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Full-Text Articles in Physics

A Demonstration Of The Infrared Activity Of Carbon Dioxide, Philip Sieg, William Berner, Peter Harnish, Philip C. Nelson Jan 2019

A Demonstration Of The Infrared Activity Of Carbon Dioxide, Philip Sieg, William Berner, Peter Harnish, Philip C. Nelson

Department of Physics Papers

Before they can talk meaningfully about anthropogenic climate change, students need to grasp basic principles of natural planetary climates, for example, the key role of trace atmospheric gases in setting surface temperature. We describe a dramatic demonstration that scales well for large audiences and that requires as little as ten classroom minutes to show the crucial difference between room air and carbon dioxide gas. Beyond its significance for public policy, the demonstration can serve as a springboard to motivate discussion of important physics concepts such as rotation and vibration spectra.


From Photon To Neuron Chapter 17: Rainbows And Other Caustics, Philip C. Nelson Dec 2018

From Photon To Neuron Chapter 17: Rainbows And Other Caustics, Philip C. Nelson

Department of Physics Papers

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, Philip C. Nelson Aug 2018

From Photon To Neuron Chapter 16: Tunneling Of Photons And Electrons, Philip C. Nelson

Department of Physics Papers

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.


A Student’S Guide To Matlab For Physical Modeling, Philip C. Nelson, Tom Dodson Aug 2018

A Student’S Guide To Matlab For Physical Modeling, Philip C. Nelson, Tom Dodson

Department of Physics Papers

This tutorial aims to help you teach yourself enough of the Matlab􏱈 programming language to get started on physical modeling, and particularly the problems appearing in Physical Models of Living Systems (Nelson, 2015). This is not an official publication of The MathWorks, Inc. We attempt to maintain it, but no claim is made that every suggestion made here will work properly with future versions of Matlab.

This is a free online document. Code listings that appear in this document, errata, and more can be found online via http://www.physics.upenn.edu/biophys/PMLS/Student ; code can also be accessed ...


Activities And Classroom Demonstrations In Biological Physics: A Resource Document, Philip C. Nelson, William Berner Jul 2018

Activities And Classroom Demonstrations In Biological Physics: A Resource Document, Philip C. Nelson, William Berner

Department of Physics Papers

We give detailed recipes for a number of classroom demonstrations relevant to biological physics instruction. We developed them mainly for use in 2nd-3rd year undergraduate Physics courses. But you can (and we do) use them for primary school, through high school, up to PhD candidates. You adapt the words for each audience, but a phenomenon is a phenomenon.

We also outline a 1-hour introduction to Python for undergraduate scientific computing.

Finally we document some outcomes from courses taught at U Pennsylvania using these resources and others cited here. This material was presented at a workshop at the AAPT meeting in ...


From Photon To Neuron Chapter 15: Planetary Climates, Philip C. Nelson Jul 2018

From Photon To Neuron Chapter 15: Planetary Climates, Philip C. Nelson

Department of Physics Papers

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.


Physics 516: Electromagnetic Phenomena (Spring 2019), Philip C. Nelson Apr 2018

Physics 516: Electromagnetic Phenomena (Spring 2019), Philip C. Nelson

Department of Physics Papers

These course notes are made publicly available in the hope that they will be useful. All reports of errata will be gratefully received. I will also be glad to hear from anyone who reads them, whether or not you find errors: pcn@upenn.edu.


The Role Of Quantum Decoherence In Fret, Philip C. Nelson Jan 2018

The Role Of Quantum Decoherence In Fret, Philip C. Nelson

Department of Physics Papers

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 ...


Time To Stop Telling Biophysics Students That Light Is Primarily A Wave, Philip C. Nelson Jan 2018

Time To Stop Telling Biophysics Students That Light Is Primarily A Wave, Philip C. Nelson

Department of Physics Papers

Standard 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 ...


Effect Of Interstitial Fluid On The Fraction Of Flow Microstates That Precede Clogging In Granular Hoppers, Juha Koivisto, Douglas J. Durian Mar 2017

Effect Of Interstitial Fluid On The Fraction Of Flow Microstates That Precede Clogging In Granular Hoppers, Juha Koivisto, Douglas J. Durian

Department of Physics Papers

We report on the nature of flow events for the gravity-driven discharge of glass beads through a hole that is small enough that the hopper is susceptible to clogging. In particular, we measure the average and standard deviation of the distribution of discharged masses as a function of both hole and grain sizes. We do so in air, which is usual, but also with the system entirely submerged under water. This damps the grain dynamics and could be expected to dramatically affect the distribution of the flow events, which are described in prior work as avalanche-like. Though the flow is ...


Student Resources For: From Photon To Neuron, Light, Imaging, Vision, Philip C. Nelson Feb 2017

Student Resources For: From Photon To Neuron, Light, Imaging, Vision, Philip C. Nelson

Department of Physics Papers

This zip archive contains datasets and additional media associated to the book "From Photon to Neuron (Princeton University Press, 2017).


Rheology Of Sediment Transported By A Laminar Flow, Morgane Houssais, Carlos P. Ortiz, Douglas J. Durian, Douglas J. Jerolmack Dec 2016

Rheology Of Sediment Transported By A Laminar Flow, Morgane Houssais, Carlos P. Ortiz, Douglas J. Durian, Douglas J. Jerolmack

Department of Physics Papers

Understanding the dynamics of fluid-driven sediment transport remains challenging, as it occurs at the interface between a granular material and a fluid flow. Boyer, Guazzelli, and Pouliquen [Phys. Rev. Lett.107, 188301 (2011)] proposed a local rheology unifying dense dry-granular and viscous-suspension flows, but it has been validated only for neutrally buoyant particles in a confined and homogeneous system. Here we generalize the Boyer, Guazzelli, and Pouliquen model to account for the weight of a particle by addition of a pressure P0 and test the ability of this model to describe sediment transport in an idealized laboratory river. We ...


Coding And Data Visualization In The Science Classroom, Philip C. Nelson Sep 2016

Coding And Data Visualization In The Science Classroom, Philip C. Nelson

Department of Physics Papers

No abstract provided.


Intermittency And Velocity Fluctuations In Hopper Flows Prone To Clogging, C. C. Thomas, Douglas J. Durian Aug 2016

Intermittency And Velocity Fluctuations In Hopper Flows Prone To Clogging, C. C. Thomas, Douglas J. Durian

Department of Physics Papers

We study experimentally the dynamics of granular media in a discharging hopper. In such flows, there often appears to be a critical outlet size Dc such that the flow never clogs for D > Dc. We report on the time-averaged velocity distributions, as well as temporal intermittency in the ensemble-averaged velocity of grains in a viewing window, for both D < Dc and D > Dc, near and far from the outlet. We characterize the velocity distributions by the standard deviation and the skewness of the distribution of vertical velocities. We propose a measure for intermittency based on the two-sample ...


Old And New Results About Single-Photon Sensitivity In Human Vision, Philip C. Nelson Apr 2016

Old And New Results About Single-Photon Sensitivity In Human Vision, Philip C. Nelson

Department of Physics Papers

It is sometimes said that 'our eyes can see single photons'. 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.


Divergence Of Voronoi Cell Anisotropy Vector: A Threshold-Free Characterization Of Local Structure In Amorphous Materials, Jennifer M. Rieser, Carl P. Goodrich, Andrea J. Liu, Douglas J. Durian Feb 2016

Divergence Of Voronoi Cell Anisotropy Vector: A Threshold-Free Characterization Of Local Structure In Amorphous Materials, Jennifer M. Rieser, Carl P. Goodrich, Andrea J. Liu, Douglas J. Durian

Department of Physics Papers

Characterizing structural inhomogeneity is an essential step in understanding the mechanical response of amorphous materials. We introduce a threshold-free measure based on the field of vectors pointing from the center of each particle to the centroid of the Voronoi cell in which the particle resides. These vectors tend to point in toward regions of high free volume and away from regions of low free volume, reminiscent of sinks and sources in a vector field. We compute the local divergence of these vectors, where positive values correspond to overpacked regions and negative values identify underpacked regions within the material. Distributions of ...


Deformation-Driven Diffusion And Plastic Flow In Amorphous Granular Pillars, Wenbin Li, Jennifer M. Rieser, Andrea J. Liu, Douglas J. Durian, Ju Li Jun 2015

Deformation-Driven Diffusion And Plastic Flow In Amorphous Granular Pillars, Wenbin Li, Jennifer M. Rieser, Andrea J. Liu, Douglas J. Durian, Ju Li

Department of Physics Papers

We report a combined experimental and simulation study of deformation-induced diffusion in compacted quasi-two-dimensional amorphous granular pillars, in which thermal fluctuations play a negligible role. The pillars, consisting of bidisperse cylindrical acetal plastic particles standing upright on a substrate, are deformed uniaxially and quasistatically by a rigid bar moving at a constant speed. The plastic flow and particle rearrangements in the pillars are characterized by computing the best-fit affine transformation strain and nonaffine displacement associated with each particle between two stages of deformation. The nonaffine displacement exhibits exponential crossover from ballistic to diffusive behavior with respect to the cumulative deviatoric ...


Fraction Of Clogging Configurations Sampled By Granular Hopper Flow, C. C. Thomas, Douglas J. Durian Apr 2015

Fraction Of Clogging Configurations Sampled By Granular Hopper Flow, C. C. Thomas, Douglas J. Durian

Department of Physics Papers

We measure the fraction F of flowing grain configurations that precede a clog, based on the average mass discharged between clogging events for various aperture geometries. By tilting the hopper, we demonstrate that F is a function of the hole area projected in the direction of the exiting grain velocity. By varying the length of slits, we demonstrate that grains clog in the same manner as if they were flowing out of a set of smaller independent circular openings. The collapsed data for F can be fit to a decay that is exponential in hole width raised to the power ...


Identifying Structural Flow Defects In Disordered Solids Using Machine-Learning Methods, E. D. Cubuk, Samuel Schoenholz, Jennifer M. Rieser, B. D. Malone, J. Rottler, Douglas J. Durian, E. Kaxiras, Andrea J. Liu Mar 2015

Identifying Structural Flow Defects In Disordered Solids Using Machine-Learning Methods, E. D. Cubuk, Samuel Schoenholz, Jennifer M. Rieser, B. D. Malone, J. Rottler, Douglas J. Durian, E. Kaxiras, Andrea J. Liu

Department of Physics Papers

We use machine-learning methods on local structure to identify flow defects—or particles susceptible to rearrangement—in jammed and glassy systems. We apply this method successfully to two very different systems: a two-dimensional experimental realization of a granular pillar under compression and a Lennard-Jones glass in both two and three dimensions above and below its glass transition temperature. We also identify characteristics of flow defects that differentiate them from the rest of the sample. Our results show it is possible to discern subtle structural features responsible for heterogeneous dynamics observed across a broad range of disordered materials.


Penetration Depth Scaling For Impact Into Wet Granular Packings, Theodore A. Brzinski Iii, Jonathan Schug, K. Mao, Douglas J. Durian Feb 2015

Penetration Depth Scaling For Impact Into Wet Granular Packings, Theodore A. Brzinski Iii, Jonathan Schug, K. Mao, Douglas J. Durian

Department of Physics Papers

We present experimental measurements of penetration depths for the impact of spheres into wetted granular media. We observe that the penetration depth in the liquid saturated case scales with projectile density, size, and drop height in a fashion consistent with the scaling observed in the dry case, but with smaller penetrations. Neither viscous drag nor density effects can explain the enhancement to the stopping force. The penetration depth exhibits a complicated dependence on liquid fraction, accompanied by a change in the drop-height dependence, that must be the consequence of accompanying changes in the conformation of the liquid phase in the ...


Physical Models Of Living Systems: Contents, Preface, And Prolog, Philip C. Nelson Jan 2015

Physical Models Of Living Systems: Contents, Preface, And Prolog, Philip C. Nelson

Department of Physics Papers

Brief contents; To the Student; To the Instructor; A Breakthrough on HIV


Kinetics Of Gravity-Driven Water Channels Under Steady Rainfall, Cesare M. Cejas, Yuli Wei, Rémi Barrois, Christian Frétigny, Douglas J. Durian, Rémi Dreyfus Oct 2014

Kinetics Of Gravity-Driven Water Channels Under Steady Rainfall, Cesare M. Cejas, Yuli Wei, Rémi Barrois, Christian Frétigny, Douglas J. Durian, Rémi Dreyfus

Department of Physics Papers

We investigate the formation of fingered flow in dry granular media under simulated rainfall using a quasi-two-dimensional experimental setup composed of a random close packing of monodisperse glass beads. Using controlled experiments, we analyze the finger instabilities that develop from the wetting front as a function of fundamental granular (particle size) and fluid properties (rainfall, viscosity). These finger instabilities act as precursors for water channels, which serve as outlets for water drainage. We look into the characteristics of the homogeneous wetting front and channel size as well as estimate relevant time scales involved in the instability formation and the velocity ...


Morphology Of Rain Water Channeling In Systematically Varied Model Sandy Soils, Yuli Wei, Cesare M. Cejas, Rémi Barrois, Rémi Dreyfus, Douglas J. Durian Oct 2014

Morphology Of Rain Water Channeling In Systematically Varied Model Sandy Soils, Yuli Wei, Cesare M. Cejas, Rémi Barrois, Rémi Dreyfus, Douglas J. Durian

Department of Physics Papers

We visualize the formation of fingered flow in dry model sandy soils under different rain conditions using a quasi-2D experimental setup and systematically determine the impact of the soil grain diameter and surface wetting properties on the water channeling phenomenon. The model sandy soils we use are random closely packed glass beads with varied diameters and surface treatments. For hydrophilic sandy soils, our experiments show that rain water infiltrates a shallow top layer of soil and creates a horizontal water wetting front that grows downward homogeneously until instabilities occur to form fingered flows. For hydrophobic sandy soils, in contrast, we ...


Granular Discharge Rate For Submerged Hoppers, T. J. Wilson, C. R. Pfeifer, N. Meysingier, Douglas J. Durian Jan 2014

Granular Discharge Rate For Submerged Hoppers, T. J. Wilson, C. R. Pfeifer, N. Meysingier, Douglas J. Durian

Department of Physics Papers

The discharge of spherical grains from a hole in the bottom of a right circular cylinder is measured with the entire system underwater. We find that the discharge rate depends on filling height, in contrast to the well-known case of dry non-cohesive grains. It is further surprising that the rate increases up to about twenty five percent, as the hopper empties and the granular pressure head decreases. For deep filling, where the discharge rate is constant, we measure the behavior as a function of both grain and hole diameters. The discharge rate scale is set by the product of hole ...


Structure And Coarsening At The Surface Of A Dry Three-Dimensional Aqueous Foam, R. E. Roth, B. G. Chen, Douglas J. Durian Dec 2013

Structure And Coarsening At The Surface Of A Dry Three-Dimensional Aqueous Foam, R. E. Roth, B. G. Chen, Douglas J. Durian

Department of Physics Papers

We utilize total-internal reflection to isolate the two-dimensional surface foam formed at the planar boundary of a three-dimensional sample. The resulting images of surface Plateau borders are consistent with Plateau's laws for a truly two-dimensional foam. Samples are allowed to coarsen into a self-similar scaling state where statistical distributions appear independent of time, except for an overall scale factor. There we find that statistical measures of side number distributions, size-topology correlations, and bubble shapes are all very similar to those for two-dimensional foams. However, the size number distribution is slightly broader, and the shapes are slightly more elongated. A ...


Transformation Of Stimulus Correlations By The Retina, Kristina D. Simmons, Jason S. Prentice, Gasper Tkacik, Jan Homann, Heather K. Yee, Stephanie E. Palmer, Philip C. Nelson, Vijay Balasubramanian Dec 2013

Transformation Of Stimulus Correlations By The Retina, Kristina D. Simmons, Jason S. Prentice, Gasper Tkacik, Jan Homann, Heather K. Yee, Stephanie E. Palmer, Philip C. Nelson, Vijay Balasubramanian

Department of Physics Papers

Redundancies and correlations in the responses of sensory neurons may seem to waste neural resources, but they can also carry cues about structured stimuli and may help the brain to correct for response errors. To investigate the effect of stimulus structure on redundancy in retina, we measured simultaneous responses from populations of retinal ganglion cells presented with natural and artificial stimuli that varied greatly in correlation structure; these stimuli and recordings are publicly available online. Responding to spatio-temporally structured stimuli such as natural movies, pairs of ganglion cells were modestly more correlated than in response to white noise checkerboards, but ...


Depth-Dependent Resistance Of Granular Media To Vertical Penetration, Theodore A. Brzinski Iii, Patrick Mayor, Douglas J. Durian Oct 2013

Depth-Dependent Resistance Of Granular Media To Vertical Penetration, Theodore A. Brzinski Iii, Patrick Mayor, Douglas J. Durian

Department of Physics Papers

We measure the quasistatic friction force acting on intruders moving downwards into a granular medium. By utilizing different intruder geometries, we demonstrate that the force acts locally normal to the intruder surface. By altering the hydrostatic loading of grain contacts by a sub-fluidizing airflow through the bed, we demonstrate that the relevant frictional contacts are loaded by gravity rather than by the motion of the intruder itself. Lastly, by measuring the final penetration depth versus airspeed and using an earlier result for inertial drag, we demonstrate that the same quasistatic friction force acts during impact. Altogether this force is set ...


The Syncytial Drosophila Embryoas A Mechanically Excitable Medium, Timon Idema, Julien Dubuis, Louis Kang, M. Lisa Manning, Philip C. Nelson, Tom Lubensky, Andrea J. Liu Oct 2013

The Syncytial Drosophila Embryoas A Mechanically Excitable Medium, Timon Idema, Julien Dubuis, Louis Kang, M. Lisa Manning, Philip C. Nelson, Tom Lubensky, Andrea J. Liu

Department of Physics Papers

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 ...


Coffee Rings And Coffee Disks: Physics On The Edge, Peter J. Yunker, Douglas J. Durian, Arjun G. Yodh Aug 2013

Coffee Rings And Coffee Disks: Physics On The Edge, Peter J. Yunker, Douglas J. Durian, Arjun G. Yodh

Department of Physics Papers

As many a coffee drinker knows, a drying drop of coffee typically leaves behind a ring-shaped stain of small grounds. Though the phenomenon is common, the mechanisms that drive it are rich with physics. As first elucidated by Robert Deegan and colleagues in 1997, the coffee ring results from radially outward fluid flows induced by so-called contact line pinning: The outer edge of a spilled coffee droplet grabs onto rough spots on the solid surface and becomes pinned in place. The evaporating drop thus retains its pinned diameter and flattens while it dries. That flattening, in turn, is accompanied by ...


Spin Dynamics Of Trimers On A Distorted Kagome Lattice, A. Brooks Harris, Taner Yildirim Jul 2013

Spin Dynamics Of Trimers On A Distorted Kagome Lattice, A. Brooks Harris, Taner Yildirim

Department of Physics Papers

We treat the ground state, elementary excitations, and neutron scattering cross section for a system of trimers consisting of three tightly bound spins 1/2 on a distorted kagome lattice, subject to isotropic nearest-neighbor (usually antiferromagnetic) Heisenberg interactions. The interactions between trimers are assumed to be weak compared to the intratrimer interactions. We compare the spin-wave excitation spectrum of trimers with that obtained from standard spin-wave theory and attribute the differences at low energy to the fact that the trimer formulation includes exactly the effects of intratrimer zero-point motion.