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News and Upcoming Events

Upcoming Events

UNT Smart Talks: Beautiful Data: Materials as Musical Muses
Dr. Marco Buongiorno Nardelli
Date: October 24, 2019
Time: 4:00PM
Location: UNT Lyceum (Student Union)

Contact Information

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).

CASCaM Professor presents UNT SMART Talk
Dr. Marco Buongiorno Nardelli (Physics) will present the talk "Beautiful Data: Materials as Musical Muses" as part of the UNT College of Science SMART Talks series. The talk will be on Thursday, October 24, 2019, at 4PM in the UNT Lyceum.

According to the College of Science website: S.M.A.R.T = Science & Mathematics Advancing Research & Technology. Formerly known as the Faculty Lecture Series, the series of talks was created to highlight the outstanding scholarly work of COS faculty and bring the UNT community together to discuss scientific breakthroughs and learn about the building blocks of the world around us. All S.M.A.R.T. Talks are free and open to the public.

You can see the official flyer here.

You can read the College of Science announcement here.

New Publication: Ewald-based methods for Gaussian integral evaluation: application to a new parameterization of GEM*
Dr. Andrés Cisneros (Chemistry), and others, recently published "Ewald-based methods for Gaussian integral evaluation: application to a new parameterization of GEM*" in the journal Journal of the Molecular Modeling.

Abstract: The development of accurate potentials for computational simulations has been an active area of research. Our group has been involved in the development of the Gaussian electrostatic model (GEM), a force field based on molecular densities. The philosophy of GEM is based on the pioneering work of N. Gresh and co-workers of the reproduction of individual inter-molecular interaction components obtained from quantum mechanical (QM) energy decomposition analysis (EDA). The molecular densities used in GEM are represented by fitting accurate QM molecular densities using auxiliary basis sets (comprised of Hermite Gaussians). The use of these molecular densities results in the need to evaluate a large number of Gaussian integrals. We have previously shown that the particle-mesh Ewald (PME), and fast Fourier Poisson (FFP) methods can be used for efficiently evaluating these types of integrals. Here, we present the latest parameterization of GEM* and its application for an extensive study of PME and FFP for molecular dynamics (MD) simulations using a hybrid version of our potential, GEM*. The temperature dependence of various bulk properties is presented and discussed, as well as the effect of various parameters affecting the performance/accuracy of both methods.

You can view the article here.

CASCaM professor receives W.E.S. Turner Award of International Commission on Glass
Dr. Jincheng Du, Material Science and Engineering, has received the Prof. W.E.S. Turner Award of International Commission on Glass. According to the International Commission on Glass (ICG) website, the award “rewards those who have made a noteworthy contribution to the ICG Technical Committees.” Dr. Du was presented with the award during the ceremony of the 25th International Congress on Glass, Boston, MA, in June 2019.

Chemistry student receives TAMS Scholarship
Christopher Zhou, a TAMS student working with Dr. Thomas Cundari, was the recipient of the 2019 Steve and Kathy Weiner Research Scholarship, presented by the TAMS program at their Fall Convocation, August 28, 2019. The scholarship recognizes students who have conducted research in the area of engineering or computer science.

Chemistry student receives Travel Award from American Chemical Society
Azadeh Nazemi, a graduate student working with Dr. Thomas Cundari, received a Travel Award from the Division of Inorganic chemistry of the American Chemical Society (ACS) to help cover the cost of attending the Spring 2019 ACS National Meeting in March/April 2019.

New Publication: Ground State Destabilization in Uracil DNA Glycosylase (UDG): Let's Not Forget "Tautomeric Strain" in Substrates
Dr. Andrés Cisneros (Chemistry), and others, recently published "Ground State Destabilization in Uracil DNA Glycosylase (UDG): Let's Not Forget "Tautomeric Strain" in Substrates" in the journal Journal of the American Chemical Society.

Abstract: Enzymes like uracil DNA glycosylase (UDG) can achieve ground state destabilization, by polarizing substrates to mimic rare tautomers. Based on computed nucleus independent chemical shifts, NICS(1)zz, and harmonic oscillator model of electron delocalization (HOMED) analyses, of QM and QM/MM models of the UDG active site, uracil is strongly polarized when bound to UDG, and resembles a tautomer > 12 kcal/mol higher in energy. Natural resonance theory (NRT) analyses identified a dominant O2 imidate resonance form for residue bound 1-methyl-uracil. This "tautomeric strain" raises the energy of uracil, making uracilate a better than expected leaving group. Computed gas-phase SN2 reactions of free and hydrogen bonded 1-methyl-uracil demonstrate the relationship between degree of polarization in uracil and leaving group ability of uracilate.

You can view the article here.

CASCaM professors receives NSF and NIH grants to further research
Dr. Andrés Cisneros, Chemistry, has received a 3-year NSF grant in collaboration with Prof. P. Ren from UT-Austin to develop accurate computational methodologies to study enzymatic reactions in ionic liquid solutions to investigate the effect of solvent on enzyme catalysis. Dr. Cisneros also received a 4-year renewal of a single PI NIH R01 grant to continue the development of advanced methods for QM/MM simulations and their application to characterize the effect of cancer biomarkers on DNA modification enzymes.

Recent CASCaM graduate receives 2019 Toulouse Dissertation Award
Riffat Parveen, a Spring 2019 Chemistry graduate that worked with Dr. Cundari, has received the 2019 Toulouse Dissertation Award. 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.

You can view the UNT College of Science announcement here.

Former Graduate Student joins Northeastern State University
Dr. Hector Gonzalez, Fall 2012 Chemistry graduate that worked with Dr. Cundari, has joined the Northeastern State University in Tahlequah, OK, as the Executive Director of Prehealth Professions Programing and Advising. Dr. Gonzalez will be the lead academic advisor and primary contact for students interested in prehealth professions.

New Publication: Dynamics of the E. coli beta clamp dimer interface and its influence on DNA loading
Dr. Andrés Cisneros (Chemistry), and others, recently had an article, "Dynamics of the E. coli beta clamp dimer interface and its influence on DNA loading", accepted for publication to Biophysical Journal.

The journal can be found here.

In Remembrance of Dr. Clemens C.J. Roothaan
Clemens Charles John Roothaan was born on 29 August, 1918 and passed away on 17 June, 2019 just short of his 101st birthday. He was a pioneer in the development and application of rigorous theory to the electronic structure of atoms and molecules. His theoretical approaches have also been extended to condensed phase systems. As well as establishing the theoretical foundations, he contributed a great deal to the development of numerical methods that made it possible to compute wavefunctions using digital computers. He guided the first calculations on atoms and molecules on digital computers using programs that he and his students and post-docs wrote.

In a very real sense, CASCaM continues to build on the foundations that Clemens Roothaan laid down in the early years of Theoretical Chemistry at the the University of Chicago's Laboratory of Molecular Structure and Spectra. Indeed, on the staff are two people who have directly collaborated with Clemens. We are all grateful to the contributions that Clemens made and we shall strongly miss him. He was a true giant in our discipline.

Please read more about Dr. Roothaan here.

Please read the article "Prof. Emeritus Clemens C.J. Roothaan turns 100 on August 29th", written by Dr. David Bevington, currently posted on the University of Chicago website.

New Publication: Towards Large Scale Hybrid QM/MM Dynamics of Complex Systems with Advanced Point Dipole Polarizable Embeddings
Dr. Andrés Cisneros (Chemistry), and others, recently published "Towards Large Scale Hybrid QM/MM Dynamics of Complex Systems with Advanced Point Dipole Polarizable Embeddings" in the journal Chemical Science.

Abstract: In this work, we present a general route to hybrid quantum mechanics/molecular mechanics dynamics for complex systems using a polarizable embedding. We extend the capabilities of our hybrid framework, combining the Gaussian and Tinker/Tinker-HP packages in the context of the polarizable force field AMOEBA to treat large (bio)systems where the QM and the MM subsystems are covalently bound, adopting pseudopotentials at the boundaries between the two regions.We discuss in details the implementation and demonstrate the global energy conservation using density functional theory. Finally, the approach is assessed on the electronic absorption properties of an organic dye embedded in a DNA matrix in solution, extending the hybrid method to a time-dependent density functional theory approach. The results obtained comparing different partitions between the quantum and the classical subsystems also suggest that large QM portions are not necessary if accurate polarizable force fields are used in a variational formulation of the embedding, properly including the QM/MM mutual polarization.

You can view the article here.

New Publication: Probing Actinide Covalency: Plutonium Electronic Structure Studies Using High Energy Resolution X-Ray Spectroscopy
Dr. Paul Bagus (Chemistry), and others, recently published "Probing Actinide Covalency: Plutonium Electronic Structure Studies Using High Energy Resolution X-Ray Spectroscopy" in the Los Alamos National Laboratory Actinide Research Quarterly (Second Quarter of 2018 Edition).

Snippet: The nature of chemical bonds in compounds with actinide (An) elements and the role of covalency is a topic of extensive research. Understanding these bonds ultimately allows us to design actinide material properties or predict their behavior in the environment. Covalency is a very important component of bonding that affects the chemical properties of a compound, and can be broadly defined for actinide complexes as the amount of mixing between metal-ligand orbitals in a bonding inter¬action. Advanced spectroscopic methods can provide new insights into the nature of these chemical bonds and can help the development and optimization of theoretical approaches for predicting chemical and physical properties.

You can view the article here.

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