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

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

Non-Gaussian Lineshapes and Dynamics of Time-Resolved Linear and Nonlinear (Correlation) Spectra

Signatures of nonlinear and non-Gaussian dynamics in time-resolved linear and nonlinear (correlation) 2D spectra are analyzed in a model considering a linear plus quadratic dependence of the spectroscopic transition frequency on a Gaussian nuclear coordinate of the thermal bath (quadratic coupling). This new model is contrasted to the commonly assumed linear dependence of the transition frequency on the medium nuclear coordinates (linear coupling). The linear coupling model predicts equality between the Stokes shift and equilibrium correlation functions of the transition frequency and time-independent spectral width. Both predictions are often violated, and we are asking here the question of whether a nonlinear solvent response and/or non-Gaussian dynamics are required to explain these observations. We find that correlation functions of spectroscopic observables calculated in the quadratic coupling model depend on the chromophore’s electronic state and the spectral width gains time dependence, all in violation of the predictions of the linear coupling models. Lineshape functions of 2D spectra are derived assuming Ornstein–Uhlenbeck dynamics of the bath nuclear modes. The model predicts asymmetry of 2D correlation plots and bending of the center line. The latter is often used to extract two-point correlation functions from 2D spectra. The dynamics of the transition frequency are non-Gaussian. However, the effect of non-Gaussian dynamics is limited to the third-order (skewness) time correlation function, without affecting the time correlation functions of higher order. The theory is tested against molecular dynamics simulations of a model polar–polarizable chromophore dissolved in a force field water

On the Density Dependence of the Integral Equation Coarse-Graining Effective Potential

Coarse-graining (CG) procedures provide computationally efficient methods for investigating the corresponding long time- and length-scale processes. In the bottom-up approaches, the effective interactions between the CG sites are obtained using the information from the atomistic simulations, but reliable CG procedures are required to preserve the structure and thermodynamics. In this regard, the integral equation coarse-graining (IECG) method is a promising approach that uses the first-principles Ornstein–Zernike equation in liquid state theory to determine the effective potential between CG sites. In this work, we present the details of the IECG method while treating the density as an intrinsic property and active variable of the CG system. Performing extensive simulations of polymer melts, we show that the IECG theory/simulation and atomistic simulation results are consistent in structural properties such as the pair-correlation functions and form factors, and also thermodynamic properties such as pressure. The atomistic simulations of the liquids show that the structure is largely sensitive to the repulsive part of the potential. Similarly, the IECG simulations of polymeric liquids show that the structure can be determined by the relatively short-range CG repulsive interactions, but the pressure is only accurately determined once the long-range, weak CG attractive interactions are included. This is in agreement with the seminal work by Widom on the influence of the potential on the phase diagram of the liquid [Widom, B. Science 1967, 157, 375–382]. Other aspects of the IECG theory/simulations are also discussed