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Biophysics

Content About: Biophysics

Published: 03/02/2017 - 1:45pm Type of Content: Article-Research Highlight

The Perkins group continues to extend the performance of its unique Atomic Force Microscope (AFM) technology, revealing for the first time a dozen new short-lived intermediate states in the folding and unfolding of a membrane protein that controls the exchange of chemicals and ions into and out of living cells. Measuring the energetics and dynamics of membrane proteins is crucial to...

Published: 02/03/2017 - 1:36pm Type of Content: News

Ralph Jimenez received a Department of Commerce Bronze Medal for Superior Federal Service at a ceremony held in mid-December 2016. The Medal is the highest honor presented by the National Institute of Standards and Technology (NIST). Under Secretary of Commerce for Standards and Technology and NIST Director Willie E. May presided over the awards ceremony, which was held concurrently at NIST's...

Published: 10/31/2016 - 7:58am Type of Content: Article-Research Highlight

Far-red fluorescent light emitted from proteins could one day illuminate the inner workings of life. But before that happens, scientists like Fellow Ralph Jimenez must figure out how fluorescent proteins’ light-emitting structures work. As part of this effort, Jimenez wants to answer a simple question: How do we design red fluorescent proteins to emit longer-wavelength, or redder, light?

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Published: 05/11/2015 - 11:20am Type of Content: Article-Research Highlight

A wildly successful JILA (Nesbitt Group)-NIH collaboration is opening the door to studies of RNA behavior, including binding, folding and other factors that affect structural changes of RNA from living organisms. Such structural changes determine RNA enzymatic functions, including the regulation of genetic information.

Yun-Xing Wang of the National Institutes of Health (NIH) and his...

Published: 04/01/2015 - 12:21pm Type of Content: News

JILA graduate students Stephen Okoniewski (Perkins group), Jake Pettine (Nesbitt group), and Lindsay Sonderhouse (Ye group) have won coveted 2015 National Science Foundation Graduate Research Fellowships, NSF announced March 31. The five-year Graduate Research Fellowships provide three years of support, with a per-year stipend of $34,000 and cost of education allowance of $12,000. Tuition and...

Published: 01/20/2015 - 9:09am Type of Content: Article-Research Highlight

Because red fluorescent proteins are important tools for cellular imaging, the Jimenez group is working to improve them to further biophysics research. The group’s quest for a better red-fluorescent protein began with a computer simulation of a protein called mCherry that fluoresces red light after laser illumination. The simulation identified a floppy (i.e., less stable) portion of the...

Published: 05/22/2014 - 9:11am Type of Content: Article-Research Highlight

Biomolecules may not always behave the same way in test tubes as they do in living cells, a fact underscored by important new work by former research associate Nick Dupuis, graduate student Erik Holmstrom, and Fellow David Nesbitt. The researchers found that under crowded conditions that begin to mimic those found in cells, single RNA molecules folded 35 times faster than in the dilute...

Published: 04/17/2014 - 10:33am Type of Content: Article-Research Highlight

Graduate student Erik Holmstrom and Fellow David Nesbitt have applied their laboratory research on the rates of RNA folding and unfolding to the medically important enzyme telomerase. Telomerase employs both protein and RNA components to lengthen chromosomes, which are shortened every time they are copied.

If one short piece of the RNA in telomerase is folded into an organized structure...

Published: 02/04/2014 - 10:25am Type of Content: Article-Research Highlight

The groups of Fellow Adjoint Markus Raschke and Fellow Tom Perkins joined forces recently to shine light onto a bacterial membrane protein called bacteriorhodopsin (bR). They used a new infrared (IR) light imaging system with a spatial resolution and chemical sensitivity of just a few bR molecules. In their experiment, the tip of an atomic force microscope (AFM) acted like an antenna for the...

Published: 01/09/2013 - 10:19am Type of Content: Article-Research Highlight

Gold glitters because it is highly reflective, a quality once considered important for precision measurements made with gold-coated probes in atomic force microscopy (AFM). In reality, the usual gold coating on AFM probes is a major cause of force instability and measurement imprecision, according to research done by the Perkins group. The group has shown that gold-coated probes are a...

Published: 08/17/2012 - 2:26pm Type of Content: Article-Research Highlight

The Nesbitt group has been investigating RNA folding since the early 2000s. The group’s goal has been to gain a detailed understanding of the relationship between structure and function in this important biomolecule. One challenge has been figuring out how unfolded RNA molecules assume the proper three-dimensional (3D) shape to perform their biological activities. To accomplish this, the...

Published: 10/18/2011 - 6:00pm Type of Content: Article-Research Highlight

Graduate student Jennifer Lubbeck (Jimenez Group) spent the summer of 2011 doing research in the Molecular Spectroscopy Laboratory at the RIKEN Institute in Wako, Japan (near Tokyo). Her host's group included 16 postdocs and four graduate students (Figure 1). The group was under the direction of Chief Scientist Tahei Tahara. However, Lubbeck actually worked directly with just five other young...

Published: 04/20/2011 - 6:00pm Type of Content: Article-Research Highlight

JILA experiment shows nicks and free ends are not required for DNA overstretching

In science, it can be fun and interesting to upend conventional wisdom. A good example is what just happened to a widely accepted explanation for overstretching of double-stranded DNA (dsDNA). Overstretching occurs suddenly when researchers add a tiny increment of force to dsDNA that is already...

Published: 11/23/2010 - 5:00pm Type of Content: Article-Research Highlight

Atomic force microscopy (AFM) just got a whole lot more efficient for studying proteins and other biomolecules. Graduate student Allison Churnside, former research associate Gavin King, and Fellow Tom Perkins recently used a laser to detect the position of sparsely distributed biomolecules on a glass cover slip. Since the same laser is also used to locate the AFM tip, it is now possible to...

Published: 02/09/2010 - 5:00pm Type of Content: Article-Research Highlight

Fellow Ralph Jimenez is applying his knowledge of lasers, microscopy, and the precise control of tiny amounts of fluids to the development of a battery-powered blood analyzer for use "off-grid" in Third World countries. He is collaborating with Jeff Squier, David Marr, and their students from the Colorado School of Mines and Charles Eggleton and his student from the University of Maryland,...

Published: 04/08/2009 - 6:00pm Type of Content: Article-Research Highlight

Quantum dots are tiny structures made of semiconductor materials. With diameters of 1–5 nm, they are small enough to constrain their constituents in all three dimensions. This constraint means that when a photon of light knocks an electron into the conduction band and creates an electron/hole pair, the pair can’t get out of the dot. In terms of quantum mechanics, this confinement...

Published: 04/08/2009 - 6:00pm Type of Content: Article-Research Highlight

The most important step for a microscope wanting to marry another microscope is finding the right partner. A professional matchmaker, such as the Perkins lab, might be just the ticket. The group recently presided over the nuptials of atomic force microscopy and optical-trapping microscopy. Research associate Gavin King, graduate students Ashley Carter and Allison Churnside, CU freshman...

Published: 02/09/2009 - 5:00pm Type of Content: Article-Research Highlight

Imagine being able to study how molecules form on the quantum level. It turns out that researchers have already figured out some nifty techniques involving lasers and jets of reactive atoms for doing just that in a gaseous environment. Now graduate student Alex Zolot, former Visiting Fellow Paul Dagdikian of Johns Hopkins University, and Fellow David Nesbitt have taken this kind of study...

Published: 07/08/2008 - 6:00pm Type of Content: Article-Research Highlight

For many years, chemists have explored the differences between liquids and solids. One difference is that liquid surfaces tend to be softer than solid surfaces (from the perspective of molecules crashing onto them). Another difference is that the surface of at least one oily liquid (perfluorinated polyether, or PFPE) actually gets stickier as it gets hotter, according to a new study by...

Published: 02/09/2008 - 5:00pm Type of Content: Article-Research Highlight

An excellent way to watch proteins fold is to probe the inside of a microfluidics device with light. This tiny device contains micron-sized three-dimensional (3D) transparent channels that carry small amounts of liquid. Inside the channels, the fluid flow is laminar, i.e., there is no turbulence. Consequently, fluid flow through them is predictable and easily modeled. Microfluidics devices...

Published: 02/09/2008 - 5:00pm Type of Content: Article-Research Highlight

The Perkins group is helping to develop DNA as a force standard for the nano world. Polymers of DNA act like springs, and DNA's elasticity may one day provide a force standard from 0.1–10 piconewtons (pN). One pN is the force exerted when 1 mW of light reflects off a mirror or the approximate weight of one hundred E. coli cells. DNA is an excellent candidate for a force standard...

Published: 09/29/2007 - 6:00pm Type of Content: Article-Research Highlight

Fellows Ralph Jimenez and Henry Kapteyn and their groups recently helped develop optical technology that will make femtosecond laser experiments much simpler to perform, opening the door to using such lasers in many more laboratories.

The technology, which employs reflection grisms as laser pulse compressors, has been patented and is now available commercially. A reflection grism...

Published: 07/08/2006 - 6:00pm Type of Content: Article-Research Highlight

Life can be challenging on the biophysics research frontier. Consider gold nanoparticles as a research tool, for example. Gold is ductile and malleable as well as being a good conductor of heat and electricity. Its unique chemistry allows proteins and DNA to be easily attached to these nanoparticles. Physicists have been investigating gold nanoparticles in optical-trapping experiments...

Published: 04/08/2006 - 6:00pm Type of Content: Article-Research Highlight

Our lives depend on heme. As part of hemoglobin, it carries oxygen to our tissues. As part of cytochrome c, it helps transform the energy in food into the energy-rich molecule ATP (adenosine triphosphate) that powers biochemical reactions that keep us alive and moving. As part of cytochrome P450, it helps break down toxic chemicals in our bodies.

What is this thing called heme? And...

Published: 02/09/2006 - 5:00pm Type of Content: Article-Research Highlight

Chemical physicists investigate the structure and behavior of atoms and molecules on the quantum level. Such research is particularly challenging when the molecule under investigation appears in small amounts and is rapidly transformed into something else, e.g., during combustion, chemical synthesis, or atmospheric chemical reactions. Happily, Research Associate Feng Dong, Fellow David Nesbitt...

Published: 09/29/2005 - 6:00pm Type of Content: Article-Research Highlight

RNA molecules can perform amazing biological feats, including storing, transporting, and reading genetic blueprints as well as catalyzing chemical reactions inside living cells. To manage the latter feat, RNA molecules must rapidly fold into an exact three-dimensional (3D) shape. Understanding how RNA accomplishes this is a major scientific challenge. Former JILA postdoc Jose Hodak,...

Published: 04/08/2005 - 6:00pm Type of Content: Article-Research Highlight

Lora Nugent-Glandorf and Tom Perkins have come up with an optical trap motion detector that can "see" protein motors moving one base at a time along a DNA helix. For some time scientists have been able to make optical traps that can track the movement of attached beads, but the method had a resolution of 1-2 nanometers, which was not sensitive enough to resolve .338 nm DNA base...

Published: 10/18/2012 - 3:28pm Type of Content: People - Faculty & Research Groups
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Published: 03/04/2013 - 2:50pm Type of Content: Research Areas

The Tom Perkins group investigates biological molecules as force standards at the pico-Newton scale (10-12 N). The forces applied by Atomic Force Microscopes (AFMs) and optical traps cannot be directly linked to an internationally accepted force standard (i.e., SI traceable) over the force range from pico-Newtons (10-12 N) to nano-Newtons (10-9 N). For AFM applications, SI traceability...

Published: 03/15/2013 - 12:06pm Type of Content: Biblio
Published: 02/28/2013 - 3:48pm Type of Content: Research Areas

The Ralph Jimenez group specializes in molecular biophysics, a relatively new field that employs concepts and techniques from physics, chemistry, and biology to elucidate the behaviors of biomolecules found in nature. The group’s eclectic research topics include (1) studies of the elastic properties of single cells, (2) the characterization of cellular fluorescent proteins, (3) investigations...

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Single-Molecule Studies of DNA, RNA, and Protein

The study of single molecules of DNA, RNA, and protein is revolutionizing biophysics. To investigate the structure and function of selected biomolecules in all three categories, the Thomas Perkins group has developed and is using precision single-molecule biophysics techniques such as atomic force microscopy (AFM), single-molecule force...

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