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We present the results of molecular dynamics simulations of a nanoscale electrochemical cell. The simulations include an aqueous electrolyte solution with varying ionic strength (i.e., concentrations ranging from 0-4M) between a pair of metallic electrodes held at constant potential difference. We analyze these simulations by computing the electrostatic potential profile of the electric double-layer region and find it to be nearly independent of ionic concentration, in stark contrast to the predictions of standard continuum-based theories. We attribute this lack of concentration dependence to the molecular influences of water molecules at the electrode-solution interface. These influences include the molecular manifestation of water's dielectric response, which tends to drown out the comparatively weak screening requirement of the ions. To support our analysis, we decompose water's interfacial response into three primary contributions: molecular layering, intrinsic (zero-field) orientational polarization, and the dipolar dielectric response. 

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. 

The local hydration around tetrameric hemoglobin (Hb) in its T0 and R4 conformational substates is analyzed based on molecular dynamics simulations. Analysis of the local hydrophobicity (LH) for all residues at the α1β2 and α2β1 interfaces, responsible for the quaternary T → R transition, which is encoded in the Monod–Wyman–Changeux model, as well as comparison with earlier computations of the solvent accessible surface area, makes clear that the two quantities measure different aspects of hydration. Local hydrophobicity quantifies the presence and structure of water molecules at the interface, whereas “buried surface” reports on the available space for solvent. For simulations with Hb frozen in its T0 and R4 states, the correlation coefficient between LH and buried surface is 0.36 and 0.44, respectively, but it increases considerably if the 95% confidence interval is used. The LH with Hb frozen and flexible changes little for most residues at the interfaces but is significantly altered for a few select ones: Thr41α, Tyr42α, Tyr140α, Trp37β, Glu101β (for T0) and Thr38α, Tyr42α, Tyr140α (for R4). The number of water molecules at the interface is found to increase by ∼25% for T0 → R4, which is consistent with earlier measurements. Since hydration is found to be essential to protein function, it is clear that hydration also plays an essential role in allostery. 

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.