Article
Polymer Science
Dirk Grommes, Martin R. Schenk, Olaf Bruch, Dirk Reith
Summary: In this study, the thermo-mechanical relaxation and crystallization behavior of polyethylene were investigated using mesoscale molecular dynamics simulations. The results show how chain length, temperature, local entanglements, and orientation of chain segments influence crystallization and relaxation behavior. The temperature dependent crystallization rate of polyethylene, including crystallization onset temperature, was determined from the models.
Article
Polymer Science
Dirk Grommes, Martin R. Schenk, Olaf Bruch, Dirk Reith
Summary: This study investigates the initial stage of thermo-mechanical crystallization behavior for uni- and biaxially stretched polyethylene using a mesoscale molecular dynamics approach. The effects of stretching procedures on the micro-mechanical state of the systems are discussed, with a focus on entanglement behavior and nematic ordering of chain segments. The study reveals that the main stretching direction dominates the microscopic states of the different systems and that crystallization mainly depends on the (dis-)entanglement behavior, with nematic ordering playing a secondary role.
Article
Biochemistry & Molecular Biology
Adam Liwo, Cezary Czaplewski, Adam K. Sieradzan, Agnieszka G. Lipska, Sergey A. Samsonov, Rajesh K. Murarka
Summary: This review article discusses the physical basis, force fields, equations of motion, numerical integration algorithms, and applications of coarse-grained molecular dynamics. By integrating out secondary degrees of freedom, the motion of coarse-grained sites is controlled, leading to simulations at a coarse-grained level.
Article
Materials Science, Multidisciplinary
Katiana Kontolati, Darius Alix-Williams, Nicholas M. Boffi, Michael L. Falk, Chris H. Rycroft, Michael D. Shields
Summary: A generalized machine learning framework is proposed to probabilistically parameterize upper-scale models based on coarse-grained atomistic simulation data of mechanical deformation and flow processes. The framework utilizes manifold learning and surrogate-based optimization techniques to link coarse-grained microscale simulations to macroscale observables, achieving a high level of parity between the models across scales.
Article
Polymer Science
Anastassia Rissanou, Antonis Chazirakis, Patrycja Polinska, Craig Burkhart, Manolis Doxastakis, Vagelis Harmandaris
Summary: The study presents a bottom-up methodology to obtain coarse-grained models for copolymers through detailed atomistic simulations, using a dual-stage multi-component iterative Boltzmann inversion optimization scheme to derive effective CG interactions. The transferability of the PB copolymer model across molecular weight and copolymer composition is examined, with a focus on the impact of different isomers on conformational properties. The CG model is used to predict time mapping factors for segmental and center-of-mass dynamics of PB copolymers, showing potential applications in predicting polymer behavior.
Article
Optics
Carlos Pineda, David Davalos, Carlos Viviescas, Antonio Rosado
Summary: Using the quantum map formalism, a framework is provided to construct fuzzy and coarse-grained quantum maps for many-body systems that consider limitations in measurement device resolution. These maps are applied to a spin-1/2 XX chain to obtain a blurred picture of entanglement generation and propagation. It is shown that the volume of tomographically accessible states decreases at a double-exponential rate with the number of particles, imposing severe bounds on the ability to read and use information from a many-body quantum system.
Article
Mathematics, Applied
Michel Moreau, Bernard Gaveau
Summary: This article investigates the relationship between the evolution of mesoscopic systems and entropy, finding that under certain conditions, mesoscopic systems can be approximated by Markov processes and introduces the concept of Kolmogorov entropy. It demonstrates the connection between Kolmogorov entropy and basic aspects of time, such as irreversibility.
Article
Physics, Multidisciplinary
Nicolas Martzel
Summary: We first introduce the Zwanzig-Kawasaki version of the generalized Langevin equation and show that the commonly used term for the Markovian approximation of the dissipation is vanishing, necessitating the use of the next-order term. Independently, we provide a comprehensive description of complex coarse-grained molecules and derive their dynamics, which enriches considerably the dynamics at the coarse-grained level and could serve as a foundation for developing more holistic and accurate numerical models for complex molecular systems. This advancement opens up new possibilities for understanding and predicting the behavior of such systems in various scientific and engineering applications.
JOURNAL OF PHYSICS A-MATHEMATICAL AND THEORETICAL
(2023)
Article
Chemistry, Physical
Xiangyun Lei, Andrew J. Medford
Summary: Machine-learning force fields have limitations in scalability due to their use of element-specific features. This work introduces a new featurization scheme that utilizes Gaussian multipole expansions to generate feature vectors with fixed dimensions, regardless of the number of elements. The combination of this scheme with neural networks results in high computational efficiency and systematically improvable accuracy.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Materials Science, Multidisciplinary
A. A. Madadi, A. R. Khoei
Summary: In this paper, a multi-scale method is proposed to couple atomistic and coarse-grained systems for modeling the mechanical properties of materials with defects and heterogeneity. By combining Molecular Dynamics analysis with a coarse-grained approach, the method reduces computational costs and allows for the effective study of material behavior and properties.
COMPUTATIONAL MATERIALS SCIENCE
(2021)
Article
Mathematics, Interdisciplinary Applications
Moris Kalderon, Edward Smith, Catherine O'Sullivan
Summary: The discrete element method (DEM) is a well-established approach for studying granular materials in various fields of application, where each granular particle is modeled individually. Different coarse-graining methods have been proposed and reviewed in this work, with two novel porosity coarse-graining strategies being introduced and compared with existing methods. These methods are validated for accuracy and computational cost, providing users with options to adjust between accuracy and computational time.
COMPUTATIONAL PARTICLE MECHANICS
(2022)
Article
Oceanography
Angelina Cassianides, Camille Lique, Anne-Marie Treguier, Gianluca Meneghello, Charly De Marez
Summary: In this study, comprehensive data sets from Ice Tethered Profilers and moorings were analyzed to understand the dynamics of the ocean under sea ice in the Arctic Basin. It was found that the surface dynamics in seasonally ice-covered regions were greatly influenced by the presence of sea ice, while the influence of sea ice conditions on first order dynamics beyond these regions was less clear. The analysis also revealed a large variety of regimes in the sea ice pack, independent of time and space variations of sea ice conditions. The study highlighted the presence of hundreds of eddies in the subsurface layer, with potential impacts on sea ice locally.
JOURNAL OF GEOPHYSICAL RESEARCH-OCEANS
(2023)
Article
Physics, Condensed Matter
Fabian Berressem, Christoph Scherer, Denis Andrienko, Arash Nikoubashman
Summary: The study demonstrates that CG models with two-body potential interactions alone cannot accurately simulate stable polymer films and droplets, while CG simulations with a local density-dependent potential (LDP) can achieve this. Minor quantitative differences between reference and CG simulations, such as slightly broadened interfaces and reduced surface tension in the CG simulations, are attributed to the inability to resolve polymer deformations near interfaces in the CG representation.
JOURNAL OF PHYSICS-CONDENSED MATTER
(2021)
Article
Physics, Condensed Matter
Bing Li, Kostas Daoulas, Friederike Schmid
Summary: A dynamic coarse-graining scheme is proposed to map heterogeneous polymer fluids onto extremely CG models in a dynamically consistent manner, utilizing a wave-vector dependent mobility function and internal friction parameters. This method allows for mapping over a range of relevant wave vectors and constructing dynamically consistent CG models, suitable for homopolymers with a CG chain length of 4.
JOURNAL OF PHYSICS-CONDENSED MATTER
(2021)
Article
Biochemistry & Molecular Biology
Rafal Slusarz, Emilia A. Lubecka, Cezary Czaplewski, Adam Liwo
Summary: This paper reports the improvements and extensions of the UNRES server, including code optimization and the addition of a scale-consistent variant. The server has also been extended to handle data-assisted simulations with NMR and XL-MS restraints.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Engineering, Chemical
Michael C. Baker, Bo Kong, Jesse Capecelatro, Olivier Desjardins, Rodney O. Fox
Article
Engineering, Chemical
N. Panicker, A. Passalacqua, R. O. Fox
CHEMICAL ENGINEERING SCIENCE
(2020)
Article
Engineering, Chemical
A. D. Ilgun, A. Passalacqua, R. O. Fox
CHEMICAL ENGINEERING SCIENCE
(2020)
Article
Physics, Fluids & Plasmas
M. C. Baker, R. O. Fox, B. Kong, J. Capecelatro, O. Desjardins
PHYSICAL REVIEW FLUIDS
(2020)
Article
Thermodynamics
A. D. Ilgun, A. Passalacqua, R. O. Fox
Summary: Two solution algorithms were developed for conditional moment closure using quadrature-based moment methods, aiming to eliminate the need for additional grid. Both algorithms were tested for multi-step H 2 combustion and achieved expected results with at most six quadrature nodes. The proposed algorithms ensure constant scalar mean during molecular mixing, providing accurate, cost-effective, and direct alternatives to traditional CMC solution methods.
PROCEEDINGS OF THE COMBUSTION INSTITUTE
(2021)
Article
Mechanics
S. Beetham, R. O. Fox, J. Capecelatro
Summary: In this study, model closures for multiphase Reynolds-averaged Navier-Stokes (RANS) equations are developed using sparse regression and Eulerian-Lagrangian simulations to ensure accuracy and robustness of the models across different flow conditions. The focus is on capturing the dynamics of gas-particle flows, particularly the generation of particle clusters and interphase momentum exchange, in a compact and algebraic manner.
JOURNAL OF FLUID MECHANICS
(2021)
Article
Physics, Fluids & Plasmas
Elise Almeras, Frederic Risso, Olivier Masbernat, Rodney O. Fox
Summary: This study experimentally investigates a liquid-solid fluidized bed involving inertial particles at a large Reynolds number. The flow dynamics exhibit three distinctive properties, which allow for the derivation of a model for the probability density functions of the velocity fluctuations. This model accurately describes experimental data and captures unique features such as skewness of fluctuations and symmetry between different volume fractions.
PHYSICAL REVIEW FLUIDS
(2021)
Article
Mechanics
Alessio Innocenti, Rodney O. Fox, Sergio Chibbaro
Summary: Modeling particle-laden turbulent flows at high volume fractions requires considering the coupling between phases, which is not straightforward due to the sensitive nature of the interaction. By extending a Lagrangian probability-density-function model to channel flow, consistent two-way coupling and the decomposition of particle velocity have been achieved, allowing for statistical treatment of collisions in dense flows.
Article
Mechanics
Emmanuel Hitimana, Rodney O. Fox, James C. Hill, Michael G. Olsen
Summary: This study investigates the coherent structures of turbulent swirling flow within the multi-inlet vortex reactor, revealing elliptical shapes of velocity and concentration fluctuations with positive correlations near basepoints and surrounded by negatively correlated regions. Linear stochastic estimation shows obliquely oriented counter-rotating vortical structures that depend on local concentration gradient.
Article
Computer Science, Interdisciplinary Applications
Jeffrey C. Heylmun, Rodney O. Fox, Alberto Passalacqua
Summary: This study presents a quadrature-based moment method for solving the evolution of joint size-velocity number density function of particle populations, successfully applied to numerical simulations of aggregation, breakup, collisions, and other scenarios.
COMPUTER PHYSICS COMMUNICATIONS
(2021)
Article
Mathematics, Applied
Rodney O. Fox, Frederique Laurent
Summary: A tractable solution is proposed to a classical problem in kinetic theory by introducing the Hyperbolic Quadrature Method of Moments (HyQMOM) to close even-order moments, strictly based on properties of monic orthogonal polynomials. The method is shown to converge with increasing order, demonstrating efficiency and accuracy in closure of moment equations.
SIAM JOURNAL ON APPLIED MATHEMATICS
(2022)
Article
Mechanics
Krishnamurthy Ravichandar, R. Dennis Vigil, Rodney O. Fox, Stephanie Nachtigall, Andreas Daiss, Michal Vonka, Michael G. Olsen
Summary: Droplet dispersion in liquid-liquid systems is a crucial step in various industries. This study investigates droplet breakup using a novel method and finds that breakage time and breakage probability increase with increasing parent droplet size, while the shape of the child drop size distribution depends on the size of the parent droplet.
Article
Engineering, Chemical
Rodney O. Fox, Frederique Laurent, Alberto Passalacqua
Summary: The quadrature method of moments (QMOM) is a method to close the moment source terms based on the properties of orthogonal polynomials. The generalized quadrature method of moments (GQMOM) extends QMOM by using recursion coefficients and provides a more accurate moment closure.
JOURNAL OF AEROSOL SCIENCE
(2023)
Article
Mechanics
Palas Kumar Farsoiya, Zehua Liu, Andreas Daiss, Rodney O. Fox, Luc Deike
Summary: In this study, we investigate the morphology, occurrence, time, and size distribution of drop break-up in homogeneous isotropic turbulence through numerical simulations. The results show that the critical Weber number for drop break-up is nearly constant for viscosity ratio mu(r) <= 20, while it increases with mu(r) (and Reynolds number) for mu(r) > 20. The break-up time is delayed and is influenced by the distance to criticality. The first break-up child-size distribution transitions from M to U shape as the distance to criticality increases for mu(r) <= 20. The distribution shape is modified at high mu(r). At high We, a d(-3/2) size distribution is observed for mu(r) <= 20, while for mu(r) > 20, most of the drops formed by fragmentation are at the smallest scale, controlled by the diameter of the filament.
JOURNAL OF FLUID MECHANICS
(2023)
Article
Mechanics
Victor Boniou, Rodney O. Fox
Summary: The main goal of this study is to explore the closures used in two-fluid models for representing interphase forces between particles and high-speed flows. By employing a hyperbolic two-fluid model, the interaction between an incident shock with Mach number M-s and a thin, moderately dense particle curtain is investigated. The two-fluid model is able to reproduce the experimental data, with some discrepancies observed in configurations with the smallest M-s. Furthermore, the study highlights the importance of investigating the particle-Mach number (M-p) dependence of drag and added-mass coefficients, which have not been extensively explored in the literature.
INTERNATIONAL JOURNAL OF MULTIPHASE FLOW
(2023)