Related papers: Root Cause Analysis of Hydrogen Bond Separation in…

We examine the phenomenon of dynamical heterogeneity in computer simulations of an equilibrium, glass-forming liquid. We describe several approaches to quantify the spatial correlation of single-particle motion, and show that spatial…

Intermolecular and long-range interactions are central to phenomena as diverse as gene regulation, topological states of quantum materials, electrolyte transport in batteries, and the universal solvation properties of water. We present a…

First shells of hydration and bulk solvent plays a crucial role in the folding of proteins. Here, the role of water in the dynamics of proteins has been investigated using a theoretical protein-solvent model and a statistical physics…

Machine learning approaches commonly rely on the assumption of independent and identically distributed (i.i.d.) data. In reality, however, this assumption is almost always violated due to distribution shifts between environments. Although…

In this study, we address causal inference when only observational data and a valid causal ordering from the causal graph are available. We introduce a set of flow models that can recover component-wise, invertible transformation of…

This article studies clogging phenomena using a velocity-based model for pedestrian dynamics. First, a method to identify prolonged clogs in simulations was introduced. Then bottleneck simulations were implemented with different initial and…

Most work on causality in machine learning assumes that causal relationships are driven by a constant underlying process. However, the flexibility of agents' actions or tipping points in the environmental process can change the qualitative…

A three-dimensional simulation model is proposed here to study the erosive wear of structure caused by solid particles, which accounts for the accumulation of surface deformation and degradation during the erosion process. Although there…

Modeling the dynamics of colloidal rods remains a central challenge in soft-matter physics due to the anisotropic and long-ranged nature of their interactions. Hydrodynamic interactions in rods suspensions are often assumed to be screened…

The coarse-grained molecular dynamics (MD) or Brownian dynamics (BD) simulation is a particle-based approach that has been applied to a wide range of biological problems that involve interactions with surrounding fluid molecules or the…

Effects of presence of ions, at moderate to high concentrations, on dynamical properties of water molecules are investigated through classical molecular dynamics simulations using two well known non-polarizable water models. Simulations…

Causal systems often exhibit variations of the underlying causal mechanisms between the variables of the system. Often, these changes are driven by different environments or internal states in which the system operates, and we refer to…

The microscopic description of the local structure of water remains an open challenge. Here, we adopt an agnostic approach to understanding water's hydrogen bond network using data harvested from molecular dynamics simulations of an…

Structural causal models postulate noisy functional relations among a set of interacting variables. The causal structure underlying each such model is naturally represented by a directed graph whose edges indicate for each variable which…

Multivariate time series anomaly detection has numerous real-world applications and is being extensively studied. Modeling pairwise correlations between variables is crucial. Existing methods employ learnable graph structures and graph…

Supercooled liquids exhibit spatial heterogeneity in the dynamics of their fluctuating atomic arrangements. The length and time scales of the heterogeneous dynamics are central to the glass transition and influence nucleation and growth of…

Finite mixture models are fitted to spherical data. Kent distributions are used for the components of the mixture because they allow considerable flexibility. Previous work on such mixtures has used an approximate maximum likelihood…

Due to the challenge posed by multi-source and heterogeneous data collected from diverse environments, causal relationships among features can exhibit variations influenced by different time spans, regions, or strategies. This diversity…

A hydrophilic liquid, such as water, forms hydrogen bonds with a hydrophilic substrate. The strength and locality of the hydrogen bonding interactions prohibit slip of the liquid over the substrate. The question then arises how the contact…

Context: Chemical models of dense cloud cores often utilize the so-called pseudo-time-dependent approximation, in which the physical conditions are held fixed and uniform as the chemistry occurs. In this approximation, the initial…