Pitt research predicts unpredictable reactions

Research from Pitt and Politecnico di Milano paves the way for simulating catalysts under reaction conditions

Computational catalysis, a field that simulates and accelerates the discovery of catalysts for chemical production, has largely been limited to simulations of idealized catalyst structures that do not necessarily represent structures under realistic reaction conditions.

New research from the University of Pittsburgh's Swanson School of Engineering, in collaboration with the Laboratory of Catalysis and Catalytic Processes (Department of Energy) at Politecnico di Milano in Milan, Italy, advances the field of computational catalysis by paving the way for the simulation of realistic catalysts under reaction conditions. The work, published in ACS Catalysis, was authored by Raffaele Cheula, a Ph.D. student in the Maestri group; Matteo Maestri, a full professor of chemical engineering at Politecnico di Milano; and Giannis "Yanni" Mpourmpakis, Bicentennial Alumni Faculty Fellow and associate professor of chemical engineering at Pitt. CAPTION An illustration of nanoparticles under reaction conditions was featured on the cover of ACS Catalysis.  CREDIT Raffaele Cheula{module INSIDE STORY}

"With our work, one can see, for example, how metal nanoparticles that are commonly used as catalysts can change morphology in a reactive environment and affect catalytic behavior. As a result, we can now simulate nanoparticle ensembles, which can advance any field of nanoparticle application, like nanomedicine, energy, the environment, and more," says Mpourmpakis. "Although our application is focused on catalysis, it has the potential to advance nanoscale simulations as a whole."

In order to model catalysts in reaction conditions, the researchers had to account for the dynamic character of the catalyst, which is likely to change throughout the reaction. To accomplish this, the researchers simulated how the catalysts change the structure, how probable this change is, and how that probability affects the reactions taking place on the surface of the catalysts.

"Catalysis is behind most of the important processes in our daily lives: from the production of chemicals and fuels to the abatement of pollutants," says Maestri. "Our work paves the way towards the fundamental analysis of the structure-activity relation in catalysis. This is paramount in any effort in the quest of engineering chemical transformation at the molecular level by achieving a detailed mechanistic understanding of the catalyst functionality. Thanks to Raffaele's stay at Pitt, we were able to combine the expertise in microkinetic and multiscale modeling of my group with the expertise in nanomaterials simulations and computational catalysis of Yanni's group."

Lead author Raffaele Cheula, a PhD student in the Maestri Lab, worked for a year in the Mpourmpakis Lab at Pitt on this research.

"It has been very nice to be involved in this collaboration between Yanni and Matteo," says Cheula. "The combination of my research experiences at Pitt and at PoliMi has been very important for the finalization of this work. It was a challenging topic and I am very happy with this result."

Magnetic liquid structure elucidated through hybrid reverse Monte Carlo simulation at Shinshu University

A research team lead by Ryusuke Futamura of Shinshu University investigated the response of magnetic ionic liquids (MIL) to magnetic fields from the microscopic viewpoints. Magnetic fluids, which can respond to magnetic fields, can be made by dispersing ferromagnetic nanoparticles in a solvent. Some pure liquids that are not mixtures also respond to magnetic fields. For example, oxygen is a liquid around -200°C and is attracted to magnets. In this study, pure magnetic ionic liquids Emim[FeCl4] and Bmim[FeCl4] were examined on the microscopic scale. These liquids are attracted to magnets at room temperature, but the former also undergo a change from paramagnetic to antiferromagnetic behavior at 3.8K.

Ferromagnetism is found in the objects which we think of as "magnets", such as refrigerator magnets. Magnetic atoms or ions have magnetic dipoles (north and south) in the molecular scale that interact with each other and show Ferro- or antiferromagnetism over a long distance in their crystal structures. Bmim[FeCl4] does not crystalize even at low temperatures and are amorphous, or formless. It was shown in this study that even in this amorphous state, there is structurality in the short-range and several magnetic ions form an aligned association structure. This is thought to be the reason for the negative Curie-Weiss temperature, which can be observed as a macroscopic physical property. CAPTION Magnetic ionic liquid structures were elucidated through hybrid reverse Monte Carlo simulation. The research results elucidated fundamental understanding of pure liquids with magnetic responses as well as lead to the development of MIL for a variety of practical applications.  CREDIT Ryusuke Futamura, Faculty of Science, Department of Chemistry, Shinshu University{module INSIDE STORY}

It was difficult to investigate and understand the formation of the liquid structure of Emim[FeCl4] and Bmim[FeCl4]. Liquids and amorphous objects do not have a long-range ordered structure, which means structural analysis of such materials is performed through X-ray scattering measurements followed by radial distribution analysis. However, MILs are binary systems consisting of cations and anions. This makes examination by ordinary radial distribution analysis difficult. This is where the hybrid reverse Monte Carlo (HRMC) method helped. It combined the X-ray scattering measurement with molecular simulation to clearly demonstrate the precise coordination structures of the two MIL. This has made it possible to discuss the cation-cation, anion-anion, and cation-anion of the liquid structure.

By the use of spatial distribution function analysis, it has become possible to visualize the ion coordination structure. The temperature dependence of the spatial distribution function showing the coordination structure of the anions around the cations in the MIL can be seen that the lower the temperature, the wider the coordination sphere and more blurred the site. The researchers were able to clarify the characteristics of substances that appear in macroscopic physical properties from a microscopic perspective.

First author Futamura specializes in the nano spaces of porous materials. He hopes to synthesize new composite materials by combining porous materials and ionic liquids. By confining MIL in the nano space of porous materials, he hopes to create new functional materials for various applications. These MIL are considered organic-inorganic hybrid functional materials that hold potential for outstanding chemical and physical uses.

Seven bridges collaborates on personalized treatment for kids with cancer

Seven Bridges has announced a collaborative partnership between The Gabriella Miller Kids First Data Resource Center (Kids First DRC), ZERO Childhood Cancer (ZERO), the Children's Brain Tumor Tissue Consortium (CBTTC), the Australian BioCommons and the Australian Research Data Commons (ARDC). The multinational genomic cancer research project aims to establish internationally federated computational infrastructure that will enable the harmonization of pediatric cancer data from ZERO Australia with the extensive genomic datasets from CBTTC and Kids First DRC. Through this collaboration, researchers hope to better understand rare pediatric brain cancer subtypes and improve interventions for patients and their families.

Large-scale cancer whole-genome sequencing (WGS), RNA-Seq and methylome analyses have made a substantial impact on our understanding of many cancers, including their etiology, identifying disease subtypes, novel pathways, and new drug targets. While there are a number of extensive genomic cancer research programs globally, most focus on adult cancer; however, as all high-risk pediatric cancer subtypes are rare diseases, statistically significant correlation between subtype and genomic variation is inherently dependent on large sample numbers.

"Childhood cancer kills more children than any other disease in Australia and every week three children and adolescents in Australia die because of cancer," said Mark Cowley, Ph.D., Associate Professor of the Children's Cancer Institute. "Every child is different, every cancer is unique, so treatment has to be tailored for each individual. Through an international data collaboration on pediatric cancer subtypes, we hope to better understand how to treat the cancers we find in Australia, based on information that was previously inaccessible."

The research will be done on the CAVATICA Platform, a cloud-based system for collaboratively accessing, sharing, and analyzing childhood cancer data. The CAVATICA Platform, powered by Seven Bridges, allows clinicians and scientists worldwide to rapidly access large amounts of genomic data and workflows within a computation and storage environment where they can share, process, integrate and analyze data. Complex and comparative analyses can be achieved using various open-source R and Python packages; and through the Data Cruncher feature, data can be shared through interactive Jupyter Notebooks.

"The CAVATICA Platform enables us to seamlessly collaborate, share, interoperate and connect with other researchers studying pediatric cancer, driving improved outcomes and novel research," said Adam Resnick, Ph.D., Kids First Data Resource Principal Investigator. "The platform has enabled us to harmonize and process over 15,000 whole genomes, whole becomes, and RNA-seq, including alignment, somatic variant calling, copy number calls, structural variants, RNA expression, and fusions. Additionally, integrations with the Kids First Data Resource Center portal allow users to create cohorts and manage their analysis in secure, cloud-based projects in CAVATICA."

To enable this multinational collaboration, the CAVATICA Platform is being expanded to enable harmonized analyses across geographically separated and jurisdictionally protected data datasets, in this case across Australia and the United States. The extended CAVATICA orchestration engine will allow ZERO and Kids First workflows and analysis tools to be used interchangeably and seamlessly across both datasets. From the researcher's perspective, the platform aggregates the separate datasets into a single virtual pan-continental dataset that is highly accessible through a global best practice analysis platform.

"By connecting pediatric researchers across international borders through the CAVATICA platform, we are also breaking down borders between data silos through the use of the global standard Common Workflow Language (CWL) and the ease of multi-cloud computing," said Brandi Davis-Dusenbery, Ph.D., Chief Scientific Officer of Seven Bridges. "This enables our researchers to focus on treatments for kids with rare cancers rather than data challenges."