arXiv subjects

Homin Shin

Publications and source records attributed to Homin Shin.

12 recordsLinked to original sources

arXiv2026

A Comparative Study of Molecular Dynamics Approaches for Simulating Ionic Conductivity in Solid Lithium Electrolytes

Accurate prediction of ionic conductivity is critical for the design of high-performance solid-state electrolytes in next-generation batteries. We benchmark molecular dynamics (MD) approaches for computing ionic conductivity in 21 lithium solid electrolytes for which experimental ionic conductivity has been previously reported in the literature. In particular, we compare simulations driven by density functional theory (DFT) and by universal machine-learning interatomic potentials (uMLIPs), namely a MACE foundation model. We find comparable performance between DFT and MACE, despite MACE on one GPU more than 350 times faster than DFT on a 64-CPU node. The framework developed here is designed to enable systematic comparisons with additional uMLIPs and fine-tuned models in future work.

cond-mat.mtrl-sci↗

arXiv2025

OBELiX: A Curated Dataset of Crystal Structures and Experimentally Measured Ionic Conductivities for Lithium Solid-State Electrolytes

Solid-state electrolyte batteries are expected to replace liquid electrolyte lithium-ion batteries in the near future thanks to their higher theoretical energy density and improved safety. However, their adoption is currently hindered by their lower effective ionic conductivity, a quantity that governs charge and discharge rates. Identifying highly ion-conductive materials using conventional theoretical calculations and experimental validation is both time-consuming and resource-intensive. While machine learning holds the promise to expedite this process, relevant ionic conductivity and structural data is scarce. Here, we present OBELiX, a database of $\sim$600 synthesized solid electrolyte materials and their experimentally measured room temperature ionic conductivities gathered from literature and curated by domain experts. Each material is described by their measured composition, space group and lattice parameters. A full-crystal description in the form of a crystallographic information file (CIF) is provided for $\sim$320 structures for which atomic positions were available. We discuss various statistics and features of the dataset and provide training and testing splits carefully designed to avoid data leakage. Finally, we benchmark seven existing ML models on the task of predicting ionic conductivity and discuss their performance. The goal of this work is to facilitate the use of machine learning for solid-state electrolyte materials discovery.

cond-mat.mtrl-sci↗

arXiv2024

GAP-DFT: A graph-based alchemical perturbation density functional theory for catalytic high-entropy alloys

High-entropy alloys (HEAs) exhibit exceptional catalytic performance due to their complex surface structures. However, the vast number of active binding sites in HEAs, as opposed to conventional alloys, presents a significant computational challenge in catalytic applications. To tackle this challenge, robust methods must be developed to efficiently explore the configurational space of HEA catalysts. Here, we introduce a novel approach that combines alchemical perturbation density functional theory (APDFT) with a graph-based correction scheme to explore the binding energy landscape HEAs. Our results demonstrate that APDFT can accurately predict binding energies for isoelectronic permutations in HEAs at minimal computational cost, significantly accelerating configurational space sampling. However, APDFT errors increase substantially when permutations occur near binding sites. To address this issue, we developed a graph-based Gaussian process regression model to correct discrepancies between APDFT and conventional density functional theory values. Our approach enables the prediction of binding energies for hundreds of thousands of configurations with a mean average error of 30 meV, requiring a handful of ab initio simulations.

cond-mat.mtrl-sci↗

arXiv2011

Morphology of Nematic and Smectic Vesicles

Recent experiments on vesicles formed from block copolymers with liquid-crystalline side-chains reveal a rich variety of vesicle morphologies. The additional internal order ("structure") developed by these self-assembled block copolymer vesicles can lead to significantly deformed vesicles as a result of the delicate interplay between two-dimensional ordering and vesicle shape. The inevitable topological defects in structured vesicles of spherical topology also play an essential role in controlling the final vesicle morphology. Here we develop a minimal theoretical model for the morphology of the membrane structure with internal nematic/smectic order. Using both analytic and numerical approaches, we show that the possible low free energy morphologies include nano-size cylindrical micelles (nano-fibers), faceted tetrahedral vesicles, and ellipsoidal vesicles, as well as cylindrical vesicles. The tetrahedral vesicle is a particularly fascinating example of a faceted liquid-crystalline membrane. Faceted liquid vesicles may lead to the design of supra-molecular structures with tetrahedral symmetry and new classes of nano-carriers.

cond-mat.soft↗

arXiv2011

Filling the void in confined polymer nematics: phase transitions in a minimal model of dsDNA packing

Inspired to understand the complex spectrum of space-filling organizations the dsDNA genome within the capsid of bacterial viruses, we study a minimal, coarse-grained model of single chains densely-packed into a finite spherical volume. We build the three basic elements of the model--i) the absence of chain ends ii) the tendency of parallel-strand alignment and iii) a preference of uniform areal density of chain segments--into a polymer nematic theory for confined chains. Given the geometric constraints of the problem, we show that axially symmetric packings fall into one of three topologies: the coaxial spool; the simple solenoid; and the twisted-solenoid. Among these, only the twisted-solenoid fills the volume without the presence of line-like disclinations, or voids, and are therefore generically preferred in the incompressible limit. An analysis of the thermodynamics behavior of this simple model reveals a rich behavior, a generic sequence of phases from the empty state for small container sizes, to the coaxial spool configuration at intermediate sizes, ultimately giving way, via a second-order, symmetry-breaking transition, to the twisted-solenoid structure above a critical sphere size.

cond-mat.soft↗

arXiv2010

Structural Reorganization of Parallel Actin Bundles by Crosslinking Proteins: Incommensurate States of Twist

We construct a coarse-grained model of parallel actin bundles crosslinked by compact, globular bundling proteins, such as fascin and espin, necessary components of filapodial and mechanosensory bundles. Consistent with structural observations of bundles, we find that the optimal geometry for crosslinking is overtwisted, requiring a coherent structural change of the helical geometry of the filaments. We study the linker-dependent thermodynamic transition of bundled actin filaments from their native state to the overtwisted state and map out the "twist-state'' phase diagram in terms of the availability as well as the flexibility of crosslinker proteins. We predict that the transition from the uncrosslinked to fully-crosslinked state is highly sensitive to linker flexibility: flexible crosslinking smoothly distorts the twist-state of bundled filaments, while rigidly crosslinked bundles undergo a phase transition, rapidly overtwisting filaments over a narrow range of free crosslinker concentrations. Additionally, we predict a rich spectrum of intermediate structures, composed of alternating domains of sparsely-bound (untwisted) and strongly-bound (overtwisted) filaments. This model reveals that subtle differences in crosslinking agents themselves modify not only the detailed structure of parallel actin bundles, but also the thermodynamic pathway by which they form.

cond-mat.soft↗

arXiv2009

Cooperativity and Frustration in Protein-Mediated Parallel Actin Bundles

We examine the mechanism of bundling of cytoskeletal actin filaments by two representative bundling proteins, fascin and espin. Small-angle X-ray studies show that increased binding from linkers drives a systematic \textit{overtwist} of actin filaments from their native state, which occurs in a linker-dependent fashion. Fascin bundles actin into a continuous spectrum of intermediate twist states, while espin only allows for untwisted actin filaments and fully-overtwisted bundles. Based on a coarse-grained, statistical model of protein binding, we show that the interplay between binding geometry and the intrinsic \textit{flexibility} of linkers mediates cooperative binding in the bundle. We attribute the respective continuous/discontinous bundling mechanisms of fascin/espin to differences in the stiffness of linker bonds themselves.

cond-mat.soft↗

arXiv2009

Mesophases of soft-sphere aggregates

Soft spheres interacting via a hard core and range of attractive and repulsive "soft-shoulder" potentials self-assemble into clusters forming a variety of mesophases. We combine a mean field theory developed from a lattice model with a level surface analysis of the periodic structures of soft-sphere aggregates to study stable morphologies for all clustering potentials. We develop a systematic approach to the thermodynamics of mesophase assembly in the low-temperature, strong-segregation and predict a generic sequence of phases including lamella, hexagonal-columnar and body-center cubic phases, as well as the associated inverse structures. We discuss the finite-temperature corrections to strong segregation theory in terms of Sommerfeld-like expansion and how these corrections affect the thermodynamic stability of bicontinuous mesophase structures, such as gyroid. Finally, we explore the opposite limit of weakly-segregated particles, and predict the generic stability of a bicontinuous cluster morphology within the mean-field phase diagram.

cond-mat.soft↗

arXiv2008

Topological Defects in Spherical Nematics

We study the organization of topological defects in a system of nematogens confined to the two-dimensional sphere (S^2). We first perform Monte Carlo simulations of a fluid system of hard rods (spherocylinders) living in the tangent plane of S^2. The sphere is adiabatically compressed until we reach a jammed nematic state with maximum packing density. The nematic state exhibits four +1/2 disclinations arrayed on a great circle rather than at the vertices of a regular tetrahedron. This arises from the high elastic anisotropy of the system in which splay (K_1) is far softer than bending (K_3). We also introduce and study a lattice nematic model on S^2 with tunable elastic constants and map out the preferred defect locations as a function of elastic anisotropy. We establish the existence of a one-parameter family of degenerate ground states in the extreme splay-dominated limit K_1/K_3 -> 0. Thus the global defect geometry is controllable by tuning the relative splay to bend modulus.

cond-mat.soft↗

arXiv2007

Bubble Raft Model for a Paraboloidal Crystal

We investigate crystalline order on a two-dimensional paraboloid of revolution by assembling a single layer of millimeter-sized soap bubbles on the surface of a rotating liquid, thus extending the classic work of Bragg and Nye on planar soap bubble rafts. Topological constraints require crystalline configurations to contain a certain minimum number of topological defects such as disclinations or grain boundary scars whose structure is analyzed as a function of the aspect ratio of the paraboloid. We find the defect structure to agree with theoretical predictions and propose a mechanism for scar nucleation in the presence of large Gaussian curvature.

cond-mat.soft↗

arXiv2007

Interstitial Fractionalization and Spherical Crystallography

Finding the ground states of identical particles packed on spheres has relevance for stabilizing emulsions and a venerable history in the literature of theoretical physics and mathematics. Theory and experiment have confirmed that defects such as disclinations and dislocations are an intrinsic part of the ground state. Here we discuss the remarkable behavior of vacancies and interstitials in spherical crystals. The strain fields of isolated disclinations forced in by the spherical topology literally rip interstitials and vacancies apart, typically into dislocation fragments that combine with the disclinations to create small grain boundary scars. The fractionation is often into three charge-neutral dislocations, although dislocation pairs can be created as well. We use a powerful, freely available computer program to explore interstitial fractionalization in some detail, for a variety of power law pair potentials. We investigate the dependence on initial conditions and the final state energies, and compare the position dependence of interstitial energies with the predictions of continuum elastic theory on the sphere. The theory predicts that, before fragmentation, interstitials are repelled from 5-fold disclinations and vacancies are attracted. We also use vacancies and interstitials to study low energy states in the vicinity of "magic numbers" that accommodate regular icosadeltahedral tessellations.

cond-mat.soft↗

arXiv2007

Dynamics and Instabilities of Defects in Two-Dimensional Crystals on Curved Backgrounds

Point defects are ubiquitous in two dimensional crystals and play a fundamental role in determining their mechanical and thermodynamical properties. When crystals are formed on a curved background, finite length grain boundaries (scars) are generally needed to stabilize the crystal. We provide a continuum elasticity analysis of defect dynamics in curved crystals. By exploiting the fact that any point defect can be obtained as an appropriate combination of disclinations, we provide an analytical determination of the elastic spring constants of dislocations within scars and compare them with existing experimental measurements from optical microscopy. We further show that vacancies and interstitials, which are stable defects in flat crystals, are generally unstable in curved geometries. This observation explains why vacancies or interstitials are never found in equilibrium spherical crystals. We finish with some further implications for experiments and future theoretical work.

cond-mat.soft↗