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We have implemented the VSS-RNEMD algorithm in OpenMD, our |
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group molecular dynamics code. A 1188 atom gold slab was |
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equilibrated at 1 atm and 200 K. The periodic box was then expanded |
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in the z direction to expose two Au(111) faces on either side of the 11-atom thick slab. |
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in the $z$-direction to expose two Au(111) faces on either side of the 11-atom thick slab. |
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A full monolayer of thiolates (1/3 the number of surface gold atoms) was placed on three-fold hollow sites on the gold interfaces. To efficiently test the effect of thiolate binding sites on the thermal conductance, all systems had one gold interface with thiolates placed only on fcc hollow sites and the other interface with thiolates only on hcp hollow sites. To test the effect of thiolate chain length on interfacial thermal conductance, full coverages of five chain lengths were tested: butanethiolate, hexanethiolate, octanethiolate, decanethiolate, and dodecanethiolate. To test the effect of mixed chain lengths, full coverages of butanethiolate/decanethiolate and butanethiolate/dodecanethiolate mixtures were created in short/long chain percentages of 25/75, 50/50, 62.5/37.5, 75/25, and 87.5/12.5. The short and long chains were placed on the surface hollow sites in a random configuration. |
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The simulation box z dimension was set to roughly double the length of the gold/thiolate block. Hexane solvent molecules were placed in the vacant portion of the box using the packmol algorithm. Hexane, a straight chain flexible alkane, is very structurally similar to the thiolate alkane tails; previous work has shown that UA models of hexane and butanethiolate have a high degree of vibrational overlap.\cite{Kuang2011} This overlap should provide a mechanism for thermal energy transfer from the thiolates to the solvent. |
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The simulation box $z$-dimension was set to roughly double the length of the gold/thiolate block. Hexane solvent molecules were placed in the vacant portion of the box using the packmol algorithm. Hexane, a straight chain flexible alkane, is very structurally similar to the thiolate alkane tails; previous work has shown that UA models of hexane and butanethiolate have a high degree of vibrational overlap.\cite{Kuang2011} This overlap should provide a mechanism for thermal energy transfer from the thiolates to the solvent. |
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The system was equilibrated to 220 K in the NVT ensemble, allowing the thiolates and solvent to warm gradually. Pressure correction to 1 atm was done in an NPT ensemble that allowed expansion or contraction only in the z direction, so as not to disrupt the crystalline structure of the gold. The diagonal elements of the pressure tensor were monitored during the pressure correction step. If the xx and/or yy elements had a mean above zero throughout the simulation -- indicating residual pressure in the plane of the gold slab -- an additional short NPT equilibration step was performed allowing all box dimensions to change. Once the pressure was stable at 1 atm, a final NVT simulation was performed. All systems were equilibrated in the microcanonical (NVE) ensemble before proceeding with the VSS-RNEMD step. |
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