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In standard molecular junctions, a molecular structure is placed between and connected to metal leads. Understanding how mechanical tuning in such molecular junctions can change heat conductance has interesting applications in nanoscale energy transport. In this work, we use nonequilibrium molecular dynamics simulations to address the effect of stretching on the phononic contribution to the heat conduction of molecular junctions consisting of single long-chain alkanes and various metal leads, such as Ag, Au, Cu, Ni, and Pt. The thermal conductance of such junctions is found to be much smaller than the intrinsic thermal conductance of the polymer and significantly depends on the nature of metal leads as expressed by the metal–molecule coupling and metal vibrational density of states. This behavior is expected and reflects the mismatch of phonon spectra at the metal molecule interfaces. As a function of stretching, we find a behavior similar to what was observed earlier [M. Dinpajooh and A. Nitzan, J. Chem. Phys. 153, 164903 (2020)] for pure polymeric structures. At relatively short electrode distances, where the polyethylene chains are compressed, it is found that the thermal conductances of the molecular junctions remain almost constant as one stretches the polymer chains. At critical electrode distances, the thermal conductances start to increase, reaching the values of the fully extended molecular junctions. Similar behaviors are observed for junctions in which several long-chain alkanes are sandwiched between various metal leads. These findings indicate that this behavior under stretching is an intrinsic property of the polymer chain and not significantly associated with the interfacial structures.

 

Abstract Regulatory protein access to the DNA duplex ‘interior’ depends on local DNA ‘breathing’ fluctuations, and the most fundamental of these are thermally-driven base stacking-unstacking interactions. The smallest DNA unit that can undergo such transitions is the dinucleotide, whose structural and dynamic properties are dominated by stacking, while the ion condensation, cooperative stacking and inter-base hydrogen-bonding present in duplex DNA are not involved. We use dApdA to study stacking-unstacking at the dinucleotide level because the fluctuations observed are likely to resemble those of larger DNA molecules, but in the absence of constraints introduced by cooperativity are likely to be more pronounced, and thus more accessible to measurement. We study these fluctuations with a combination of Molecular Dynamics simulations on the microsecond timescale and Markov State Model analyses, and validate our results by calculations of circular dichroism (CD) spectra, with results that agree well with the experimental spectra. Our analyses show that the CD spectrum of dApdA is defined by two distinct chiral conformations that correspond, respectively, to a Watson–Crick form and a hybrid form with one base in a Hoogsteen configuration. We find also that ionic structure and water orientation around dApdA play important roles in controlling its breathing fluctuations. 

The integral equation coarse-graining (IECG) approach is a promising high-level coarse-graining (CG) method for polymer melts, with variable resolution from soft spheres to multi CG sites, which preserves the structural and thermodynamical consistencies with the related atomistic simulations. When compared to the atomistic description, the procedure of coarse-graining results in smoother free energy surfaces, longer-ranged potentials, a decrease in the number of interaction sites for a given polymer, and more. Because these changes have competing effects on the computational efficiency of the CG model, care needs to be taken when studying the effect of coarse-graining on the computational speed-up in CG molecular dynamics simulations. For instance, treatment of long-range CG interactions requires the selection of cutoff distances that include the attractive part of the effective CG potential and force. In particular, we show how the complex nature of the range and curvature of the effective CG potential, the selection of a suitable CG timestep, the choice of the cutoff distance, the molecular dynamics algorithms, and the smoothness of the CG free energy surface affect the efficiency of IECG simulations. By direct comparison with the atomistic simulations of relatively short chain polymer melts, we find that the overall computational efficiency is highest for the highest level of CG (soft spheres), with an overall improvement of the computational efficiency being about 10 6 –10 8 for various CG levels/resolutions. Therefore, the IECG method can have important applications in molecular dynamics simulations of polymeric systems. Finally, making use of the standard spatial decomposition algorithm, the parallel scalability of the IECG simulations for various levels of CG is presented. Optimal parallel scaling is observed for a reasonably large number of processors. Although this study is performed using the IECG approach, its results on the relation between the level of CG and the computational efficiency are general and apply to any properly-constructed CG model.