Unsupervised Machine Learning Method for the Phase Behavior of the Constant Magnetization Ising Model in Two and Three Dimensions.

Machine learning methods have been important in the study of phase transitions. Unsupervised methods are particularly attractive because they do not require prior knowledge of the existence of a phase transition. In this work we focus on the constant magnetization Ising model in two (2D) and three (3D) dimensions.

Sensitive and selective polymer condensation at membrane surface driven by positive co-operativity.

Biomolecular phase separation has emerged as an essential mechanism for cellular organization. How cells respond to environmental stimuli in a robust and sensitive manner to build functional condensates at the proper time and location is only starting to be understood. Recently, lipid membranes have been recognized as an important regulatory center for biomolecular condensation.

Importance of feature construction in machine learning for phase transitions.

Machine learning is an important tool in the study of the phase behavior from molecular simulations. In this work, we use un-supervised machine learning methods to study the phase behavior of two off-lattice models, a binary Lennard-Jones (LJ) mixture and the Widom-Rowlinson (WR) non-additive hard-sphere mixture. The majority of previous work has focused on lattice models, such as the 2D Ising model, where the values of the spins are used as the feature vector that is input into the machine learning algorithm, with considerable success.

Chemically realistic coarse-grained models for polyelectrolyte solutions.

Polyelectrolyte solutions are of considerable scientific and practical importance. One of the most widely studied polymer is polystyrene sulfonate (PSS), which has a hydrophobic backbone with pendant charged groups. A polycation with similar chemical structure is poly(vinyl benzyltri methyl) ammonium (PVBTMA).

Fast estimation of ion-pairing for screening electrolytes: A cluster can approximate a bulk liquid.

The propensity for ion-pairing can often dictate the thermodynamic and kinetic properties of electrolyte solutions. Fast and accurate estimates of ion-pairing can thus be extremely valuable for supplementing design and screening efforts for novel electrolytes. We introduce an efficient cluster model to estimate the local ion-pair potential-of-mean-force between ionic solutes in electrolytes.

Effect of diffusion constant on the morphology of dendrite growth in lithium metal batteries.

Lithium dendrites can lead to a short circuit and battery failure, and developing strategies for their suppression is of considerable importance. In this work, we study the growth of dendrites in a simple model system where the solvent is a continuum and the lithium ions are hard spheres that can deposit by sticking to existing spheres or the electrode surface. Using stochastic dynamics simulations, we investigate the effect of applied voltage and diffusion constant on the growth of dendrites.

Deep Eutectic Solvents: Molecular Simulations with a First-Principles Polarizable Force Field.

The unique properties of deep eutectic solvents make them useful in a variety of applications. In this work we develop a first-principles force field for reline, which is composed of choline chloride and urea in the molar ratio 1:2. We start with the symmetry adapted perturbation theory (SAPT) protocol and then make adjustments to better reproduce the structure and dynamics of the liquid when compared to first-principles molecular dynamics (FPMD) simulations.

Why Lithium Ions Stick to Some Anions and Not Others.

Designing battery electrolytes for lithium-ion batteries has been a topic of extensive research for decades. The ideal electrolyte must have a large conductivity as well as high Li transference number. The conductivity is very sensitive to the nature of the anions and dynamical correlations between ions.

Liquid-Liquid Phase Separation As the Second Step of Complex Coacervation.

Liquid-liquid phase separation (LLPS) between tyrosine- and arginine-rich peptides are of biological importance. To understand the interactions between proteins in the condensed phase in close analogy to complex coacervation, we run multiple umbrella calculations between oligomers containing tyrosine (pY) and arginine (pR). We find pR-pY complexation to be energetically driven.

Phase Behavior of Poly(ethylene oxide) in Room Temperature Ionic Liquids: A Molecular Simulation and Deep Neural Network Study.

The phase behavior of polymers in room temperature ionic liquids is a topic of considerable interest. In this work we study the phase diagram of poly(ethylene oxide) in four imidazolium ionic liquids (ILs) using molecular simulation. We develop united atom models for 1-butyl-2,3-dimethylimidazolium ([BMMIM]), 1-ethyl-2,3-dimethylimidazolium ([EMMIM]), and 1-ethyl-3-methylimidazolium ([EMIM]) in an analogous fashion to previously developed models for 1-butyl-3-methylimidazolium ([BMIM]) and tetrafluoroborate ([BF]) using symmetry-adapted perturbation theory.

Phase behavior of continuous-space systems: A supervised machine learning approach.

The phase behavior of complex fluids is a challenging problem for molecular simulations. Supervised machine learning (ML) methods have shown potential for identifying the phase boundaries of lattice models. In this work, we extend these ML methods to continuous-space systems.

A Transferable Polarizable Force Field for Urea Crystals and Aqueous Solutions.

Urea is an important chemical with many biological and industrial applications. In this work, we develop a first-principles polarizable force field for urea crystals and aqueous solutions within the symmetry-adapted perturbation theory (SAPT) protocol with the SWM4-NDP model for water. We make three adjustments to the SAPT force field protocol: We augment the carbonyl oxygen atom of urea with additional interaction sites in order to address the "chelated" bent double hydrogen bonds in urea, we reduce the polarizability of urea by a factor of 0.

Solvation Induced Ring Puckering Effect in Fluorinated Prolines and Its Inclusion in Classical Force Fields.

Strategic incorporation of fluorinated prolines can accelerate folding and increase thermal stability of proteins. It has been suggested that this behavior emerges from puckering effects induced by fluorination of the proline ring. We use electronic structure calculations to characterize the potential energy surface (PES) along puckering coordinates for a simple dipeptide model of proline and its fluorinated derivatives.

Nematic ordering of hard rods under strong confinement in a dense array of nanoposts.

The effect of confinement on the behavior of liquid crystals is interesting from a fundamental and practical standpoint. In this work, we report Monte Carlo simulations of hard rods in an array of hard nanoposts, where the surface-to-surface separations between nanoposts are comparable to or less than the length of hard rods. This particular system shows promise as a means of generating large-scale organization of the nematic liquid by introducing an entropic external field set by the alignment of nanoposts.

Driving Force for the Complexation of Charged Polypeptides.

The phase separation of oppositely charged polyelectrolytes in solution is of current interest. In this work, we study the driving force for polyelectrolyte complexation using molecular dynamics simulations. We calculate the potential of mean force between poly(lysine) and poly(glutamate) oligomers using three different force fields, an atomistic force field and two coarse-grained force fields.

Proper Thermal Equilibration of Simulations with Drude Polarizable Models: Temperature-Grouped Dual-Nosé-Hoover Thermostat.

An explicit treatment of electronic polarization is critically important to accurate simulations of highly charged or interfacial systems. Compared to the iterative self-consistent field (SCF) scheme, extended Lagrangian approaches are computationally more efficient for simulations that employ a polarizable force field. However, an appropriate thermostat must be chosen to minimize heat flow and ensure an equipartition of kinetic energy among all unconstrained system degrees of freedom.

Influence of Charge Scaling on the Solvation Properties of Ionic Liquid Solutions.

Scaled-charge force fields (FFs) are widely employed in the simulation of neat ionic liquids (ILs), where the charges on the ions are empirically scaled to approximately account for electronic polarization and/or charge transfer. Such charge scaling has been found to yield significant improvement in liquid-state thermodynamic and dynamic properties (when compared to experiment). However, the mean field approximation inherent in charge scaling becomes suspect when applied to IL mixtures or solutions.

Understanding the Properties of Ionic Liquids: Electrostatics, Structure Factors, and Their Sum Rules.

The properties of room-temperature ionic liquids (ILs) may be viewed as resulting from a balance of electrostatic interactions that can be tuned at short range but constrained to satisfy universal, asymptotic screening conditions. Short-range interactions and ion packing provide ample opportunity for chemical tunability, while asymptotic sum rules dictate that the long-range structure and charge oscillation be similar to those of molten alkali halide salts. In this work, we study the structure factors and long-range electrostatic interactions in six ILs.

Non-universality of the dynamic exponent in two-dimensional random media.

The diffusion of solutes in two-dimensional random media is important in diverse physical situations including the dynamics of proteins in crowded cell membranes and the adsorption on nano-structured substrates. It has generally been thought that the diffusion constant, D, should display universal behavior near the percolation threshold, i.e.

Ion-Specific Confined Water Dynamics in Convex Nanopores of Gemini Surfactant Lyotropic Liquid Crystals.

The impact of pore geometry and functionality on the dynamics of water nanoconfined in porous media are the subject of some debate. We report the synthesis and small-angle X-ray scattering (SAXS) characterization of a series of perdeuterated gemini surfactant lyotropic liquid crystals (LLCs), in which convex, water-filled nanopores of well-defined dimensions are lined with carboxylate functionalities. Quasielastic neutron scattering (QENS) measurements of the translational water dynamics in these dicarboxylate LLC nanopores as functions of the surfactant hydration state and the charge compensating counterion (Na, K, NMe) reveal that the measured dynamics depend primarily on surfactant hydration, with an unexpected counterion dependence that varies with hydration number.

Influence of Electronic Polarization on the Structure of Ionic Liquids.

The liquid structure and electrical screening ability of ionic liquids are fundamentally intertwined. The molecular nature of the charge carriers means that screening distances of external fields depend sensitively on the ion packing and structure of the ionic liquid. In this work, we quantitatively illustrate how the liquid structure itself is directly modulated by electrostatic screening conditions.