Ralph Jimenez

JILA Hosts the Inaugural Workshop on Quantum Light Generation, Detection, and Applications

Steven Burrows — Fri, 19 Jul 2024 19:31:51 +0000

JILA Hosts the Inaugural Workshop on Quantum Light Generation, Detection, and Applications Steven Burrows Fri, 07/19/2024 - 13:31

Kenna Hughes-Castleberry / JILA Science Communicator

The group photo taken at the Quantum Light Conference hosted by JILA in July 2024. Credit: Kenna Hughes-Castleberry/JILA

The event invited speakers from various prestigious institutions, including Texas A&M University, the National Autonomous University of Mexico, Columbia University, Wake Forest University, Livermore National Lab, the University of Illinois Urbana-Champaign, Caltech, Oak Ridge National Lab, Cornell University, William & Mary, University College London, the University of Oregon, the University of Toronto, and the University of Virginia, along with multiple representatives from NIST.

The conference was dedicated to recent advancements in the field of quantum light, particularly in nonlinear optics, integrated photonics, and materials synthesis. These fields of physics have significantly contributed to our ability to generate various quantum states of light. The workshop also highlighted the innovative applications of these advancements in imaging, sensing, and spectroscopy.

"I'm really excited about this workshop as it brings people working on quantum light generation with people thinking about metrology applications with quantum light, we hope that the workshop could seed many fruitful science discussions!” Stated JILA Associate Fellow and University of Colorado Boulder Assistant Professor of Physics Shuo Sun, one of the conference organizers.

The workshop brought together leading experts and researchers from diverse fields, such as nonlinear photonics, quantum optics, single-photon detectors, and chemical physics. The aim was to foster a collaborative community to discuss these transformative advancements and implement the use of quantum light in physics, chemistry, and biology. The conference included afternoon poster sessions, allowing graduate students time to present their research to senior researchers, and laboratory tours for visitors to learn more about the innovative quantum research happening at JILA.

This gathering marked a significant step towards harnessing the full potential of quantum light in various scientific domains.

JILA, a joint institute of the University of Colorado Boulder and the National Institute of Standards and Technology (NIST) hosted its inaugural workshop on recent technological and research advancements in quantum light from July 17 to 19, 2024. The conference was sponsored by the National Science Foundation (NSF)-funded JILA Physics Frontier Center (PFC), the CUbit Quantum Initiative, and laser company Toptica.

The event invited speakers from various prestigious institutions, including Texas A&M University, the National Autonomous University of Mexico, Columbia University, Wake Forest University, Livermore National Lab, the University of Illinois Urbana-Champaign, Caltech, Oak Ridge National Lab, Cornell University, William & Mary, University College London, the University of Oregon, the University of Toronto, and the University of Virginia, along with multiple representatives from NIST.

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The Prime Suspect: Hot Band Absorption

Steven Burrows — Mon, 07 Mar 2022 18:20:45 +0000

The Prime Suspect: Hot Band Absorption Steven Burrows Mon, 03/07/2022 - 11:20

Kenna Hughes-Castleberry / JILA Science Communicator

An artistic depiction of the hot band absorption process in the LDS798 molecule. Image credit: Steven Burrows / JILA

The hunt was afoot within the laboratory of JILA and NIST Fellow Ralph Jimenez as his team continued to unravel the mystery of entangled two-photon absorption. Entangled photons are pairs of light particles whose quantum states are not independent of each other, so they share aspects of their properties, such as their energies and angular momenta. For many years, these photons have been studied by physicists who are trying to create quantum networks and other technologies. The Jimenez lab has been researching whether entangled photons can excite molecules with greater, even super, efficiency as compared with normal photons.

In a new paper published in the Journal of Physical Chemistry Letters, Jimenez and his team report a new experimental setup to search for the cause of a mysterious fluorescent signal that appears to be from entangled photon excitation. According to Jimenez: “We built a setup where you could use either a classical laser or entangled photons to look for fluorescence. And the reason we built it is to ask: ‘What is it that other people were seeing when they were claiming to see entangled photon-excited fluorescence?’ We saw no signal in our previous work published a year ago, headed by Kristen Parzuchowski. So now, we're wondering, people are seeing something, what could it possibly be? That was the detective work here.” The results of their new experiments suggested that hot-band absorption (HBA) by the subject molecules, could be the potential culprit for this mysterious fluorescent signal, making it the prime suspect.

Case Notes on Hot-Band Absorption

HBA is a classical one-photon absorption process. According to graduate student Kristen Parzuchowski,: “[HBA is] process in which a single photon excites a one-photon transition from thermally populated vibrational levels of the ground electronic state.” Normally, this doesn’t happen for less energetically vibrating molecules, which require two infrared photons to be excited and transition to a higher state.

In order to determine if HBA was the source of the mysterious fluorescence, Jimenez and his team tested two different molecules: Rhodamine 6G (Rh6G) and LDS798 (a fluorophore or fluorescent chemical compound that can re-emit light upon light excitation) dissolved in solvents. “A 1060-nanometer laser was used to directly excite the sample,” Jimenez explained. “The excited molecules emit red light, which is measured by a photomultiplier tube.” To create entangled photons, Jimenez added: “We used a 532-nanometer laser and focused it into a ppKTP crystal where one in a million photons is turned into an entangled pair of 1064-nanometer photons… which can excite the sample. This way we have a classical and a quantum side of the experiment to compare.”

With their setup, the researchers focused on the “cross section” of the absorption process. “The crosssection tells you how much area a molecule presents for being hit by a photon pair,” Jimenez stated. The cross section sizehas a history of being somewhat controversial, as Parzuchowski explained that: “Right now there is significant controversy about the size of entangled two-photon absorption (E2PA) cross sections.” Jimenez added: “Other groups claimed that the E2PA cross-section was almost as large as that for a single photon, which implies very strong absorption.” The Jimenez group’s previous work showed that other investigators were over-estimating cross-sections by a factor of 10,000 or more. The team was eager to see if their experiment could validate previous observations, or if it would offer something new.

In looking at the cross-sections of the Rh6G and LDS798 molecules, Jimenez pointed out some important parameters. “For regular two-photon absorption, the cross-section is very small. That's why people need to use high-powered lasers with short pulses of light to get a signal,” he stated. “So, the implication was that big cross-sections for entangled two-photon absorption would allow ultralow-power imaging.” But this was where the HBA became important. “If the signal is from hot band absorption, that doesn't allow you to do two-photon imaging, which is 3D.” Jimenez explained that: “For at least one of the molecules we showed here, the signal could be pretty much entirely due to this hot band absorption. The other molecule we looked at did not show this absorption.”

The Evidence Points to Overestimating

In seeing HBA happen in the LDS798 molecule, the researchers realized this small signal may have big implications for the study of entangled photons interacting with molecules. “What we found is that if you calculate the hot band absorption cross-section, it can account for most of the overestimated cross-section that people were reporting for entangled two-photon absorption,” Jimenez said. “We're showing that HBA can mimic what people think is entangled two-photon absorption, so additional tests are needed to verify which process is occurring. We don't know if that's happening with every molecule that others have studied.” Jimenez hopes that others will take this new factor into account when looking at entangled two-photon absorption. In observing the similarities between the entangled two-photon flux and HBA, Parzuchowski noted that: “These two processes share one signature: a linear scaling with excitation photon flux. This is an exciting finding because some researchers who claim to measure E2PA only look for evidence of this one signature. They may have been measuring HBA all along!”

The Case Isn’t Closed

While the researchers found a potential explanation, they still want to understand how to generate a bona fide entangled photon absorption signal. According to Jimenez: “ Now, we know that the real signal is going to be around 10,000 times smaller than what people claimed to see before. But it could still be hundreds or thousands of times stronger than a classical signal under the same conditions.” The team is hoping to tweak their experimental setup to better their chances to find the signal, “There are various ways you can think of doing this experiment,” Jimenez added. “Either by using a different type of quantum light source that provides stronger excitation or by building your experiment in such a way that you get a much stronger interaction between the photons and the sample.” The researchers hope that with their new setup, and results from their previous research they can definitively identify the source of the mystery fluorescent signal, and find a real fluorescence signal from tangled photon excitation. That would be case closed.

In a new paper published in the Journal of Physical Chemistry Letters, Jimenez and his team report a new experimental setup to search for the cause of a mysterious fluorescent signal that appears to be from entangled photon excitation. The results of their new experiments suggested that hot-band absorption (HBA) by the subject molecules, could be the potential culprit for this mysterious fluorescent signal, making it the prime suspect.

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The Case of the Missing Signal

Steven Burrows — Wed, 02 Jun 2021 19:01:34 +0000

The Case of the Missing Signal Steven Burrows Wed, 06/02/2021 - 13:01

Kenna Hughes-Castleberry / JILA Science Communicator

A model of two entangled photons converging on a Rh6G molecule. Image credit: Steven Burrows

Most researchers would agree that it is much easier to write a paper about an observed effect than a paper proving the nonexistence of the effect when it is not observed. NIST JILA Fellow Ralph Jimenez found this to be the case in contributing to a recent paper published in Physical Review Applied. The authors of this paper were originally hoping to observe the increased efficiency in two-photon absorption, a special type of process used in microscopy of living tissue, that had been reported by other research labs.This increased efficiency would be determined by an absorption signal in additional to the one being producted from classical light that comes from using entangled photons. This additional signal came from using entangled photons. Instead, Jimenez and his team of collaborators from NIST found no additional signal in their measurements, indicating a lack of absorption entirely from the entangled photons. When speaking to other researchers around the world performing similar experiments, Jimenez found that sometimes the signal was seen and sometimes it wasn't. This randomness in signal appearance began a mystery for Jimenez to solve when it came to the process of using entangled photons in two-photon absorption.

A Brief History of two-Photon Absorption

According to NIST scientist Martin Stevens: "Two-photon absorption is a very inefficient process. If two photons happen to be in the same place at the same time, and hit the molecule that you're trying to excite, there's a chance you'll get absorption." However, the chances of this absorption happening are very slim. That is why teams like Jimenez's and Stevens' use high-powered lasers with short light pulses. This increases the probability of two photons being next to each other and being absorbed. Previous studies suggested that the efficiency of two-photon absorption could be enhanced up to 10 orders of magnitude by using entangled photons. Quantum entanglement of light occurs when quantum states of two photons are not independent of each other. As Stevens explained: "The hope is that by generating entangled photon pairs, we can make photons that are highly correlated in energy and time, so they arrive at the same place at the same time with exactly the right energy, making the absorption process very efficient.” If an entangled photon pair is absorbed, the instruments would be able to detect a signature of this absorption.

The Clues of Fluorescence

In order to test this theory, graduate students and postdocs from both the Jimenez and Stevens labs joined forces to build a state-of-the-art quantum optics laboratory starting with an empty room. This laboratory was specifically built by co-first authors Kristen Parzuchowski and Alexander Mikhaylov of the Jimenez laboratory. Stevens commented: "That's been a really rewarding part of this work with myself, Thomas Gerrits and Mike Mazurek---with quantum optics backgrounds---interacting with Ralph his postdocs, and students---who did not have this background---and merging these different streams of talent together with these different areas of expertise." The team did several tests on this proposed efficiency by looking for the absorption of entangled photon pairs by molecules in liquids, without seeing any signals that corroborated previous studies.

After this initial testing with a transmission-based experiment didn’t turn up any clues, "we then realized that the more sensitive experiment would detect fluorescence," Jimenez stated. This would allow for more thorough testing. "In that case, if the molecules absorb a pair of photons, then a fluorescence photon will come out. If there's no two-photon absorption, you shouldn't see any signal, unless it's something else. So, we built this new experiment to detect two-photon absorption with fluorescence, and again, we didn't see a signal." Frustrated about their lack of signal, Jimenez and Stevens began informal discussions with other teams around the world to determine if other researchers were getting the same result that they were. These discussions, which includes a group in Geneva that has detected entangled two-photon absorption, evolved into a biweekly global seminar series, where different labs presented their findings. The results puzzled Jimenez and Stevens, as some labs have found a signal showing entangled photons being absorbed in two-photon absorption, while others haven't. Jimenez commented: "We thought there's something going on around the world as different people are seeing different things, such as a group in South America saw this process, and there's a group in Mexico that sees the same thing we do, with no signal. There's a group at the University of Oregon that also saw no signal. And we've been trying to understand what's going on here."

The Mystery Deepens:

In their fluorescence experiments, graduate student Kristen Parzuchowski and postdoc Alex Mikhaylov worked together with the NIST-campus team to show that even in the absence of a signal from entangled photon absorption, they could precisely calibrate their experiment and estimate upper bounds for the enhancement which are up to 10,000 times smaller than what was reported by others. The next steps are clear for both Jimenez and Stevens, who have a number of experiments lined up as they try to find the reason for why some labs are seeing a signal and others aren't. "I think what's come out of this is that we've been able to largely come to a consensus as a community about what measurements need to be done to verify this process." Stevens explained. With global established protocols, both Jimenez and Stevens are excited to try to solve the answer to the case of the missing entangled photon absorption signal.

Most researchers would agree that it is much easier to write a paper about an observed effect than a paper proving the nonexistence of the effect when it is not observed. NIST JILA Fellow Ralph Jimenez found this to be the case in contributing to a recent paper published in Physical Review Applied. The authors of this paper were originally hoping to observe the increased efficiency in two-photon absorption, a special type of process used in microscopy of living tissue, that had been reported by other research labs. This increased efficiency would be determined by an additional absorption signal than the one being produced by classical light. This additional signal came from using entangled photons. Instead, Jimenez and his team of collaborators from NIST found no additional signal in their measurements, indicating a lack of absorption entirely from the entangled photons.

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Sorting the Glow from the Flow

Steven Burrows — Mon, 02 Mar 2020 18:46:12 +0000

Sorting the Glow from the Flow Steven Burrows Mon, 03/02/2020 - 11:46

Rebecca Jacobson / JILA Science Communicator

The Jimenez Lab has built a fast flow cytometry system which quickly sorts fluorescing cells from non-fluorescing ones. Image credit: Steven Burrows / JILA

How do you find a single cell in a sea of thousands? You make it glow.

Adding fluorescence helps track movement and changes in small things like cells, DNA, and bacteria. In a library of millions of cells or bacteria, flow cytometry sorts the glowing material you want to study from the non-glowing material.

In short, “it’s a fluorescence filter,” said Srijit Mukherjee, a graduate student in the Jimenez Lab at JILA.

With the help of JILA’s electronics shop and clean room, the Jimenez Lab has found a way to take droplet sorting time from days to hours. Their new setup not only improves the time it takes, you can better sort your material by how long or how brightly it glows.

“You gain an enrichment off a population in a matter of a few hours,” Mukherjee explained. “Then you can repeat the process again and again to enrich this population of a very rare event.”

Drop by drop

Here’s how flow cytometry works: You have a large library of material—cells, for example—which have been genetically modified so the cells with the traits you want to study glow. You encapsulate a group of those cells (and the medium they’re floating in) into individual droplets of water in oil. The droplets flow through a tube past a focused laser beam. When a glowing group is detected, it is separated out with an electric field which “pushes” it into the “keep” pile.

There are two obstacles scientists run into with flow cytometry systems. First, there’s a lot of junk floating around with the glowing material you want to study. The odds of getting any fluorescent cells at all in your droplet are low, Mukherjee pointed out—at single cell loading, fewer than 10% of the droplets have a cell, glowing or not. The other 90% are just oil and water.

“Even in that 10% the probability that you have a fluorescent droplet is even lower, so your throughput is really, really low,” Mukherjee explained.

Second, flow cytometry can be really tedious. That low throughput means it can take a long time to sort through with a large library of material, even with good flow cytometry systems.

The Jimenez Lab wanted to sort fluorescing E. coli bacteria. For their experiment, they needed to not only sort out the glowing bacteria, but sort by the lifetime of that fluorescence. The flow cytometry system they were using could only sort 50 cells a second; sorting through millions of bacteria would have taken days.

Plus, the system was complicated to use.

“To most of us, it was just a black box…it was just a cobweb of Labview codes,” Mukherjee said. “Getting it to sort was a challenge.”

Pumping up the drops

The group took a mathematical approach, Mukherjee said: if you increase the number of cells in each droplet, the probability that a droplet contains a fluorescing cell increases too.

“It's basically dumping out most of the non-fluorescing junk and selecting out the fluorescing population,” Mukherjee said.

Then, they repeat the flow cytometry process with the traditional single-cell per droplet approach—but this time, they sort out the material by more specific characteristics, such as a fluorescence lifetime or brightness.

The power of collaboration

To do that, they needed faster electronics and clean, precise tools. Those were all available in house at JILA, and the Jimenez Lab built their fast flow cytometry system completely at JILA.

JILA’s electronics shop was able to craft field-programmable gate array (FPGA) electronics which operate on a nanosecond scale—much faster than what they could order elsewhere. The clean room at JILA was used to fabricate all the microfluidic chips, so they were super clean. Being able to make everything in house also made this new system extremely cost-effective, Mukherjee added.

As a result, the Jimenez Lab enriched the proportion of fluorescing cells in their samples from 10% to 94%. They went from sorting 50 cells per second to about 2500 droplets per second—greater than a hundredfold improvement, Mukherjee said.

This type of system could make a difference not only to labs, but to anyone who needs to sort through a large library for a particular event, such as biomedical researchers who need to find the few abnormal cells in a pool of millions.

“We are trying to use it to approach fluorescent protein libraries but this is a very general approach to enrich any fluorescent event in a library of events.”

This study was published in Royal Society of Chemistry’s Lab on a Chip on February 21, 2020, and was supported by the NSF Physics Frontier Center Grant, and the NIH/CU Molecular Biophysics Training Program.

Written by Rebecca Jacobson

Fluorescence and dyes are great tools to study cells, proteins, bacteria, or DNA. But scientists need to efficiently sort out the glowing material from the non-glowing stuff in their samples. The Jimenez Lab and the JILA Electronics Shop teamed up to create an improved flow cytometry system which can not only sort fluorescent material faster, it can sort by fluorescence lifetime and brightness faster than a commercially available system.

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Molecule Movies, Now Filming at NIST

Steven Burrows — Sat, 03 Nov 2018 17:19:18 +0000

Molecule Movies, Now Filming at NIST Steven Burrows Sat, 11/03/2018 - 11:19

Catherine Klauss / JILA Science Communicator

Ralph Jimenez and a team at NIST break a molecular bond in CO-heme (Carbon-monoxy- iron protoporphyrin IX) with a laser. They then use X-rays to watch how the electron configurations and bond lengths change, with a time resolution of < 6 picoseconds. The combined frames from a movie of sorts, depicting the real-life drama of everyday molecules. Credit: Jimenez Group and Brad Baxley, JILA

The team at NIST built a microcalorimeter X-ray spectrometer capable of performing time-resolved spectroscopy; in other words: a camera to film molecules. They use this camera to learn how molecules break their bonds – do the electrons rearrange, do the other atoms quake?

The microcalorimeter spectrometer is not the only tool that can film molecules, but it is the smallest. Previously, only huge, multibillion dollar synchrotrons were capable of producing X-rays and probing molecules. Beam time at these facilities has to be reserved in advance, sometimes months, or even years. These long wait times, combined with the expense of building and operating synchrotrons, can limit opportunities for new research.

In contrast, NIST’s spectrometer fits on a tabletop and costs a fraction of an entire synchrotron system. But most importantly, NIST’s spectrometer is easily accessible – it’s like having the ability to film a Hollywood movie on your smartphone. Jimenez hopes that this new device will “broaden access and enable a wider range of molecules to be studied.”

Despite its small size and modest cost, the NIST spectrometer is faster and more efficient than previous systems. The new spectrometer combines ultrafast X-ray pulses with an array of cryogenic microcalorimeter detectors. The microcalorimeter detectors are superconductors held at their transition temperature, where the resistance is maximally sensitive to temperature. When one of the superconductors absorbs an X-ray photon, it’s temperature is raised, and the energy of the X-ray photon can be deduced from the change in resistance. This enables the microcalorimeter array to count individual emitted X-rays and simultaneously measure their energies.

While a fascinating tool, you can’t make a movie without actors. Jimenez is the casting director of the experiment, and writes the leading roles into the scripts. But not every molecule is charismatic enough for the big screen. “[I] tell them the reality,” said Jimenez, “what science you can actually do with the system.”

Jimenez worked tirelessly to find a worthy molecule, considering “how much light it absorbs, signal to noise, structure change … if we broke this bond, would it give a large enough signal? We can’t just pop a molecule in the experiment and see it.” So far, all of the molecules have had a metal atom.

The film begins rolling after the film crew breaks a molecular bond with a laser. The crew then blast that same laser onto a material to create a plasma (a gas of free electrons). The free electrons collide into each other, causing them to emit X-rays. The result in an X-ray light bulb that glows over a fairly broad range.

When the X-ray lightbulb shines over the newly broken molecule, it excites transitions in the core electrons of the metal atom. The timing between when the molecule breaks and the X-rays probe can be delayed with picosecond resolution (trillionth of a second). “And that’s the kind of resolution you need to see molecular motions,” said Jimenez.

Depending on the state of the core electrons, a specific energy of X-rays is absorbed by the metal atom in the molecule. This absorption spectrum can then be analyzed to determine the electronic state of the metal atom, and the positions of the other atoms in the molecule. This means that the team can see whether the electrons move around before a bond breaks, and watch the other bond lengths change. These measurements are repeated with picosecond time resolution, and the combined frames create a molecular movie.

With their setup, the NIST team has already made two new films. One film, documenting a bond breaking in a ferrioxalate complex, settled a controversy in the literature about the important atmospheric chemistry reaction. Because molecules with heavy atoms, such as a ferrioxalate complex, have multiple oxidation states, they are useful for storing both energy and data. Filming how these molecules react to chemical changes can help develop more energy-efficient batteries, computer memories and optical display technologies.

With a couple of molecular movies under his belt, Jimenez’s casting is ready to move from high school drama kids to Hollywood hotshots. “We [plan to] do in vitro measurements of purified proteins… we’re going to try it this fall.”

Filming proteins no easy task. Proteins are much larger than the previously filmed molecules. And, as anyone who has had a medical X-ray knows, human bodies, and the proteins they are made of, are mostly transparent to X-rays.

But Jimenez is not one to back down from a challenging experiment. “I think everyone who was on the team said, ‘these were the hardest experiments we’ve ever done.’"

The NIST detector experts are Joe Ullom, William Doriese, and Dan Swetz, as well as the tireless film crew, Luis Miaja-Avila and Galen O’Neil. Ralph Jimenez recruited casting assistance from Niels Damrauer and JILA postdoc D. M. Sagar. The team’s recent work was published in Physical Review X and the Journal of Physical Chemistry Letters.

The actors are molecules. The plot, broken molecular bonds. JILA Fellow Ralph Jimenez and a team of detector experts at the National Institute of Standards and Technology (NIST) are working together to make X-ray movies of a molecular drama. The team at NIST built a microcalorimeter X-ray spectrometer capable of performing time-resolved spectroscopy; in other words: a camera to film molecules. They use this camera to learn how molecules break their bonds – do the electrons rearrange, do the other atoms quake?

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Ralph Jimenez Receives Arthur S. Flemming Award for Outstanding Public Service

Steven Burrows — Wed, 30 May 2018 19:59:17 +0000

Ralph Jimenez Receives Arthur S. Flemming Award for Outstanding Public Service Steven Burrows Wed, 05/30/2018 - 13:59

Catherine Klauss / JILA Science Communicator

JILA Fellow and NIST Physicist Ralph Jimenez received the 2017 Arthur S. Flemming Award for outstanding public service as a Federal employee. Jimenez was one of 12 honorees across all parts of the Federal government to receive the Flemming Award this cycle. Jimenez was a winner in the Applied Science and Engineering category for his pioneering research on combining microfluidics, ultrafast lasers, biochemistry and molecular biology to dramatically accelerate the creation and characterization of specialized biomolecules to serve as sensors within living cells.

“I'm honored to join a very distinguished group of JILA/NIST colleagues who have won this award, including Tom Perkins, Jun Ye, Debbie Jin and David Nesbitt,” said Jimenez.

The Flemming Award program, established in 1948, is administered by the George Washington University’s Trachtenberg School of Public Policy and Public Administration to recognize outstanding accomplishments by Federal government employees within the first 15 years of their service. Awards are presented in the categories of Applied Science and Engineering (Jimenez’s category), Basic Science, Social Science, Clinical Trials, Legal Achievement, and Leadership and Management.

JILA Flemming Award winners have included David Nesbitt (1991), Debbie Jin (2003), Jun Ye (2005), and Tom Perkins (2013), as well as former JILAns Lewis Branscomb, Pete Bender, David Hummer, and Steve Leone. Other well-known Flemming winners have included astronaut Neil Armstrong, Francis Collins (NIH Director and Human Genome Project leader), Anthony Fauci (Director of the National Institute of Allergy and Infectious Disease and pioneer in characterizing HIV), and NIST Nobel Physics Laureate Bill Phillips, among many other prominent winners.

Jimenez will officially receive the award in a ceremony at George Washington University in Washington, DC on June 4, 2018.

Congratulations to Ralph!

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Ralph Jimenez Awarded Department of Commerce Bronze Medal

Steven Burrows — Thu, 02 Feb 2017 21:05:38 +0000

Ralph Jimenez Awarded Department of Commerce Bronze Medal Steven Burrows Thu, 02/02/2017 - 14:05

Catherine Klauss / JILA Science Communicator

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 Gaithersburg, Maryland, and Boulder, Colorado, campuses.

Jimenez received his Bronze Medal Award "for pioneering innovative tools for transforming the measurement, characterization and collection of biomolecules and cells for applications in industry, medicine, and research." He was recognized for leading a multidisciplinary program combining ultrafast lasers, custom microfluidics, biochemistry, and directed evolution to measure and use large biomolecules and living cells for a range of applications, including more efficiently making biofuels, revealing the details of how enzymes work within cells, as well as developing new molecular tools for nondestructively imaging and measuring chemical reactions within living cells. His accomplishments include

Inventing a new high-throughput cytometer that uses ultrafast lasers and microfluidics to nondestructively identify and collect individual living cells with unique and highly desirable properties,
Pioneering methods to measure complex three-dimensional motions of large biomolecules, such as enzymes and proteins, in their natural cellular environments, and,
Developing and characterizing fluorescent proteins for use in measurements of chemical and physical reactions within living cells.

Jimenez' innovations and patented innovations are accelerating the ability of basic and applied researchers to study, understand, and apply their new understanding of the biochemistry of cells in both normal and diseased states.

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The Red Light District

Steven Burrows — Mon, 31 Oct 2016 18:30:42 +0000

The Red Light District Steven Burrows Mon, 10/31/2016 - 12:30

Julie Phillips / Science Communicator

Light-emitting molecular arrangement in the chromophore of an mPlum fluorescent protein. The incorporation of a water molecule into this structure causes the emission of red light. Image credit: Steven Burrows / JILA

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?

The reason for working on this problem is that far-red light emitted by fluorescent proteins would be more useful for “seeing” into the intact organs of live animals such as mice. Far-red light more readily passes through living tissue than do green or blue wavelengths, as those people who have covered a flashlight with their hands can attest.

There are two basic approaches to making red fluorescent proteins redder, according to Jimenez. The first one is to change the structure of the small group of atoms called the chromophore that absorb and emit light. In the past, researchers thought that that the longer-wavelength emission from red fluorescent proteins was due to a particularly strong interaction between specific atoms in the chromophore (known as acylimine) and atoms in the barrel-shaped protein surrounding the chromophore. This interaction supposedly gave the electrons in the chromophore more room to move around, which lowered the energy of the photons absorbed and emitted by the chromophore.

The second approach is to fine-tune the motions of the barrel around the chromophore. This approach is favored by the Jimenez group, which studied a protein called mPlum that emits the longest-wavelength red light of any of “mFruit” family of fluorescent proteins. The Jimenez group’s experiments show that mPlum’s redder emission is due to the flexibility of interactions between the barrel and chromophore’s acylimine atoms.

“Water is available in and around the barrel, and water can pop in and pop out as the (floppy) side chain rotates,” Jimenez explained. “This rotation is correlated with the red shift.” In other words, after mPlum absorbs a photon, a water molecule gets in between the chromophore and a sidechain of the protein, causing the chromophore to fluoresce red rather than orange light.

The Jimenez group recently measured this process in detail and determined that after the mPlum’s chromophore is excited with a short pulse of laser light, it takes precisely 37 picoseconds (10-12 s) to convert from a structure without water to a lower-energy structure containing a water molecule.

Following this enlightening experiment, the group collaborated on an analysis of a fluorescent protein known as TagRFP675, which emits even redder light than mPlum. TagRFP675 has two different interactions between the acylimine group of its chromophore and the protein barrel, both of which can interact with water and with other protein structures, with everything in constant motion. The question was whether the two interactions in TagRFP675 responsible for the redder emission occurred via the same mechanism identified for mPlum.

“Two interactions turned out to be too much of a good thing,” Jimenez said, adding that the system is so complex that it emits light from multiple structures simultaneously, and it’s difficult to nail down which ones are responsible for the reddest emission.

“We discovered that there may be an avenue to making a more red-shifted fluorescent protein by learning how to lock down, or immobilize, one of the structures in TagRFP675,” he said.

Jimenez worked on the mPlum and TagRFP675 projects with recently minted JILA Ph.D. Patrick Konold, graduate student Samantha Allen, and colleagues from Pohang University of Science and Technology (South Korea), Florida International University, Virginia Tech, the Massachusetts Institute of Technology, and Albert Einstein College of Medicine.

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Mutant Chronicles: The quest for a better red-fluorescent protein

Steven Burrows — Tue, 20 Jan 2015 20:30:30 +0000

Mutant Chronicles: The quest for a better red-fluorescent protein Steven Burrows Tue, 01/20/2015 - 13:30

Julie Phillips / Science Communicator

Microfluidics system used in the Jimenez lab to select the top-performing cells during a directed evolution experiment. Lasers measure the fluorescent properties of mutated fluorescent proteins in each cell passing through the system, and another laser provides a “tractor beam” to grab onto the best mutant cells for further investigation. This system allows the group to rapidly investigate tens of thousands of different proteins. Image credit: Steven Burrows / JILA

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 protein “barrel” enclosing the red-light emitting compound, or chromophore. The thought was that when the barrel flopped open, it would allow oxygen in to degrade the chromophore, thus destroying its ability to fluoresce.

The group decided that its next step(s) would be to tweak the natural protein to make it more stable. Tweaking proteins is a huge challenge because most combinations of mutations result in a complete loss of the necessary structure to maintain fluorescence. Even so, the group succeeded in developing a new approach to real-world protein improvement that employs a laboratory strategy for directed evolution.

Directing evolution is challenging. The first step requires creating a library of hundreds of thousands of cells containing different mutations of a single protein. This step is now relatively easy, thanks to the tools of molecular biology. The second step requires screening the fluorescence properties of each cell to select only those few that contain top-performing mutant proteins.

To accomplish the selection process, the group uses microfluidics combined with several laser beams. Its microfluidics system contains micron-sized three-dimensional transparent channels that carry small streams of liquid and allow cells to flow through them one at a time. As the mutant cells pass through the microfluidics channel, lasers measure the fluorescent properties of each mutant cell to assess how well the cells maintain their fluorescence when repeatedly excited by the series of laser beams. Another laser acts as an optical trap that works like a tractor beam to grab onto the best mutant cells for further investigation. The microfluidics setup itself readily removes the cells that are poor performers by simply allowing them flow out of the device.

To make matters more challenging, directed evolution requires repeating the two steps described above multiple times. The Jimenez group is currently in the middle of round three of its quest to evolve a better red-fluorescent protein.

Although the group has already shown that the specific improvements suggested by the computer simulation don’t work, the first round of the directed evolution experiment has come up with an improved red-fluorescent protein with a less floppy barrel that is 2–4 times more stable than mCherry. The combination of mutations that resulted in this improvement has not been previously observed in nature and was completely unexpected.

The group named its new mutant protein Kriek, after a Belgian beer made via the fermentation of cherries. Clearly, the researchers are adept at doing more than biophysics. They include JILA Ph.D. Jennifer Lubbeck (2013) and Fellow Ralph Jimenez, Kevin Dean and Amy Palmer of CU’s Department of Chemistry and Biochemistry, as well as colleagues from the University of Tennessee Space Institute and Florida International University.

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