Tuning Colloidal Reactions.

The precise control of complex reactions is critical for biological processes, yet our inability to design for specific outcomes limits the development of synthetic analogs. Here, we leverage differentiable simulators to design nontrivial reaction pathways in colloidal assemblies. By optimizing over external structures, we achieve controlled disassembly and particle release from colloidal shells.

Programming patchy particles for materials assembly design.

Direct design of complex functional materials would revolutionize technologies ranging from printable organs to novel clean energy devices. However, even incremental steps toward designing functional materials have proven challenging. If the material is constructed from highly complex components, the design space of materials properties rapidly becomes too computationally expensive to search.

Uncovering the mechanism for aggregation in repeat expanded RNA reveals a reentrant transition.

RNA molecules aggregate under certain conditions. The resulting condensates are implicated in human neurological disorders, and can potentially be designed towards specified bulk properties in vitro. However, the mechanism for aggregation-including how aggregation properties change with sequence and environmental conditions-remains poorly understood.

Correlation Tracking: Using simulations to interpolate highly correlated particle tracks.

Despite significant advances in particle imaging technologies over the past two decades, few advances have been made in particle tracking, i.e., linking individual particle positions across time series data.

Designing self-assembling kinetics with differentiable statistical physics models.

The inverse problem of designing component interactions to target emergent structure is fundamental to numerous applications in biotechnology, materials science, and statistical physics. Equally important is the inverse problem of designing emergent kinetics, but this has received considerably less attention. Using recent advances in automatic differentiation, we show how kinetic pathways can be precisely designed by directly differentiating through statistical physics models, namely free energy calculations and molecular dynamics simulations.

Impact of Rigidity on Molecular Self-Assembly.

Rigid, cage-like molecules, like diamondoids, show unique self-assembly behavior, such as templating 1-D nanomaterial assembly via pathways that are typically blocked for such bulky substituents. We investigate molecular forces between diamondoids to explore why molecules with high structural rigidity exhibit these novel assembly pathways. The rigid nature of diamondoids significantly lowers configurational entropy, and we hypothesize that this influences molecular interaction forces.