Team – ICMS HPC

Our mission

Taking Innovation Into the Real World

Our mission is to use the knowledge and tools of molecular evolution to advance research and product development in biomedical biodiversity. We accomplish this mission by making fundamental discoveries, developing informatics resources and training the next generation of young scientists.

Please, join us!

Michael L. Klein, Carnell Professor

Meet Our Team

Michael L. Klein

Laura H. Carnell Professor of Science / ICMS Director / TMI Director / Former CST Dean

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Michael L. Klein

COLLEGE OF SCIENCE AND TECHNOLOGY

Laura H. Carnell Professor of Science / ICMS Director / TMI Director / Former CST Dean

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Biography

My research interests focus on the use of theoretical & computational methods to study the properties of molecular solids and liquids and the self-assembly of both natural and synthetic macromolecules. In collaboration with brilliant students and postdocs, I have developed computational methodologies and carried out computer simulations to understand the phase behavior and properties of systems ranging from small molecules, such as water, to larger molecules such as surfactants and lipid bilayers, as well as natural and synthetic macromolecules. Other applications have been aimed at understanding the sensing and gating mechanisms Nature’s nano-scale machines, such as membrane-bound ion channels, as well as designing molecular therapeutics to combat both viral and bacterial infections.

Axel Kohlmeyer

Associate Dean

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Axel Kohlmeyer

COLLEGE OF SCIENCE AND TECHNOLOGY

Associate Dean

Biography

Axel Kohlmeyer is Associate Director of the Institute for Computational Molecular Science, and the Leader of the High-Performance Computing (HPC) Team at Temple University in Philadelphia, USA.

He is also an External Associate of the International Centre for Theoretical Physics in Trieste, Italy, where he collaborates with ICTP HPC staff on HPC-related activities and teaches in the International HPC Master program hosted by ICTP and SISSA in Trieste.

His main research interests are in software development and engineering for scientific software in general and for simulation and analysis of molecular dynamics simulation on highly parallel modern computer architectures in particular. He also is interested in improving HPC education for scientists and engineers. He is a core developer and co-maintainer of the LAMMPS Molecular Dynamics softwarepackage and has contributed to several other popular scientific software packages like VMD, Quantum-Espresso, HOOMD-blue,CPMD or CP2k.

Past positions of his academic career include the International Centre for Theoretical Physics in Trieste, Italy, the Center for Molecular Modeling at the University of Pennsylvania in Philadelphia, USA, the Center for Theoretical Chemistry at the Ruhr-University Bochum, Germany, and the Department for Theoretical Chemistry at the University of Ulm, Germany.

He obtained his PhD (= Dr.rer.nat.) and Dipl.-Chem. degrees in Theoretical Chemisty at the University of Ulm under the supervision of Professor Wolfgang Witchel and Dr. Eckhard Spohr.

X-ray diffraction and computation yield the structure of alkanethiols on gold(111), A. Cossaro, R.Mazzarello, R. Rousseau, L. Casalis, A. Verdini, A. Kohlmeyer, L. Floreano, S. Scandolo, A. Morgante, M.L. Klein, G. Scoles, Science 321, 943-946 (2008). (Link)

LAMMPS – a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales, Aidan P. Thompson, H. Metin Aktulg, Richard Berger, Dan S.Bolintineanu, W. Michael Brown, Paul S. Crozier, Pieter J .in ‘t Veld, Axel Kohlmeyer, Stan G. Moore, Trung Dac Nguyen, RayShan, Mark J. Stevens, Julien Tranchida, Christian Trott, Steven J. Plimpton, Computer Physics Communications 271 (2022). Link

Fast Analysis of Molecular Dynamics Trajectories with Graphics Processing Units: Radial Distribution Function Histogramming, B.G. Levine, J.E. Stone, A. Kohlmeyer, J. Comput. Phys. 230(9), 3556-3569 (2011) (Link)
TopoGromacs: Automated Topology Conversion from CHARMM to GROMACS within VMD,Josh V. Vermaas, David J. Hardy, John E. Stone, Emad Tajkhorshid, and Axel Kohlmeyer, AC Publications (2016). Link

Michele Young

Executive Assistant

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Simona Percec

Research Professor

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Simona Percec

COLLEGE OF SCIENCE AND TECHNOLOGY

Research Professor

Biography

Dr. Simona Percec is a Research Professor in the Department of Chemistry in the College of Science and Technology and an Associate Editor of the ACS journal, Biomacromolecules. Simona has a broad technical background through working at Standard Oil/BP/Amoco CR&D (1982-1999) where she led various research programs in the fields of polymer and catalysis. As a Research Fellow at DuPont CRD (1999-2016) Simona was involved in a wide range of research areas and led programs in organic, polymer and biopolymer design and synthesis with particular emphasis on applications including molecular electronics, biosensors, electrochromics, anticorrosive coatings, polymer-glass hybrids, thermoplastic carbon fiber composites, renewably-resourced polymers and self-assembled systems. Simona has authored 58 original publications, 39 patents issued and 5 patent applications. She has been an invited speaker and chairperson at National and International meetings. She served in numerous committees including the DuPont Young Professor Grant Nomination Committee, Biomacromolecules/Macromolecules Young Investigator ACS Award, and as the Chair of the DuPont Discovery Chemistry Series Seminars and the Carothers Award Committee.

Vincenzo Carnevale

Associate Professor

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Vincenzo Carnevale

COLLEGE OF SCIENCE AND TECHNOLOGY

Associate Professor

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PhD: 2007, SISSA – Scuola Internazionale Superiore di Studi Avanzati, Trieste, Italy

Affiliation: Department of Biology, Temple University

Phone: 215-204-4214

Email: [email protected]

Office: SERC 710

Bio and Research description:

Vincenzo Carnevale received B.Sc. and M.Sc. degrees in Physics from the University of Pisa and a PhD from SISSA – Scuola Internazionale Superiore di Studi Avanzati in Trieste, Italy. He currently holds the position of Associate Professor in the Department of Biology.

The Carnevale research group uses statistical physics and machine learning approaches to investigate sequence-structure-function relations in proteins. A central theme of the group’s research is how interactions give rise to collective phenomena and complex emergent behaviors. At the level of genes, the group is interested in epistasis – the complex entanglement phenomenon that causes amino acids to evolve in a concerted fashion – and how this shapes molecular evolution. At the cellular level, the group investigates how intermolecular interactions drive biomolecules toward self-organization and pattern formation. A long-term goal of the group is understanding the molecular underpinnings of electrical signaling in excitable cells. Toward these goals, the group applies and actively develops an extensive arsenal of theoretical and computational approaches including statistical (mean)field theories, Monte Carlo and molecular dynamics simulations, statistical inference of generative models, and deep learning.

Jeff Tolliver

Director of Finance & Research

Steve Plimpton

Adjunct Research Professor

Mark DelloStritto

Research Assistant Professor

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Mark DelloStritto

COLLEGE OF SCIENCE AND TECHNOLOGY

Researcher

Biography

Mark DelloStritto received a Ph.D. in Physics from the Pennsylvania State University in 2017 and joined Professor Klein’s research group as a postdoctoral fellow. Mark’s research is focused on studying the relationship between structure, dynamics, and chemistry in fluids and polymers. Recent topics include the adsorption of water and ions at oxide interfaces, the dependence of the structural and electronic properties of ion solvation on the choice of density functional, vibrational spectroscopy of water and polymer systems, improving the properties of polymer systems by modifying polymer chemistry, and the application of neural network potentials to extend ab-initio calculations.

Manal A Nael

Researcher Assistant Professor

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Manal A Nael

COLLEGE OF SCIENCE AND TECHNOLOGY

Researcher Assistant Professor

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Biography

Dr. Nael has expertise in medicinal chemistry, molecular modeling, and computational drug design, and she is adept at using several techniques of medicinal chemistry, computational chemistry, bioinformatics, and theoretical biophysics. Dr. Nael uses computational methods to explore the properties of polymer materials as well as doing experiments on different ways of processing these materials to enhance performance.

Khaled M. Elokely

Associate Professor of Research

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Khaled M. Elokely

COLLEGE OF SCIENCE AND TECHNOLOGY

Researcher

Biography

Dr. Elokely is an Associate Professor of Chemistry (Research) and director of the Forensic Chemistry PSM program. His research interests include drug design and development to understand the molecular determinants of drug recognition using computational and medicinal chemistry tools. Dr. Elokely has experiences in medicinal and analytical chemistry with advanced training in the areas of computer aided drug design (CADD) and quality assurance of active pharmaceutical ingredients. He includes in his research the use of rational drug design, structure-based approaches, ligand-based techniques, bioisosteric replacement strategies, and manipulation of medicinal chemistry approaches in the design of biologically active agents. Currently, he is working on targeting the Kv1.3 voltage-gated potassium channel to design safe and novel immunomodulators by applying medicinal chemistry and conventional computational approaches, and on the development of new inhibitors for the main protease of SARS-CoV-2.

George Petersson

Distinguished Adjunct Professor of Chemistry

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George Petersson

COLLEGE OF SCIENCE AND TECHNOLOGY

Distinguished Adjunct Professor of Chemistry

Biography

Selected Awards

Ph.D. California Institute of Technology

B.Sc. The City College of New York

Kitasato Medal, John S. Burlew Award from the Connecticut Valley Section of the American Chemical Society

Interests

Electron correlation in atoms and molecules, particularly as applied to transition states for chemical reactions. Development of efficient computational models for thermochemistry, kinetics, and reactive dynamics. The nature of bond energies. Computational spectroscopy in collaborations with Experimental Chemists.

Select Publications

“Improved Geometries and Frequencies with the PFD-3B DFT Method” Jason M. Breslin, Michael J. Frisch, and George A. Petersson, J. Phys. Chem.,A, 126, 5814-5820 (2022) LINK

“A Bond-Energy/Bond-Order and Populations Relationship” Zulueta, Barbaro; Tulyani, Sonia; Westmoreland, Phillip; Frisch, Michael; Petersson, E. James; Petersson, George; Keith, John Journal of Chemical Theory and Computation 18, 4774-4794(2022). LINK

“Synthesis and characterization of fluorescent amino acid dimethylaminoacridonylalanine (PJ-11498VP)” Chloe M. Jones, George A. Petersson, and E. James Petersson, Arkivoc 2021,97 (2021). LINK

“Three Body Dispersion Corrections to the Spherical Atom Model: the PFD-3B Density Functional” George A. Petersson, Michael J. Frisch, Frank Dobek, and Barbaro Zulueta, J. Phys. Chem. 124, 10296 (2020). LINK

Lamont Speller

Graphic Designer

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Ahmed M. Abdelwaly

Postdoctoral Research Associate

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Ahmed M. Abdelwaly

COLLEGE OF SCIENCE AND TECHNOLOGY

Postdoctoral Research Associate

Biography

Ahmed Abdelwaly obtained a bachelor’s degree in Pharmacy from Sana’a University – Yemen in 2004, with a cumulative grade of very good. He joined the academic sector in 2008 and worked as a teaching assistant at Thamar University in Yemen for four years , then he moved to Egypt to finish his postgraduate studies. He obtained a master’s degree in Medicinal Chemistry from Suez Canal University in 2016, then a Ph.D. in the same field from Cairo University in 2021. His research was conducted during the past ten years in drug design and discovery laboratories, and he focused on the design and organic synthesis of small molecules to target medical conditions such as chronic obstructive pulmonary disease, bronchial asthma, addiction, Alzheimer’s disease, and inflammatory diseases.

After obtaining his master’s degree, he worked as an assistant lecturer at the Department of Pharmaceutical Chemistry at Suez Canal University for two years. In 2017, he joined the Biomedical Sciences Program at Zewail City of Science and Technology as an assistant lecturer and Researcher, then was promoted in 2022 to become an Assistant Professor and postdoctoral research associate at the same university.

Ahmed is currently a postdoctoral research associate in the Institute for Computational Molecular Sciences (ICMS) at Temple University.

Pradeep Bhetwal

Post Doctoral Fellow

Ahmed H. Ibrahim

Post Doctoral Fellow

Andrés Felipe Ortíz Almazo

Research Assistant Professor

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Venkata Surya Kumar Choutipalli

Postdoctoral Research Fellow

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