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Alex Pacheco

I am a High Performance Computing (HPC) administrator currently working as an Associate CIO - Advanced Research Computing at New Jersey Institute of Technology.

From September 2014 to July 2022, I was the Manager of Research Computing at Lehigh University and from August 2010 to September 2014, I was a HPC User Services Consultant with HPC@LSU and LONI, helping users with

  • Building codes on HPC clusters.
  • Install and use of software packages on HPC clusters.
  • Gaussian, GAMESS, NWChem, CPMD, AMBER, GROMACS, LAMMPS, NAMD, AutoDock
  • Troubleshoot problems running jobs on HPC clusters.
  • Provide Training to new and advanced users.
  • Computational Chemistry/Biology, Fortran, Parallel Programming
  • Maintain Grid Services.

I'm a computational chemist by training with interest in Ab-Initio Molcular Dynamics, Spectroscopy, and Scientific Computing. I routinely program in Fortran, R, bash and tcsh, OpenMP and have taught programming in C, python, OpenACC and MPI.

Education

  • B.Sc. St. Xavier's College, Mumbai, 1997
  • M.Sc. University of Pune, Pune, 1999
  • Ph.D. University of Florida, Gainesville, 2006

Employment

  • Associate CIO - Advanced Research Computing, New Jersey Institute of Technology (08/2022-Present)
  • Manager of Research Computing, Lehigh University (09/2014-07/2022)
  • HPC User Services Consultant, Louisiana State University (08/2010-09/2014)
  • Postdoctoral Fellow, Indiana University (10/2006-08/2010)
  • Graduate Research & Teaching Assistant, University of Florida (08/1999-09/2006)

Publications

  • J. Li, A. B. Pacheco, K. Raghavacharia and S. S. Iyengar, "A Grotthuss-like proton shuttle in the anomalous C2H3+ carbocation: energetic and vibrational properties for isotopologues", Phys. Chem. Chem. Phys., 18, 29395 (2016).
  • A. B. Pacheco, S. M. Dietrick, P. S. Stevens and S. S. Iyengar, "Pump-probe atom-centered density matrix propagation studies to gauge anharmonicity and energy repartitioning in atmospheric reactive adducts: Case study of OH + Isoporene and OH + Butadiene reaction intermediates", J. Phys. Chem. A 116, 4108 (2012).
  • S. M. Dietrick, A. B. Pacheco, P. S. Stevens and S. S. Iyengar, "The influence of water on anharmonicity, stability and vibrational energy distribution of hydrogen-bonded adducts in atmospheric reactions: Case study of the OH + Isoprene reaction intermediate using ab-initio Molecular Dynamics", J. Phys. Chem. A 116, 399 (2012).
  • A. B. Pacheco and S. S. Iyengar, "Multi-Stage Ab-initio Quantum Wavepacket Dynamics for Electronic Structure and Dynamics in open systems: Momentum Representation, Coupled Electron Nuclear dynamics and External Fields", J. Chem. Phys. 134, 074107 (2011). g * A. B. Pacheco and S. S. Iyengar, "A Multi-Stage Ab-initio Quantum Wavepacket Dynamics Formalism for Electronic Structure and Dynamics in Open Systems", J. Chem. Phys. 133, 044105 (2010).
  • D. Vimal, A. B. Pacheco, S. S. Iyengar and P. S. Stevens, "Experimental and theoretical study of the kinetics of the OH + 1,3-butadiene reaction between 263 and 423 K at low pressure", J. Phys. Chem. A 112, 7227 (2008).
  • A. B. Pacheco, B. Thorndyke, A. Reyes, and D. A. Micha, "Quantum dynamics of an excited alkali atom in a noble gas cluster: Lithium attached to a helium cluster", J. Chem. Phys. 127, 244504 (2007)
  • A. B. Pacheco, A. Reyes, and D. A. Micha, "First principles dynamics treatment of light emission in alkali atom-noble gas atom collisions around 10 keV", Phys. Rev. A 74, 062714 (2006)
  • A. B. Pacheco, A. Reyes, and D. A. Micha, "Light absorption during alkali atom-noble gas atom interactions at thermal energies: A quantum dynamics treatment", J. Chem. Phys. 125, 154313 (2006)
  • First Principles Dynamics of Transient Light Absorption and Emission of Alkali Atoms Interacting with Rare Gas Atoms, Ph. D. Thesis, University of Florida (2006).

Conference Presentations

Posters

  • A. B. Pacheco and S. S. Iyengar, A Multi-Stage Ab-initio Quantum Wavepacket Dynamics Formalism for Electronic Structure and Dynamics in Open Systems. 42nd MidWest Theoretical Chemistry Conference, West Lafayette, IN (2010).
  • A. B. Pacheco and S. S. Iyengar, Quantum Wavepacket Ab-initio Molecular Dynamics Formalism for Calculating Electron Transport in Molecular Wires. American Conference on Theoretical Chemistry Conference, Evanston, IL. (2008).
  • S. M. Dietric, A. B. Pacheco and S. S. Iyengar, Study of the reactivity of OH radical adducts with isoprene in gas phase and adsorbed on an aerosol using Ab-Initio Molecular Dynamics. American Conference on Theoretical Chemistry Conference, Evanston, IL. (2008).
  • A. B. Pacheco and S. S. Iyengar, Quantum Wavepacket Ab-initio Molecular Dynamics Formalism for Calculating Electron Transport in Molecular Wires. 40th MidWest Theoretical Chemistry Conference, Ann Arbor, MI. (2008).
  • S. M. Dietric, A. B. Pacheco and S. S. Iyengar, Study of the reactivity of OH radical adducts with isoprene in gas phase and adsorbed on an aerosol using Ab-Initio Molecular Dynamics. 40th MidWest Theoretical Chemistry Conference, Ann Arbor, MI. (2008).
  • A. B. Pacheco and S. S. Iyengar, Quantum Wavepacket Ab-initio Molecular Dynamics Formalism for Calculating Electron Transport in Molecular Wires. 39th MidWest Theoretical Chemistry Conference, Bloomington, IN. (2007).
  • A. B. Pacheco and D. A. Micha, Light Emission during Interactions of an Excited Alkali Atom inside or at the surface of a Noble Gas Atom Cluster: A Density Matrix Treatment. 46th Sanibel Symposium, St. Simon's Island, GA. (2006).
  • A. B. Pacheco and D. A. Micha, Calculation of Light Absorption Intensities during Alkali Atom - Noble Gas Atom Interactions from a First Principles Dynamics. 45th Sanibel Symposium, St. Simon's Island, GA. (2005).
  • A. B. Pacheco and D. A. Micha, Dynamics of Light Emission during Alkali Atom - Rare Gas Atom Interactions: From Atom-Atom Collisions to Interactions in Clusters. 44th Sanibel Symposium, St. Augustine, FL. (2004).
  • A. Reyes, D. A. Micha and A. Pacheco, First Principles Quantum Dynamics of Electronic Excitation and Spin-Orbit Recoupling in Alkali-Noble Gas Atom Interactions. 43rd Sanibel Symposium, St. Augustine, FL. (2003).
  • A. B. Pacheco and D. A. Micha, Electronic State-to-State Collision Cross Sections using Transition Integrals. 42nd Sanibel Symposium, St. Augustine, FL. (2002).

Oral and Contributed Talks

  • A. B. Pacheco, A Multi-Stage Ab-initio Wavepacket Dynamics Formalism for Electronic Structure and Dynamics in Open Systems. Center for Computation and Technology, Louisiana State University, Baton Rouge, LA, June 10 (2010).
  • A. B. Pacheco and S. S. Iyengar, A Multi-Stage Ab-initio Wavepacket Dynamics Formalism for Electron Dynamics in Open Systems. 41st MidWest Theoretical Chemistry Conference. Carbondale, IL. (2009).
  • D. A. Micha, A. Leathers, A. Pacheco, A. Sudhyadhom and B. R. Thorndyke. Dissipative Femtosecond Dynamics of Electronically Excited Systems: A Density Matrix Approach. Amer. Chem. Soc. National Meeting, Atlanta, Ga. (2006).
  • D. A. Micha, A. Reyes, A. Pacheco and B. Thorndyke, Time-Propagation of the Quantum-Classical Density Matrix for Electronically Excited Molecular Systems. Amer. Chem. Soc. National Meeting, Anaheim, Ca. (2004).
  • A. Reyes, D. A. Micha and A. Pacheco, Electronic Excitation and Spin-Orbit Recoupling Cross Sections for Alkali-Atom/Noble Gas-Atom Collisions from a First Principles Quantum Dynamics. Amer. Phys. Soc. DAMOP Meeting, Boulder, Co. (2003).

Downloads

LaTeX Presentations

I use LaTeX for my documents, presentations and posters. For presentations I almost always use LaTeX Beamer and have tried Powerdot once. I created beamer themes rather than the use the standard themes that come with TeXLive for use at LSU and Lehigh University. The themes are based on the official color schemes but are not officially endorsed by either schools. Feel free to use and modify for personal use.

Molecular Dynamics Code

Quite often there is someone attending the HPC Training session who asks that unavoidable question "How do I use this in my research?". So I've written a Molecular Dynamics code for my training sessions on Fortran, OpenMP and OpenACC.

This code covers some but not all concepts of MD.