency and low frequency vibrations, and this can lead to the anomalous patterns of temperature dependence seen in this system. Thus, electron transfer in photosynthesis depends on an interplay of classical and quantum dynamics, at biologically relevant tem peratures.
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Efficient hydrogen transfer in biological molecules thus depends on an interplay between classical and quantum dynamics, in many ways parallel to the case of photosynthetic electron transfer. scales comparable to the initial electron transfer rate.
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. Even beyond its in trinsic importance, the physics of how the photosynthetic reaction center captures the energy of sunlight thus provides an entrance point for studying mechanisms of energy conversion that are shared across all forms of life on Earth.
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. The larger movement of the 14.5-nm reflection suggests that the centres of mass, presumably the catalytic domains of the myosin heads, separate by an additional ,0.03 nm from each other as they are pulled towards the Z-disk by the thin filaments.
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. The biological physics community made a major effort to develop these single molecule manipulation experiments, which have now been exported to the broader community of biologists.
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They are driven by the world's smallest rotary engine, as schematized in Figure 1.4. As noted above, this motor is powered directly by the difference in chemical potential for protons FIGURE 1.3 Single molecule experiments help us to understand molecular motors, including force generation in muscle.
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As they make more of the protein, the rotation rate (bottom, for a cell tethered to a glass slide) increases in steps as individual proteins are inserted into the structure, each contributing a discrete unit of torque.
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This rotation is visible in single molecules that are fixed to a glass slide and running "backward," degrading ATP molecules to pump protons, as in Figure 1.5. Strikingly, unlike the linear motors myosin and kinesin, which have irreversible cycles and convert only a fraction of the energy from ATP into mechanical work, the ATP synthases are nearly 100 percent efficient; they are thus reversible and can be run in either direction (i.e., to consume or to produce ATP)
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The number of the beads at th eed, the histogram of angular Sciences U.S.A. method102:1333, distribution of centroid Creative Commons License CC BY-NC-ND 4.0.
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The effort to explore these nanomachines has led to the development of new methods for single molecule measurement and manipulation, and to sharp new theoretical ideas about the relations between ther modynamics and information on small scales and away from equilibrium. These developments in biological physics are continuous with a broader renaissance in non-equilibrium statistical mechanics (Chapter 5)
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More profoundly, at very low Reynolds number, the viscous forces from the surrounding fluid balance the active forces that an organism generates in order to move, and this balance is enforced moment by moment. As a consequence, as the organism goes through one cycle of movement -- one rotation of a bacterial flagellum, one beat of a eukaryotic cilium, one full squirm or writhe
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The ratio of inertial to viscous forces is the Reynolds number R = avρ/η; it is convenient to define the kinematic viscos ity ν = η/ρ. The sketches at the right indicate typical Reynolds numbers for swimming humans, fish, and bacteria.
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. Both brains and leaves devote considerable resources to their vasculature, and the biological physics community has explored whether there might be general physi cal principles governing the distribution of these resources.
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. This theoretical work raises questions about how to characterize the "loopiness" of flow networks, and how such networks could develop.
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This example also illustrates how the questions asked by the biological physics community connect to questions asked by neurobiologists, engineers, control theorists, and others, as explored more fully in Part II of this report. Faced with the wide range of questions associated even with one movement, many physicists and biologists have made progress by constraining animal behavior so that some more limited set of movements could be studied more precisely.
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In many ways, the challenge ethologists raise is paradigmatic for modern biological physics: Can the complexity of a living system be tamed in its functional context? In the spirit of physicists' approaches to other complex prob lems, the goal is not just to build better tools for characterizing behavior, but to discover some underlying principles that govern these complex dynamics.
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These measurements reveal highly stereotyped responses on time scales of tens of milliseconds, which can be understood in terms of feedback from gyroscopic sensors called halteres. Perspective The motion of organisms through fluids -- from swimming bacteria to soar ing birds -- has long provided inspiration for the physics community, pushing our
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Altun, edi tor of www.wormatlas.org, https://en.wikipedia.org/wiki/Caenorhabditis_elegans, Creative Commons license CC BY-SA 2.5. understanding into new regimes and far eclipsing what human-made machines can accomplish.
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The second is the torque due to the asym- that these insects drive their corrective response using an auto metric wing motions, N fly ¼ γ · Δα, and it is proportional to Δα stabilizing feedback loop in which the sensed angular velocity with a second aerodynamic constant γ. Combining Eqs.
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The absorption of one photon triggers a change in the struc ture of one rhodopsin molecule. As in photosynthesis, the first molecular events that follow photon absorption happen within trillionths of a second, so fast that these events compete with the loss of quantum mechanical coherence.
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Figure sive flash was four times brigh N CASCADE the electrical current for this r closed all the channels in the o Figure 4(c) shows superimposed d the rod outer segment as a and completely shut off the cur cident photons to a change in brief light flashes recorded from a Dim flashes produced respons igate the biophysical mecha- the average of 4–5 individual r lasted about 5 seconds.
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But a single molecule makes transitions between states at random times, and this randomness would be passed through the cascade, ultimately resulting in a highly variable current across the cell membrane. Such variability would make it impossible for cells to report reliably that different numbers of photons had been counted; in fact the current pulses in response to single photons are stereotyped and reproducible.
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The commonality of vesicle release mechanisms was crucial in the identification of the key protein molecules involved in the process, which was recognized by a Nobel Prize in 2013. Today, vesicle release is studied with the full range of experimental methods from the biological physics community, down to the single molecule level.
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A challenge for the coming decade is to determine whether these physical principles can predict the dynamics of signal processing at synapses in the retina more generally. Molecule Counting Photon counting is not the only example where biological signaling systems encounter fundamental physical limits to performance.
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Clément, 2020, 3D spatial exploration by E coli echoes motor temporal variability, Physical Review X 10:021004, Creative Commons License Attribution 4.0 International (CC BY 4.0)
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