Nelson, Philip C.
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Publication Spontaneous Expulsion of Giant Lipid Vesicles Induced by Laser Tweezers(1997) Moroz, J David; Nelson, Philip C; Bar-Ziv, Roy; Moses, ElishaIrradiation of a giant unilamellar lipid bilayer vesicle with a focused laser spot leads to a tense pressurized state which persists indefinitely after laser shutoff. If the vesicle contains another object it can then be gently and continuously expelled from the tense outer vesicle. Remarkably, the inner object can be almost as large as the parent vesicle; its volume is replaced during the exit process. We offer a qualitative theoretical model to explain these and related phenomena. The main hypothesis is that the laser trap pulls in lipid and ejects it in the form of submicron objects, whose osmotic activity then drives the expulsion.Publication Stress Tensor Perturbations in Conformal Field Theory(1991-11-01) Campbell, Marc; Nelson, Philip C; Wong, EugeneWe reconsider the problem of deforming a conformal field theory to a neighboring theory which is again critical. An invariant formulation of this problem is important for understanding the underlying symmetry of string theory. We give a simple derivation of A. Sen’s recent formula for the change in the stress tensor and show that, when correctly interpreted, it is coordinate-invariant. We give the corresponding superconformal perturbation for superfield backgrounds and explain why it has no direct analog for spin-field backgrounds.Publication Colloidal Particle Motion as a Diagnostic of DNA Conformational Transitions(2007-12-01) Nelson, Philip CTethered 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.Publication First-Principles Calculation of DNA Looping in Tethered Particle Experiments(2009-07-01) Towles, Kevin; Beausang, John; Garcia, Hernan; Phillips, Rob; Nelson, Philip CWe calculate the probability of DNA loop formation mediated by regulatory proteins such as Lac repressor (LacI), using a mathematical model of DNA elasticity. Our model is adapted to calculating quantities directly observable in tethered particle motion (TPM) experiments, and it accounts for all the entropic forces present in such experiments. Our model has no free parameters; it characterizes DNA elasticity using information obtained in other kinds of experiments. It assumes a harmonic elastic energy function (or wormlike chain type elasticity), but our Monte Carlo calculation scheme is flexible enough to accommodate arbitrary elastic energy functions. We show how to compute both the 'looping J factor' (or equivalently, the looping free energy) for various DNA construct geometries and LacI concentrations, as well as the detailed probability density function of bead excursions. We also show how to extract the same quantities from recent experimental data on TPM, and then compare to our model's predictions. In particular, we present a new method to correct observed data for finite camera shutter time and other experimental effects. Although the currently available experimental data give large uncertainties, our first-principles predictions for the looping free energy change are confirmed to within about 1 k(B)T, for loops of length around 300 basepairs. More significantly, our model successfully reproduces the detailed distributions of bead excursion, including their surprising three-peak structure, without any fit parameters and without invoking any alternative conformation of the LacI tetramer. Indeed, the model qualitatively reproduces the observed dependence of these distributions on tether length (e.g., phasing) and on LacI concentration (titration). However, for short DNA loops (around 95 basepairs) the experiments show more looping than is predicted by the harmonic-elasticity model, echoing other recent experimental results. Because the experiments we study are done in vitro, this anomalously high looping cannot be rationalized as resulting from the presence of DNA-bending proteins or other cellular machinery. We also show that it is unlikely to be the result of a hypothetical 'open' conformation of the LacI tetramer.Publication Electrostatic Repulsion of Positively Charged Vesicles and Negatively Charged Objects(1999-03-01) Aranda-Espinoza, Helim; Chen, Yi; Lubesnky, T C; Dan, Nily; Nelson, Philip C; Ramos, Lauren; Weitz, D. AA positively charged, mixed bilayer vesicle in the presence of negatively charged surfaces (for example, colloidal particles) can spontaneously partition into an adhesion zone of definite area, and another zone that repels additional negative objects. Although the membrane itself has nonnegative charge in the repulsive zone, negative counterions on the interior of the vesicle spontaneously aggregate there, and present a net negative charge to the exterior. Beyond the fundamental result that oppositely charged objects can repel, our mechanism helps explain recent experiments on surfactant vesicles.Publication Physical Models of Living Systems new chapter: Single Particle Reconstruction in Cryo-electron Microscopy(2021-06-05) Nelson, Philip CThis chapter extends Part III of the book 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.Publication Direct Determination of DNA Twist-Stretch Coupling(1996-11-01) Kamien, Randall; Lubensky, Tom; Nelson, Philip C; O'Hern, Corey S.The symmetries of the DNA double helix require a new term in its linear response to stress: the coupling between twist and stretch. Recent experiments with torsionally constrained single molecules give the first direct measurement of this important material parameter. We extract its value from a recent experiment of Strick et al. [Science 271 (1996) 1835] and find rough agreement with an independent experimental estimate recently given by Marko. We also present a very simple microscopic theory predicting a value comparable to the one observed.Publication Twirling of Actin by Myosins II and V Observed via Polarized TIRF in a Modified Gliding Assay(2008-12-01) Beausang, John F; Schroeder, Harry W; Nelson, Philip C; Goldman, Yale EThe force generated between actin and myosin acts predominantly along the direction of the actin filament, resulting in relative sliding of the thick and thin filaments in muscle or transport of myosin cargos along actin tracks. Previous studies have also detected lateral forces or torques that are generated between actin and myosin, but the origin and biological role of these sideways forces is not known. Here we adapt an actin gliding filament assay in order to measure the rotation of an actin filament about its axis (“twirling”) as it is translocated by myosin. We quantify the rotation by determining the orientation of sparsely incorporated rhodamine-labeledactin monomers, using polarized total internal reflection (polTIRF) microscopy. In order to determine the handedness of the filament rotation, linear incident polarizations in between the standard s- and p-polarizations were generated, decreasing the ambiguity of our probe orientation measurement four-fold. We found that whole myosin II and myosin V both twirl actin with a relatively long (~ µm), left-handed pitch that is insensitive to myosin concentration, filament length and filament velocity.Publication The Syncytial Drosophila Embryoas a Mechanically Excitable Medium(2013-10-01) Idema, Timon; Dubuis, Julien; Kang, Louis; Manning, M. Lisa; Nelson, Philip C; Lubensky, Tom; Liu, Andrea J.Mitosis in the early syncytial Drosophila embryo is highly correlated in space and time, as manifested in mitotic wavefronts that propagate across the embryo. In this paper we investigate the idea that the embryo can be considered a mechanically-excitable medium, and that mitotic wavefronts can be understood as nonlinear wavefronts that propagate through this medium. We study the wavefronts via both image analysis of confocal microscopy videos and theoretical models. We find that the mitotic waves travel across the embryo at a well-defined speed that decreases with replication cycle. We find two markers of the wavefront in each cycle, corresponding to the onsets of metaphase and anaphase. Each of these onsets is followed by displacements of the nuclei that obey the same wavefront pattern. To understand the mitotic wavefronts theoretically we analyze wavefront propagation in excitable media. We study two classes of models, one with biochemical signaling and one with mechanical signaling. We find that the dependence of wavefront speed on cycle number is most naturally explained by mechanical signaling, and that the entire process suggests a scenario in which biochemical and mechanical signaling are coupled.Publication Time to Stop Telling Biophysics Students That Light Is Primarily a Wave(2018-01-01) Nelson, Philip CStandard pedagogy introduces optics as though it were a consequence of Maxwell’s equations, and only grudgingly admits, usually in a rushed aside, that light has a particulate character that can somehow be reconciled with the wave picture. Recent revolutionary advances in optical imaging, however, make this approach more and more unhelpful: How are we to describe two-photon imaging, FRET, localization microscopy, and a host of related techniques to students who think of light primarily as a wave? I was surprised to find that everything I wanted my biophysics students to know about light, including image formation, x-ray diffraction, and even Bessel beams, could be expressed as well (or better) from the quantum viewpoint pioneered by Richard Feynman. Even my undergraduate students grasp this viewpoint as well as (or better than) the traditional one, and by mid-semester they are already well positioned to integrate the latest advances into their understanding. Moreover, I have found that this approach clarifies my own understanding of new techniques.