Amphiphilic salts as single-component, solvent-free, lithium electrolytes
Not Available
Liu, Jiacheng↗
Engineering topics
Whitmer, Jonathan K.
Publications and source records attributed to Whitmer, Jonathan K..
Transfer Learning Facilitates the Prediction of Polymer–Surface Adhesion Strength
Not provided.
Chemistry↗
Combined Force-Frequency Sampling for Simulation of Systems Having Rugged Free Energy Landscapes.
An adaptive, machine learning-based sampling method is presented for simulation of systems having rugged, multidimensional free energy landscapes. The method's main strength resides in its ability to learn both from the frequency of visits to distinct states and the generalized force estimates that arise in a system as it evolves in phase space. This is accomplished by introducing a self-integrating artificial neural network, which generates an estimate of the free energy directly from its derivatives. The usefulness of the proposed combined approach is examined in the context of two concrete examples, namely, an alanine dipeptide molecule in water and a polymer diffusing through a narrow pore. This new method is found to be robust, faster, and more accurate than approaches that rely only on frequency-based or generalized force-based estimations. After combining the proposed approach with overfill protection and support for sparse data storage and training, the method is shown to be more effective than comparable, previously available techniques and capable of scaling efficiently to larger numbers of collective variables.
Sevgen, Emre↗
Novel elastic response in twist-bend nematic models
We demonstrate that a simple lattice model of a twist-bend nematic exhibits nonmonotonic elastic behavior strikingly similar to recent experiments.
Shi, Jiale↗
Adaptive enhanced sampling by force-biasing using neural networks
A machine learning assisted method is presented for molecular simulation of systems with rugged free energy landscapes. The method is general and can be combined with other advanced sampling techniques. In the particular implementation proposed here, it is illustrated in the context of an adaptive biasing force approach where, rather than relying on discrete force estimates, one can resort to a self-regularizing artificial neural network to generate continuous, estimated generalized forces. By doing so, the proposed approach addresses several shortcomings common to adaptive biasing force and other algorithms. Specifically, the neural network enables smooth estimates of generalized forces in sparsely sampled regions, force estimates in previously unexplored regions, and continuous force estimates with which to bias the simulation, as opposed to biases generated at specific points of a discrete grid. The usefulness of the method is illustrated with three different examples, chosen to highlight the wide range of applicability of the underlying concepts. In all three cases, the new method is found to enhance considerably the underlying traditional adaptive biasing force approach. Furthermore, the method is also found to provide improvements over previous implementations of neural network assisted algorithms.
97 MATHEMATICS AND COMPUTING↗
In Silico Measurement of Elastic Moduli of Nematic Liquid Crystals
Experiments on confined droplets of the nematic liquid crystal 5CB have questioned long-established bounds imposed on the elastic free energy of nematic systems. This elasticity, which derives from molecular alignment within nematic systems, is quantified through a set of moduli which can be difficult to measure experimentally and, in some cases, can only be probed indirectly. This is particularly true of the surfacelike saddle-splay elastic term, for which the available experimental data indicate values on the cusp of stability, often with large uncertainties. Here, we demonstrate that all nematic elastic moduli, including the saddle-splay elastic constant k 24 , may be calculated directly from atomistic molecular simulations. Importantly, results obtained through in silico measurements of the 5CB elastic properties demonstrate unambiguously that saddle-splay elasticity alone is unable to describe the observed confined morphologies.
36 MATERIALS SCIENCE↗
SSAGES: Software Suite for Advanced General Ensemble Simulations
Molecular simulation has emerged as an essential tool for modern-day research, but obtaining proper results and making reliable conclusions from simulations requires adequate sampling of the system under consideration. To this end, a variety of methods exist in the literature that can enhance sampling considerably, and increasingly sophisticated, effective algorithms continue to be developed at a rapid pace. Implementation of these techniques, however, can be challenging for experts and non-experts alike. There is a clear need for software that provides rapid, reliable, and easy access to a wide range of advanced sampling methods, and that facilitates implementation of new techniques as they emerge. Here we present SSAGES, a publicly available Software Suite for Advanced General Ensemble Simulations designed to interface with multiple widely used molecular dynamics simulations packages. SSAGES allows facile application of a variety of enhanced sampling techniques—including adaptive biasing force, string methods, and forward flux sampling—that extract meaningful free energy and transition path data from all-atom and coarse grained simulations. A noteworthy feature of SSAGES is a user-friendly framework that facilitates further development and implementation of new methods and collective variables. In this study, the use of SSAGES is illustrated in the context of simple representative applications involving distinct methods and different collective variables that are available in the current release of the suite.
97 MATHEMATICS AND COMPUTING↗
Charge Transport and Phase Behavior of Imidazolium-Based Ionic Liquid Crystals from Fully Atomistic Simulations
Ionic liquid crystals occupy an intriguing middle ground between room-temperature ionic liquids and mesostructured liquid crystals. Here, we examine a non-polarizable, fully atomistic model of the 1-alkyl-3-methylimidazolium nitrate family using molecular dynamics in the constant pressure–constant temperature ensemble. These materials exhibit a distinct “smectic” liquid phase, characterized by layers formed by the molecules, which separate the ionic and aliphatic moieties. In particular, we discuss the implications this layering may have for electrolyte applications.
36 MATERIALS SCIENCE↗
Sculpting bespoke mountains: Determining free energies with basis expansions
Not Available
Whitmer, Jonathan K.↗
Chirality-selected phase behaviour in ionic polypeptide complexes
In this study, polyelectrolyte complexes present new opportunities for self-assembled soft matter. Factors determining whether the phase of the complex is solid or liquid remain unclear. Ionic polypeptides enable examination of the effects of stereochemistry on complex formation. Here we demonstrate that chirality determines the state of polyelectrolyte complexes, formed from mixing dilute solutions of oppositely charged polypeptides, via a combination of electrostatic and hydrogen-bonding interactions. Fluid complexes occur when at least one of the polypeptides in the mixture is racemic, which disrupts backbone hydrogen-bonding networks. Pairs of purely chiral polypeptides, of any sense, form compact, fibrillar solids with a β-sheet structure. Analogous behaviour occurs in micelles formed from polypeptide block copolymers with polyethylene oxide, where assembly into aggregates with either solid or fluid cores, and eventually into ordered phases at high concentrations, is possible. Chirality is an exploitable tool for manipulating material properties in polyelectrolyte complexation.
36 MATERIALS SCIENCE↗
Surface Adsorption in Nonpolarizable Atomic Models
Many ionic solutions exhibit species dependent properties, including surface tension and the salting out of proteins. These effects may be loosely quantified in terms of the Hofmeister series, first identified in the context of protein solubility. Here, our interest is to develop atomistic models capable of capturing Hofmeister effects rigorously. Importantly, we aim to capture this dependence in computationally cheap “hard” ionic models, which do not exhibit dynamic polarization. To do this, we have performed an investigation detailing the effects of the water model on these properties. Though incredibly important, the role of water models in simulation of ionic solutions and biological systems is essentially unexplored. We quantify this via the ion-dependent surface attraction of the halide series (Cl, Br, I) and, in so doing, determine the relative importance of various hypothesized contributions to ionic surface free energies. Importantly, we demonstrate surface adsorption can result in hard ionic models combined with a thermodynamically accurate reprsenation of the water molecule (TIP4Q). The effect observed in simulations of iodide is commensurate with previous calculations of the surface potential of mean force in rigid molecular dynamics and polarizable density- functional models. Our calculations are direct simulation evidence of the subtle but sensitive role of water thermodynamics in atomistic simulations.
Whitmer, Jonathan K.↗
Basis Function Sampling: A New Paradigm for Material Property Computation
Not Available
Whitmer, Jonathan K.↗
Coarse-grained modeling of DNA curvature
The interaction of DNA with proteins occurs over a wide range of length scales, and depends critically on its local structure. In particular, recent experimental work suggests that the intrinsic curvature of DNA plays a significant role on its protein-binding properties. In this work, we present a coarse grained model of DNA that is capable of describing base-pairing, hybridization, major and minor groove widths, and local curvature. The model represents an extension of the recently proposed 3SPN.2 description of DNA [D. M. Hinckley, G. S. Freeman, J. K. Whitmer, and J. J. de Pablo, J. Chem. Phys. 139, 144903 (2013)], into which sequence-dependent shape and mechanical properties are incorporated. The proposed model is validated against experimental data including melting temperatures, local flexibilities, dsDNA persistence lengths, and minor groove width profiles.
Freeman, Gordon S.↗
Orientationally Glassy Crystals of Janus Spheres
Colloidal Janus spheres in water (one hemisphere attractive and the other repulsive) assemble into two-dimensional hexagonal crystals with orientational order controlled by anisotropic interactions. We exploit the decoupled translational and rotational order to quantify the orientational dynamics. Via imaging experiments and Monte Carlo simulations we demonstrate that the correlations in the orientation of individual Janus spheres exhibit glasslike dynamics that can be controlled via the ionic strength. Furthermore, these colloidal building blocks provide a particularly suitable model glass system for elucidating nontrivial dynamics arising from directional interactions, not captured by the consideration of just translational order.
42 ENGINEERING↗