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Biological membranes are self-assembled complex fluid interfaces that host proteins, molecular motors and other macromolecules essential for cellular function. These membranes have a distinct in-plane fluid response with a surface viscosity…
We demonstrate the application of the Dynamic Mode Decomposition (DMD) for the diagnostic analysis of the nonlinear dynamics of a magnetized plasma in resistive magnetohydrodynamics. The DMD method is an ideal spatio-temporal matrix…
Theoretical studies of protein folding on lattice models relie on the assumption that water close to amino-acids is always in thermal equilibrium all along the folding pathway. Within this framework, it has always been considered that…
In recent years, molecular dynamics (MD) simulations have emerged as a pivotal tool for understanding the structure, dynamics, and phase behavior in charged soft matter systems. To explore phenomena across greater length and time scales in…
Accurate and efficient plasma models are essential to understand and control experimental devices. Existing magnetohydrodynamic or kinetic models are nonlinear, computationally intensive, and can be difficult to interpret, while often only…
Active gel theory has recently been very successful in describing biologically active materials such as actin filaments or moving bacteria in temporally fixed and simple geometries such as cubes or spheres. Here we develop a computational…
Molecular models of real fluids are validated by comparing the vapor-liquid surface tension from molecular dynamics (MD) simulation to correlations of experimental data. The considered molecular models consist of up to 28 interaction sites,…
The diffusivity of water in aqueous cesium iodide solutions is larger than that in neat liquid water, and vice versa for sodium chloride solutions. Such peculiar ion-specific behavior, called anomalous diffusion, is not reproduced in…
Space plasma simulations have seen an increase in the use of magnetohydrodynamic (MHD) with embedded Particle-in-Cell (PIC) models. This combined MHD-EPIC algorithm simulates some regions of interest using the kinetic PIC method while…
We present a robust immersed boundary (IB) method for high density ratio multiphase flows that is capable of modeling complex wave-structure interaction (WSI) problems arising in marine and coastal engineering applications. The IB/WSI…
Numerical simulation of the complex plasma dynamics associated with high power, high frequency microwave breakdown at high pressures, leading to the formation of filamentary plasma structures such as self-organized plasma arrays, is a…
We present a method to simulate fluid flow on evolving surfaces, e.g., an oil film on a water surface. Given an animated surface (e.g., extracted from a particle-based fluid simulation) in three-dimensional space, we add a second simulation…
Understanding the nature of solvated electrons is important in studying a range of chemical and biological phenomena. This study investigates the structural and dynamical behavior of an excess electron in water, examining different…
We present a hybrid continuum-atomistic scheme which combines molecular dynamics (MD) simulations with on-the-fly machine learning techniques for the accurate and efficient prediction of multiscale fluidic systems. By using a Gaussian…
Massively-parallel molecular dynamics simulation is applied to systems containing electrolytes, vapour-liquid interfaces, and biomolecules in contact with water-oil interfaces. Novel molecular models of alkali halide salts are presented and…
Ultrafast, time-resolved spectroscopies enable the direct observation of non-equilibrium processes in condensed-phase systems and have revealed key insights into energy transport, hydrogen-bond dynamics, and vibrational coupling. While ab…
Generative models have achieved impressive results in many domains including image and text generation. In the natural sciences, generative models have led to rapid progress in automated drug discovery. Many of the current methods focus on…
Simultaneous Localization and Mapping (SLAM) systems are fundamental building blocks for any autonomous robot navigating in unknown environments. The SLAM implementation heavily depends on the sensor modality employed on the mobile…
We extend the use of the adaptive resolution method (AdResS) in its Grand Canonical-like version (GC-AdResS) to the molecular dynamics simulation of 1,3-dimethylimidazolium chloride. We show that the partitioning of the total system in a…
Molecular dynamics (MD) simulations present a data-mining challenge, given that they can generate a considerable amount of data but often rely on limited or biased human interpretation to examine their information content. By not asking the…