arXiv subjects

Ji Woong Yu

Publications and source records attributed to Ji Woong Yu.

3 recordsLinked to original sources

arXiv2024

Depletion interaction between cylindrical inclusions in polymer brushes

Inclusions in mobile brushes experience apparent (depletion) attraction, which arises from a tendency to minimize the volume of depletion zones around the inclusions, thereby to maximize the entropy of the surrounding polymers. Here, we study the brush-induced depletion attraction between cylindrical inclusions using molecular dynamics simulations and the Asakura-Oosawa theory. Our considerations find that the correlation blobs defined in the brush environment serve as the fundamental units of the attraction. In tall brushes, however, the entropy of the overgrown polymer competes with the depletion attraction between the inclusions. As a result, the brush-induced depletion interaction displays non-monotonic variations with the brush height. Our study not only expands the repertoire of colloid-polymer mixtures to depletion interactions in brushes, but also suggests the brush-induced depletion interaction as a previously unappreciated mechanism for glycocalyx-induced protein cluster formation on cell surfaces.

cond-mat.soft↗

arXiv2021

A2I Transformer: Permutation-equivariant attention network for pairwise and many-body interactions with minimal featurization

The combination of neural network potential (NNP) with molecular simulations plays an important role in an efficient and thorough understanding of a molecular system's potential energy surface (PES). However, grasping the interplay between input features and their local contribution to NNP is growingly evasive due to heavy featurization. In this work, we suggest an end-to-end model which directly predicts per-atom energy from the coordinates of particles, avoiding expert-guided featurization of the network input. Employing self-attention as the main workhorse, our model is intrinsically equivariant under the permutation operation, resulting in the invariance of the total potential energy. We tested our model against several challenges in molecular simulation problems, including periodic boundary condition (PBC), $n$-body interaction, and binary composition. Our model yielded stable predictions in all tested systems with errors significantly smaller than the potential energy fluctuation acquired from molecular dynamics simulations. Thus, our work provides a minimal baseline model that encodes complex interactions in a condensed phase system to facilitate the data-driven analysis of physicochemical systems.

physics.comp-ph↗

arXiv2020

Active microrheology of a bulk metallic glass

The glass transition remains unclarified in condensed matter physics. Investigating the mechanical properties of glass is challenging because any global deformation that may result in shear rejuvenation requires an astronomical relaxation time. Moreover, it is well known that a glass is heterogeneous and a global perturbation cannot explore local mechanical/transport properties. However, an investigation based on a local probe, i.e. microrheology, may overcome these problems. Here, we establish active microrheology of a bulk metallic glass: a probe particle driven into host medium glass. This is a technique amenable for experimental investigations. We show that upon cooling the microscopic friction exhibits a second-order phase transition; this sheds light on the origin of friction in heterogeneous materials. Further, we provide distinct evidence to demonstrate that a strong relationship exists between the microscopic dynamics of the probe particle and the macroscopic properties of the host medium glass. These findings establish active microrheology as a promising technique for investigating the local properties of bulk metallic glass.

cond-mat.soft↗