Article
Chemistry, Multidisciplinary
Gustavo Giordani, Domenico Scaramozzino, Ignacio Iturrioz, Giuseppe Lacidogna, Alberto Carpinteri
Summary: Proteins play a crucial role in biological functions, with low-frequency modes and modal analysis being key in understanding their structural processes. Biochemical researchers use dynamic simulation techniques, while new proposals of simplified elastic models offer alternative approaches. Comparing experimental data with numerical solutions allows for the assessment of protein flexibility.
APPLIED SCIENCES-BASEL
(2021)
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
Biochemistry & Molecular Biology
Esmat Mohammadi, Soumil Y. Joshi, Sanket A. Deshmukh
Summary: Interactions between amino acids and water play a crucial role in determining the stability and function of biological macromolecules in aqueous solutions. We have developed nonbonded interaction parameters between coarse-grained models of amino acids and water models, and optimized them using an artificial neural network-assisted particle swarm optimization method. These models accurately reproduce the Gibbs hydration free energies and show good agreement with experimental data, demonstrating their transferability and applicability in studying the self-assembly of biomaterials and biomolecules.
Article
Physics, Fluids & Plasmas
Enrico Skoruppa, Aderik Voorspoels, Jocelyne Vreede, Enrico Carlon
Summary: Investigations on the influence of nonlocal couplings on DNA torsional and bending elasticities revealed strong off-site couplings for tilt-tilt and twist-twist, while they were weaker in the roll-roll case. Analysis indicated that off-site interactions generate a length-scale-dependent elasticity in DNA models. Simulation-generated data predicted significant length-scale-dependent effect on torsional fluctuations, but only a modest effect on bending fluctuations, consistent with experimental observations probing DNA mechanics.
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
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
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
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
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
Aleksander E. P. Durumeric, Gregory A. Voth
Summary: Bottom-up CG molecular dynamics models, parameterized using complex effective Hamiltonians, are often optimized to approximate high dimensional data from atomistic simulations. However, human validation of these models may not differentiate between the CG model and the atomistic simulations. We propose using classification to estimate high dimensional errors and utilizing explainable machine learning to convey this information to scientists. This approach is demonstrated using Shapley additive explanations and two CG protein models, and may be valuable for assessing the accuracy of allosteric effects in CG models at the atomistic level.
JOURNAL OF CHEMICAL PHYSICS
(2023)
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
Polymer Science
Akash Arora, Tzyy-Shyang Lin, Bradley D. Olsen
Summary: The research developed a coarse-grained simulation framework to calculate the fracture strength of elastomers and elucidated the role of topological defects in controlling the fracture properties of networks.
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
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
Computer Science, Interdisciplinary Applications
Yanlin Su, Guoqing Cai, Fengjie Yin, Yepeng Shan, Annan Zhou
Summary: This paper presents a novel elastic-viscoplastic constitutive model that takes into account particle breakage to reproduce the time-dependent behavior of coarse-grained soil. The model integrates the Unified Hardening (UH) model, the elastic-viscoplastic (EVP) model, and the overstress theory. The relationship between particle breakage and loading rate is established, and state variables associated with the critical state of coarse-grained soil are derived to consider both time and particle breakage. A three-dimensional elastic-viscoplastic constitutive model is constructed by combining a one-dimensional viscoplastic hardening parameter with a secondary consolidation coefficient considering particle breakage. The proposed model requires 19 parameters and effectively describes the influence of time-dependency and particle breakage on the shear, dilatancy, and compression behaviors of coarse-grained soil with different confining pressures or initial void ratios. Experimental data comparisons validate the model's ability to replicate the time-dependent behavior of coarse-grained soil.
COMPUTERS AND GEOTECHNICS
(2024)