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We develop a Split Reactive Brownian Dynamics (SRBD) algorithm for particle simulations of reaction-diffusion systems based on the Doi or volume reactivity model, in which pairs of particles react with a specified Poisson rate if they are…
Dislocations are the carriers of plasticity in crystalline materials. Their collective interaction behavior is dependent on the strain rate and sample size. In small specimens, details of the nucleation process are of particular importance.…
Integration of physics principles with data-driven methods has attracted great attention in recent few years. In this study, a physics-informed dynamic mode decomposition (piDMD) method, where the mass conservation law is integrated with a…
The present study explores combining machine learning (ML) algorithms with standard optical diagnostics (such as time-integrated emission spectroscopy and imaging) to accurately predict operating conditions and assess the emission…
This work presents the mathematical and computational aspects of a smooth dissipative particle dynamics with dynamic virtual particle allocation method (SDPD-DV) for modeling and simulation of mesoscopic fluids in wall-bounded domains. The…
Large language model (LLM) inference often suffers from high decoding latency and limited scalability across heterogeneous edge-cloud environments. Existing speculative decoding (SD) techniques accelerate token generation but remain…
We present Latent Diffeomorphic Dynamic Mode Decomposition (LDDMD), a new data reduction approach for the analysis of non-linear systems that combines the interpretability of Dynamic Mode Decomposition (DMD) with the predictive power of…
The dynamical properties of classical fluids at pico-liter scale attract experimentally and theoretically much attention in the soft-matter and biophysics communities, due to the appearance of the microfluidics, also called 'lab-on-a-chip',…
Dissipative particle dynamics (DPD) is a novel particle method for mesoscale modeling of complex fluids. DPD particles are often thought to represent packets of real atoms, and the physical scale probed in DPD models are determined by the…
Dissipative particle dynamics (DPD) belongs to a class of models and computational algorithms developed to address mesoscale problems in complex fluids and soft matter in general. It is based on the notion of particles that represent…
Discrete dislocation dynamics (DDD) is a widely employed computational method to study plasticity at the mesoscale that connects the motion of dislocation lines to the macroscopic response of crystalline materials. However, the…
Recent advances in light microscopy have spawned new research frontiers in microbiology by working around the diffraction barrier and allowing for the observation of nanometric biological structures. Microrheology is the study of the…
Soft particles suspended in fluids flowing through microchannels are often encountered in biological flows such as cells in vessels. They can deform under flow or when subject to mechanical stresses as they interact with themselves.…
We study the effect of varying the mass and volume fraction of a suspension of rigid spheres dispersed in a turbulent channel flow. We performed several Direct Numerical Simulations using an Immersed Boundary Method for finite-size…
Predicting the binding structure of a small molecule ligand to a protein -- a task known as molecular docking -- is critical to drug design. Recent deep learning methods that treat docking as a regression problem have decreased runtime…
Dissipative particle dynamics (DPD) is a relatively new technique which has proved successful in the simulation of complex fluids. We caution that for the equilibrium achieved by the DPD simulation of a simple fluid the temperature depends…
Standard Latent Diffusion Models rely on a complex, three-part architecture consisting of a separate encoder, decoder, and diffusion network, which are trained in multiple stages. This modular design is computationally inefficient, leads to…
Recent numerical analyses to optimize the design of microfluidic devices for more effective entrapment or segregation of surrogate circulating tumor cells (CTCs) from healthy cells have been reported in the literature without concurrently…
In this paper, we describe the unification and extension of multiple kinematic theories on the advection of colloidal particles through periodic obstacle lattices of arbitrary geometry and infinitesimally small obstacle size. We focus…
Confined active particles constitute simple, yet realistic, examples of systems that converge into a non-equilibrium steady state. We investigate a run-and-tumble particle in one spatial dimension, trapped by an external potential, with a…