Demian Riccardi (Fed)

Research Interests

My research interests are in two distinct (yet miscible) categories:

1. Thermodynamics experimental data informatics. The NIST Thermodynamics Research Center (TRC) provides critically evaluated thermophysical and thermochemical property data complete with provenance and uncertainty. We develop software tools to transform information from primary sources into digital resources that drive model development and process engineering. Here are a few recent projects existing on both sides of the information flow:

   • Combuston Calorimetry Tool (CCTool) 

   • Calculation Support Page for IUPAC Project #2011-037-2-100

   • ThermoML Archive
   CCTool and the Calculation support page for IUPAC Project #2011-037-2-100 are tools that may be used to improve the quality of experimental data. CCTool is a standard reference data (SRD) web application that facilitates accurate standard-state corrections to enthalpies of formation for combustion calorimetry experiments.  The focus of the ongoing IUPAC Project #2011-037-2-100 is to develop carefully vetted phase-equilibrium reference systems (LLE, SLE, VLE) for use in calibration and method validation. The ThermoML Archive contains a large collection of thermophysical and thermochemical properties that comprises a subset of Thermodynamics Research Center (TRC) data holdings. The collection was engineered using FAIR Principles (Findable, Accessible, Interoperable, and Reusable) and contains 2.69 million data points complete with metadata including compound, purification, experimental method, and publication information. The archive can be explored using an interactive web application or downloaded in a single click from data.nist.gov (doi:10.18434/mds2-2422).
2. Multiscale modeling of complex molecular processes. The molecular details of condensed-phase processes are complex and often require the application of theory and computation to provide complementary interpretations.  My research has applied multiscale computational methods ranging from quantum chemical calculations of ion solvation to molecular simulation and elastic network models (ENM) of crystalline biomolecules and their associated diffuse X-ray scattering.  My graduate work focused on the validation and application of hybrid QM/MM (quantum mechanics/molecular mechanics) potentials to pKa and proton transfer processes in enzymes. Recently (in collaboration with other division 647 researchers) we have been applying molecular dynamics and quantum-chemistry to predict NMR chemical shifts of aqueous ions. In another recent project (carried out in collaboration with CU-Boulder researchers), long conventional molecular dynamics simulations were used to explore the role of activation-loop conformational states in allosteric regulation of the mitogen-activated protein extracellular signal-regulated protein kinase 2, ERK2 (preprint available here).

NIST supports research opportunities for US Citizens at different stages of their career

If you are an undergraduate student interested in applying molecular dynamics simulations to condensed-phase systems, you may apply to the Summer Undergraduate Research Fellowship (SURF) (application typically due February 1).

If you are a postdoctoral candidate, we have openings available through the NRC Research Associateship Program. The application process involves developing a research proposal within the scope of listed opportunities; deadlines are February 1 and August 1. Please email me if you are interested in developing a proposal; here are my NRC-RAP opportunities:

• Computational Investigations of Molecular Interface Formation from the Perspective of Cosolvent Preferential Interactions
• Computational investigations of proton transfer between ionizable moieties in heterogeneous molecular environments
• Molecular Dynamics Studies of Electrostatic Driving Forces in the Erk2 Enzyme

Selected Publications

D. Riccardi, Z. Trautt, A. Bazyleva, E. Paulechka, V. Diky, J.W. Magee, A.F. Kazakov, S.A. Townsend, C. D. Muzny, Towards improved FAIRness of the ThermoML Archive. Journal of Computational Chemistry 2022, 43 (12), 879-887 (doi:10.1002/jcc.26842)

A. Fang, K. Kroenlein, D. Riccardi, and A. Smolyanitsky, Highly mechanosensitive ion channels from graphene-embedded crown ethers. Nature Materials 2019, 18 (1), 76-81 (doi:10.1038/s41563-018-0220-4)

D. Riccardi, H.B. Guo, J.M. Parks, B. Gu, A.O. Summers, S.M. Miller, L. Liang, J.C. Smith, Why mercury prefers soft ligands, Journal of Physical Chemistry Letters 2013, 4 (14), 2317-2322 (doi:10.1021/jz401075b )

D. Riccardi, Q. Cui, G.N. Phillips Jr Evaluating elastic network models of crystalline biological molecules with temperature factors, correlated motions, and diffuse X-ray scattering, Biophysical Journal 2010, 99 (8), 2616-2625 (doi:10.1016/j.bpj.2010.08.013)

D. Riccardi, P. König, X. Prat-Resina, H. Yu, M. Elstner, T. Frauenheim, Q. Cui, “Proton holes” in long-range proton transfer reactions in solution and enzymes: A theoretical analysis, Journal of the American Chemical Society 2006, 128 (50), 16302-16311 (doi:10.1021/ja065451j)

Google Scholar Page

Brief

I have lived in CT, NY, WI, TN, IN, and CO:  (CT) grew up in West Haven; (NY) majored in biochemistry and found a passion for computational chemistry in the lab of Maria Gomez at Vassar College and then spent a year as a cooperative student at IBM in East Fishkill; (WI) executed thesis work on enzyme pK_a and long-range proton transfer in the lab of Qiang Cui at the UW-Madison, Theoretical Chemistry Institute and then researched protein crystal dynamics in the lab of George N Phillips, Jr as a National Library of Medicine Computation and Informatics in Biology and Medicine Trainee; (TN) researched speciation of the mercuric ion as a postdoctoral fellow in the UT/ORNL Center for Molecular Biophysics; (IN) taught chemistry at Earlham College in Richmond for two years at a rate of twelve contact hours per semester; (CO) joined NIST/MML/ACMD/TRC as a research chemist in 2016.