The Center for Advanced Scientific Computing and Modeling (CASCaM)

07/08/2022

Emmett Leddin, a Spring 2022 Chemistry graduate that worked with Drs. Andrés Cisneros (Chemistry) and Oliviero Andreussi (Physics), has received the 2022 Toulouse Dissertation Award in the Physical Sciences category. According to the Toulouse Graduate School, the Toulouse Dissertation Award is an annual award that "recognizes individuals who have completed dissertations that represent original work and make an unusually significant contribution to a discipline" and is given to UP TO 4 individuals.

More information about the award can be found here:

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05/03/2022

Dr. Jincheng Du, Materials Science and Engineering, and others, recently published a book Atomistic Simulations of Glasses: Fundamentals and Applications through Wiley Publishing.

Brief Description: In Atomistic Simulations of Glasses: Fundamentals and Applications, a team of distinguished researchers and active practitioners delivers a comprehensive review of the fundamentals and practical applications of atomistic simulations of inorganic glasses. The book offers concise discussions of classical, first principles, Monte Carlo, and other simulation methods, together with structural analysis techniques and property calculation methods for the models of glass generated from these atomistic simulations, before moving on to practical examples of the application of atomistic simulations in the research of several glass systems.

You can learn more about the book here:

A complete referenceto computer simulations of inorganic glass materials InAtomistic Simulations of Glasses: Fundamentals and Applications, a team of distinguished researchersand active practitionersdeliversa comprehensive review of the fundamentals and practical applications of atomistic simulation...

05/03/2022

Dr. Paul Marshall, Chemistry, and others, recently published "An Experimental and Modeling Study on Auto-Ignition Kinetics of Ammonia/Methanol Mixtures at Intermediate Temperature and High Pressure" in the journal Combustion and Flame.

Abstract: A rapid compression machine (RCM) has been applied to measure the ignition delay times of NH3/CH3OH mixtures covering pressures of 20 and 40 bar, equivalence ratios of 0.5, 1.0 and 2.0, and temperatures between 845 and 1100 K. The measurements show that the NH3/CH3OH mixtures become more reactive with increasing methanol addition. Addition of merely 1% (molar basis) of CH3OH to NH3 lowers the ignition temperature around 100 K at 40 bar in comparison to pure NH3. The ignition delay is a complex function of fuel mixture and stoichiometry. For the 1% CH3OH mixture, the leaner mixtures are more reactive, while the reverse trend is found for mixtures with 5%, 20% and pure CH3OH. Analysis of the pressure profiles shows three distinct ignition modes for NH3/CH3OH mixtures, facilitated by the pre-ignition heat release from NH3 consumption. A detailed mechanism for ignition of NH3/CH3OH fuel blends has been developed, capable of reproducing the ignition behavior of mixtures with reasonable accuracy. A subset for amine / methanol interactions was established, with rate constants for the key reaction between NH2 and CH3OH calculated from ab initio theory. A sensitivity analysis indicates that the critical reactions during the auto-ignition process vary with the CH3OH mole fraction in the fuel. The ammonia chemistry, namely NH2 + NO, NH2 + NO2 and NH2 + HO2, is dominant for the mixture with 1% CH3OH, while the reactions related to CH3OH and H2O2 are more important for the 20% CH3OH mixture. The interaction between ammonia and methanol shows a more prominent effect on auto-ignition for mixtures with 5% CH3OH in fuel as compared to those with 1% and 20% CH3OH. According to the modeling results, methanol addition is found to enrich the O/H radical pool, consuming ammonia and promoting auto-ignition through different reaction pathways.

You can view the article here:

A rapid compression machine (RCM) has been applied to measure the ignition delay times of NH3/CH3OH mixtures covering pressures of 20 and 40 bar, equi…

05/03/2022

Dr. Paul Marshall, Chemistry, and others, recently published "Challenges in Kinetic Modeling of Ammonia Pyrolysis" in the journal Fuel Communications.

Abstract: Ammonia pyrolysis reactions have implications for its ignition and oxidation in engines and gas turbines. In the present work, the chemistry of ammonia pyrolysis is investigated by kinetic modeling and theory. Rate constants for key reactions are carefully evaluated based on available experimental and theoretical results. The high pressure limit k1,∞ for NH2 + H (+M) ⇄ NH3 (+M) (R1) is calculated to be essentially the collision frequency, indicating that dissociation of ammonia in combustion processes will be at or close to the low pressure limit even at engine and gas turbine conditions. The chemical kinetic model is validated against reported shock tube measurements of NH3, NH2, and NH in ammonia pyrolysis. Predictions are in good agreement with observations for dilute conditions (≤ 0.5% NH3), but the model appears to underpredict the NH3 consumption rate at longer times in less dilute mixtures. At short reaction times, thermal dissociation of NH3, together with the NH3 + H reaction, controls conversion. At longer times, secondary reactions involving NH2 and NH become important due to their impact on the radical pool. Predictions become sensitive to formation and consumption of diazene (tHNNH and cHNNH). Several of the key steps in the ammonia pyrolysis mechanism are radical-radical reactions that are difficult to measure accurately and challenging to calculate theoretically, and a more comprehensive experimental characterization is desirable to support further model development.

You can view the article here:

Ammonia pyrolysis reactions have implications for its ignition and oxidation in engines and gas turbines. In the present work, the chemistry of ammoni…

05/03/2022

Dr. Paul Marshal, Chemistry, and others, recently published "New Reactions of Diazene and Related Species for Modeling Combustion of Amine Fuels" in the journal Molecular Physics.

Abstract: Potential energy surfaces for reactions involving N2H2 isomers of diazene (diimide) have been explored using density functional theory, with energies based on coupled-cluster theory. A focus is on processes that create or consume these species, and isomerisation between the E (trans) and Z (cis) forms of HNNH. These include isomerisation and dissociation pathways for HNNH, addition of H atoms to form N2H3, abstraction by H atoms yielding short-lived NNH, and abstraction reactions of H with N2H3. Transition state and capture theories are applied for high-pressure-limiting behaviour, while low-pressure and falloff regions are characterised via the methods of Troe and coworkers. Rate constants and thermochemistry are provided to improve models of diamine chemistry, relevant to the combustion of NH3 especially at high concentrations, high pressures or under reducing conditions. Results indicate that amine radical recombination mainly yields the E HNNH isomer, while H-abstraction from N2H3 results in E HNNH and H2NN. However, at elevated temperature E → Z isomerisation becomes competitive, and Z HNNH, being more reactive, acts to enhance the diazene consumption rate.

You can view the article here:

(2021). New reactions of diazene and related species for modelling combustion of amine fuels. Molecular Physics: Vol. 119, The Beauty of Chemical Reaction Kinetics: A Festschrift in Honour of Jürgen Troe, e1979674.

05/03/2022

Congratulations to Emmett Leddin, a UNT Chemistry doctoral candidate, for winning the UNT Golden Eagle Award! Soon-to-be Dr. Leddin recently completed his dissertation work in computational biochemistry under the advisement of Profs. Andres Cisneros and Oliviero Andreussi.

According to the Division of Student Affairs website (https://studentaffairs.unt.edu/student-activities-center/programs-and-services/eagle-awards), the Golden Eagle Award is the “most prestigious award that UNT bestows upon a student leader; recipients show a tremendous commitment to co-curricular activities and enhancing campus life at UNT by engaging in considerable service and displaying great leadership, all while achieving excellence in the classroom.”

When asked to comment on winning the award, Dr. Leddin stated “I am honored to be named as a recipient of the Golden Eagle Award for my impact as a student leader on the campus community. When I started at UNT, I did not set out to become as involved as I did. I intended to keep my head down and focus on research in order to complete my degree. However, I quickly found a number of activities and projects that I was passionate about and wanted to contribute to, particularly those focused on mental health and diversity in science.

I started by volunteering with Crisis Text Line. A few months later, I helped found the UNT chapter of Out in Science, Technology, Engineering, and Mathematics (oSTEM), and served as their first President. After attending my first oSTEM conference, I realized I could contribute to some of the work happening behind the scenes, and I became a global oSTEM volunteer. One of these projects grew into its own non-profit, THRIVE Lifeline, a text-based crisis hotline for people in Science, Technology, Engineering, Mathematics, and Medicine (STEMM) fields with marginalized identities. I have also gotten involved in science communication and mentorship efforts, including Skype-a-Scientist, Letters to a Pre-Scientist, and Científico Latino’s Graduate Student Mentorship Initiative.

I would never have been able to be so involved without the unwavering support of my PhD advisor, Dr. G. Andrés Cisneros. He encouraged me to strike a balance between research and community involvement.”

Dr. Leddin’s nomination was supplemented by recommendations from Drs. Andres Cisneros and Timothy Stephens. Dr. Cisneros commented that “Emmett is an indefatigable advocate and leader in our group and our department.” Meanwhile, Dr. Stephens remarked that “Emmett Leddin has done the most amazing things I have ever seen a student do here at UNT. I have been associated with UNT since 2009 and have never met anyone more deserving of this award. Emmett created the oSTEM chapter and immediately came on as their president for their first semester. The response to the creation of this oSTEM chapter was overwhelmingly positive here at UNT. I remember attending the first meeting and the small room that they reserved in the library was standing room only. Emmett saw this need for his fellow students to find a place where they belonged and he made it happen.”

Again, we want to congratulate Dr. Emmett Leddin on winning this prestigious UNT award!

To learn more about the award and view past winners and (hopefully soon) all of the 2022 winners, please visit the Golden Eagle Award website (https://studentaffairs.unt.edu/student-activities-center/programs-and-services/eagle-awards/golden-eagle-award).

In connection to UNT's 125th anniversary celebrated in 2015-2016, the Center for Leadership and Service and Student Activities created the Golden Eagle Award. The Golden Eagle Award is the most prestigious award that UNT bestows on a student leader. Any student who has been a leader in campus life,....

04/05/2022

Dr. Jincheng Du, Materials Science and Engineering, received a Department of Energy Advanced Research Projects Agency-Energy (ARPA-E) award to study and develop “a safer and more efficient method of containing and recycling molten salt nuclear waste from nuclear reactors and other sources — a critical link in making these plants feasible.” Dr. Du will conduct the ARPA-E research in collaboration with Citrine Informatics, Inc. (https://citrine.io/) and Pacific Northwest National Laboratory (PNNL) (https://www.pnnl.gov/).

For more information about the research, please read the article on the Materials Science and Engineering website (https://materials.engineering.unt.edu/news/next-generation-nuclear-power).

PNNL advances the frontiers of knowledge, taking on some of the world’s greatest science and technology challenges.

04/05/2022

Congratulations to Anay Gupta and Neel Shanmugam, Chemistry TAMS students, for being recipients of the 2022 Goldwater Scholarship Award.

Anay Gupta worked in the research laboratory of Drs. Thomas Cundari (UNT), Gad Getz (Broad Institute of MIT & Harvard) and Anshul Kundaje (Stanford), investigating the relation of genomics and drug resistance via computational analysis of 25 different cancerous cell lines treated with a wide variety of chemotherapy drugs at different doses, predictive deep-learning modeling and Methane functionalization.

Neel Shanmugam worked in the research laboratories of Drs. William Acree and Andres Cisneros, helping to advance environmental chemistry via computational and analytical chemistry methods that stand to develop safer replacements for hazardous solvents and drugs, and developing computational compound designs for novel drugs and solvents.

According to the Goldwater Foundation website [https://goldwaterscholarship.gov/], "The Barry Goldwater Scholarship and Excellence in Education Foundation was established by Congress in 1986 to serve as a living memorial to honor the lifetime work of Senator Barry Goldwater, who served his country for 56 years as a soldier and statesman, including 30 years in the U.S. Senate."

The complete list [https://goldwaterscholarship.gov/2022-goldwater-scholars-by-legal-state-of-residence/] of 2022 Goldwater Scholarship Award recipients by Institution State includes a brief description of each recipient's career goals.

The Barry Goldwater Scholarship and Excellence in Education Foundation The Barry Goldwater Scholarship and Excellence in Education Foundation was established by Congress in 1986 to serve as a living memorial to honor the lifetime work of Senator Barry Goldwater, who served his country for 56 years a...

01/04/2022

Dr. Ahmad Najafian, former Chemistry Ph.D. student working with Dr. Cundari, will join the research team at EMD Serono (Merck KGaA) in the Boston, MA area as a Senior Scientist. He will be supporting the team to generate hypotheses, design and optimize drug-like molecules and biologics from early stages to lead optimization for the company's programs and therapeutics areas using various computational tools and methods in collaboration with medicinal chemistry and biology departments. Dr. Najafian will begin his new position in January 2022.

12/02/2021

Kurt Bodenstedt, Sheikh Islam, Jacob Fripp, Shan Li, Zhou Lu (graduate students) and Allison Myers (undergraduate student), from the Omary Research Group presented the following shared posters at the 2021 Southwest Regional Meeting (SWRM) in October/November 2021:
• Advantages and Challenges for MOFs using Texas-sized Extended Poly-carboxylate Linkers
• Further Advancements in Dopant-free Organic Light-emitting Diodes (DFW-OLEDs)
• Luminescent Metal Inorganic Framework Sensors: Chemo- and Baro-sensing
• “Research for the Classroom” Discovery Labs 2021: Can You “Alchemize” Gold via Copper in Tetranuclear Dithiophosphinate-Diphosphine Complexes as Potential (O)LED and/or Thermochromic-Sensing Materials
• “Research for the Classroom” Discovery Labs 2021: You Get What You Pay for via Dinuclear Gold(I) Dithiophosphinate-Diphosphine Complexes as Potential (O)LED Materials
• Strong Heteroatomic Metal–Metal Coordinate-Covalent Bonding and Charge-Transfer Interactions Between Two Cyclic Trinuclear Coinage-Metal Complexes