Colloidal particle motion as a diagnostic of DNA conformational transitions

Tethered particle motion is an experimental technique to monitor conformational changes in single molecules of DNA in real time, by observing the position fluctuations of a micrometer-size particle attached to the DNA. This article reviews some recent work on theoretical problems inherent in the interpretation of TPM experiments, both in equilibrium and dynamical aspects.Comment: 19pp. Accepted for publication in Curr Op Colloid Interf Scienc

Hitchhiking Through the Cytoplasm

We propose an alternative mechanism for intracellular cargo transport which results from motor induced longitudinal fluctuations of cytoskeletal microtubules (MT). The longitudinal fluctuations combined with transient cargo binding to the MTs lead to long range transport even for cargos and vesicles having no molecular motors on them. The proposed transport mechanism, which we call ``hitchhiking'', provides a consistent explanation for the broadly observed yet still mysterious phenomenon of bidirectional transport along MTs. We show that cells exploiting the hitchhiking mechanism can effectively up- and down-regulate the transport of different vesicles by tuning their binding kinetics to characteristic MT oscillation frequencies

Covariant Insertions of General Vertex Operators

We provide a very simple prescription for inserting an arbitrary state into a string amplitude. The corresponding string measure is defined without any additional information whenever the state is Becchi-Rouet-Stora-Tyutin (BRST) invariant, generalizing the usual physical conditions. In particular no world-sheet metric is needed. We recover and interpret in a simple way the b^ prescription of Polchinski and explain geometrically how it secures the decoupling of BRST spurious states

The Role of Quantum Decoherence in FRET

Resonance energy transfer has become an indispensable experimental tool for single-molecule and single-cell biophysics. Its physical underpin- nings, however, are subtle: It involves a discrete jump of excitation from one molecule to another, and so we regard it as a strongly quantum- mechanical process. And yet, its kinetics differ from what many of us were taught about two-state quantum systems; quantum superpositions of the states do not seem to arise; and so on. Although J. R. Oppenheimer and T. Förster navigated these subtleties successfully, it remains hard to find an elementary derivation in modern language. The key step involves acknowledging quantum decoherence. Appreciating that aspect can be helpful when we attempt to extend our understanding to situations where Fo ̈rster’s original analysis is not applicable

Biological Physics Student Edition 2020: Chapter 1

Chapter 1: What the Ancients Kne

Physical Models of Living Systems 2nd ed, new chapter: Demographic Variation in Epidemic Spread

This chapter extends the first edition of Physical Models of Living Systems (WH Freeman 2015). This preliminary version is made freely available as-is in the hope that it will be useful

From Photon to Neuron Chapter 17: Rainbows and other Caustics

This chapter extends Part III of the book From Photon to Neuron (Princeton Univ Press 2017). This preliminary version is made freely available as-is in the hope that it will be useful

From Photon to Neuron Chapter 16: Tunneling of Photons and Electrons

This chapter extends Part III of the book From Photon to Neuron (Princeton Univ Press 2017). This preliminary version is made freely available as-is in the hope that it will be useful

Old and New Results About Single-Photon Sensitivity in Human Vision

It is sometimes said that \u27our eyes can see single photons\u27. This article begins by finding a more precise version of that claim and reviewing evidence gathered for it up to around 1985 in two distinct realms, those of human psychophysics and single-cell physiology. Finding a single framework that accommodates both kinds of result is then a nontrivial challenge, and one that sets severe quantitative constraints on any model of dim-light visual processing. This article presents one such model and compares it to a recent experiment

Cohomology and the Operator Formalism

This letter points a close parallel between the operator formalism for string theory and the action of a Lie algebra on a differential complex. The construction of conformal field theories can then be regarded as a cohomology problem; we suggest that this viewpoint may survive the generalization beyond finite genus Riemann surfaces