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
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)
Review
Physics, Multidisciplinary
Tanja Schilling
Summary: This article discusses the construction of coarse-grained models for systems out of thermal equilibrium, including both equilibrium and non-equilibrium coarse-graining methods and numerical schemes.
PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS
(2022)
Article
Multidisciplinary Sciences
Riccardo Alessandri, Jonathan Barnoud, Anders S. Gertsen, Ilias Patmanidis, Alex H. de Vries, Paulo C. T. Souza, Siewert J. Marrink
Summary: The recent re-parametrization of the Martini coarse-grained force field, Martini 3, has improved the accuracy of the model in predicting molecular packing and interactions in molecular dynamics simulations. The use of higher resolution coarse-grained particles to describe ring-like structures in small molecules has resulted in excellent partitioning behavior and solvent properties, as well as capturing miscibility trends between different bulk phases.
ADVANCED THEORY AND SIMULATIONS
(2022)
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
Polymer Science
Ting Ge, Jiuling Wang, Mark O. Robbins
Summary: As the degree of coarse-graining increases, the stress level during strain hardening decreases, but the stress-strain curves can be collapsed with a simple rescaling factor. In the same strain range, the conformational changes in local chain segments are almost the same.
Article
Polymer Science
Kevin R. Hinkle
Summary: Molecular dynamics simulations were used to verify the accuracy of using coarse-grained models to describe diblock-arm star polymers. The results showed agreement with atomistic models, reproduced general trends, and investigated structure-property relationships by varying arm number and length. This work is an important first step towards improved design of polymeric nanoparticles for drug delivery applications.
EUROPEAN POLYMER JOURNAL
(2021)
Review
Chemistry, Multidisciplinary
Rui Shi, Hu-Jun Qian, Zhong-Yuan Lu
Summary: Coarse-grained (CG) molecular dynamics simulations are important for the simulations of polymeric systems due to their computational efficiency and ability to provide structural and dynamical properties. CG models have been developed in two directions: generic models focusing on capturing general properties, and chemically-specific models retaining chemical-physical properties. However, faithfully reproducing structure and dynamics is a major challenge due to the reduction of atomistic degree of freedom. This review provides an overview of recent achievements and remaining challenges in the development of chemically-specific CG approaches for polymer systems simulations.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE
(2023)
Article
Pharmacology & Pharmacy
Xiaoyu Liu, Mostafa Sulaiman, Jari Kolehmainen, Ali Ozel, Sankaran Sundaresan
Summary: This study evaluated the effectiveness of two coarse-grained CFD-DEM approaches in drug delivery via dry powder inhalers, finding that the representative particle approach can approximate CFD-DEM results with reasonable accuracies.
INTERNATIONAL JOURNAL OF PHARMACEUTICS
(2021)
Article
Chemistry, Multidisciplinary
Giuliana Giunta, Gerardo Campos-Villalobos, Marjolein Dijkstra
Summary: Colloidal nanoparticles can self-assemble into superstructures with distinctive properties. This study proposes a machine-learning approach to construct effective coarse-grained many-body interaction potentials for investigating the self-assembly behavior of complex colloidal systems. The key advantage of this method is its generality.
Article
Multidisciplinary Sciences
Hugues Meyer, Steffen Wolf, Gerhard Stock, Tanja Schilling
Summary: A method is presented to infer the memory kernel in non-equilibrium processes, using ion dissociation in water as an example. This method improves a previously published numerical scheme and addresses the issue of truncation.
ADVANCED THEORY AND SIMULATIONS
(2021)
Article
Chemistry, Physical
Mamta Yadav, Yashwant Singh
Summary: We have developed a theory to trace the solvent degrees of freedom in colloid-solvent mixtures based on the grand partition function. Our approach uses density functional formalism and considers the solvent-induced interactions expressed in terms of two functionals. The theory provides insights into the nature of the potential and its dependence on thermodynamic state, packing fractions, and size ratio. We applied the theory to additive and nonadditive binary hard-sphere mixtures and observed interesting features such as non-monotonic dependence of the attractive part of the potential on the packing fraction.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Chemistry, Physical
Aditi Khot, Brett M. Savoie
Summary: Coarse-grained molecular dynamics (CGMD) simulations address critical lengthscales and timescales in chemical and material applications. The development of black-box CGMD methodologies similar to density functional theory for electronic structure is still lacking. Machine learning (ML)-based CGMD potentials show promise in simplifying model development, but they have yet to outperform physics-based CGMD methods. In this study, λ-learning models are explored to combine the advantages of both approaches. The λ-models outperform ML-only CGMD models and provide essentially free gains in reproducing atomistic properties. However, neither the λ-learning models nor the ML-only models significantly outperform elementary pairwise models in reproducing atomistic properties due to the large irreducible force errors associated with coarse-graining.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Mechanics
T. Venkatesh Varma, Saikat Sarkar
Summary: Designing protective armors is crucial for civilian and defense applications, with ceramic-polymer composite armors providing high strength, light weight, and energy absorption capabilities. By replacing bulk polymer panels with polymer-based metamaterials, energy absorption of the armor can be greatly enhanced. Computational challenges in studying metamaterial properties can be overcome by utilizing a novel coarse-grained methodology based on the energetics of the structure.
Article
Chemistry, Multidisciplinary
Marc Stieffenhofer, Christoph Scherer, Falk May, Tristan Bereau, Denis Andrienko
Summary: In this study, the quality of different coarse-grained models is evaluated at the atomistic resolution using reverse-mapping strategies. Significant discrepancies between the all-atom and coarse-grained ensembles are revealed, and the reintroduced details allow for force computations and a clear ranking of the coarse-grained models.
FRONTIERS IN CHEMISTRY
(2022)
Article
Chemistry, Physical
Kai-Yang Leong, Feng Wang
JOURNAL OF CHEMICAL PHYSICS
(2019)
Article
Chemistry, Physical
Lin Zhuang, Rui Wang, Gerrick E. Lindberg, Hongyi Hu, Xin-Zheng Li, Feng Wang
JOURNAL OF PHYSICAL CHEMISTRY B
(2019)
Article
Chemistry, Physical
Ying Yuan, Zhonghua Ma, Feng Wang
JOURNAL OF CHEMICAL PHYSICS
(2019)
Article
Chemistry, Physical
T. Ryan Rogers, Feng Wang
JOURNAL OF PHYSICAL CHEMISTRY B
(2020)
Article
Chemistry, Physical
Cameron C. Crane, Ryan H. Manso, Jun Li, Mourad Benamara, Jing Tao, Yimei Zhu, Feng Wang, Jingyi Chen
JOURNAL OF PHYSICAL CHEMISTRY C
(2020)
Article
Chemistry, Multidisciplinary
Preeti Pandey, Ulrich H. E. Hansmann, Feng Wang
Article
Chemistry, Physical
T. Ryan Rogers, Feng Wang
JOURNAL OF CHEMICAL PHYSICS
(2020)
Article
Chemistry, Physical
Dong Zheng, Ying Yuan, Feng Wang
Summary: Force fields for seven small solute molecules were created using the AFM method with good agreement between predicted and experimental hydration free energies, except for 1,4-butanediol. Further investigation suggested that LMP2 may not be accurate for computing HFEs for alcohols with AFM. Other properties like enthalpy of hydration, diffusion constants, and vibrational spectra were also computed using the developed force fields.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
Ying Yuan, Zhonghua Ma, Feng Wang
Summary: A new force field AFM2020 has been developed using the adaptive force matching method for simulating hydrated alanine polypeptides, showing better accuracy compared to other models. The force field predicts different conformations for Ala(7), with a higher helical population than previous estimates based on the same experimental data. Gas-phase simulations suggest that the force field developed from AFM solution-phase data may produce a reasonable conformation distribution in the absence of hydration water, such as the interior of a protein.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Chemistry, Physical
Ariel Rogers, Isabelle I. Niyonshuti, Alice Cai, Feng Wang, Mourad Benamara, Jingyi Chen, Yong Wang
Summary: The study focuses on the kinetics of laser-induced nanowelding of silver nanoparticles (AgNPs), with an observation that laser illumination leads to the formation of higher-order structures of AgNPs. An analytical model based on simple polymerization was developed to predict and understand the dynamics, and experimental verification was conducted by varying laser power and AgNP concentration. The merging of assemblies and diffusion-limited kinetics of laser-induced assembling were taken into account for improved modeling, and the asynchronous blinking behaviors of different regions within formed structures were observed.
JOURNAL OF PHYSICAL CHEMISTRY C
(2021)
Article
Chemistry, Physical
Ying Yuan, Feng Wang
Summary: This study tested the performance of three DFT exchange-correlation functionals in predicting conformational distributions of a hydrated glycine peptide, with B3LYP showing better accuracy than BP86 and PBE. The study also introduced the AFM2021 model, demonstrating the potential of using DFT as a reference for developing force fields for proteinogenic peptides.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
Dong Zheng, Ying Yuan, Feng Wang
Summary: A new fragmentation approach called SORForM is introduced for efficient computation of quantum mechanical forces for large molecules. The method is validated in the framework of AFM and used to develop solute models in water. The performance of the method is confirmed and compared with experimental results.
JOURNAL OF PHYSICAL CHEMISTRY A
(2022)
Article
Chemistry, Physical
Raymond Weldon, Feng Wang
Summary: This study investigates two methods to convert flexible models into rigid models. The rigid model can be created based on the Model's Geometry (MG) without molecular interaction or the ensemble averaged geometry (EG) under specific thermodynamic conditions. While the MG model is more straightforward, it has relatively poor performance compared to the EG model, which behaves similarly to the corresponding flexible model (FL model) and agrees better with experiments. The difference between the EG and FL models is mainly due to flexibility, and the MG and EG models have different dipole moments in the condensed phase.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Ying Yuan, Feng Wang
Summary: The physical driving forces behind the secondary structure preferences of hydrated alanine peptide are investigated using B3LYP-D3(BJ) and adaptive force matching (AFM) methods. The AFM model accurately reproduces the experimental results of nuclear magnetic resonance scalar coupling constants, providing insights into the underlying physical driving forces. DFT calculations, with and without the Conductor-like Screening Model (COSMO), reveal that solvent polarization due to dipole cooperativity stabilizes the alpha helix, while the finite size of water molecules frustrates the polarization stabilization for the near-planar trapezoid formed by adjacent amide groups in the beta strand.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Chemistry, Physical
Dong Zheng, Feng Wang
Summary: This study mapped potential energy surfaces for eight solutes in dilute aqueous solutions into pairwise additive force field expressions using the AFM method at the B3LYP-D3-(BJ) level. By force matching B3LYP-D3-(BJ), the predictions from the models showed good agreement with experimental data, providing confidence on the quality of producing potential energy surfaces for thermodynamic property calculations. Accurate computational predictions could potentially validate experimental measurements in cases where measurements from different sources do not agree.
ACS PHYSICAL CHEMISTRY AU
(2021)