What do we do?

Data Science Integrated with Chemistry, Modeling and Simulation – Applied to Study Solutions and Their Interfaces

What do we value?

“We pursue scientific truth.” (Dan Pope, PhD student)

The Clark lab recognizes that pursuit of truth goes hand in hand with the just and honorable treatment of all people. We are lifelong learners that do not do not become complacent in our knowledge. Recognizing our individual strengths and weaknesses, we seek to teach our colleagues our strengths and learn from others to grow from our weaknesses. We are honest and forthright, challenging each other to grow as scientists and human beings. Our group is diverse, accepting, and respectful of each other and our personal and cultural backgrounds. We all succeed when we support each other as a team and as individuals.

A Window Into Our Projects

1) Graphs, Topology and Geometry – The Integration of Applied Mathematics and Chemistry

Simulation data contains much more information than we often consider. Why not use the patterns and shapes of data from simulation to explore and generate new knowledge that we might miss using chemical intuition alone? Our group develops graph theory techniques based upon networks of chemical interactions to identify complex correlations of behavior across time and length scales. We apply techniques of topological data analysis and geometry to identify hierarchically organized structures in complex chemical systems and to probe the energy landscapes that underpin chemical transformations.

Example publications:

A Geometric Measure Theory Approach to Identify Complex Structural Features on Soft Matter Surfaces, Journal of Chemical Theory and Computation, 2020, ASAP article. DOI: 10.1021/acs.jctc.0c00260.

PageRank as a Collective Variable to Study Complex Chemical Transformations and Their Energy Landscapes, The Journal of Chemical Physics, 2019, 150, 134102. DOI: 10.1063/1.5082648  

2) Complex Multicomponent Solutions

Solutions that contain more than 1 solute type are pervasive, underpinning chemical synthesis (catalysis), purification, and the cleanup of contaminated sites that affect human health. There are many transcending characteristics of complex solutions, for example their properties cannot be described without many body effects. They also exhibit close coupling of different length and timescale behavior. In multicomponent systems the degrees of freedom are increased dramatically: local organization of solutes into a supramolecular assembly can then create a percolated network of aggregated assemblies that in turn supports a phase transition. Or, in a concentrated electrolyte, the local motions of water are coupled to longer length scale dynamics of evolving ion solvation networks. The collective organization of the solution across different length scales and the dynamic motion across time-scales, challenges study of the features of the underlying free energy landscape (minima and barriers) that directs reaction outcomes, kinetics of motion and reactions, and phase behavior. To truly understand multicomponent complex solutions our group takes a holistic view to understand and create both a local and global description from state-of-the-art simulations.

Example publications:

Servis, M. J.; Martinez-Baez, E.; Clark, A. E. Hierarchical Phenomena in Multicomponent Liquids: Methods, Analysis, Chemistry. Physical Chemistry Chemical Physics 2020, 22, 9850-9874.  DOI: 10.1039/D0CP00164C.

Martinez-Baez, E.; Pearce, C.; Schenter, G.; Clark, A. E. ²⁷Al NMR chemical shift of Al(OH)₄^– calculated from first principles: Assessment of error cancellation in chemically distinct reference and target systems. Journal of Chemical Physics. 2020. 152, 134303. DOI: 10.1063/1.5144294

3) Complex Liquid Interfaces

Liquid/liquid interfaces support a number of important chemical processes, from enhanced reactivity, to transport phenomena associated with chemical purification. Although they are  highly heterogeneous, we use modeling and simulations to create a molecular-scale understanding of the balance of forces that tune their reactivity. We elucidate mechanisms of reactions, changes to speciation, and the formation of hierarchically organized structures that cause unique microenvironment for transport. These efforts are currently focused upon optimizing transport in solvent extraction for chemical purification and environmental cleanup.

Example Publications:

Liu, Z.; Clark, A. E. An Octanol Hinge Opens the Door to Water Transport, Chemical Science, 2021, Advance Article, DOI: 10.1039/D0SC04782A

Kumar, N. ; Servis, M. J.; Liu, Z.; Clark, A. E. Competitive Interactions at Electrolyte/Octanol Interfaces – A Molecular Perspective. Journal of Physical Chemistry C. 2020, 124, 10924–10934 DOI: 10.1021/acs.jpcc.0c00302