In the News
Journal Dedicated to Emeritus Raymond Barnes
An interdisciplinary team of UMass Amherst researchers had their recently published article chosen as a “hot” article in the journal Physical Chemistry Chemical Physics. The team, led by chemistry professor Scott Auerbach and chemical engineering professor Wei Fan, reported breakthrough computer simulations confirmed by experiments showing faster crystallization of nanoporous catalysts known as zeolites.
“Understanding how to make zeolites, and how to make them faster, is incredibly important. Zeolites are the most used synthetic catalysts on planet earth, and they show great potential for making green fuels and capturing carbon dioxide – both critical for battling climate change,” said Dr. Auerbach.
The team also includes lead author Dr. Cecilia Bores, a former postdoctoral fellow at UMass Amherst and now a physics professor at Union College, as well as chemical engineering PhD student Song Luo and undergraduate researchers J. David Lonergan, Eden Richardson, and Alexander Engstrom.
“Simulating zeolite crystallization is one of the grand challenges in materials science because the process can take days to weeks, so our simulations have to efficiently model very slow assembly processes,” said Dr. Bores. She continued, “The key to our work is capturing only the essential aspects of zeolite bonding and intentionally omitting some interactions between particles that would only slow down the simulation.”
Also critical to the work are experimental tests confirming that the simulation predictions are correct. Such experiments, carried out by Fan and Luo, involve using additives called “structure directing agents” to help steer the crystallization. Fan and Luo confirmed the prediction that using multiple structure directing agents that match the different nanopore sizes within a zeolite can speed up crystallization, by as much as a factor of three.
“Learning how faster zeolite crystallization occurs by using several structure directing agents is a real breakthrough for my lab,” said Dr. Fan. “We spend countless hours trying to fabricate new zeolites, so being able to speed up the process can lead to much faster discovery of new and useful materials.”
The team plans to continue the research, which is funded by the Department of Energy’s program in Synthesis and Processing Science, by applying artificial intelligence to analyze the simulated crystallization trajectories to identify key steps that lead to crystals, and by testing those predictions using advanced experimental methods such as Raman spectroscopy.
“Being able to combine computer simulations with experiments so seamlessly is critical to this research,” said Dr. Auerbach. “Our collaboration with Wei Fan and his team has been fantastic. As we like to say: ‘Without Wei, there’s no way!’”
Sun Receives Paul Hatheway Terry Scholarship
Zhining (Jennings) Sun received Paul Hatheway Terry Scholarship in recognition of excellence in research. Research Summary: Genetically encodable RNA-based fluorescent sensors have been a revolutionary tool for real-time imaging of important biological small molecules in live cells. Guanosine tetraphosphate (also known as ppGpp or “Magic Spot”) in particular is one of the targets that plays an integral role in cell regulation. Its presence in bacteria cells triggers the stringent response which helps the cells to survive the harsh living conditions via various pathways. Although many researches have been done to study its functions, people still have not been able to fully understand it due to the lack of tools to monitor it in live cells. I engineered a naturally occurring ppGpp riboswitch into an RNA-based fluorescent sensor and achieved imaging of ppGpp in live E. coli cells. After half a century since its discovery, we are the first group to ever visualize ppGpp and provide information on its cellular dynamics and cell-to-cell variations. Now I’m working on the multiplex imaging project to study ppGpp and other related targets simultaneously, which will discover the potential correlation between the targets as well as how they affect the cell biology.
Zhou Lin, assistant professor in chemistry, and her co-authors received the (“science + dialog") Scialog Award for their proposal to develop a new electrosynthetic route that reduces the emissions of two most significant greenhouse gases from waste management and treatment activities, carbon dioxide, and methane. The $55,000 grant will help the team design unconventional electrochemical reactors and catalysts to enable direct coupling of carbon dioxide and methane into valuable liquid feedstock.
Jianhan Chen, a University of Massachusetts Amherst chemistry and biochemistry and molecular biology professor, has received a five-year, $2 million National Institutes of Health (NIH) grant to support research in his computational biophysics lab aimed at better understanding the role of intrinsically disordered proteins (IDPs) in biology and human disease.
The grant falls under the National Institute of General Medical Sciences MIRA program, which stands for Maximizing Investigators’ Research Award. It’s designed to give highly talented researchers more flexibility and stability to achieve important scientific advances in their labs.
“The MIRA award enables us to continue working on several central problems regarding the study of disordered proteins and dynamic interactions. The flexibility of this funding mechanism also allows us to follow new research directions as they emerge,” Chen says.
Until relatively recently, it was thought that proteins needed to adopt a well-defined structure to perform their biological function. But about two decades ago, Chen explains, IDPs were recognized as a new class of proteins that rely on a lack of stable structures to function. They make up about one-third of proteins that human bodies make, Chen explains, and two-thirds of cancer-associated proteins contain large, disordered segments or domains.
“This disorder seems to provide some unique functional advantage, and that’s why we have so much disorder in certain kinds of proteins,” Chen says. “These IDPs play really important roles in biology, and when something breaks down, they lead to very serious diseases, like cancers and neurodegenerative diseases.”
In his lab, Chen and colleagues focus on using computer simulations to model the molecular structure and dynamics of proteins. “IDPs are a mess; it’s difficult to determine the details of their properties because they are not amenable to traditional techniques that are designed to resolve stable protein structures,” he says.
Because of their chaotic state, IDPs must be described using ensembles of structures, and computer simulations play a crucial role in the quantitative description of these disordered ensembles. “Our goal is really trying to combine simulation and experiments in collaboration with other labs to tease out what are the hidden features of these disordered proteins that are crucial to their function,” Chen says. “Then we can look at how these specific features might be perturbed by disease-related mutations or conditions.”
The next step would be to develop effective strategies for targeting disordered protein states. Toward that end, Chen’s lab will study the molecular basis of how the anti-cancer drug EGCG, an antioxidant found in green tea extract, and their derivatives interact with the p53 gene, a tumor suppressor and the most important protein involved in cancer.
The key, he says, is knowing how to design drug molecules to bind well enough to IDPs to achieve a therapeutic effect. Traditional, structure-based drug design strategies are faced with significant challenges, Chen says, because IDPs do not contain stable, “druggable” pockets.
“We believe that targeting IDPs requires new strategies that explore the dynamic nature of IDP interactions,” Chen says. “If we can do this, it could really open up a whole class of drugs that were previously thought impossible.”
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Craig Martin, professor of chemistry at the University of Massachusetts Amherst, will lead a UMass team that will spend the next three years developing a process that can deliver the quantity and quality of messenger RNA (mRNA) demanded by a new class of medicines, including the COVID vaccines, faster, cheaper and more effectively than any other method. Martin and his colleagues will be joining Wellcome’s R3 program, which seeks to create a global network of “biofoundaries” capable of producing high quality, low-cost mRNA, increasing global access to these new therapies, wherever they’re needed.
Martin whose co-principal investigators include Sarah Perry and Shelly Peyton, both professors of chemical engineering at UMass Amherst, is at the cutting edge of a new approach to medicine. Traditionally, illnesses have been cured by medicines that come from outside the human body: herbs, chemicals and vaccines. Recently, there’s been a new approach, using biologics, or therapies that delivers missing proteins to the human body and which can be used to treat a very wide range of illnesses that result from missing or damaged cell proteins.
But, says, Martin, this process can be taken one step further. “Instead of making the protein in some other organism and delivering it to humans,” he says, “we can make the RNA that encodes the protein, deliver that RNA as the biologic, and the patient’s own cells then make that protein from the delivered RNA.” The result is that, when the body makes the protein itself, “everything gets done correctly.” Furthermore, says Martin, “once you know how to make the RNA for one disease, it’s comparatively easy to swap in a different RNA so it can treat another disease. You don’t have to reinvent the wheel, saving money, and, crucially, saving time.”
If RNA therapies have not yet reached their full potential, it’s because making RNA that is pure enough, in great enough quantities, has proved very difficult—and the purity is of utmost importance. Impure RNA looks, to the body’s immune system like an invader and triggers an immune response. “This is actually ok for vaccines,” says Martin, “because what vaccines do is train the body’s immune system to recognize disease."
For certain diseases, though, especially those that are caused by genetic deficiencies, and for which the immune system plays no role, purity is important. Take cystic fibrosis, for example. Impure RNA would cause swelling in the lungs, making it even harder for a patient to breathe—a potentially deadly complication. Many cancers, too, are the result of genetic malfunctions, and could be treated with RNA therapies.
Martin, whose lab has been studying RNA for more than 30 years, has developed an approach to making RNA that employs a “flow reactor.” This method results in much larger quantities of much purer RNA. It is also scalable and can provide small amounts of RNA that could, for instance, address a particular person’s cancer, as well as the enormous amounts needed for something like a COVID vaccine.
While the Martin and Perry labs have already developed an initial smaller-scale version of their process, Perry and Peyton will help refine the process and be responsible for helping to scale the initial to industrial uses. “The microfluidic aspects of this technology rely critically on their small size,” Perry says. “Therefore, we will not ‘scale up’ so much as ‘scale out,’ creating many parallel reactors that can operate simultaneously to produce sufficient product for commercial use.” This scaling out, says Peyton, relies on a series of porous scaffolds, which Perry will engineer. Peyton will incorporate these porous scaffolds into the reactors. “Without both,” she says, “such an ambitious goal of continuous production of long mRNAs would not be possible.”
The work is part of the larger Wellcome Foundation’s Leap Health Breakthrough Network, a web of more than 70 world-class institutions, non-profits and commercial entities representing a network of over 650,000 scientists and engineers across six continents and is supported by a major grant. Early support for this work was provided by UMass Amherst’s Institute for Applied Life Sciences (IALS), which combines deep and interdisciplinary expertise from 29 departments on the UMass Amherst campus to translate fundamental research into innovations that benefit human health and well-being.
Buz Awarded a PPG Fellowship
Enes Buz (Kittlestved Group) Awarded a PPG Fellowship Award for outstanding research in the area of materials chemistry. Research summary: Transition-metal doped metal oxide semiconductors, in particular Zn1-xMxO, have attracted tremendous interest as potential candidates not only for the semiconductor-compatible magnetic components for spintronic applications but also room-temperature magnetism. While ZnO is a diamagnetic semiconductor, introduction of magnetic dopants such as Fe imparts magnetism on ZnO. In the Kittilstved research group, I study on different methods to tune the oxidation state of Fe dopants in ZnO nanocrystals (NCs) in a controlled way which will allow us to control the properties of ZnO NCs in turn. With the support of the PPG fellowship, I will be furthering my studies to investigate and directly show the specific oxidation state of Fe in ZnO NCs by utilizing various dopant-specific spectroscopic techniques. This study will help us to shed light on the mechanism of magnetism in ZnO NCs and to develop materials of interest for magnetism-related applications.
Wang Awarded PPG Fellowship
Tongkun Wang (Auerbach Group) Awarded a PPG Fellowship Award for outstanding research in the area of materials chemistry. Research summary: People in Prof. Scott Auerbach’s group focus on the study of zeolites, which are atomic crystals formed by tetrahedral atoms like Si with bridging atoms like O. As noticeable members of molecular sieves, zeolites have interesting porous structures and channels. To better understand their formation mechanism, we performed periodic density functional theory simulations and probed key precursors. Combined with experimental results from our collaborators, we successfully used Raman spectroscopy and thermodynamics calculations to reveal defects and explained why or why not they can be healed with the presence of organic structure directing agents. In future works, I will extend my ab initio molecular dynamics simulations in aqueous environment and study processes from monomers, via important building units, to full crystalline, which will help us to predict and design the synthesis for zeolites we want.