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Sevgen, Emre

Publications and source records attributed to Sevgen, Emre.

6 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Dissociation of salts in water under pressure

The investigation of salts in water at extreme conditions is crucial to understanding the properties of aqueous fluids in the Earth. We report first principles (FP) and classical molecular dynamics simulations of NaCl in the dilute limit, at temperatures and pressures relevant to the Earth's upper mantle. Similar to ambient conditions, we observe two metastable states of the salt: the contact (CIP) and the solvent-shared ion-pair (SIP), which are entropically and enthalpically favored, respectively. We find that the free energy barrier between the CIP and SIP minima increases at extreme conditions, and that the stability of the CIP is enhanced in FP simulations, consistent with the decrease of the dielectric constant of water. The minimum free energy path between the CIP and SIP becomes smoother at high pressure, and the relative stability of the two configurations is affected by water self-dissociation, which can only be described properly by FP simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

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↗
DOE OSTI2018

Nanocrystalline Oligo(ethylene sulfide)- b -poly(ethylene glycol) Micelles: Structure and Stability

Micelle formation generally relies on hydrophobic or electrostatic interactions between distinct regions of amphiphilic molecules. In this work, a different mechanism is considered in which nanocrystalline domains are formed from short ethylene sulfide oligomers at the core of the micelles, leading to exceptionally stable, uniform micellar structures. The structure and thermodynamic properties of the resulting micelles are examined through a combination of experiments, theory, and simulations. It is found that in oligo(ethylene sulfide)- b -poly(ethylene glycol) amphiphiles as few as three ethylene sulfide monomers are sufficient to form a highly crystalline core, surrounded by a water-soluble ethylene glycol corona of arbitrary size. Sulfur-sulfur interactions induce formation of rhombohedral lattice crystalline regions, which exhibit well-defined intramolecular and intermolecular order. An atomistic model is used to determine the free energy of the micelles; the critical micelle concentration (CMC) is found to be extremely small, on the order of 10 -8 mol/L. The size distribution of these micelles is nearly monodisperse. The crystalline core also includes amorphous regions that could serve as hosts for other molecules. Taken together, these properties serve to underscore that controlled crystallization provides a useful and underexploited mechanism for assembly of ultrastable micelles for applications in a variety of settings, including drug delivery and immunology.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

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↗
DOE OSTI2018

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↗