August 24, 2012
Physics News Highlights of the American Institute of Physics (AIP) contains summaries of interesting research from the AIP journals, notices of upcoming meetings, and other information from the AIP Member Societies. Copies of papers are available to journalists upon request.
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TOPICS IN THIS ISSUE:
1. Wind Concentrates Pollutants with Unexpected Order in an Urban Environment: When blown by chaotic winds in an urban environment, pollutants tend to accumulate in specific neighborhoods.
2. Modeling Metastasis: A technique used by animators helps scientists model how cancer cells enter the bloodstream.
3. Virus Detector Harnesses Ring of Light in ‘Whispering Gallery Mode’: Light alters pitch to detect and weigh the world’s smallest viruses one at a time.
4. New Model Gives Hands-on Help for Learning the Secrets of Molecules: Squishy models are anything but child’s play as they help researchers understand the building-block nature of proteins.
1. Wind Concentrates Pollutants with Unexpected Order in an Urban Environment
Cities – with their concrete canyons, isolated greenery, and congested traffic – create seemingly chaotic and often powerful wind patterns known as urban flows. Carried on these winds are a variety of environmental hazards, including exhaust particles, diesel fumes, chemical residues, ozone, and the simple dust and dander produced by dense populations.
In a paper published in the American Institute of Physics (AIP) journal Physics of Fluids, researchers present the unexpected finding that pollutant particles, rather than scattering randomly, prefer to accumulate in specific regions of the urban environment and even form coherent structures. "The unexpected finding is coherent patterns in fluid flows were thought to have no real analog in nature," said Wenbo Tang of Arizona State University in Tempe. "In previous studies, the existence of these patterns in fluid flows was only verified with idealized 'theoretical' flows. It was not known if such structures were robust enough to manifest in the environment."
The researchers were able to verify this by using a new mathematical formula, the first of its kind, to simulate the long-term random motion of pollutant particles as would be found in the real world. These more realistic simulations revealed that coherent patterns emerged from the random motions of particles carried along by the urban flow. The results can be used to generate maps of well and poorly mixed regions and highlight urban areas that are most susceptible to high concentrations of pollutants, indicating locations that should be avoided or remedied.
According to the researchers, the modeling capabilities developed in this project directly benefit decision makers addressing issues related to urban pollution, human comfort, and the effects of climate change on urban areas. The research also aims to understand the interconnection of urban flows with the regional and global atmosphere.
Article: “The geometry of inertial particle mixing in urban flows, from deterministic and random displacement models” is published in Physics of Fluids.
Authors: Wenbo Tang (1), Brent Knutson (1), Alex Mahalov (1), and Reneta Dimitrova (2)
(1) School of Mathematical and Statistical Sciences, Arizona State University, Tempe, Arizona
(2) Environmental Fluid Dynamics, University of Notre Dame, Notre Dame, Indiana
2. Modeling Metastasis
Cancer metastasis, the escape and spread of primary tumor cells, is a common cause of cancer-related deaths. But metastasis remains poorly understood. Studies indicate that when a primary tumor breaks through a blood vessel wall, blood's "stickiness" tears off tumor cells the way a piece of tape tears wrapping paper. Until now, no one knew the physical forces involved in this process, the first step in metastasis. Using a statistical technique employed by animators, scientists created a new computer simulation that reveals how cancer cells enter the bloodstream. The researchers present their work in a paper accepted to the American Institute of Physics (AIP) journal Physics of Fluids.
To create the simulation, a group of scientists from the University of Southern California in Los Angeles, Oregon Health and Science University in Portland, Ore., and The Scripps Research Institute in La Jolla, Calif., first had to describe the physics of the process. The researchers couldn't directly measure the fluid forces acting on a tumor cell in the body. Instead, they imaged blood flowing at different velocities over a breast cancer cell on a glass plate. Then, they bridged the gap between known and unknown with an Active Shape Model, a statistical technique that animators use to create furry monsters. Active Shape Models track the shape of an object as it dynamically deforms. When combined with the experimental data, the modeling enabled the team to compute the fluid forces acting on the cell, and that in turn helped them tune the simulation.
The study is an important first step toward understanding the mechanical properties of cancer cells and how they travel over the course of the disease, the researchers say. The ultimate goal is developing computer simulations of metastasis' multi-step process, and thus new therapies to target metastasis.
Article: “A low-dimensional deformation model for cancer cells in flow” is accepted for publication in Physics of Fluids.
Authors: A.M. Lee (1), M.A. Berny-Lang (2), S. Liao (1), E. Kanso (1), P. Kuhn (3), O.J.T. McCarty (2), and P.K. Newton (1)
(1) Department of Aerospace & Mechanical Engineering and Department of Mathematics, University of Southern California, Los Angeles
(2) Department of Biomedical Engineering, Oregon Health & Science University, Portland
(3) The Scripps Research Institute, La Jolla, California
3. Virus Detector Harnesses Ring of Light in ‘Whispering Gallery Mode’
By affixing nanoscale gold spheres onto a microscopic bead of glass, researchers have created a super-sensor that can detect even single samples of the smallest known viruses. The sensor uses a peculiar behavior of light known as “whispering gallery mode,” named after the famous circular gallery in St. Paul’s Cathedral in London, where a whisper near the wall can be heard around the gallery. In a similar way, waves of light are sent whirling around the inside of a small glass bead, resonating at a specific frequency. Just as a small object on a vibrating violin string can change its frequency – ever so slightly – so too can a virus landing on the sensor change the resonant frequency of the light. With the initial glass sphere, researchers were able to detect changes in frequency from viruses about the size of influenza, a relatively large virus. The system, however, was not sensitive enough to detect anything smaller, such as the Polio virus. The researchers were able to increase the sensitivity of the device nearly seventyfold by adding gold nanospheres to the surface of the glass, which created what the researchers referred to as “plasmonic hot spots” – areas where the light waves coupled with waves of electrons. This hybrid sensor not only detected the presence of the MS2 virus – the current light-weight in the world of RNA viruses – it also was able to determine the weight of the virus by measuring the precise frequency change of the light. With a few minor adjustments, the sensor should also be able to detect single proteins, such as cancer markers that appear in the blood long before outward signs of cancer can be detected. The results were published in the American Institute of Physics (AIP) journal Applied Physics Letters.
Article: “Taking whispering gallery-mode single virus detection and sizing to the limit” is published in Applied Physics Letters.
Authors: V.R. Dantham (1), S. Holler (1,2) , V. Kochenko (3) , Z. Wan (4), and S. Arnold (1)
(1) Polytechnic Institute of New York University, Brooklyn New York
(2) Fordham University, Bronx, New York
(3) New York City College of Technology, Brooklyn, New York
4. New Model Gives Hands-on Help for Learning the Secrets of Molecules
For biology researchers, the complex world of molecular proteins – where tens of thousands of atoms can comprise a single protein – may be getting clearer with the help of a new soft, transparent, and squishy silicone model they can hold in their hands. Its advantage over traditional computer and solid models is that it is mostly transparent and easy to manipulate, which will help researchers more intuitively understand protein structures, positions, and interactions. The models will enable researchers to quickly and collaboratively see, touch, and test ideas about molecular interactions and the behavior of proteins. These insights are keys to innovation in drug design because they help generate discussion about what a particular molecular surface might be like and how a protein is shaped and structured. The models also allow researchers to simulate docking maneuvers involving molecules known as ligands and their partners, a chemical binding step that can turn a biological process on or off.
This boost to molecular modeling comes from Masaru Kawakami, Ph.D., a biophysicist researcher at JAIST (Japan Advanced Institute of Science and Technology) in Ishikawa, Japan. It appears in the current issue of the American Institute of Physics (AIP) journal Review of Scientific Instruments. "Because my new model is soft, users can deform the model and experience ligand binding or protein-protein association, which has never been possible with other physical molecule models", said Kawakami. "I believe my model would be an effective discussion tool for the classroom or laboratory to stimulate inspired learning."
Article: “A soft and transparent handleable protein model” is published in Review of Scientific Instruments.
Author: Masaru Kawakami (1)
(1) School of Materials Science, Japan Advanced Institute of Science and Technology, Nomi, Ishikawa, Japan
Upcoming Conferences of Interest
- OSA Annual Meeting and Exhibit: The Frontiers in Optics meeting will be held October 14 - 18, 2012, in Rochester, New York
- AVS Symposium: The AVS 59th International Symposium and Exhibition will be held October 28 - November 2, 2012, in Tampa, Florida
- ASA Meeting: The 164th meeting of the Acoustical Society of America will be held October 22 - 26, 2012, in Kansas City, Missouri
- APS/DFD Meeting: The American Physical Society/Division of Fluid Dynamics meeting will be held November 18 - 20, 2012, in San Diego, California
Physics Today: August Articles
1. Strange kinetics of single molecules in living cells: The irreproducibility of time-averaged observables in living cells poses fundamental questions for statistical mechanics and reshapes our views on cell biology.
2. Nanotechnology in cancer medicine: Because of a previously unexploited weakness in tumor architecture, nanomaterials may offer a way to treat cancer without doing too much damage to healthy tissue. The weakness isn’t really a property of the tumors themselves but of the blood vessels that feed them.
3. Theoretical challenges in understanding galaxy evolution: The concordance cosmological model provides initial conditions and a reliable framework for simulating the evolution of primordial fluctuations into galaxies. But many unsolved problems remain.
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