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Many methods have been developed to predict static protein structures, however understanding the dynamics of protein structure is essential for elucidating biological function. While molecular dynamics (MD) simulations remain the in silico…
We construct the molecular model and the tensor model for the dynamics of the nematic phases of bent-core molecules and star molecules in incompressible fluid. We start from the molecular interaction and the molecule--fluid friction, and…
By combining methods of kinetic and density functional theory, we present a description of molecular fluids which accounts for their microscopic structure and thermodynamic properties as well as for the hydrodynamic behavior. We focus on…
The nature of glassy states in realistic finite dimensions is still under fierce debate. Lattice models can offer valuable insights and facilitate deeper theoretical understanding. Recently, a disordered-interacting lattice model with…
Despite decades of research, the modeling of moving contact lines has remained a formidable challenge in fluid dynamics whose resolution will impact numerous industrial, biological, and daily life applications. On the one hand, molecular…
In this work, we aimed to replicate and extend the results presented in the DiffFluid paper[1]. The DiffFluid model showed that diffusion models combined with Transformers are capable of predicting fluid dynamics. It uses a denoising…
Modern computational science and engineering applications are being improved by the advances in scientific machine learning. Data-driven methods such as Dynamic Mode Decomposition (DMD) can extract coherent structures from spatio-temporal…
Efficient molecular dynamics (MD) simulation is vital for understanding atomic-scale processes in materials science and biophysics. Traditional density functional theory (DFT) methods are computationally expensive, which limits the…
Molecular Dynamics (MD) codes predict the fundamental properties of matter by following the trajectories of a collection of interacting model particles. To exploit diverse modern manycore hardware, efficient codes must use all available…
We present a data-driven method for separating complex, multiscale systems into their constituent time-scale components using a recursive implementation of dynamic mode decomposition (DMD). Local linear models are built from windowed…
DNA-interacting proteins have roles multiple processes, many operating as molecular machines which undergo dynamic metastable transitions to bring about their biological function. To fully understand this molecular heterogeneity, DNA and…
Inspired by recent progress in dynamic programming approaches for weighted model counting, we investigate a dynamic-programming approach in the context of boolean realizability and synthesis, which takes a conjunctive-normal-form boolean…
Emergent phenomena share the fascinating property of not being obvious consequences of the design of the system in which they appear. This characteristic is no less relevant when attempting to simulate such phenomena, given that the outcome…
For molecular dynamics simulations of hard particles, we define dynamic neighbors as the distinct particles that collide with a given reference one during a specific time interval. This definition allows us to determine the distribution of…
Controlling polymorphism in molecular crystals is crucial in the pharmaceutical, dye, and pesticide industries. However, its theoretical description is extremely challenging, due to the associated long timescales ($ > 1 \, \mu s$). We…
Tracer-diffusion of small molecules through dense systems of chain polymers is studied within an athermal lattice model, where hard core interactions are taken into account by means of the site exclusion principle. An approximate mapping of…
The output of molecular dynamics simulations is high-dimensional, and the degrees of freedom among the atoms are related in intricate ways. Therefore, a variety of analysis frameworks have been introduced in order to distill complex motions…
Over times shorter than that required for relaxation of enthalpy, a liquid can exhibit striking heterogeneities. The picture of these heterogeneities is complex with transient patches of rigidity, irregular yet persistent, intersected by…
In recent years, soft robotics simulators have evolved to offer various functionalities, including the simulation of different material types (e.g., elastic, hyper-elastic) and actuation methods (e.g., pneumatic, cable-driven, servomotor).…
Stress tensors are derived for the multiparticle collision dynamics algorithm, a particle-based mesoscale simulation method for fluctuating fluids, resembling those of atomistic or molecular systems. Systems with periodic boundary…