Computational Modeling
Molecular modeling and simulation can provide crucial insights into the structure, dynamics, and interactions of various systems at the molecular level, to both complement and enrich experimental measurements. Computational and Modeling Core of the UMass Institute for Applied Life Sciences (IALS) provides expert consultative and collaborative services to both academic and industrial partners. As a collaborative partner, we contribute directly to research and development, such as performing simulations, interpreting results, providing actionable decisions, and preparing materials for scientific manuscripts and grant applications. We also assist scientists who are unfamiliar with computational tools and high-performance computing to apply these techniques in their research projects. Our expertise includes ab-initio/classical molecular dynamics simulations, quantum chemistry/electronic structure calculations, computational spectroscopy, small molecule design, and protein-ligand docking and screening.
Modeling and Simulation of Biomolecules and Biomaterials
Modeling of Infrared Spectra of Biological Systems
Small Molecule Property Prediction and Virtual Screening
High-Performance Computing (HPC)
Pikes: An in-house GPU cluster with a total 704 Xeon cores, 176 Titan X Pascal and GTX 1080 GPU cards, and 396 TB storage.
UMass Green Cluster: A shared HPC cluster with 14,376 cores available (Intel and AMD), and 660 TB of high performance EMC Isilon X series storage, and 513 TB of Farline storage. See wiki: http://wiki.umassrc.org/
We seek long-term collaborators/users both in academia and industry for biological and chemical-related research projects. The initial project consultation/discussion will be free of charge. In the exploration phase (typically for three months), a project initiation fee of $3,000 will be charged once the modeling/simulation approaches prove the feasibility and provide insights into those research questions. For the following phases, a financial plan for service charge will be customized upon mutual agreement of both parties.
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Services |
Internal | Other Academic | External |
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| Technician | $65/hour | $90/hour |
$120/hour |
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FY22 Specialized Service Center Approved Fees |
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Computational Modeling Core Facility: The Core provides simulation and modeling services to both academic and industrial partners, including ab-initio/classical molecular dynamics simulations, quantum chemistry/electronic structure calculations, computational spectroscopy, small molecule design, and protein-ligand docking and screening. The Core equips an in-house GPU cluster (Pikes) with a total of 704 Xeon cores, 176 Titan X Pascal and GTX 1080 GPU cards, and 396 TB storage. The Core also has access two shared HPC clusters: (1) UMass Green Cluster with 14,376 cores available (Intel and AMD), and (2) XSEDE Comet GPU cluster with a total 228 NVIDIA GPU cards (144 K80 and 144 P100), and Intel Xeon CPUs with 1872 cores in total.
FY20-21 Specialized Service Center Approved Fees
Updated January 2021
Key Personnel
Sergey Savinov, Extension Associate Professor
Dr. Savinov obtained his PhD in Chemistry from Yale University. Currently, he is an Extension Associate Professor of Biochemistry and Molecular Biology in University of Massachusetts, Amherst. He also serves as a Co-Director of Small-Molecule Screening Facility at UMass Medical School, where he offers integrated cheminformatics and computational modeling services for the purpose of discovery and further elaboration of drug candidates. His research interests aim to discover and harness medicinal properties of plant-derived metabolites, with particular emphasis on resistance-resilient solutions for antibacterial, antifungal, and antiparasite control. Additional information about Dr. Savinov can be found at: https://www.umass.edu/biochem/faculty/sergey-savinov/.
Core Advisory Committee
Jianhan Chen, PhD
Dr. Chen received his PhD in University of California at Irvine. He is currently a Professor of Chemistry and Professor of Biochemistry and Molecular Biology in University of Massachusetts, Amherst. His research interests are mainly in the development of advanced computational methods and their applications to the study of biomolecules and biomaterials. One of the particular emphasis has been on understanding how intrinsically disorder of proteins mediate function and how such functional mechanisms may be altered in human diseases. Additional information on Dr. Chen and his research can be found at: http://people.chem.umass.edu/jchenlab/.
Li-Jun Ma, PhD
Dr. Ma received her PhD in Molecular Biology from the State University of New York. She is currently an Associate Professor in Department of Biochemistry and Molecular Biology in University of Massachusetts, Amherst. Her lab studies genetic mechanisms that sustain structural and functional flexibility while maintaining the integrity of the organism using the model fungal system Fusarium oxysporum. Specifically, Specifically, her research combines experimental and computational biology approaches to study the molecular interactions within the genome and between the “core genome” and the horizontally transferred chromosomes, to investigate the plant-fungal interactions using a Fusarium-Arabidopsis pathosystem for the development of optimized management strategies to control the Fusarium vascular wilt diseases; and to dissect virulence factors that contribute to emerging infectious disease using Fusarium-animal model systems for the development of novel therapeutics.
Craig T. Martin, PhD
Dr. Martin obtained his PhD in Chemistry from California Institution of Technology. He is currently a Professor in Department of Chemistry in University of Massachusetts, Amherst. The overall goal of his research is to understand the chemical and enzymological basis of complex and fundamental processes in biology. His research group combines the powerful quantitative tools of biophysical chemistry with equally powerful techniques found in modern molecular biology to provide detailed information on specific chemical interactions in enzymology.
Woody Sherman, PhD
Dr. Sherman received his PhD in Physics Chemistry Massachusetts Institute of Technology. He was Global Head of Application Science at Schrodinger, where he lead research efforts in broad areas, including induced-fit docking, water thermodynamics, free energy simulations, custom method development, and modeling services. He is currently a CSO of Silicon Therapeutics, leading physics-based simulation efforts and overall scientific strategy for the company. He is also the Founder and CEO of MolySym, Inc. Dr. Sherman has co-authored over 80 peer-reviewed publications with an emphasis on drug design and protein-ligand interactions.
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