Correlated atomic dynamics in liquid seen in real space and time

Identical Diffusion Distributions and Co-Cluster Formation Dictate Azeotrope Formation: Microscopic Evidences and Experimental Signatures

What selects azeotropic pairs and governs the azeotropic conditions (composition and temperature) is an open and intriguing question. A combined simulation and experimental work presented here investigates this by considering ethanol-water mixtures. We find identical distributions of center-of-mass diffusion coefficients for ethanol and water molecules under the azeotropic condition (95.5 wt % ethanol +4.5 wt % water, Tazeo = 351.1K). Moreover, the particle displacements show strong interspecies correlations at Tazeo. Interestingly, simulated reorientation time distributions become identical at Tazeo but at a composition different from that at which the translational diffusion distributions overlapped. Cluster analyses indicate that solutions at Tazeo with xwater ≤ 15 wt % are more microheterogeneous than those with higher water content, although no anomaly in the composition-dependent solution structural properties was detected. Ethanol-water and ethanol-ethanol interaction energies show pronounced nonideal composition dependence, but the size of the relative fluctuations in them remained small (∼0.5kBT). Rare water-water H-bonding, predominant water-ethanol H-bonding, and a sizable population of "free" water molecules characterize the azeotropic solutions. The red edge excitation spectroscopic (REES) measurements with a dissolved anionic fluorescent dye, coumarin343 (C343), support the predicted solution microheterogeneity by showing a nonmonotonic composition dependence of the excitation energy-induced changes in the fluorescence emission spectral frequencies and bandwidths, the largest changes being under the azeotropic condition. Subsequent dynamic anisotropy measurements reveal a nonmonotonic composition dependence of C343 rotation times with a peak under the azeotropic condition. In summary, equalization of the component translational diffusion coefficients and solution microheterogeneity with regular composition dependence of the solution structure appear to characterize the ethanol-water azeotrope.

Relevance of structural defects to the mechanism of mechanical deformation in metallic glasses

It is known that deformation in disordered materials such as metallic glasses and supercooled liquids occurs via the cooperative rearrangement of atoms or constituent particles at dynamical heterogeneities, commonly regarded as point-like defects. We show via molecular-dynamics simulations that there is no apparent relationship between atomic rearrangements and the local atomic environment as measured by the atomic-level stresses, kinetic and potential energies, and the per-atom Voronoi volume. In addition, there is only a weak correlation between atomic rearrangements and the largest and smallest eigenvalues of the dynamical matrix. Our results confirm the transient nature of dynamical heterogeneities and suggest that the notion of defects may be less relevant than that of a propensity for rearrangement.

Real Space and Time Imaging of Collective Headgroup Dipole Motions in Zwitterionic Lipid Bilayers

Lipid bilayers are supramolecular structures responsible for a range of processes, such as transmembrane transport of ions and solutes, and sorting and replication of genetic materials, to name just a few. Some of these processes are transient and currently, cannot be visualized in real space and time. Here, we developed an approach using 1D, 2D, and 3D Van Hove correlation functions to image collective headgroup dipole motions in zwitterionic phospholipid bilayers. We show that both 2D and 3D spatiotemporal images of headgroup dipoles are consistent with commonly understood dynamic features of fluids. However, analysis of the 1D Van Hove function reveals lateral transient and re-emergent collective dynamics of the headgroup dipoles-occurring at picosecond time scales-that transmit and dissipate heat at longer times, due to relaxation processes. At the same time, the headgroup dipoles also generate membrane surface undulations due a collective tilting of the headgroup dipoles. A continuous intensity band of headgroup dipole spatiotemporal correlations-at nanometer length and nanosecond time scales-indicates that dipoles undergo stretching and squeezing elastic deformations. Importantly, the above mentioned intrinsic headgroup dipole motions can be externally stimulated at GHz-frequency scale, enhancing their flexoelectric and piezoelectric capabilities (i.e., increased conversion efficiency of mechanical energy into electric energy). In conclusion, we discuss how lipid membranes can provide molecular-level insights about biological learning and memory, and as platforms for the development of the next generation of neuromorphic computers.

SPEADI: Accelerated Analysis of IDP-Ion Interactions from MD-Trajectories

The disordered nature of Intrinsically Disordered Proteins (IDPs) makes their structural ensembles particularly susceptible to changes in chemical environmental conditions, often leading to an alteration of their normal functions. A Radial Distribution Function (RDF) is considered a standard method for characterizing the chemical environment surrounding particles during atomistic simulations, commonly averaged over an entire or part of a trajectory. Given their high structural variability, such averaged information might not be reliable for IDPs. We introduce the Time-Resolved Radial Distribution Function (TRRDF), implemented in our open-source Python package SPEADI, which is able to characterize dynamic environments around IDPs. We use SPEADI to characterize the dynamic distribution of ions around the IDPs Alpha-Synuclein (AS) and Humanin (HN) from Molecular Dynamics (MD) simulations, and some of their selected mutants, showing that local ion-residue interactions play an important role in the structures and behaviors of IDPs.

Medium-range atomic correlation in simple liquids. II. Theory of temperature dependence

The spatial atomic correlations in liquids and glasses extend often significantly beyond the nearest neighbors. Such correlations, called the medium-range order (MRO), affect many physical properties, but their nature is not well understood. In this article the variation of the MRO with temperature is calculated based upon the concept of the atomic-level pressure, focusing on simple liquids, such as metallic liquids. It is shown that the structural coherence length that characterizes MRO follows the Curie-Weiss law with a negative Curie temperature as observed by experiment and simulation. It is also shown that the glass transition is induced by freezing of the MRO, rather than the freezing of the nearest-neighbor shell. The implications of these results are discussed.

Investigating the Accuracy of Water Models through the Van Hove Correlation Function

We present molecular-simulation-based calculations of the Van Hove correlation function (VHF) of water using multiple modeling approaches: classical molecular dynamics with simple three-site nonpolarizable models, with a polarizable model, and with a reactive force field; density functional tight-binding molecular dynamics; and ab initio molecular dynamics. Due to the many orders of magnitude difference in the computational cost of these approaches, we investigate how small and short the simulations can be while still yielding sufficiently accurate and interpretable results for the VHF. We investigate the accuracy of the different models by comparing them to recently published inelastic X-ray scattering measurements of the VHF. We find that all of the models exhibit qualitative agreement with the experiments, and in some models and for some properties, the agreement is quantitative. This work lays the foundation for future simulation approaches to calculating the VHF for aqueous solutions in bulk and under nanoconfinement.