Related papers: Chemistry Across Multiple Phases (CAMP) version 1.…
A model of multicellular systems with several types of cells is developed from the phase field model. The model is presented as a set of partial differential equations of the field variables, each of which expresses the shape of one cell.…
We report a novel hybrid method of simultaneous atomistic simulation of solids in critical regions (contacts surfaces, cracks areas, etc.), along with continuum modeling of other parts. The continuum is treated in terms of quasi-atoms of…
Multiphase gas, with hot ($\sim10^6$K) and cold ($\sim10^4$K) gas, is ubiquitous in astrophysical media across a wide range of scales. However, simulating multiphase gas has been a long-standing challenge, due to the large separation…
Multiphase systems are ubiquitous in engineering, biology, and materials science, where understanding their complex interactions and rheological behavior is crucial for advancing applications ranging from emulsion stability to cellular…
We introduce a mathematical framework for retrosynthetic analysis, an important research method in synthetic chemistry. Our approach represents molecules and their interaction using string diagrams in layered props - a recently introduced…
A new, more comprehensive model of gas-grain chemistry in hot molecular cores is presented, in which nondiffusive reaction processes on dust-grain surfaces and in ice mantles are implemented alongside traditional diffusive surface/bulk-ice…
In this paper, a mathematical model is developed to describe the evolution of the concentration of compounds through a gas chromatography column. The model couples mass balances and kinetic equations for all components. Both single and…
Multi-phase phenomena remain at the heart of many challenging fluid dynamics problems. Molecular fluxes at the interface determine the fate of neighboring phases, yet their closure far from the continuum needs to be modeled. Along the…
Stochastic chemical systems with diffusion are modeled with a reaction-diffusion master equation. On a macroscopic level, the governing equation is a reaction-diffusion equation for the averages of the chemical species. On a mesoscopic…
Performing alchemical transformations, in which one molecular system is nonphysically changed to another system, is a popular approach adopted in performing free energy calculations associated with various biophysical processes, such as…
A coarse-grained model for solutions of polymers in supercritical fluids is introduced and applied to the system of hexadecane and carbon dioxide as a representative example. Fitting parameters of the model to the gas-liquid critical point…
MCPlas is introduced as a powerful tool for automated fluid model generation with application to the analysis of dielectric barrier discharges operating in different regimes. MCPlas consists of a number of…
Computer simulation is an important tool for scientific progress, especially when lab experiments are either extremely costly and difficult or lack the required resolution. However, all of the simulation methods come with limitations. In…
This work expands on our recently introduced low Mach enthalpy method [1] for simulating the melting and solidification of a phase change material (PCM) alongside (or without) an ambient gas phase. The method captures PCM's volume change…
We present a phase field-based electro-chemo-mechanical formulation for modelling mechanics-enhanced corrosion and hydrogen-assisted cracking in elastic-plastic solids. A multi-phase-field approach is used to present, for the first time, a…
Chemical reactions are the fundamental building blocks of drug design and organic chemistry research. In recent years, there has been a growing need for a large-scale deep-learning framework that can efficiently capture the basic rules of…
There are various methods for modeling phase transformations in materials science, including general classes of phase-field methods and reactive diffusion methodologies, which most importantly differ in their treatment of interface energy.…
We have designed an improved algorithm that enables us to simulate the chemistry of cold dense interstellar clouds with a full gas-grain reaction network. The chemistry is treated by a unified microscopic-macroscopic Monte Carlo approach…
Soft condensed matter structures often challenge us with complex many-body phenomena governed by collective modes spanning wide spatial and temporal domains. In order to successfully tackle such problems mesoscopic coarse-grained (CG)…
In this paper, we consider a class of models for multiphase fluids, in the framework of mixture theory. The considered system, in its more general form, contains both the gradient of a hydrostatic pressure, generated by an incompressibility…