We investigate using transient non-equilibrum molecular dynamics simulation the temperature relaxation process of three structurally different proteins in water, namely; myoglobin, green fluorescence protein (GFP) and two conformations of the Ca²⁺ -ATPase protein. By modeling the temperature relaxation process using the solution of the heat diffusion equation we compute the thermal conductivity and thermal diffusivity of the proteins, as well as the thermal conductance of the protein–water interface. Our results indicate that the temperature relaxation of the protein can be described using a macroscopic approach. The protein–water interface has a thermal conductance of the order of 100–270 MW K⁻¹ m⁻² , characteristic of water–hydrophilic interfaces. The thermal conductivity of the proteins is of the order of 0.1–0.2 W K⁻¹ m⁻¹ as compared with ≈0.6 W K⁻¹ m⁻¹ for water, suggesting that these proteins can develop temperature gradients within the biomolecular structures that are larger than those of aqueous solutions. We find that the thermal diffusivity of the transmembrane protein, Ca²⁺ -ATPase is about three times larger than that of myoglobin or GFP. Our simulation shows that the Kapitza length of these structurally different proteins is of the order of 1 nm, showing that the protein–water interface should play a major role in defining the thermal relaxation of biomolecules.

We investigate the response of bulk liquid water to a temperature gradient using nonequilibrium molecular dynamics simulations. It is shown that the thermal gradient polarizes water in the direction of the gradient, leading to a non-negligible electrostatic field whose origin lies in the water reorientation under nonequilibrium conditions. The dependence of the magnitude of the electrostatic field with the temperature gradient is in agreement with nonequilibrium thermodynamics theory. We conclude that temperature gradients of the order of ${10}^8\mathrm{K}/\mathrm{m}$ could result in fairly large polarizations $\sim {10}^6\mathrm{V}/\mathrm{m}$.

We report an extensive nonequilibrium molecular dynamics investigation of the thermal conductivity of water using two of the most accurate rigid nonpolarizable empirical models available, SPC/E and TIP4P/2005. Our study covers liquid and supercritical states. Both models predict the anomalous increase of the thermal conductivity with temperature and the thermal conductivity maximum, hence confirming their ability to reproduce the complex anomalous behaviour of water. The performance of the models strongly depends on the thermodynamic state investigated, and best agreement with experiment is obtained for states close to the liquid coexistence line and at high densities and temperatures. Considering the simplicity of these two models the overall agreement with experiments is remarkable. Our results show that explicit polarizability and molecular flexibility are not needed to reproduce the anomalous heat conduction of water.

The pH of liquid water is determined by the infrequent process in which water molecules split into short-lived hydroxide and hydronium ions. This reaction is difficult to probe experimentally and challenging to simulate. One of the open questions is whether the local water structure around a slightly stretched OH bond is actually initiating the eventual breakage of this bond or whether this event is driven by a global ordering that involves many water molecules far away from the reaction center. Here, we investigated the self-ionization of water at room temperature by rare-event ab initio molecular dynamics and obtained autoionization rates and activation energies in good agreement with experiments. Based on the analysis of thousands of molecular trajectories, we identified a couple of local order parameters and show that if a bond stretch occurs when all these parameters are around their ideal range, the chance for the first dissociation step (double-proton jump) increases from $10^{-7}$ to $0.4$. Understanding these initiation triggers might ultimately allow the steering of chemical reactions. Significance The dissociation of water is arguably the most fundamental chemical reaction occurring in the aqueous phase. Despite that the splitting of a water molecule very seldom occurs, the reaction is of major importance in many areas of chemistry and biology. Direct experimental probing of the event is still impossible and also simulating the event via accurate computer simulations is challenging. Here, we achieved the latter via specialized rare-event algorithms estimating rates of dissociation in agreement with indirect experimental measurements. Even more interestingly, by a rigorous analysis of our results we identified anomalies in the water structure that act as initiators of the reaction, a finding that suggests paradigms for steering and catalyzing chemical reactions.

We investigate, using transient non-equilibrium molecular-dynamics simulations, heat-transfer through nanometer-scale interfaces consisting of n-decane (2–12 nm diameter) droplets in water. Using computer simulation results of the temperature relaxation of the nanodroplet as a function of time we have computed the thermal conductivity and the interfacial conductance of the droplet and the droplet/water interface respectively. We find that the thermal conductivity of the n-decane droplets is insensitive to droplet size, whereas the interfacial conductance shows a strong dependence on the droplet radius. We rationalize this behavior in terms of a modification of the n-decane/water surface-tension with droplet curvature. This enhancement in interfacial conductance would contribute, in the case of a suspension, to an increase in the thermal conductivity with decreasing particle radius. This notion is consistent with recent experimental studies of nanofluids. We also investigate the accuracy of different diffusion equations to model the temperature relaxation in non stationary non equilibrium processes. We show that the modeling of heat transfer across a nanodroplet/fluid interface requires the consideration of the thermal conductivity of the nanodroplet as well as the temperature discontinuity across the interface. The relevance of this result in diffusion models that neglect thermal conductivity effects in the modeling of the temperature relaxation is discussed.

The algorithmic development in the field of path sampling has made tremendous progress in recent years. Although the original transition path sampling method was mostly used as a qualitative tool to sample reaction paths, the more recent family of interface‐based path sampling methods has paved the way for more quantitative rate calculation studies. Of the exact methods, the replica exchange transition interface sampling (RETIS) method is the most efficient, but rather difficult to implement. This has been the main motivation to develop the open‐source Python‐based computer library PyRETIS that was released in 2017. PyRETIS is designed to be easily interfaced with any molecular dynamics (MD) package using either classical or ab initio MD. In this study, we report on the principles and the software enhancements that are now included in PyRETIS 2, as well as the recent developments on the user interface, improvements of the efficiency via the implementation of new shooting moves, easier initialization procedures, analysis methods, and supported interfaced software. © 2019 The Authors. Journal of Computational Chemistry published by Wiley Periodicals, Inc.