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The hydration shells of proteins mediate interactions, such as small molecule binding, that are vital to their biological function or in some cases their dysfunction. However, even when the structure of a protein is known, the properties of its hydration environment cannot be easily predicted due to the complex interplay between protein surface heterogeneity and the collective structure of water’s hydrogen bonding network. This manuscript presents a theoretical study of the influence of surface charge heterogeneity on the polarization response of the liquid water interface. We focus our attention on classical point charge models of water, where the polarization response is limited to molecular reorientation. We introduce a new computational method for analyzing simulation data that is capable of quantifying water’s collective polarization response and determining the effective surface charge distribution of hydrated surfaces over atomistic length scales. To illustrate the utility of this method, we present the results of molecular dynamics simulations of liquid water in contact with a heterogeneous model surface and the CheY protein. 

DNA scaffolds enable the activation and suppression of photochemistry between strongly-coupled synthetic chromophores. 

Abstract The Tafel slope is a key parameter often quoted to characterize the efficacy of an electrochemical catalyst. In this paper, we develop a Bayesian data analysis approach to estimate the Tafel slope from experimentally-measured current-voltage data. Our approach obviates the human intervention required by current literature practice for Tafel estimation, and provides robust, distributional uncertainty estimates. Using synthetic data, we illustrate how data insufficiency can unknowingly influence current fitting approaches, and how our approach allays these concerns. We apply our approach to conduct a comprehensive re-analysis of data from the CO 2 reduction literature. This analysis reveals no systematic preference for Tafel slopes to cluster around certain "cardinal values” (e.g. 60 or 120 mV/decade). We hypothesize several plausible physical explanations for this observation, and discuss the implications of our finding for mechanistic analysis in electrochemical kinetic investigations. 

Abstract The influenza B M2 protein forms a water-filled tetrameric channel to conduct protons across the lipid membrane. To understand how channel water mediates proton transport, we have investigated the water orientation and dynamics using solid-state NMR spectroscopy and molecular dynamics (MD) simulations. 13 C-detected water 1 H NMR relaxation times indicate that water has faster rotational motion in the low-pH open channel than in the high-pH closed channel. Despite this faster dynamics, the open-channel water shows higher orientational order, as manifested by larger motionally-averaged 1 H chemical shift anisotropies. MD simulations indicate that this order is induced by the cationic proton-selective histidine at low pH. Furthermore, the water network has fewer hydrogen-bonding bottlenecks in the open state than in the closed state. Thus, faster dynamics and higher orientational order of water molecules in the open channel establish the water network structure that is necessary for proton hopping. 

This manuscript presents a strategy for controlling the transformation of excitonic states through the design of circuits made up of coupled organic dye molecules. Specifically, we show how unitary transformation matrices can be mapped to the Hamiltonians of physical systems of dye molecules with specified geometric and chemical properties. The evolution of these systems over specific time scales encodes the action of the unitary transformation. We identify bounds on the complexity of the transformations that can be represented by these circuits and on the optoelectronic properties of the dye molecules that comprise them. We formalize this strategy and apply it to determine the excitonic circuits of the four universal quantum logic gates: NOT, Hadamard, π/8 and CNOT. We discuss the properties of these circuits and how their performance is expected to be influenced by the presence of environmental noise.