26 papers · ranked by Valyu relevance
Lin Deng, Suo Fan, Yun Zhang, Zhigao Huang + 7 more
'Shaofei Jiang' 'Jiquan Li' 'Célio Bruno Pinto Fernandes' 'Salah Aldin Faroughi' 'Luís L. Ferrás' 'Alexandre M. Afonso'] Modeling and simulation of the morphology evolution of immiscible polymer blends during injection molding is crucial for predicting and tailoring the products’ performance. This paper reviews the…
Mengke Ren, Junfeng Gu, Zheng Li, Shilun Ruan + 2 more
'Ming-Shyan Huang'] In this article, a multiscale simulation method of polymer melt injection molding filling flow is established by combining an improved smoothed particle hydrodynamics method and clustered fixed slip-link model. The proposed method is first applied to the simulation of HDPE melt in a classic…
Lionel Kusch, Sandra Diaz, Wouter Klijn, Kim Sontheimer + 3 more
Integration of information across heterogeneous sources creates added scientific value. It is, however, a challenge to progress, often a barrier, to interoperate data, tools and models across spatial and temporal scales. Here we present a design template for coupling simulators operating at different scales and…
Huandong Wang, Huan Yan, Can Rong, Yuan Yuan + 5 more
'Zhenyu Han' 'Hongjie Sui' 'Depeng Jin' 'Yong Li'] Complex system simulation has been playing an irreplaceable role in understanding, predicting, and controlling diverse complex systems. In the past few decades, the multi-scale simulation technique has drawn increasing attention for its remarkable ability to overcome…
Bin Sun, Alec Loftus, Peter Kekenes-Huskey
We review the Brownian dynamics (BD) modeling of biomolecular binding events, with an emphasis on enzyme-substrate interactions in cellular environments. We begin with theoretical foundations of BD and its applications to association and dissociation binding processes in both homogeneous and heterogeneous media. Next…
Matteo Capone, Marco Romanelli, Davide Castaldo, Giovanni Parolin + 3 more
The rise of modern computer science enabled physical chemistry to make enormous progresses in understanding and harnessing natural and artificial phenomena. Nevertheless, despite the advances achieved over past decades, computational resources are still insufficient to thoroughly simulate extended systems from first…
Xiaoming Liu, Kun Gao, Peng Chen, Lijun Yin + 2 more
'Norbert Robert Radek'] Nanowear-resistant coatings are critical for extending the service life of mechanical components, yet their performance optimization remains challenging due to the complex interplay between atomic-scale defects and macroscopic wear behavior. While experimental characterization struggles to…
Pariksheet Nanda, Maral Budak, Christian T. Michael, Kathryn Krupinsky + 1 more
Although infectious disease dynamics are often analyzed at the macro-scale, increasing numbers of drug-resistant infections highlight the importance of within-host modeling that simultaneously solves across multiple scales to effectively respond to epidemics. We review multiscale modeling approaches for complex…
Wacław Kuś, Waldemar Mucha, Iyasu Tafese Jiregna, Beomjoo Yang
Structures made of heterogeneous materials, such as composites, often require a multiscale approach when their behavior is simulated using the finite element method. By solving the boundary value problem of the macroscale model, for previously homogenized material properties, the resulting stress maps can be obtained.…
Authors not listed
Our study focused on the implementation and testing of machine learning interatomic potentials (MLIPs) into the AMBER software suite. This implementation enables us to perform a novel type of molecular dynamics simulation utilizing the hybrid machine learning/molecular mechanics (ML/MM) potentials. To underpin the…
Anupam Ojha, Lane Votapka, Gary Huber, Shang Gao + 1 more
SEEKR2 (Simulation enabled estimation of kinetic rates v. 2) is a powerful and versatile software tool designed to computationally estimate the kinetics and thermodynamics of complex molecular processes, particularly emphasizing the process of receptor-ligand binding and unbinding. We present a suite of tutorials for…
Junfeng Wang, Guohui Li
Computational chemistry methods are playing an increasingly pivotal role in chemical experiments. From quantum chemistry simulations to finite element simulations, researchers can always find an appropriate simulation method to elucidate the specific mechanisms at a certain resolution scale. However, in organic or…
Wenqiang Guo, Mikhail Sheremet, Tianbai Xiao, Yuan Hu + 1 more
In this work, the Simpson method is proposed to calculate the interface flux of a discrete unified gas kinetic scheme (DUGKS) according to the distribution function at the node and the midpoint of the interface, which is noted by Simpson-DUGKS. Moreover, the optimized DUGKS and Simpson-DUGKS considering the force term…
Authors not listed
We present the next generation of AMP, a neural network potential (NNP) with anisotropic message passing designed to study large biomolecular systems at DFT accuracy in the condensed phase using a multiscale approach similar to quantum-mechanics/molecular-mechanics (QM/MM) with electrostatic embedding. We trained AMPv3…
Giorgos Tatsios, Arun Kumar Chinnappan, Arshad Kamal, Nikolaos Vasileiadis + 6 more
'Nikolaos Vasileiadis' 'Stephanie Y. Docherty' 'Craig White' 'Livio Gibelli' 'Matthew K. Borg' 'James R. Kermode' 'Duncan A. Lockerby'] A new Micro-Macro-Surrogate (MMS) hybrid method is presented that couples the Direct Simulation Monte Carlo (DSMC) method with Computational Fluid Dynamics (CFD) to simulate low-speed…
Hao Jin, Sha Liu, Sirui Yang, Junzhe Cao + 2 more
The Direct Simulation Monte Carlo (DSMC) method provides a particle-based numerical solution to the Boltzmann equation, and is widely employed for simulating rarefied nonequilibrium gas flows. With advances in aerospace engineering and micro/nano-scale technologies, gas flows increasingly exhibit the coexistence of…
Yue Zhang, Wenpei Long, Junzhe Cao, Kun Xu
Simulating multiscale flows with moving boundaries, such as hypersonic multi-body separation and flows in micro-electro-mechanical systems (MEMS), requires robust numerical methods that couple mesh deformation with complex flow physics. This paper presents a hybrid overlapping moving-mesh technique developed within the…
Shubin Fu, Eric T. Chung, Lina Zhao
In this paper, we study the generalized multiscale finite element method (GMsFEM) for single phase compressible flow in highly heterogeneous porous media. We follow the major steps of the GMsFEM to construct permeability dependent offline basis for fast coarse-grid simulation. The offline coarse space is efficiently…
Parima Ahmadipour, Omid G. Sani, Bijan Pesaran, Maryam M. Shanechi
Learning dynamical latent state models for multimodal spiking and field potential activity can reveal their collective low-dimensional dynamics and enable better decoding of behavior through multimodal fusion. Toward this goal, developing unsupervised learning methods that are computationally efficient is important…
Sonata Kvedaravičiūtė, Andrej Antalík, Olivier Adjoua, Thomas Plé + 4 more
In this work, we present the development of a fully-polarizable KS-DFT/AMOEBA embedding scheme for delocalized basis sets such as plane-waves and real-space grids. The augmented problem of electron spill-out inherent to a polarizable QM/MM implementation with plane-wave basis sets is addressed and the periodicity for…
Christian Y Song, Han-Lin Hsieh, Bijan Pesaran, Maryam M Shanechi
Realizing neurotechnologies that enable long-term neural recordings across multiple spatial-temporal scales during naturalistic behaviors requires new modeling and inference methods that can simultaneously address two challenges. First, the methods should aggregate information across all activity scales from multiple…
S. L. Yang, Sha Liu, Junzhe Cao, Chengwen Zhong
Rykov model Authors: ['S. L. Yang' 'Sha Liu' 'Junzhe Cao' 'Chengwen Zhong'] During the past decades, the numerical methods based on Navier-Stokes (N-S) equations and direct simulation Monte Carlo (DSMC) methods have been proved effective in simulating flows in the continuum and rarefied regimes, respectively. However…
Martin Kutscherauer, Scott Anderson, Sebastian Böcklein, Gerhard Mestl + 2 more
Modeling catalytic fixed bed reactors with a small tube-to-particle diameter ratio requires a detailed description of the interactions between fluid flow, intra-particle transport, and the chemical reaction(s) within the catalyst. Particle-resolved computational fluid dynamics (PRCFD) simulations are the most promising…
Aaron Finney, Matteo Salvalaglio
Nucleation is the initial step towards the formation of crystalline materials from solutions. Various factors, such as environmental conditions, composition, and external fields, can influence its outcomes and rates. Indeed, controlling this rate-determining step towards phase separation can affect the resulting…
Authors not listed
Computing the free energy of protein-ligand binding by employing molecular dynamics (MD) simulations is becoming a valuable tool in the early stages of drug discovery. However, the cost and complexity of such simulations are often prohibitive for high-throughput studies. We present an automated workflow for the…
Authors not listed
Computational simulations of biomolecules provide a wealth of information about the thermodynamic landscape of biologically important systems, kinetics of important cellular processes, and the biophysical basis of life. Despite the ubiquity of molecular simulations in biophysical literature, major challenges persist…