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Center for Advanced Scientific Computing and Modeling
Department of Chemistry
University of North Texas
1155 Union Circle #305070
Denton, Texas 76203-5017

Phone: (940) 565-4372
Fax: (940) 565-4318

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The chemistry building at the University of North Texas. CASCaM Instituted at UNT   [ Official UNT News Story ]
The University of North Texas is the home of the Center for Advanced Scientific Computing and Modeling (CASCaM), whose central mission involves research, education, training and outreach in all facets of advanced scientific computing and modeling. The CASCaM facility, supported by the United States Department of Education, the United States Department of Energy, and the United States Air Force Research Laboratory, affords excellent opportunities for collaboration with UNT computational chemists for students and faculty mentors in Texas and the surrounding states. You can download the official brochure here (PDF format).

New Publication: Computational and Spectroscopic Tools for the Detection of Bond Covalency in Pu(IV) Materials
Dr. Paul Bagus, Chemistry, and others, recently published "Computational and Spectroscopic Tools for the Detection of Bond Covalency in Pu(IV) Materials" in the journal Inorganic Chemistry.

Abstract: Plutonium is used as a major component of new-generation nuclear fuels and of radioisotope batteries for Mars rovers, but it is also an environmental pollutant. Plutonium clearly has high technological and environmental importance, but it has an extremely complex, not well-understood electronic structure. The level of covalency of the Pu 5f valence orbitals and their role in chemical bonding are still an enigma and thus at the frontier of research in actinide science. We performed fully relativistic quantum chemical computations of the electronic structure of the Pu4+ ion and the PuO2 compound. Using four different theoretical tools, it is shown that the 5f orbitals have very little covalent character although the 5f(7/2) a2u orbital with the highest orbital energy has the greatest extent of covalency in PuO2. It is illustrated that the Pu M4,5 edge high-energy resolution X-ray absorption near-edge structure (Pu M4,5 HR-XANES) spectra cannot be interpreted in terms of dipole selection rules applied between individual 3d and 5f orbitals, but the selection rules must be applied between the total wavefunctions for the initial and excited states. This is because the states cannot be represented by single determinants. They are shown to involve major redistributions on the 5f electrons over the different 5f orbitals. These redistributions could be viewed as shake-up-like excitations in the 5f shell from the lowest orbital energy from J = 5f(5/2) into higher orbital energy J = 5f(7/2). We show that the second peak in the Pu M4 edge and the high-energy shoulder of the Pu M5 edge HR-XANES spectra probe the 5f(7/2) a2u orbital; thus, these spectral features are expected to change upon bond variations. We describe theoretical and spectroscopy tools, which can be applied for all actinide elements in materials with cubic structure.

You can view the article here.

New Publication: Computational investigations of selected enzymes from two iron and α-ketoglutarate-dependent families
Madison Berger, Graduate Student in the Cisneros Research Group, and others, recently published "Computational investigations of selected enzymes from two iron and α-ketoglutarate-dependent families" in the journal Physical Chemistry Chemical Physics.

Abstract: DNA alkylation is used as the key epigenetic mark in eukaryotes, however, most alkylation in DNA can result in deleterious effects. Therefore, this process needs to be tightly regulated. The enzymes of the AlkB and Ten-Eleven Translocation (TET) families are members of the Fe and alpha-ketoglutarate-dependent superfamily of enzymes that are tasked with dealkylating DNA and RNA in cells. Members of these families span all species and are an integral part of transcriptional regulation. While both families catalyze oxidative dealkylation of various bases, each has specific preference for alkylated base type as well as distinct catalytic mechanisms. This perspective aims to provide an overview of computational work carried out to investigate several members of these enzyme families including AlkB, ALKB Homolog 2, ALKB Homolog 3 and Ten-Eleven Translocate 2. Insights into structural details, mutagenesis studies, reaction path analysis, electronic structure features in the active site, and substrate preferences are presented and discussed.

You can view the article here.

New Publication: Structural and electronic analysis of the octarepeat region of prion protein with four Cu2+ by polarizable MD and QM/MM simulations
Dr. Jorge Nochebuena-Hernandes, Post-Doc in the Cisneros Research Group, and others, recently published "Structural and electronic analysis of the octarepeat region of prion protein with four Cu2+ by polarizable MD and QM/MM simulations" in the journal Physical Chemistry Chemical Physics.

Abstract: Prions have been linked to neurodegenerative diseases that affect various species of mammals including humans. The prion protein, located mainly in neurons, is believed to play the role of metal ion transporter. High levels of copper ions have been related to structural changes. A 32-residue region of the N-terminal domain, known as octarepeat, can bind up to four copper ions. Different coordination modes have been observed and are strongly dependent on Cu2+ concentration. Many theoretical studies carried out so far have focused on studying the coordination modes of a single copper ion. In this work we investigate the octarepeat region coordinated with four copper ions. Molecular dynamics (MD) and hybrid quantum mechanics/molecular mechanics (QM/MM) simulations using the polarizable AMOEBA force field have been carried out. The polarizable MD simulations starting from a fully extended conformation indicate that the tetra-Cu2+/octarepeat complex forms a globular structure. The globular form is stabilized by interactions between Cu2+ and tryptophan residues resulting in some coordination sites observed to be in close proximity, in agreement with experimental results. Subsequent QM/MM simulations on several snapshots suggests the system is in a high-spin quintet state, with all Cu2+ bearing one single electron, and all unpaired electrons are ferromagnetically coupled. NMR simulations on selected structures provides insights on the chemical shifts of the first shell ligands around the metals with respect to inter-metal distances.

You can view the article here.

CASCaM Professors Part of Multidepartmental Team Receiving Grant from National Science Foundation for Major Upgrade of Computational Facilities
Dr. Andrés Cisneros (Chemistry) and collaborators Drs. Oliviero Andreussi (Physics), Thomas Cundari (Chemistry), Jincheng Du (Materials Science) and Hao Yan (Chemistry), received a National Science Foundation Major Research Instrumentation (NSF-MRI) grant to upgrade the high-performance computing system housed in the Chemistry Building and affiliated with the Center for Advanced Scientific Computing and Modeling (CASCaM).

CASCaM researchers span multiple departments and colleges at UNT and are united by their interest in developing and applying computational tools to solve leading-edge problems in chemical, biomolecular, and material-related research. CASCaM has a strong emphasis on promoting research and research training of early-career scientists, including Ph.D., undergraduate, and high school students, via outstanding faculty mentorship and access to world-class resources. This new award is the latest in a serious of four major grants from the NSF that have helped to grow and maintain this this HPC system, which serves as a major research asset to UNT. It will provide a significant boost to the capabilities of CASCaM-affiliated researchers at UNT.

CASCaM Professor Appointed to SFI External Faculty
Dr. Marco Buongiorno Nardelli, Physics, has been appointed to a Santa Fe Institute (SFI) External Faculty position, making him one of only 9 new appointees. Dr. Buongiorno Nardelli received this honor due to his interdisciplinary and cross-disciplinary research.

According to the SFI website, "external faculty are central to SFI's identity as a world-class research institute. They enrich our networks of interactions, help us push the boundaries of complex systems science, and connect us to over 70 institutions around the globe."

You can read the UNT College of Science article here.

You can view all of the new SFI External Faculty here.

CASCaM Professor Part of Team Using NIH Grant to Establish G-RISE
Dr. Andrés Cisneros, Chemistry, is part of the UNT team that received a new NIH grant to create the Graduate Research Training Initiative for Student Enhancement (G-RISE), which will "develop a diverse pool of Ph.D. scientists for careers in the biomedical research fields."

According to the UNT article, "The program aims to increase diversity in Ph.D. science and engineering programs, not just by providing financial support, but also by expanding mentorship with faculty and staff and providing relevant career development."

Dr. Cisneros is one of four principal investigators on this major grant, which is expected to be a game changer for research training of graduate students at UNT. Incoming graduate students in Chemistry, Biological Sciences, Biomedical Engineering, and related fields will have the opportunity to apply for 3-year fellowships provided by the G-RISE program, which includes partial tuition, benefits and travel support in addition to a stipend.

You can read the entire UNT article here and visit the G-RISE program website here.

CASCaM Professor Named Fellow of ASM International
Dr. Jincheng Du, Materials Science and Engineering, was recently named a 2021 Fellow of ASM International for his research of glasses, ceramics and other materials for functional and structural applications.

According to the ASM International website, "ASM International established the honor of Fellow of ASM (FASM) in 1969 to provide recognition to ASM members for their distinguished contributions to materials science and engineering. Recipients of one of the highest honors in the field of materials, ASM Fellows are technical and professional leaders who have been recognized by their colleagues and now serve as advisors to the society."

Please see the article on the College of Engineering website for more details.

CASCaM professor received NSF grant to support collaborative research
Dr. Thomas Cundari, Chemistry, and his UNT collaborators, Drs. Francis D'Souza and Jeffry Kelber, have received an NSF grant to investigate fundamental chemical interactions relevant to the conversion of dinitrogen to ammonia via more energy-efficient routes. Ammonia production is vital to agriculture, but is currently produced by an energy-intensive process that also produces significant amounts of CO2. Electrocatalysis is an energetically and environmentally friendly alternative for production of ammonia, and for making other products sustainably for a clean environment. Involved student researchers will learn a wide range of experimental and computational skills while they study Earth-abundant transition metal oxides and oxynitrides, as these materials are leading catalysts for synthesis of ammonia from dinitrogen, which comprises 78% of Earth's atmosphere. The studies will help to understand the chemical and material factors that are most important for optimizing catalysts for ammonia production from dinitrogen, and also applications to other important industrial reactions.

UPDATE: On September 1, 2021, UNT pubished an article about this research collaboration. You can view the UNT article here.

CASCaM professor received the 2021 Air Force Research Lab Summer Faculty Fellowship
Dr. Yuri Rostovtsev, Physics, and his student Mr. Colin Roy have received the 2021 Air Force Research Lab (AFRL) Summer Faculty Fellowship at the Air Force Institute of Technology (May-August, 2021) to work on Quantum multiplexer for quantum communications.

According to the AFRL website, "The U.S. Air Force Research Lab Summer Faculty Fellowship Program offers hands-on exposure to Air Force research challenges through 8- to 12-week research residencies at participating Air Force research facilities for full-time science, mathematics, and engineering faculty at U.S. colleges and universities."

New Publication: Combining Evolutionary Conservation and Quantum Topological Analyses To Determine Quantum Mechanics Subsystems for Biomolecular Quantum Mechanics/Molecular Mechanics Simulations
Dr. Andrés Cisneros, Chemistry, and others, recently published "Combining Evolutionary Conservation and Quantum Topological Analyses To Determine Quantum Mechanics Subsystems for Biomolecular Quantum Mechanics/Molecular Mechanics Simulations" in the journal Biomolecular Systems.

Abstract: Selection of residues and other molecular fragments for inclusion in the quantum mechanics (QM) region for QM/molecular mechanics (MM) simulations is an important step for these calculations. Here, we present an approach that combines protein sequence/structure evolution and electron localization function (ELF) analyses. The combination of these two analyses allows the determination of whether a residue needs to be included in the QM subsystem or can be represented by the MM environment. We have applied this approach on two systems previously investigated by QM/MM simulations, 4-oxalocrotonate tautomerase (4OT) and ten-eleven translocation-2 (TET2), that provide examples where fragments may or may not need to be included in the QM subsystem. Subsequently, we present the use of this approach to determine the appropriate QM subsystem to calculate the minimum energy path (MEP) for the reaction catalyzed by human DNA polymerase λ (Polλ) with a third cation in the active site. Our results suggest that the combination of protein evolutionary and ELF analyses provides insights into residue/molecular fragment selection for QM/MM simulations.

You can view the article here.

CASCaM Professor Named Fellow of the American Vacuum Society
Dr. Paul Bagus, Chemistry, was recently named a 2021 American Vacuum Society (AVS) Fellow. AVS Fellowship is granted to members who "have made sustained and outstanding scientific and technical contributions in research, engineering, technical advancement, academic education, or managerial leadership for at 10 years."

Dr. Bagus, along with the other 2021 AVS Fellows, will be honored during the 67th AVS International Symposium in October 2021.

According to the AVS website, "AVS is an international community of scientists, engineers and instrument manufacturers, which strives to promote research and communicate knowledge in the important areas of surface, interface, vacuum, and thin film science and technology for the advancement of humankind."

You can view AVS Fellows here.

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