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Am J Phys 2021 Nov 22;89(11):1048-1061. Epub 2021 Oct 22.

Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon 97239.

Despite the importance of non-equilibrium statistical mechanics in modern physics and related fields, the topic is often omitted from undergraduate and core-graduate curricula. Key aspects of non-equilibrium physics, however, can be understood with a minimum of formalism based on a rigorous trajectory picture. The fundamental object is the ensemble of trajectories, a set of independent time-evolving systems, which easily can be visualized or simulated (e. Read More

Am J Phys 2016 07;84(7):522-530

Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, MD 20899 and Department of Physics, Oregon State University, Corvallis, OR 97331.

The double slit experiment provides a classic example of both interference and the effect of observation in quantum physics. When particles are sent individually through a pair of slits, a wave-like interference pattern develops, but no such interference is found when one observes which "path" the particles take. We present a model of interference, dephasing, and measurement-induced decoherence in a one-dimensional version of the double-slit experiment. Read More

Am J Phys 2016 Feb;84(2):150-158

Physics Department, Brandeis University, Waltham, Massachusetts 02453.

We have developed a programmable illumination system capable of tracking and illuminating numerous objects simultaneously using only low-cost and reused optical components. The active feedback control software allows for a closed-loop system that tracks and perturbs objects of interest automatically. Our system uses a static stage where the objects of interest are tracked computationally as they move across the field of view allowing for a large number of simultaneous experiments. Read More

Am J Phys 2016 Mar;Volume 84(Iss 3):192-201

NASA, Goddard Space Flight Center, Greenbelt, Maryland, 20771.

Dropping objects into a tunnel bored through Earth has been used to visualize simple harmonic motion for many years, and even imagined for use as rapid transport systems. Unlike previous studies that assumed a constant density Earth, here we calculate the fall-through time of polytropes, models of Earth's interior where the pressure varies as a power of the density. This means the fall-through time can be calculated as the varies from one to large within the family of polytropes. Read More

Am J Phys 2015 May;83(5):468-474

Departamento de Física and National Institute of Science and Technology of Complex Systems, ICEx, Universidade Federal de Minas Gerais, Caixa Postal 702, 30161-970, Belo Horizonte - Minas Gerais, Brazil.

We discuss a lattice model of vector-mediated transmission of a disease to illustrate how simulations can be applied in epidemiology. The population consists of two species, human hosts and vectors, which contract the disease from one another. Hosts are sedentary, while vectors (mosquitoes) diffuse in space. Read More

Am J Phys 2014 May;82(5):460-465

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike MSC 6075, Bethesda, MD 20894-6075.

The problem of electrostatics in biomolecular systems presents an excellent opportunity for cross-disciplinary science and a context in which fundamental physics is called for to answer complex questions. Due to the large density in biological cells of charged biomacromolecules such as protein factors and DNA, it is challenging to understand quantitatively the electric forces in these systems. Two questions are especially puzzling. Read More

Am J Phys 2014 Jul;82(7):708-722

Department of Physics, University of Massachusetts, Amherst, Massachusetts 01002.

Single-molecule-sensitive microscopy and spectroscopy are transforming biophysics and materials science laboratories. Techniques such as fluorescence correlation spectroscopy (FCS) and single-molecule sensitive fluorescence resonance energy transfer (FRET) are now commonly available in research laboratories but are as yet infrequently available in teaching laboratories. We describe inexpensive electronics and open-source software that bridges this gap, making state-of-the-art research capabilities accessible to undergraduates interested in biophysics. Read More

Am J Phys 2013 Sep;81(9):712

Department of Bioengineering, The University of Texas at Arlington, Arlington, TX 76019, USA, Joint Biomedical Engineering Program, The University of Texas at Arlington and The University of Texas Southwestern Medical Center at Dallas, TX 75390, USA.

Photoacoustic (PA) imaging techniques have recently attracted much attention and can be used for noninvasive imaging of biological tissues. Most PA imaging systems in research laboratories use the time domain method with expensive nanosecond pulsed lasers that are not affordable for most educational laboratories. Using an intensity modulated light source to excite PA signals is an alternative technique, known as the frequency domain method, with a much lower cost. Read More

Am J Phys 2003 Mar;71(3):201-215

Department of Biological Sciences and Department of Applied Physics, Stanford University, Stanford, California 94305-5020.

This Resource Letter provides a guide to the literature on optical tweezers, also known as laser-based, gradient-force optical traps. Journal articles and books are cited for the following main topics: general papers on optical tweezers, trapping instrument design, optical detection methods, optical trapping theory, mechanical measurements, single molecule studies, and sections on biological motors, cellular measurements and additional applications of optical tweezers. Read More

Am J Phys 2006 Feb;74(2):123-133

Department of Biophysics, University of California, San Francisco, California 94143.

We describe a simple framework for teaching the principles that underlie the dynamical laws of transport: Fick's law of diffusion, Fourier's law of heat flow, the Newtonian viscosity law, and the mass-action laws of chemical kinetics. In analogy with the way that the maximization of entropy over microstates leads to the Boltzmann distribution and predictions about equilibria, maximizing a quantity that E. T. Read More

Am J Phys 2002 Oct 12;70(10):1029-1033. Epub 2002 Sep 12.

Metabolic Magnetic Resonance Research and Computing Center, Department of Radiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104.

Fields such as temperature, current density, and static electromagnetic fields in regions with no field sources are harmonic functions that satisfy the Laplace equation. Such functions on a sphere have a well-known mean value property. A new mean value property is derived for fields that are harmonic on an annular region, with the field sources enclosed by the inner boundary. Read More

Am J Phys 1989 Jan;57(1):12-8

Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA.

This Resource Letter provides a guide to the literature about intelligent life beyond the human sphere of exploration. It offers a starting point for professionals and academics interested in participating in the debate about the existence of other technological civilizations or in the search for extraterrestrial intelligence (SETI). It can also serve as a reference for teaching. Read More

Am J Phys 1986 Nov;54(11):1031-4

Physics Department, Old Dominion University, Norfolk, Virginia 23508, USA.

We present a simple application of the three-dimensional harmonic oscillator which should provide a very nice particle physics example to be presented in introductory undergraduate quantum mechanics course. The idea is to use the nonrelativistic quark model to calculate the spin-averaged mass levels of the charmonium and bottomonium spectra. Read More