Article
Computer Science, Interdisciplinary Applications
Joseph Bakarji, Daniel M. Tartakovsky
Summary: Statistical (machine learning) tools for equation discovery require large amounts of data, typically computer generated rather than experimentally observed. Learning on simulated data in areas such as multiscale modeling and stochastic simulations can lead to discovery. Our machine-learning strategy based on sparse regression replaces human discovery of models and can be executed in two modes.
JOURNAL OF COMPUTATIONAL PHYSICS
(2021)
Article
Environmental Sciences
Bin Deng, Wen Zhang, Yu Yao, Changbo Jiang
Summary: This study investigates the hydrodynamics of bore-driven swash flows over beaches with varying slopes through laboratory experiments. The impacts of beach slope on swash hydrodynamics and the formation and evolution of vortex structures are analyzed.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Mechanics
Fernando F. Grinstein, Juan A. Saenz, Massimo Germano
Summary: The study revisits coarse-grained simulation strategies for turbulent material mixing involving shock-driven turbulence, using newly available LMC-xRAGE hydrodynamics. Improved simulated mixing and turbulence levels on coarser grids were achieved, with the more accurate models requiring less resolution and resulting in grid-coarsening savings for mixing prediction.
Article
Mechanics
F. Le Roy De Bonneville, R. Zamansky, F. Risso, A. Boulin, J. -f. Haquet
Summary: This study presents a numerical method for simulating the flow induced by bubbles rising at large Reynolds numbers and accurately estimates the hydrodynamic force exerted by the liquid on the bubbles. The simulations show good agreement with experimental results, indicating potential applications in studying industrial bubble columns and large-scale systems.
JOURNAL OF FLUID MECHANICS
(2021)
Article
Chemistry, Physical
Shu Wang, Zhan Ma, Wenxiao Pan
Summary: This work focuses on building accurate and efficient coarse-grained models for non-equilibrium systems by using dynamic equations and non-stationary generalized Langevin equations, preserving non-equilibrium dynamics and being applicable to any non-equilibrium process and observable of interest.
Article
Chemistry, Physical
J. Charlie Maier, Nicholas E. Jackson
Summary: This paper introduces a flexible and scalable method for learning electronic property distributions using deep kernel learning electronic coarse-graining. The appropriateness of Gaussian prior and the limitations of predictive distributions are examined. The resolution dependence and strong electron-phonon coupling are analyzed for coarse-grained property distributions. The ability to construct exact quantum chemical electronic density of states is demonstrated, offering an alternative method to recover all-atom property distributions from CG simulations.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Saientan Bag, Melissa K. Meinel, Florian Mueller-Plathe
Summary: In this paper, a data-driven approach to generate coarse-grained models that preserve the all-atom molecular mobility is presented. The researchers designed an artificial neural network model that can predict the simulation-ready coarse-grained potential based on the input of all-atom force field parameters. Experimental results showed that the predicted coarse-grained potential can significantly reduce the artificial acceleration in molecular mobility, making the coarse-grained models more accurate.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Biochemistry & Molecular Biology
Zhaoqian Su, Kalyani Dhusia, Yinghao Wu
Summary: The enzyme cGAS recognizes foreign pathogen DNA, triggering inflammatory genes transcription and anti-pathogen state establishment. It has been discovered that the detection of DNA by cGAS induces the formation of liquid-like droplets, yet how cells regulate this process remains unclear.
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS
(2021)
Article
Materials Science, Ceramics
Wei Cui, Fei Li, Zhaobo Tian, Jie Zhang, Songmo Du, Zhanglin Chen, Kexin Chen, Guanghua Liu
Summary: Coarse-grained beta-Si3N4 powders were prepared by combustion synthesis with N-2 pressure of 6 MPa, low diluent content not exceeding 10 wt.%, and high reaction temperature above 1900 degrees C. The powders consisted of beta-Si3N4 crystals with an average thickness of over 10 μm, with some crystals thicker than 20 μm.
JOURNAL OF THE AMERICAN CERAMIC SOCIETY
(2021)
Article
Chemistry, Multidisciplinary
Ping Gao, Julien Nicolas, Tap Ha-Duong
Summary: This study utilized coarse-grained molecular dynamics simulations to investigate the self-assembly of four representative drug-polymer conjugates, revealing the spatial organization of components within the nanoparticles. It was observed that the linkers were not fully accessible to the solvent, which may account for the low drug release efficiency from the nanoparticles.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Mathematics, Applied
Y. O. U. N. G. M. I. N. Park, P. R. A. S. H. A. N. T. Singh, Thomas G. Fai
Summary: This article investigates the dynamics of membrane vesicle motor transport into dendritic spines in neurons using an agent-based model and coarse-graining method. The study confirms that the coarse-grained model captures the bistability in velocity and waiting-time distributions observed in experiments. The results provide a new formulation for the translocation problem.
SIAM JOURNAL ON APPLIED MATHEMATICS
(2022)
Article
Mathematics, Applied
Katherine Owens, J. Nathan Kutz
Summary: In this paper, we employ data-driven methods to determine the governing equations for the emergent behavior of heterogeneous networked dynamical systems. We demonstrate how our method automatically detects boundary structures in the dynamics and matches inner and outer solutions in a data-driven manner. The proposed framework allows for the discovery of coarse-grained variables and dynamics.
SIAM JOURNAL ON APPLIED DYNAMICAL SYSTEMS
(2023)
Article
Engineering, Chemical
Stefan Madlmeir, Stefan Radl
Summary: The Discrete Element Method (DEM) is commonly used for modeling the flow of particulate materials. To reduce computational demand, parcels are introduced by coarse graining, which requires sophisticated models to preserve the original behavior. This study extends the coarse-graining concepts by introducing models for particle-fluid mass transfer and spray deposition rate, enabling precise particle-droplet-air interaction modeling at low computational cost for spray coating processes.
ADVANCED POWDER TECHNOLOGY
(2022)
Article
Engineering, Chemical
Chih-Chia Huang, Jeroen A. van Oijen, Niels G. Deen, Yali Tang
Summary: The combination of coarse-graining discrete element method (CG-DEM) with the Flamelet Generated Manifold-Large Eddy Simulation (FGM-LES) approach reduces computational burden in simulating turbulent coal combustion. The developed method maintains good accuracy and cost-effectiveness compared to conventional reactive simulations. An optimal coarse-graining factor of 2 is determined for predicting pulverized coal flow dynamics and combustion performance effectively.
CHEMICAL ENGINEERING SCIENCE
(2022)
Article
Mathematics, Applied
Jordan Snyder, Jared L. Callaham, Steven L. Brunton, J. Nathan Kutz
Summary: In this study, Langevin regression was used to understand finite-size effects in the Kuramoto model of coupled oscillators, and it was found that the dynamics of the Kuramoto order parameter across the entire bifurcation diagram are statistically consistent with a certain form of SDE.
PHYSICA D-NONLINEAR PHENOMENA
(2021)
Article
Mechanics
M. Seddighi, S. He, D. Pokrajac, T. O'Donoghue, A. E. Vardy
JOURNAL OF FLUID MECHANICS
(2015)
Article
Engineering, Civil
D. Pokrajac, M. J. S. de Lemos
JOURNAL OF HYDRAULIC ENGINEERING
(2015)
Article
Acoustics
Honglin Wang, Alan E. Vardy, Dubrayka Pokrajac
JOURNAL OF SOUND AND VIBRATION
(2015)
Article
Engineering, Civil
Honglin Wang, Alan E. Vardy, Dubravka Pokrajac
JOURNAL OF WIND ENGINEERING AND INDUSTRIAL AERODYNAMICS
(2015)
Article
Engineering, Civil
D. Pokrajac, M. J. S. de Lemos
JOURNAL OF HYDRAULIC ENGINEERING
(2015)
Article
Oceanography
Jose Carlos Pintado-Patino, Alec Torres-Freyermuth, Jack A. Puleo, Dubravka Pokrajac
JOURNAL OF GEOPHYSICAL RESEARCH-OCEANS
(2015)
Article
Engineering, Civil
Bo-Tao Chen, Gustaaf Adriaan Kikkert, Dubravka Pokrajac, Han-Jing Dai
COASTAL ENGINEERING
(2016)
Article
Engineering, Civil
T. O'Donoghue, G. A. Kikkert, D. Pokrajac, N. Dodd, R. Briganti
COASTAL ENGINEERING
(2016)
Article
Geosciences, Multidisciplinary
Francesco Ballio, Dubravka Pokrajac, Alessio Radice, Seyed Abbas Hosseini Sadabadi
JOURNAL OF GEOPHYSICAL RESEARCH-EARTH SURFACE
(2018)
Article
Computer Science, Interdisciplinary Applications
S. Gorji, M. Seddighi, C. Ariyaratne, A. E. Vardy, T. O'Donoghue, D. Pokrajac, S. He
COMPUTERS & FLUIDS
(2014)
Editorial Material
Water Resources
D. Pokrajac, M. J. S. de Lemos
HYDROLOGICAL PROCESSES
(2014)
Article
Spectroscopy
Florian M. Zehentbauer, Claudia Moretto, Ryan Stephen, Thangavel Thevar, John R. Gilchrist, Dubravka Pokrajac, Katherine L. Richard, Johannes Kiefer
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2014)
Article
Mechanics
Sara Venuleo, Dubravka Pokrajac, Anton J. Schleiss, Mario J. Franca
Article
Engineering, Civil
Sara Venuleo, Dubravka Pokrajac, Talia Tokyay, George Constantinescu, Anton J. Schleiss, Mario J. Franca
Summary: Based on the results of large eddy simulation, this study investigates the sensitivity of gravity current depth results to definition, the impact of density and velocity profile nonuniformity on coefficients in depth-averaged continuity and momentum equations, and the sensitivity of entrainment coefficient to current depth definition. The study shows that different definitions of current depth can lead to significantly different numerical results, and the entrainment coefficient is more sensitive to parameterization than the definition of current depth.
JOURNAL OF HYDRAULIC ENGINEERING
(2021)
Article
Engineering, Civil
Honglin Wang, Alan E. Vardy, Dubravka Pokrajac
PROCEEDINGS OF THE INSTITUTION OF CIVIL ENGINEERS-ENGINEERING AND COMPUTATIONAL MECHANICS
(2016)