Heat Transport with a Twist

Despite the desirability of polymers for use in many products due to their flexibility, light weight, and durability, their status as thermal insulators has precluded their use in applications where thermal conductors are required. However, recent results suggest that the thermal conductance of polymers can be enhanced and that their heat transport behaviors may be highly sensitive to nanoscale control. Here we use non-equilibrium molecular dynamics (MD) simulations to study the effect of mechanical twist on the steady-state thermal conductance across multi-stranded polyethylene wires. We find that a highly twisted double-helical polyethylene wire can display a thermal conductance up to three times that of its untwisted form, an effect which can be attributed to a structural transition in the strands of the double helix. We also find that in thicker wires composed of many parallel strands, adding just one twist can increase its thermal conductance by over 30%. However, we find that unlike stretching a polymer wire, which causes a monotonic increase in thermal conductance, the effect of twist is highly non-monotonic, and certain amounts of twist can actually decrease the thermal conductance. Finally, we apply the Continuous Chirality Measure (CCM) in an attempt to explore the correlation between heat conductance and chirality. The CCM is found to correlate with twist as expected, but we attribute the observed heat transport behaviors to structural factors other than chirality

Chemical Potential of a Flexible Polymer Liquid in a Coarse-Grained Representation

While the excess chemical potential is the key quantity in determining phase diagrams, its direct computation for high-density liquids of long polymer chains has posed a significant challenge. Computationally, the excess chemical potential is calculated using the Widom insertion method, which involves monitoring the change in internal energy as one incrementally introduces individual molecules in the liquid. However, when dealing with dense polymer liquids, inserting long chains requires generating trial configurations with a bias that favors those at low energy on a unit-by-unit basis: a procedure that becomes more challenging as the number of units increases. Thus, calculating the excess chemical potential of dense polymer liquids using this method becomes computationally intractable as the chain length exceeds $N > 30$. Here, we adopt a coarse-grained model derived from integral equation theory, for which inserting long polymer chains becomes feasible. The Integral Equation theory of Coarse-Graining (IECG) represents a polymer as a sphere or a collection of blobs interacting through a soft potential. We employ the IECG approach to compute the excess chemical potential using Widom's method for polymer chains of increasing lengths, extending up to $N=720$ monomers, and at densities reaching up to $\rho= 0.767$ g/cm$^{3}$. From a fundamental perspective, we demonstrate that the excess chemical potentials remain nearly constant across various levels of coarse-graining, offering valuable insights into the consistency of this type of procedure. Ultimately, we argue that current Monte Carlo (MC) algorithms, originally designed for atomistic simulations, such as Configurational Bias Monte Carlo (CBMC) methods, can significantly benefit from the integration of the IECG approach, thereby enhancing their performance in the study of phase diagrams of polymer liquids

Dinucleotides as simple models of the base stacking-unstacking component of DNA 'breathing' mechanisms

14 pagesRegulatory 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.This research was supported by a grant from the National Institute of Child Health and Human Development (5R01HD081 362-05) awarded to L.S. and N.B.A. The funding sources had no role in the study design, data collection and analysis, or submission process

The First Direct Detection of Kirkwood Transitions in Concentrated Aqueous Electrolytes using Small Angle X-ray Scattering

Ion-ion correlations, screening, and equilibrium bulk structure in various concentrated electrolytes are investigated using synchrotron small angle X-ray scattering (SAXS), theory, and molecular simulation. Utilizing SAXS measurements we provide estimates of the Kirkwood Transition (KT) for a variety of aqueous electrolytes (NaCl, CaCl$_2$, SrCl$_2$, and ErCl$_3$). The KT may be defined as the concentration above which the ion-ion correlations cease to decay exponentially with a single length scale given by the Debye length $\lambda_{\rm D}$ and develop an additional length scale, $d=2\pi/Q_0$ that reflects the formation of local domains of charge. Theoretical models of the KT have been known for decades for highly idealized models of electrolytes, but experimental verification of KT in real electrolytes has yet to be confirmed. Herein, we provide consistent theoretical and experimental estimates of both the inverse screening lengths $a_0$ and inverse domain size, $Q_0$ for the aforementioned electrolyte systems. Taken together, $a_0$ and $Q_0$ are known descriptors of the KT and provide a view into the complexity of ion-ion interaction beyond the well-accepted Debye-H\"{u}ckel limit. Our findings suggest a picture of interaction for real electrolytes that is more general than that found in idealized models that is manifest in the precise form of the non-local response function that we estimate through the interpretation of the experimental SAXS signal. Importantly, the additional complexity of describing ion-ion interaction of real electrolytes will implicate the short-range ion-ion interactions that can only be computed via molecular simulation and provide a quantitative approach to describe electrolyte phenomena beyond Debye-H\"{u}ckel theory.Comment: 3

Interface Dielectric Constant of Water at the Surface of a Spherical Solute

Interface dielectric constant is used to quantify polar response of water interfacing a spherical solute. This interfacial parameter, affected by the interfacial structure within about two solvation layers, is fundamentally distinct from the bulk dielectric constant (a material property). Molecular dynamics simulations are used to extract the interface dielectric constant from fluctuation relations correlating the dipole moment of the interfacial layer with the medium electrostatics. For a probe ion, one has to calculate cross-correlations between the shell dipole and the electrostatic potential, while cross-correlations between the shell dipole and the electrostatic field are required for a probe dipole. All protocols produce dielectric constants of water interfacing a nonpolar solute significantly below the bulk value. We analyze corrections imposed on the fluctuation relations by protocols using periodic boundary conditions with Ewald sums to compute electrostatic interactions. These corrections are insignificant for typical simulation protocols