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Francis W. Starr

Publications and source records attributed to Francis W. Starr.

At least 19 recordsLinked to original sources

Computationally Efficient Machine-Learned Model for GST Phase Change Materials via Direct and Indirect Learning

Phase change materials such as Ge$_{2}$Sb$_{2}$Te$_{5}$ (GST) are ideal candidates for next-generation, non-volatile, solid-state memory due to the ability to retain binary data in the amorphous and crystal phases, and rapidly transition between these phases to write/erase information. Thus, there is wide interest in using molecular modeling to study GST. Recently, a Gaussian Approximation Potential (GAP) was trained for GST to reproduce Density Functional Theory (DFT) energies and forces at a fraction of the computational cost [Zhou et al. Nature Electronics $\mathbf{6}$, 746-754 (2023)]; however, simulations of large length and time scales are still challenging using this GAP model. Here we present a machine-learned (ML) potential for GST implemented using the Atomic Cluster Expansion (ACE) framework. This ACE potential shows comparable accuracy to the GAP potential but performs orders of magnitude faster. We train the ACE potentials both directly from DFT, as well as using a recently introduced indirect learning approach where the potential is trained instead from an intermediate ML potential, in this case, GAP. Indirect learning allows us to consider a significantly larger training set than could be generated using DFT alone. We compare the directly and indirectly learned potentials and find that both reproduce the structure and thermodynamics predicted by the GAP, and also match experimental measures of GST structure. The speed of the ACE model, particularly when using GPU acceleration, allows us to examine repeated transitions between crystal and amorphous phases in device-scale systems with only modest computational resources.

cond-mat.mtrl-sci

Collective Motion in the Interfacial and Interior Regions of Supported Polymer Films and its Relation to Relaxation

To understand the role of collective motion in the often large changes in interfacial molecular mobility observed in polymer films, we investigate the extent of collective motion in the interfacial regions of a thin supported polymer film and within the film interior by molecular dynamics simulation. Contrary to commonly stated expectations, we find that the extent of collective motion, as quantified by string-like molecular exchange motion, is similar in magnitude in polymer-air interfacial layer to that in the film interior, and both are generally distinct from the bulk material. This finding is consistent with Adam-Gibbs description of the segmental dynamics within mesoscopic film regions where the extent of collective motion is related to the configurational entropy of the film as whole rather than a locally defined extent of collective motion or configurational entropy.

cond-mat.soft

Influence of sample preparation on the transformation of low-density to high-density amorphous ice: An explanation based on the Potential Energy Landscape

Experiments and computer simulations of the transformations of amorphous ices display different behavior depending on sample preparation methods, and on the rates of change of temperature and pressure to which samples are subjected. In addition to these factors, simulation results also depend strongly on the chosen water model. Using computer simulations of the ST2 water model, we study how the sharpness of the compression-induced transition from low-density amorphous ice (LDA) to high-density amorphous ice (HDA) is influenced by the preparation of LDA. By studying LDA samples prepared using widely different procedures, we find that the sharpness of the LDA-to- HDA transformation is correlated with the depth of the initial LDA sample in the potential energy landscape (PEL), as characterized by the inherent structure energy. Our results show that the complex phenomenology of the amorphous ices reported in experiments and computer simulations can be understood and predicted in a unified way from a knowledge of the PEL of the system.

cond-mat.stat-mech

Potential Energy Landscape of the Apparent First-Order Phase Transition between Low-Density and High-Density Amorphous Ice

The potential energy landscape (PEL) formalism is a valuable approach within statistical mechanics for describing supercooled liquids and glasses. Here we use the PEL formalism and computer simulations to study the pressure-induced transformations between low-density amorphous ice (LDA) and high-density amorphous ice (HDA) at different temperatures. We employ the ST2 water model for which the LDA-HDA transformations are remarkably sharp, similar to what is observed in experiments, and reminiscent of a first-order phase transition. Our results are consistent with the view that LDA and HDA configurations are associated with two distinct regions (megabasins) of the PEL that are separated by a potential energy barrier. At higher temperature, we find that low-density liquid (LDL) configurations are located in the same megabasin as LDA, and that high-density liquid (HDL) configurations are located in the same megabasin as HDA. We show that the pressure-induced LDL-HDL and LDA-HDA transformations occur along paths that interconnect these two megabasins, but that the path followed by the liquid is different than the path followed by the amorphous solid. At higher pressure, we also study the liquid-to-ice-VII first-order phase transition, and find that the behavior of the PEL properties across this transition are qualitatively similar to the changes found during the LDA-HDA transformation. This similarity supports the interpretation that the LDA-HDA transformation is a first-order-like phase transition between out-of-equilibrium states.

cond-mat.stat-mech

A Unifying Framework to Quantify the Effects of Substrate Interactions, Stiffness, and Roughness on the Dynamics of Thin Supported Polymer Films

Changes in the dynamics of supported polymer films in comparison to bulk materials involve a complex convolution of effects, such as substrate interactions, roughness and compliance, in addition to film thickness. We consider molecular dynamics simulations of substrate-supported, coarse-grained polymer films where these parameters are tuned separately to determine how each of these variables influence the molecular dynamics of thin polymer films. We find that all these variables significantly influence the film dynamics, leading to a seemingly intractable degree of complexity in describing these changes. However, by considering how these constraining variables influence string-like collective motion within the film, we show that all our observations can be understood in a unified and quantitative way. More specifically, the string model for glass-forming liquids implies that the changes in the structural relaxation of these films are governed by the changes in the average length of string-like cooperative motions and this model is confirmed under all conditions considered in our simulations. Ultimately, these changes are parameterized in terms of just the activation enthalpy and entropy for molecular organization, which have predictable dependences on substrate properties and film thickness, offering a promising approach for the rational design of film properties.

cond-mat.soft

The Relationship of Dynamical Heterogeneity to the Adam-Gibbs and Random First-Order Transition Theories of Glass Formation

We carefully examine common measures of dynamical heterogeneity for a model polymer melt and test how these scales compare with those hypothesized by the Adam and Gibbs (AG) and random first-order transition (RFOT) theories of relaxation in glass-forming liquids. To this end, we first analyze clusters of highly mobile particles, the string-like collective motion of these mobile particles, and clusters of relative low mobility. We show that the time scale of the high-mobility clusters and strings is associated with a diffusive time scale, while the low-mobility particles' time scale relates to a structural relaxation time. We find a high degree of similarity in the geometrical structure of these particle clusters. In particular, we show that the fractal dimensions of these clusters are consistent with those of swollen branched polymers or branched polymers with screened excluded-volume interactions. In contrast, the fractal dimension of the strings crosses over from that of self-avoiding walks for small strings, to simple random walks for longer, {more strongly interacting, strings, corresponding to flexible polymers with screened excluded-volume interactions. We examine the appropriateness of identifying the size scales of either mobile particle clusters or strings with the size of cooperatively rearranging regions (CRR) in the AG and RFOT theories. We find that the string size appears to be the most consistent measure of CRR for both the AG and RFOT models. Identifying strings or clusters with the "mosaic" length of the RFOT model relaxes the conventional assumption that the "entropic droplets" are compact. We also confirm the validity of the entropy formulation of the AG theory, constraining the exponent values of the RFOT theory. This constraint, together with the analysis of size scales, enables us to estimate the characteristic exponents of RFOT.

cond-mat.soft

Dynamical Behavior Near a Liquid-Liquid Phase Transition in Simulations of Supercooled Water

We examine the behavior of the diffusion coefficient of the ST2 model of water over a broad region of the phase diagram via molecular dynamics simulations. The ST2 model has an accessible liquid-liquid transition between low-density and high-density phases, making the model an ideal candidate to explore the impacts of the liquid-liquid transition on dynamics. We locate characteristic dynamical loci in the phase diagram and compare them with the previously investigated thermodynamic loci. The low-density liquid phase shows a crossover from non-Arrhenius to Arrhenius behavior, signaling the onset of a crossover from fragile-to-strong behavior. We explain this crossover in terms of the asymptotic approach of the low-density liquid to a random tetrahedral network, and show that the temperature dependence of the diffusion coefficient over a wide temperature range can be simply related to the concentration of defects in the network. Our findings thus confirm that the low-density phase of ST2 water is a well-defined metastable liquid.

cond-mat.stat-mech

Modifying Fragility and Collective Motion in Polymer Melts with Nanoparticles

We investigate the impact of nanoparticles (NP) on the fragility and cooperative string-like motion in a model glass-forming polymer melt by molecular dynamics simulation. The NP cause significant changes to both the fragility and the average length of string-like motion, where the effect depends on the NP-polymer interaction and the NP concentration. We interpret these changes via the Adam-Gibbs (AG) theory, assuming the strings can be identified with the "cooperatively rearranging regions" of AG. Our findings indicate fragility is primarily a measure of the temperature dependence of the cooperativity of molecular motion.

cond-mat.soft

Universal two-step crystallization of DNA-functionalized nanoparticles

We examine the crystallization dynamics of nanoparticles reversibly tethered by DNA hybridization. We show that the crystallization happens readily only in a narrow temperature "slot," and always proceeds via a two-step process, mediated by a highly-connected amorphous intermediate. For lower temperature quenches, the dynamics of unzipping strands in the amorphous state is sufficiently slow that crystallization is kinetically hindered. This accounts for the well-documented difficulty of forming crystals in these systems. The strong parallel to the crystallization behavior of proteins and colloids suggests that these disparate systems crystallize in an apparently universal manner.

cond-mat.soft

Theoretical description of a DNA-linked nanoparticle self-assembly

Nanoparticles tethered with DNA strands are promising building blocks for bottom-up nanotechnology, and a theoretical understanding is important for future development. Here we build on approaches developed in polymer physics to provide theoretical descriptions for the equilibrium clustering and dynamics, as well as the self-assembly kinetics of DNA-linked nanoparticles. Striking agreement is observed between the theory and molecular modeling of DNA tethered nanoparticles.

cond-mat.soft

Influence of Nanoparticle Additives on the Fragility of Polymer Glass Formation and the Buchenau Relation

We investigate the impact of the addition of nanoparticles (NP) on the fragility of a model glass-forming polymer melt by molecular dynamics simulations. We find significant changes in fragility for nanoparticle volume fractions $ϕ$ exceeding $\approx$ 5%, where fragility changes correlate with the inverse variance of the magnitude of the Debye-Waller factor $ $, a measure of local "stiffness" fluctuations. We also confirm the validity of the Buchenau relationship between $ $ and the structural relaxation time $τ$ for all $ϕ$ and polymer-NP interaction types.

cond-mat.mtrl-sci

Interpenetration as a Mechanism for Liquid-Liquid Phase Transitions

We study simple lattice systems to demonstrate the influence of interpenetrating bond networks on phase behavior. We promote interpenetration by using a Hamiltonian with a weakly repulsive interaction with nearest neighbors and an attractive interaction with second-nearest neighbors. In this way, bond networks will form between second-nearest neighbors, allowing for two (locally) distinct networks to form. We obtain the phase behavior from analytic solution in the mean-field approximation and exact solution on the Bethe lattice. We compare these results with exact numerical results for the phase behavior from grand canonical Monte Carlo simulations on square, cubic, and tetrahedral lattices. All results show that these simple systems exhibit rich phase diagrams with two fluid-fluid critical points and three thermodynamically distinct phases. We also consider including third-nearest-neighbor interactions, which give rise to a phase diagram with four critical points and five thermodynamically distinct phases. Thus the interpenetration mechanism provides a simple route to generate multiple liquid phases in single-component systems, such as hypothesized in water and observed in several model and experimental systems. Additionally, interpenetration of many such networks appears plausible in a recently considered material made from nanoparticles functionalized by single strands of DNA.

cond-mat.soft

Hierarchies of networked phases induced by multiple liquid-liquid critical points

Functionalization of nanoparticles or colloids is increasingly being used to develop customizable "atoms". Functionalization by attaching single strands of DNA allows for direct control of the binding between nanoparticles, since hybridization of double strands will only occur if the base sequences of single strands are complementary. Nanoparticles and colloids functionalized by four single strands of DNA can be thought of as designed analogs to tetrahedral network forming atoms and molecules, with a difference that the attached DNA strands allow for control of the length scale of bonding relative to the core size. We explore the behavior of an experimentally realized model for a nanoparticles functionalized by four single strands of DNA (a tetramer), and show that this single-component model exhibits a rich phase diagram with at least three critical points and four thermodynamically distinct amorphous phases. We demonstrate that the additional critical points are part of the Ising universality class, like the ordinary liquid-gas critical point. The dense phases consist of a hierarchy of interpenetrating networks, reminiscent of a woven cloth. Thus bonding specificity of DNA provides an effective route to generate new nano-networked materials with polyamorphic behavior. The concept of network interpenetration helps to explain the generation of multiple liquid phases in single-component systems, suggested to occur in some atomic and molecular network forming fluids, including water and silica.

cond-mat.soft

Dynamical heterogeneities and the breakdown of the Stokes-Einstein and Stokes-Einstein-Debye relations in simulated water

We study the Stokes-Einstein (SE) and the Stokes-Einstein-Debye (SED) relations using molecular dynamics simulations of the extended simple point charge model of water. We find that both the SE and SED relations break down at low temperature. To explore the relationship between these breakdowns and dynamical heterogeneities (DH), we also calculate the SE and SED relations for subsets of the 7% ``fastest'' and 7% ``slowest'' molecules. We find that the SE and SED relations break down in both subsets, and that the breakdowns occur on all scales of mobility. Thus these breakdowns appear to be generalized phenomena, in contrast with the view where only the most mobile molecules are the origin of the breakdown of the SE and SED relations, embedded in an inactive background where these relations hold. At low temperature, the SE and SED relations in both subsets of molecules are replaced with ``fractional'' SE and SED relations, $D_t\sim(τ/T)^{-ξ_t}$ and $D_r\sim(τ/T)^{-ξ_r}$ where $ξ_t\approx0.84<1$ and $ξ_r\approx0.75<1$. We also find that there is a decoupling between rotational and translational motion, and that this decoupling occurs in both fastest and slowest subsets of molecules. We also find that when the decoupling increases, upon cooling, the probability of a molecule being classified as both translationally and rotationally fastest also increases. To study the effect of time scale for SE and SED breakdown and decoupling, we introduce a time-dependent version of the SE and SED relations, and a time-dependent function that measures the extent of decoupling. Our results suggest that both the decoupling and SE and SED breakdowns are originated at the time scale corresponding to the end of the cage regime, when diffusion starts. This is also the time scale when the DH are more relevant.

cond-mat.stat-mech

The Effect of Nanoparticle Shape on Polymer-Nanocomposite Rheology and Tensile Strength

Nanoparticles can influence the properties of polymer materials by a variety of mechanisms. With fullerene, carbon nanotube, and clay or graphene sheet nanocomposites in mind, we investigate how particle shape influences the melt shear viscosity $η$ and the tensile strength $τ$, which we determine via molecular dynamics simulations. Our simulations of compact (icosahedral), tube or rod-like, and sheet-like model nanoparticles indicate an order of magnitude increase in the viscosity $η$ relative to the pure melt. This finding evidently can not be explained by continuum hydrodynamics and we provide evidence that the $η$ increase in our model nanocomposites has its origin in chain bridging between the nanoparticles. We find that this increase is the largest for the rod-like nanoparticles and least for the sheet-like nanoparticles. Curiously, the enhancements of $η$ and $τ$ exhibit {\it opposite trends} with increasing chain length $N$ and with particle shape anisotropy. Evidently, the concept of bridging chains alone cannot account for the increase in $τ$ and we suggest that the deformability or flexibility of the sheet nanoparticles contributes to nanocomposite strength and toughness by reducing the relative value of the Poisson ratio of the composite. Our simulations point to a substantial contribution of nanoparticle shape to both mechanical and processing properties of polymer nanocomposites.

cond-mat.mtrl-sci

Effect of water-wall interaction potential on the properties of nanoconfined water

Much of the understanding of bulk liquids has progressed through study of the limiting case in which molecules interact via purely repulsive forces, such as a hard-core potential. In the same spirit, we report progress on the understanding of confined water by examining the behavior of water-like molecules interacting with planar walls via purely repulsive forces and compare our results with those obtained for Lennard-Jones (LJ) interactions between the molecules and the walls. Specifically, we perform molecular dynamics simulations of 512 water-like molecules which are confined between two smooth planar walls that are separated by 1.1 nm. At this separation, there are either two or three molecular layers of water, depending on density. We study two different forms of repulsive confinements, when the interaction potential between water-wall is (i) $1/r^9$ and (ii) WCA-like repulsive potential. We find that the thermodynamic, dynamic and structural properties of the liquid in purely repulsive confinements qualitatively match those for a system with a pure LJ attraction to the wall. In previous studies that include attractions, freezing into monolayer or trilayer ice was seen for this wall separation. Using the same separation as these previous studies, we find that the crystal state is not stable with $1/r^9$ repulsive walls but is stable with WCA-like repulsive confinement. However, by carefully adjusting the separation of the plates with $1/r^9$ repulsive interactions so that the effective space available to the molecules is the same as that for LJ confinement, we find that the same crystal phases are stable. This result emphasizes the importance of comparing systems only using the same effective confinement, which may differ from the geometric separation of the confining surfaces.

cond-mat.soft

Fractional Stokes-Einstein and Debye-Stokes-Einstein relations in a network forming liquid

We study the breakdown of the Stokes-Einstein (SE) and Debye-Stokes-Einstein (DSE) relations for translational and rotational motion in a prototypical model of a network-forming liquid, the ST2 model of water. We find that the emergence of ``fractional'' SE and DSE relations at low temperature is ubiquitous in this system, with exponents that vary little over a range of distinct physical regimes. We also show that the same fractional SE relation is obeyed by both mobile and immobile dynamical heterogeneities of the liquid.

cond-mat.soft

Model for Assembly and Gelation of Four-Armed DNA Dendrimers

We introduce and numerically study a model designed to mimic the bulk behavior of a system composed of single-stranded DNA dendrimers. Complementarity of the base sequences of different strands results in the formation of strong cooperative intermolecular links. We find that in an extremely narrow temperature range the system forms a large-scale, low-density disordered network via a thermo-reversible gel transition. By controlling the strand length, the gel transition temperature can be made arbitrarily close to the percolation transition, in contrast with recent model systems of physical gelation. This study helps the understanding of self-assembly in this class of new biomaterials and provides an excellent bridge between physical and chemical gels.

cond-mat.soft