Basic Principles Underlying Cellular Processes
Daniel M. Zuckerman

About

$ \newcommand{\avg}[1]{\langle #1 \rangle} \newcommand{\cc}[1]{[\mathrm{#1}]^{\mathrm{cell}}} \newcommand{\cgdp}{\mathrm{C \! \cdot \! GDP}} \newcommand{\cgtp}{\mathrm{C \! \cdot \! GTP}} \newcommand{\comb}[1]{{#1}^{\mathrm{comb}}} \newcommand{\conc}[1]{[\mathrm{#1}]} \newcommand{\conceq}[1]{[\mathrm{#1}]^{\mathrm{eq}}} \newcommand{\concss}[1]{[\mathrm{#1}]^{\mathrm{ss}}} \newcommand{\conctot}[1]{[\mathrm{#1}]_{\mathrm{tot}}} \newcommand{\cu}{\conc{U}} \newcommand{\dee}{\partial} \newcommand{\dgbind}{\Delta G_0^{\mathrm{bind}}} \newcommand{\dgdp}{\mathrm{D \! \cdot \! GDP}} \newcommand{\dgtp}{\mathrm{D \! \cdot \! GTP}} \newcommand{\dmu}{\Delta \mu} \newcommand{\dphi}{\Delta \Phi} \newcommand{\dplus}[1]{\mbox{#1}^{++}} \newcommand{\eq}[1]{{#1}^{\mathrm{eq}}} \newcommand{\fidl}{F^{\mathrm{idl}}} \newcommand{\idl}[1]{{#1}^{\mathrm{idl}}} \newcommand{\inn}[1]{{#1}_{\mathrm{in}}} \newcommand{\ka}{k_a} \newcommand{\kcat}{k_{\mathrm{cat}}} \newcommand{\kf}{k_f} \newcommand{\kfc}{k_{fc}} \newcommand{\kftot}{k_f^{\mathrm{tot}}} \newcommand{\kd}{K_{\mathrm{d}}} \newcommand{\kdt}{k_{\mathrm{dt}}} \newcommand{\kdtsol}{k^{\mathrm{sol}}_{\mathrm{dt}}} \newcommand{\kgtp}{K_{\mathrm{GTP}}} \newcommand{\kij}{k_{ij}} \newcommand{\kji}{k_{ji}} \newcommand{\kkeq}{K^{\mathrm{eq}}} \newcommand{\kmmon}{\kon^{\mathrm{ES}}} \newcommand{\kmmoff}{\koff^{\mathrm{ES}}} \newcommand{\kconf}{k_{\mathrm{conf}}} \newcommand{\konf}{k^{\mathrm{on}}_{\mathrm{F}}} \newcommand{\koff}{k_{\mathrm{off}}} \newcommand{\kofff}{k^{\mathrm{off}}_{\mathrm{F}}} \newcommand{\konu}{k^{\mathrm{on}}_{\mathrm{U}}} \newcommand{\koffu}{k^{\mathrm{off}}_{\mathrm{U}}} \newcommand{\kon}{k_{\mathrm{on}}} \newcommand{\kr}{k_r} \newcommand{\ks}{k_s} \newcommand{\ku}{k_u} \newcommand{\kuc}{k_{uc}} \newcommand{\kutot}{k_u^{\mathrm{tot}}} \newcommand{\ktd}{k_{\mathrm{td}}} \newcommand{\ktdsol}{k^{\mathrm{sol}}_{\mathrm{td}}} \newcommand{\minus}[1]{\mbox{#1}^{-}} \newcommand{\na}{N_A} \newcommand{\nai}{N_A^i} \newcommand{\nao}{N_A^o} \newcommand{\nb}{N_B} \newcommand{\nbi}{N_B^i} \newcommand{\nbo}{N_B^o} \newcommand{\nc}{N_{C}} \newcommand{\nl}{N_L} \newcommand{\nltot}{N_L^{\mathrm{tot}}} \newcommand{\nr}{N_R} \newcommand{\nrl}{N_{RL}} \newcommand{\nrtot}{N_R^{\mathrm{tot}}} \newcommand{\out}[1]{{#1}_{\mathrm{out}}} \newcommand{\plus}[1]{\mbox{#1}^{+}} \newcommand{\rall}{\mathbf{r}^N} \newcommand{\rn}[1]{\mathrm{r}^N_{#1}} \newcommand{\rdotc}{R \!\! \cdot \! C} \newcommand{\rstarc}{R^* \! \! \cdot \! C} \newcommand{\rstard}{R^* \! \! \cdot \! D} \newcommand{\rstarx}{R^* \! \! \cdot \! X} \newcommand{\ss}{\mathrm{SS}} \newcommand{\totsub}[1]{{#1}_{\mathrm{tot}}} \newcommand{\totsup}[1]{{#1}^{\mathrm{tot}}} \newcommand{\ztot}{Z^{\mathrm{tot}}} % Rate notation: o = 1; w = two; r = three; f = four \newcommand{\aow}{\alpha_{f}} \newcommand{\awo}{\alpha_{u}} \newcommand{\kow}{\kf} % {\kf(12)} \newcommand{\kwo}{\ku} % {\ku(21)} \newcommand{\kor}{\conc{C} \, \konu} % \konu(13)} \newcommand{\kwf}{\conc{C} \, \konf} % \konf(24)} \newcommand{\kro}{\koffu} % {\koffu(31)} \newcommand{\kfw}{\kofff} % {\kofff(42)} \newcommand{\krf}{\kfc} % {\kfc(34)} \newcommand{\kfr}{\kuc} % {\kuc(43)} \newcommand{\denom}{ \krf \, \kfw + \kro \, \kfw + \kro \, \kfr } $

Physical Lens on the Cell attempts to offer a new perspective on physical cell biology education, both in terms of content and form.The goal is to provide interdisciplinary material, now a staple of modern science, in a modern way. Lens is not a traditional linear textbook in internet guise but a cross-linked tool intended for learners from a variety of backgrounds.

Content

Modern cellular and molecular biophysics, like so many other fields, brings together a range of disciplines starting with traditional cell biology, but including the physical and quantitative sciences. Physical Lens on the Cell uses a physical approach to organize cellular phenomena in a manner that is much more concise than the usual cell biology text of 1,000+ pages. This site makes no attempt at comprehensiveness, and thus cannot replace the traditional textbook, but rather emphasizes deeper understanding of physical driving forces that necessarily underlie the myriad cellular phenomena whose diversity often seems bewildering.

The site will most obviously be useful for physical or quantitative scientists seeking to understand cell biology without getting through the 1,000-page textbook. The basic physical driving forces are explained along with their manifestation in a surprising array of contexts - synthesis of molecules, transport of molecules to organize the cell and maintain its health, locomotion along the internal road system of filaments, and even information processing (error correction). The physics, which is largely non-equilibrium thermodynamics and statistical mechanics, is fascinating in itself but presented in a formulation that should be readily accessible to undergraduates - based on mass-action kinetics and ideal-gas thermodynamics.

Biologists also have much to gain from the site. It should deepen and quantify their understanding of the physical driving forces, the free energies, which underlie all cellular processes. After all, if there is no driving force, a process won’t happen. The goal is to understand the commonalities linking the incredible diversity of cellular phenomena. Yes, there are equations, but these are restricted to the relatively simple algebra and calculus that are common in biochemistry books. Familiarity with chemical kinetics will give the biochemist or biologist an advantage over the physical scientist.

Platform

Because Physical Lens on the Cell covers interdisciplinary material, unlike a conventional textbook, it cannot make assumptions about the reader’s level of knowledge. In fact, the notion of a knowledge “level” is not really appropriate. For example, many very able physicists may have minimal familiarity with non-equilibrium phenomena, whereas such ideas (if not the formalism) may be intuitive to biochemists. The author of a traditional book would be left to puzzle over appropriate content for a “Chapter 1.”

Physical Lens on the Cell therefore does not have traditional chapters, though it does have an organization. Most importantly, the site is fully hyperlinked so the reader can readily bring up content from both internal and external links. Thus, one can click through to just the right information. The site is organized hierarchically, with the most fundamental concepts presented “first” and progressing to cell biology phenomena. But it may be most interesting to start reading about a more biological topic and clicking through as needed to get the physical background.

Two-Panel Reading

Science is not easy and learning science rarely is linear. The two-panel layout (click on the splitscreen icon from any content page) allows ready cross-referencing of any and all material in the website. It is even possible to view two copies of the same page to allow comparison of figures or equations and the accompanying text that otherwise would cause the original item to scroll off the screen.

About the PDF Version

To enable off-line reading of the site’s content, a pdf version is available.  Readers of the pdf should be aware of two points: (i) the pdf represents a static “snapshot” taken of the site and may not include all updated material; and (ii) the pdf presents the material as it is ordered in the menus, with the result that a number of pages are duplicated.  Duplications arise because a given page (e.g., on activated carriers) may be listed, appropriately, under more than one category (e.g., Physical/Molecular Processes and Energy Economy).  Duplication seemed preferable to excluding the material from a section where it is highly relevant.