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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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CASCaM Instituted at UNT   [ Official UNT News Story ]The chemistry building at the University of North Texas.
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). A longer presentation of the CASCaM research, resources, and faculty can be downloaded here (PDF format).


Chemistry NSF-REU participant received a DOE Computational Science Graduate Fellowship
Olivia Hull, 2016 NSF-REU participant working with Dr. Thomas Cundari, has received a 4-year Department of Energy Computational Science Graduate Fellowship, beginning September 2018. According to the website, the DOE CSGF "provides outstanding benefits and opportunities to students pursuing doctoral degrees in fields that use high-performance computing to solve complex science and engineering problems. The program fosters a community of energetic and committed Ph.D. students, alumni, DOE laboratory staff and other scientists who want to have an impact on the nation while advancing their research."

You can learn more about the DOE Computational Science Graduate Fellowship here.


New Publications: Three Publications by CASCaM Professor
Dr. Mohammad Omary (Chemistry), and others, recently published three papers:


New Patent Events: Two Patent Events by CASCaM Professor
Dr. Mohammad Omary (Chemistry), and others, was recently involved in the following patent events:


Chemistry student awarded NSF Graduate Research Fellowship
Catherine Moulder, a graduate student in Dr. Thomas Cundari’s lab, has received a prestigious National Science Foundation Graduate Research Fellowship to further her research in chemistry.

From NSF Graduate Research Fellowship website: "The program recognizes and supports outstanding graduate students in NSF-supported science, technology, engineering, and mathematics disciplines who are pursuing research-based master's and doctoral degrees at accredited United States institutions."

You can read the UNT Chemistry article here.

You can learn more about the fellowship here.


CASCaM alum & collaborator shares focus in article “Cancer Fighters”
Sreekar Marpu, alumni and collaborator of Dr. Mohammad Omary (Chemistry), was one of the focuses of the article “Cancer Fighters” in the UNT publication North Texan. Drs. Andrés Cisneros (Chemistry)and Mohammad Omary and the Cisneros Research Group were also mentioned in the article.

Snippet from North Texan article: "In a laboratory at UNT, Sreekar Marpu ('11 Ph.D.) is on the hunt to kill cancer. The research assistant professor of chemistry is working to develop optical sensors that have the ability to differentiate deadly cancer cells from normal benign cells. He also is researching biocompatible nanomaterials that help obliterate cancer cells. Other UNT faculty have made their own innovative findings, from discovering a protein that could be the cause of some breast cancers to creating a device that can detect cancer in its early stages."

You can view the article here.


New Publication: Computational Investigation of Non-Covalent Interactions in 1-Butyl-3-Methylimidazolium/bis(Trifluoromethylsulfonyl)imide in EMD and NEMD
Dr. Andrés Cisneros (Chemistry), and others, recently published "Computational Investigation of Non-Covalent Interactions in 1-Butyl-3-Methylimidazolium/bis(Trifluoromethylsulfonyl)imide in EMD and NEMD" in the Journal of Chemical Physics.

Abstract: Non-covalent interactions play a crucial role in the behavior and properties of Ionic Liquids (ILs). These interactions are particularly important for non-equiliibrium properties such as the change in viscosity due to hearing forces (shear viscosity). Therefore, a detailed understanding of these interactions can improve our understanding of these important class of liquids. Here, we have employed quantum mechanical (QM) energy decomposition analysis (EDA) and non-covalent interaction (NCI) analysis to investigate a series of representative 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([bmim][Tf2 N]) ion pairs extracted from classical equilibrium and non-equilibrium molecular dynamics simulations. EDA based on symmetry adapted perturbation theory (SAPT) for the complete monomers, as well as fragment SAPT (FSAPT) for the functional fragments have been carried out. In general, the electrostatic component comprises about 80% of the intermolecular interaction and significant contributions from other components (induction and dispersion) are also observed, especially for interactions involving bifurcated hydrogen bonds. The FSAPT analysis suggests that caution is warranted when employing simplified assumptions for non-bonded interactions, e.g., focusing only on hydrogen bonds between functional fragments, since this view may not provide a complete picture of the complicated interactions between the ions. In NEMD, the total interaction energies of some fragments have a significant qualitative change as the shear rate increases. Our results indicate that the inter-fragment interactions play a fundamental role in the viscous behavior of ILs; suggesting that the exclusive use of geometric criteria to analyze inter-molecular interactions in these systems is not sufficient to investigate shear-thinning effects.

You can view the article here.


New Publication: Plasmonically Induced Transparency in Graphene Oxide Quantum Dots with Dressed Phonon States
Dr. Yuri Rostovtsev (Physics), and others, recently published "Plasmonically Induced Transparency in Graphene Oxide Quantum Dots with Dressed Phonon States" in ACS Photonics.

Abstract: The absorption in quantum dots (QDs) embedded within a semiconductor matrix can be manipulated by resonant optical excitation of phonons. The coherent interaction of photons due to localized plasmon induced a change in the transient absorption of graphene oxide quantum dots conjugated to silver nanoparticles. Resonant pumping of plasmons and phonons with 400 nm pump photons induces a coherent change in excitonic absorption within QDs which results in phonon-assisted plasmon induced transparency at room temperature. This novel effect can be related to the appearance of the coherent effects such as forming dark states and coherent population trapping related to Fano interference. A large Rabi splitting of 120 meV has been observed within 800 fs of the preparation of the dressed phonon–photon states. A theoretical model has been developed to quantitatively demonstrate that the dark states can be still formed at ultrashort time scale corresponding to the dephasing time of the carriers in the QDs.

You can view the article here.


New Publications: Four Publications by CASCaM Professor
Dr. Andrés Cisneros (Chemistry), and others, recently published three papers and had another accepted:


CASCaM professor honored with special Colloquium at the Fritz Haber Institute of the Max Planck Society
The Fritz Haber Institute of the Max Planck Society, Department of Chemical Physics, hosted a colloquium honoring Dr. Paul Bagus on November 20, 2017. Guest speakers included Professors Hajo Freund, Christof Wöll and Francesc Illas.

The program can be found here.

 


Chemistry student to receive award at the Spring 2018 ACS National Meeting
Alice Walker, a Chemistry graduate student working with Dr. Andrés Cisneros, is one of 5 winners of the Chemical Computing Group Excellence Award for Graduate Students, which will be presented during the 255th ACS National Meeting & Exposition, March 2018. The award is presented by the Computers in Chemistry Division of the American Chemical Society and decisions are based on “the quality and significance of the research to be presented, as well as the strength of the supporting letter and other materials.” (COMP Division Website)

More information about the division can be found here.

A complete list of all Computers in Chemistry Division award winners can be found here.


CASCaM professor receives UNT Foundation Eminent Faculty Award
Dr. Thomas Cundari, Chemistry, has received the UNT Foundation Eminent Faculty Award. According to the UNT Faculty Success website, the award "recognizes a faculty member, who has made outstanding and sustained contributions to scholarly-creative activity, teaching, and service and has served as an inspiration to the University of North Texas community." He will be presented with the award at the UNT Salute to Faculty Excellence Awards Dinner & Ceremony in the University Union Ballroom on Friday, October 20, 2017.

A short video about Dr. Cundari can be viewed here.

More information about the award can be found here.

A list of the other UNT Faculty Excellence award winners will soon be available here.


Chemistry student receives award at the 6th EU-US Conference on Repair of Endogenous DNA Damage
Alice Walker, a Chemistry graduate student working with Dr. Andrés Cisneros, received a “Best Of” award for her poster presentation at the 6th EU-US Conference on Repair of Endogenous DNA Damage held in Udine, Italy in September 2017. The title of the poster was “AlkBH7 variant related to prostate cancer exhibits altered substrate binding.”

Abstract: The search for prostate cancer biomarkers has received increased attention, and several DNA repair related enzymes have been linked to this dysfunction. Here we report a targeted search for single nucleotide polymorphisms (SNPs) and functional impact characterization of human ALKBH family dioxygenases related to prostate cancer. Our results uncovered a SNP on ALKBH7, rs7540, which is associated with prostate cancer disease in a statistically significantly manner in two separate cohorts, and maintained in African American men. Comparisons of molecular dynamics (MD) simulations on the wild-type and variant protein structures indicate that the resulting alteration in the enzyme induces a significant structural change that reduces ALKBH7’s ability to bind its cosubstrate. Experimental spectroscopy studies with purified proteins validate our MD predictions and corroborate the conclusion that this cancer-associated mutation affects productive cosubstrate binding in ALKBH7.

More information about the conference can be found here.






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