相关论文: Modelling an Ammonium Transporter with SCLS

Several stochastic simulation algorithms (SSAs) have been recently proposed for modelling reaction-diffusion processes in cellular and molecular biology. In this paper, two commonly used SSAs are studied. The first SSA is an on-lattice…

Generating semantic layout from scene graph is a crucial intermediate task connecting text to image. We present a conceptually simple, flexible and general framework using sequence to sequence (seq-to-seq) learning for this task. The…

Recent advances in the spectroscopy of biomolecules have highlighted the possibility of quantum coherence playing an active role in biological energy transport. The revelation that quantum coherence can survive in the hot and wet…

The stochastic block model (SBM) is a probabilistic model for community structure in networks. Typically, only the adjacency matrix is used to perform SBM parameter inference. In this paper, we consider circumstances in which nodes have an…

Sediment transport is studied as a function of the grain to fluid density ratio using two phase numerical sim- ulations based on a discrete element method (DEM) for particles coupled to a continuum Reynolds averaged description of…

We investigate the effects of bacterial activity on the mixing and transport properties of a passive scalar in time-periodic flows in experiments and in a simple model. We focus on the interactions between swimming E. coli and the…

Chemically or optically powered active matter plays an increasingly important role in materials design but its computational potential has yet to be explored systematically. The competition between energy consumption and dissipation imposes…

Earth system models (ESMs) are fundamental for understanding Earth's complex climate system. However, the computational demands and storage requirements of ESM simulations limit their utility. For the newly published CESM2-LENS2 data, which…

We construct a climatology of Lagrangian coherent structures (LCSs), the concealed skeleton that shapes transport, with a twelve-year-long data-assimilative simulation of the sea-surface circulation in the Gulf of Mexico (GoM). Computed as…

The Lattice Boltzmann Method (LBM) is a computational technique of Computational Fluid Dynamics (CFD) that has gained popularity due to its high parallelism and ability to handle complex geometries with minimal effort. Although LBM…

Static and dynamic structure factors and various transport coefficients are computed for a Lennard-Jones model of a binary fluid (A,B) with a symmetrical miscibility gap, varying both temperature and relative concentration of the mixture.…

Sequencing batch reactors (SBRs) are devices widely used in wastewater treatment, chemical engineering, and other areas. They allow for the sedimentation and compression of solid particles of biomass simultaneously with biochemical…

The efficiency of nanoparticle (NP) solar cells has grown impressively in recent years, exceeding 16%. However, the carrier mobility in NP solar cells, and in other optoelectronic applications remains low, thus critically limiting their…

Single-cell RNA sequencing (scRNA-seq) allows transcriptional profiling, and cell-type annotation of individual cells. However, sample preparation in typical scRNA-seq experiments often homogenizes the samples, thus spatial locations of…

Modeling dynamical biological systems is key for understanding, predicting, and controlling complex biological behaviors. Traditional methods for identifying governing equations, such as ordinary differential equations (ODEs), typically…

This paper introduces a stochastic hybrid system (SHS) framework in state space model to capture sensor, communication, and system contingencies in modern power systems (MPS). Within this new framework, the paper concentrates on the…

Modeling of electron transport through organic molecules is presented in order to interpret the experimental data of Rosink et al. [PRB 62, 10459 (2000)]. Such results are understand as coherent off-resonance tunneling through the junction…

The integration of large language models (LLMs) into public transit systems presents a transformative opportunity to enhance urban mobility. This study explores the potential of LLMs to revolutionize public transportation management within…

Stochastic multi-scale modeling and simulation for nonlinear thermo-mechanical problems of composite materials with complicated random microstructures remains a challenging issue. In this paper, we develop a novel statistical higher-order…

We present sMolBoxes, a dataflow representation for the exploration and analysis of long molecular dynamics (MD) simulations. When MD simulations reach millions of snapshots, a frame-by-frame observation is not feasible anymore. Thus,…