Article
Chemistry, Physical
Jaehyeok Jin, Kenneth S. Schweizer, Gregory A. Voth
Summary: The first paper of this series demonstrated the scalability of excess entropy for both fine-grained and coarse-grained systems. However, a more precise determination of the scaling relationship was not possible due to its semi-empirical nature. In this second paper, an analytical scaling relation for excess entropy is derived for bottom-up coarse-grained systems. By constructing effective hard sphere systems at the single-site resolution, the dynamics and excess entropy of the target coarse-grained systems can be accurately approximated.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Michael R. DeLyser, W. G. Noid
Summary: Investigated a new class of one-body potentials called square gradient (SG) potentials that can improve the accuracy and transferability of coarse-grained (CG) models. These SG potentials can tune interfacial properties and enhance the performance of various models.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Alfred C. K. Farris, Daniel T. Seaton, David P. Landau
Summary: Different coarse-grained protein models were compared and contrasted to investigate the impact of lattice constraints. As the complexity of the model increases, major structural transitions split into multi-step processes, with lattice coarse-graining significantly influencing the details of these processes. The level of structural coarse-graining is coupled to the level of interaction coarse-graining.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
Theodore L. Fobe, Christopher C. Walker, Garrett A. Meek, Michael R. Shirts
Summary: In this study, researchers use computational modeling techniques to address the challenges in designing non-biological foldamers. They developed CG PyRosetta, an extension to PyRosetta, which allows the folding of toy CG foldamer models. By systematically varying CG parameters in these models, they investigate different folding hypotheses and provide insights for the design process of new foldamer chemistries.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Biochemistry & Molecular Biology
Dieu Thi Doan, Manh Dat Hoang, Anna-Lena Heins, Andreas Kremling
Summary: Mathematical modeling is an important tool for studying cellular processes. Coarse-grained models are simple yet effective in describing growth conditions. This article presents a mass-conservative model for bacterial growth during biotechnological production, with applications in amino acid and metabolite production.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Chemistry, Physical
Supreet Kaur, Arun Yethiraj
Summary: Polyelectrolyte solutions are of great scientific and practical importance. In this study, coarse-grained models for polystyrene sulfonate and poly(vinyl benzyltrimethyl) ammonium with explicit coarse-grained water and sodium and chloride counterions, respectively, were developed and benchmarked against atomistic simulations. The choice of topology and partial charge distribution in the coarse-grained model was found to be crucial in reproducing results from atomistic simulations.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Tianyuan Pan, Sarit Dutta, Charles E. Sing
Summary: Bottlebrush polymers are highly branched macromolecules that have potential applications in self-assembled photonic materials and tunable elastomers. However, computational studies of these polymers are challenging due to the high cost involved in explicitly modeling the side chains. In this study, a coarse-grained molecular model with implicit side chains is proposed to accelerate simulations. The interaction potential between the coarse-grained segments is calculated systematically from explicit side chain models, and the predictions of the coarse-grained model are compared with those of explicit models. This model can be extended to different solvent conditions and monomer chemistries, and is expected to be useful for large-scale simulations of bottlebrush solutions and assembly.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Physics, Condensed Matter
Tian-Xiang Liu, Li Mao, Mats-Erik Pistol, Craig Pryor
Summary: The proposed method of connecting atomistic and quasi-continuous models can speed up tight-binding calculations for large systems, reducing computation time while maintaining high accuracy. The numerical tests show significant improvements in efficiency with minimal loss of accuracy.
JOURNAL OF PHYSICS-CONDENSED MATTER
(2022)
Article
Chemistry, Physical
Erik Weiand, James P. Ewen, Peter H. Koenig, Yuri Roiter, Steven H. Page, Stefano Angioletti-Uberti, Daniele Dini
Summary: In this study, a coarse-grained molecular model of the surface of human hair is presented, and the structural and wetting behavior of lipid monolayers at different levels of damage are studied through simulations and experiments. The model captures the transition of the hair surface from hydrophobic to hydrophilic and shows good agreement with experimental results. These models are important for understanding the adsorption and tribological behavior of hair as well as other chemically heterogeneous surfaces.
Review
Mechanics
Paolo Cermelli, Giuliana Indelicato
Summary: This review presents several mathematical models for icosahedral viral capsids, utilizing coarse-graining approximations to describe the fundamental structural units and configurational changes. The paper also discusses the computation of residual stress in the capsid using coarse-grained models, and explores its influence on the capsid structure.
INTERNATIONAL JOURNAL OF NON-LINEAR MECHANICS
(2022)
Review
Biochemistry & Molecular Biology
Jun Li, Shi-Jie Chen
Summary: Understanding the 3D structures of RNA molecules is crucial for their biological functions, leading to the development of computational methods due to the laborious and difficult experimental determination. All-atom simulations are suitable for small RNA systems, while coarse-grained models are more widely applied.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Chemistry, Multidisciplinary
Yuefei Jia, Shiwei Wu, Yongkun Mu, Long Xu, Chang Ren, Kang Sun, Jun Yi, Yandong Jia, Wentao Yan, Gang Wang
Summary: The coarse-grained superplasticity of high-strength lightweight medium entropy alloy offers a solution to the limitations of conventional superplastic alloys. It demonstrates excellent ductility, high strength, and a unique deformation mechanism, providing a pathway for highly efficient superplastic forming and the development of new alloys.
Review
Biochemistry & Molecular Biology
Tiedong Sun, Vishal Minhas, Nikolay Korolev, Alexander Mirzoev, Alexander P. Lyubartsev, Lars Nordenskiold
Summary: This review presents some well-developed bottom-up coarse-graining methods for effective modeling of DNA properties, such as DNA flexibility, conformation, melting, and condensation, based on underlying atomistic force field simulations. These methods separate fast and slow dynamic processes in molecular systems and construct coarse-grained Hamiltonian using pair-wise additive potential for efficiency in computer simulation.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
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
Chemistry, Physical
Jaehyeok Jin, Kenneth S. Schweizer, Gregory A. Voth
Summary: The ultimate goal of this series of articles is to establish a better correspondence between the dynamics of fine-grained (FG) and coarse-grained (CG) models. By utilizing the excess entropy scaling relationship, the authors show that FG and CG counterparts follow the same universal scaling relationship. They develop a new theory to calculate excess entropies for both FG and CG systems, taking into account entropy representability. Applying the excess entropy scaling idea to liquid water and methanol systems, they find that the scaling exponents remain unchanged during the coarse-graining process, indicating universality of the scaling behavior for the same underlying molecular systems. Furthermore, they demonstrate that missing entropy plays a crucial role in accelerating CG dynamics.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Marcus Mueller
Summary: Using analytical considerations and particle-based simulations, this study investigates the relaxation of a density modulation in a polymer system without nonbonded interactions. The results demonstrate that shallow density modulations, prepared by different processes but with identical amplitudes and wavevectors, exhibit different nonexponential decay behaviors, challenging the assumption that density alone characterizes the polymer system configuration. Analytic descriptions within Linear-Response Theory (LRT) and the Rouse model are provided, showing quantitative agreement with the particle-based simulations.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Ganesh Sivaraman, Nicholas E. Jackson
Summary: Scalable electronic predictions are critical for soft materials design. The Electronic Coarse-Graining (ECG) method uses deep neural networks (DNNs) to renormalize all-atom quantum chemical (QC) predictions to coarse-grained (CG) resolutions. The GPU-accelerated Deep Kernel Learning (DKL) framework enables CG QC predictions with a significant speedup, accurately reproducing molecular orbital energies.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Physics, Applied
Zheng Yu, Nicholas E. Jackson
Summary: We propose a physics-based machine learning approach that detects and simulates bond breaking events in polymer networks with near quantum-chemical accuracy in atomistic simulations. By coarse-graining highly correlated neighboring bonds, the prediction accuracy is significantly improved. Compared to existing quantum mechanics/molecular mechanics methods, our approach is approximately two orders of magnitude more efficient and exhibits improved sensitivity towards rare bond breaking events at low strain. This bond breaking molecular dynamics scheme enables fast and accurate modeling of strain hardening and material failure in polymer networks and can accelerate the design of polymeric materials under extreme conditions.
APPLIED PHYSICS LETTERS
(2023)
Article
Chemistry, Physical
Chun- Wang, Nicholas E. Jackson
Summary: There are fundamental knowledge gaps in understanding the connection between emergent properties of soft materials and the quantum mechanical world. The limitations of current quantum mechanical modeling paradigms hinder the understanding and design of soft materials where quantum mechanical phenomena are crucial. This review discusses the emerging efforts to overcome these challenges through the development of electronic prediction models that operate at a coarse-grained resolution. The success of electronic coarse-graining (ECG) and related models for soft materials is highlighted, along with the potential transformative impact of ECG models on certain classes of soft materials.
CHEMISTRY OF MATERIALS
(2023)
Article
Chemistry, Physical
Azzaya Khasbaatar, Andrew Cheng, Austin L. Jones, Justin J. Kwok, Sang Kyu Park, Jessica K. Komar, Oliver Lin, Nicholas E. Jackson, Qian Chen, Dean M. DeLongchamp, John R. Reynolds, Ying Diao
Summary: The aggregation of conjugated polymers in solution is crucial for the morphology and performance of bulk heterojunction organic solar cells (OSCs). However, the specific structures of polymer aggregates in solution and their effects on OSC morphology and performance have not been extensively studied. In this study, we investigate the impact of polymer aggregate structures on the morphology and processing resilience of OSCs using a benzodithiophene-based donor polymer (PM7) and its ester-functionalized derivatives (PM7 D1 and D2). Our results show that PM7 solution forms a combination of semi-crystalline fiber aggregates and amorphous polymer chain network aggregates, while PM7 D1 and D2 solutions primarily form amorphous network aggregates through sidechain associations. Interestingly, the fiber aggregates of PM7 break down at elevated solution temperatures, while the polymer network aggregates remain stable. This temperature-dependent behavior leads to highly processing temperature-sensitive performance in blade-coated devices fabricated from PM7 and ITIC-4F, whereas PM7 D1 and D2 polymers exhibit improved processing temperature resiliency. Furthermore, we find that amorphous, network-like aggregates contribute to superior device performance in blade-coated OSCs due to the formation of blend films with short pi-pi stacking distance, small domain spacing, and face-on preferred molecular orientation. Conversely, fiber-like aggregates result in large pi-pi stacking distance, large domain spacing, and isotropic molecular orientation, which degrade device performance.
CHEMISTRY OF MATERIALS
(2023)
Article
Polymer Science
Seonghwan Kim, Charles M. Schroeder, Nicholas E. Jackson
Summary: A grand challenge in polymer science is the predictive design of new polymeric materials with targeted functionality. Recent advances in deep generative modeling have allowed for efficient exploration of molecular design space, but data sparsity in polymer science remains a major obstacle. In this work, the Open Macromolecular Genome (OMG) database is introduced, which contains synthesizable polymer chemistries compatible with known polymerization reactions and commercially available reactants. The OMG, in conjunction with the synthetically aware generative model Molecule Chef, enables property-optimized polymer design with constituent reactants and reaction pathways.
Article
Chemistry, Physical
Jicheng Guo, Vanessa Woo, David A. A. Andersson, Nathaniel Hoyt, Mark Williamson, Ian Foster, Chris Benmore, Nicholas E. E. Jackson, Ganesh Sivaraman
Summary: Machine learning interatomic potentials have been developed to overcome the limitations of ab initio simulations, but efficient parameterization remains a challenge. The AL4GAP software workflow is presented for generating multicomposition Gaussian approximation potentials (GAP) for molten salt mixtures. The workflow includes setting up chemical spaces, configurational sampling, active learning, and Bayesian optimization. The results demonstrate the accurate prediction of molten salt structures by GAP models with density functional theory accuracy.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Editorial Material
Chemistry, Physical
Nicholas E. Jackson, Joseph M. Luther, Brett M. Savoie, Kaifeng Wu
JOURNAL OF CHEMICAL PHYSICS
(2023)
Editorial Material
Chemistry, Physical
Nicholas E. Jackson, Brett M. Savoie, Antonia Statt, Michael A. Webb
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Chun- Wang, J. Charlie Maier, Nicholas E. Jackson
Summary: Coarse-grained (CG) simulations play a vital role in computational chemistry and materials science. Recent advancements have introduced systematic bottom-up CG models to capture electronic structure variations at the CG resolution. However, the effectiveness of these models is hindered by the challenge of selecting reduced representations that preserve electronic structure information.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Bronte J. Charette, Shelby R. King, Jiaqi Chen, Annika R. Holm, Justin T. Malme, Robert D. Cook, Richard D. Schaller, Nicholas E. Jackson, Lisa Olshansky
Summary: The conversion of solar energy into chemical fuel is a crucial goal for the 21st century and has the potential to generate terawatts of power worldwide. However, the discrepancy between the time scales of photodriven charge separation and chemical reactions poses a bottleneck for solar-to-fuels technology. To address this, researchers are developing coordination complexes that undergo conformational rearrangements to accelerate charge separation and slow down charge recombination. This study presents a new series of copper coordination complexes with a twisted intramolecular charge transfer fluorophore, demonstrating improved photophysics and providing insights for future optimizations. Evaluation: 8/10.
JOURNAL OF PHYSICAL CHEMISTRY A
(2023)
Article
Chemistry, Physical
Felix Weissenfeld, Lucia Wesenberg, Masaki Nakahata, Marcus Mueller, Motomu Tanaka
Summary: The interactions between vesicle and substrate were investigated using simulation and experiment. Polyacrylic acid brushes with cysteine side chains were grafted onto planar lipid membranes. The addition of Cd2+ ions compacted the polymer brushes and influenced the adhesion of lipid vesicles. Wetting of the vesicles occurred at [CdCl2] = 0.25 mM. The shape and adhesion of vesicles were quantitatively evaluated, and simulations revealed that wetting sensitivity was dependent on the interaction range.
Article
Chemistry, Physical
David M. M. Friday, Nicholas E. E. Jackson
Summary: Conjugated polyelectrolytes (CPEs) are a rising class of organic mixed ionic-electronic conductors with applications in bio-interfacing electronics and energy devices. This study provides insights into the morphology and ion-electron transport properties of CPEs, revealing the formation of electrostatically repulsive fibers and their impact on electronic transport. The work presents a significant step forward in the ability to predict CPE morphology and ion-electron transport properties.
MOLECULAR SYSTEMS DESIGN & ENGINEERING
(2023)
Article
Polymer Science
Niklas Blagojevic, Marcus Mueller
Summary: Using a particle-based model, a free-energy functional, and a lattice model, this study investigates the structure and motion of a grain boundary between two orthogonal grains in asymmetric block copolymers. The study reveals insights into transitions and correlations in space and time. By characterizing the system using a free-energy functional and calculating the minimum free-energy path, the study identifies a minimal set of transitions. The results are used to parametrize a lattice model and investigate grain-boundary motion by kinetic Monte Carlo simulation.
Article
Materials Science, Multidisciplinary
Jicheng Guo, Logan Ward, Yadu Babuji, Nathaniel Hoyt, Mark Williamson, Ian Foster, Nicholas Jackson, Chris Benmore, Ganesh Sivaraman
Summary: This study successfully unravels the liquid structure of multicomponent molten salts at high temperatures by developing a composition-transferable Gaussian approximation potential (GAP) for molten LiCl-KCl. The results show strong agreement with high-energy x-ray diffraction experiments and open up the possibility of composition discovery.
