Anders Lervik

Heat transfer in protein-water interfaces.

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 Ca(2+)-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 approximately 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, Ca(2+)-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.

Nonequilibrium molecular dynamics simulations of the thermal conductivity of water: A systematic investigation of the SPC/E and TIP4P/2005 models

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.

Heat transfer in soft nanoscale interfaces: the influence of interface curvature

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.

On the Thermodynamic Efficiency of Ca2+-ATPase Molecular Machines

Experimental studies have shown that the activity of the reconstituted molecular pump Ca(2+)-ATPase strongly depends on the thickness of the supporting bilayer. It is thus expected that the bilayer structure will have an impact on the thermodynamic efficiency of this nanomachine. Here, we introduce a nonequilibrium-thermodynamics theoretical approach to estimate the thermodynamic efficiency of the Ca(2+)-ATPase from analysis of available experimental data about ATP hydrolysis and Ca(2+) transport. We find that the entropy production, i.e., the heat released to the surroundings under working conditions, is approximately constant for bilayers containing phospholipids with hydrocarbon chains of 18-22 carbon atoms. Our estimates for the heat released during the pump operation agree with results obtained from separate calorimetric experiments on the Ca(2+)-ATPase derived from sarcoplasmic reticulum. We show that the thermodynamic efficiency of the reconstituted Ca(2+)-ATPase reaches a maximum for bilayer thicknesses corresponding to maximum activity. Surprisingly, the estimated thermodynamic efficiency is very low, ∼12%. We discuss the significance of this result as representative of the efficiency of other nanomachines, and we address the influence of the experimental set-up on such a low efficiency. Overall, our approach provides a general route to estimate thermodynamic efficiencies and heat dissipation in experimental studies of nanomachines.

Coherent description of transport across the water interface: From nanodroplets to climate models.

Transport of mass and energy across the vapor-liquid interface of water is of central importance in a variety of contexts such as climate models, weather forecasts, and power plants. We provide a complete description of the transport properties of the vapor-liquid interface of water with the framework of nonequilibrium thermodynamics. Transport across the planar interface is then described by 3 interface transfer coefficients where 9 more coefficients extend the description to curved interfaces. We obtain all coefficients in the range 260-560 K by taking advantage of water evaporation experiments at low temperatures, nonequilibrium molecular dynamics with the TIP4P/2005 rigid-water-molecule model at high temperatures, and square gradient theory to represent the whole range. Square gradient theory is used to link the region where experiments are possible (low vapor pressures) to the region where nonequilibrium molecular dynamics can be done (high vapor pressures). This enables a description of transport across the planar water interface, interfaces of bubbles, and droplets, as well as interfaces of water structures with complex geometries. The results are likely to improve the description of evaporation and condensation of water at widely different scales; they open a route to improve the understanding of nanodroplets on a small scale and the precision of climate models on a large scale.

Kinetic and mesoscopic non-equilibrium description of the Ca 2+ pump: a comparison

We analyse the operation of the Ca2+-ATPase ion pump using a kinetic cycle diagram. Using the methodology of Hill, we obtain the cycle fluxes, entropy production and efficiency of the pump. We compare these results with a mesoscopic non-equilibrium description of the pump and show that the kinetic and mesoscopic pictures are in accordance with each other. This gives further support to the mesoscopic theory, which is less restricted and also can include the heat flux as a variable. We also show how motors can be characterised in terms of unidirectional backward fluxes. We proceed to show how the mesoscopic approach can be used to identify fast and slow steps of the model in terms of activation energies, and how this can be used to simplify the kinetic diagram.

Enhancement of the Thermal Polarization of Water via Heat Flux and Dipole Moment Dynamic Correlations

It has been recently shown that liquid water polarizes as a response to a temperature gradient. This polarization effect can be significant for temperature gradients that can be achieved at micro and nanoscales. In this paper we investigate the dependence of the polarization response of liquid and supercritical water at different thermodynamic conditions using both equilibrium and nonequilibrium molecular dynamics simulations for the extended point charge water model. We find that the thermal polarization features a nonmonotonic behavior with temperature, reaching a maximum response at specific thermodynamic states. We show that the thermal polarization is maximized when the density of states of the heat flux and dipole moment correlation functions feature the strongest overlap. The librational modes of water are shown to play an important role in determining this behavior as well as the heat transport mechanism in water. The librational frequencies show a significant dependence with temperature and pressure. This dependence provides a microscopic mechanism to explain the observed maximization of the thermal-polarization effect. Our work provides new microscopic insights on the mechanism determining the orientation of polar fluids under thermal gradients, as well as new strategies to maximize their orientation by manipulating the dynamic correlations between the heat flux and the sample dipole moment.

Gluing Potential Energy Surfaces with Rare Event Simulations

We develop a new method combining replica exchange transition interface sampling with two distinct potential energy surfaces. The method can be used to combine different levels of theory in a simulation of a molecular process (e.g., a chemical reaction), and it can serve as a dynamical version of QM-MM, connecting classical dynamics with Ab Initio dynamics in the time domain. This new method, which we coin QuanTIS, could be applied to use accurate but expensive density functional theory based molecular dynamics for the breaking and making of chemical bonds, while the diffusion of reactants in the solvent are treated with classical force fields. We exemplify the method by applying it to two simple model systems (an ion dissociation reaction and a classical hydrogen model), and we discuss a possible extension of the method in which classical force field parameters for chemical reactions can be optimized on the fly.

Active transport of the Ca 2+ -pump: introduction of the temperature difference as a driving force

We analyse a kinetic cycle of the Ca2+-ATPase molecular pump using mesoscopic non-equilibrium thermodynamics. The pump is known to generate heat, and by analysing the operation on the mesoscopic level, we are able to introduce a temperature difference and the corresponding heat flux in the description. Integration over the internal coordinates then results in non-linear flux–force relations describing the operation of the pump on the macroscopic level. Specifically, we obtain an expression for the heat flux associated with the active transport and the coupling of heat effects to the transport of ions and the rate of the ATP-hydrolysis.

PyRETIS: A well-done, medium-sized python library for rare events

Transition path sampling techniques are becoming common approaches in the study of rare events at the molecular scale. More efficient methods, such as transition interface sampling (TIS) and replica exchange transition interface sampling (RETIS), allow the investigation of rare events, for example, chemical reactions and structural/morphological transitions, in a reasonable computational time. Here, we present PyRETIS, a Python library for performing TIS and RETIS simulations. PyRETIS directs molecular dynamics (MD) simulations in order to sample rare events with unbiased dynamics. PyRETIS is designed to be easily interfaced with any molecular simulation package and in the present release, it has been interfaced with GROMACS and CP2K, for classical and ab initio MD simulations, respectively.