Article
Biochemical Research Methods
Olivier Mailhot, Rafael Najmanovich
Summary: NRGTEN is a Python toolkit that implements four different NMA models and various metrics for benchmarking. It is easily extensible and includes the Elastic Network Contact Model developed by the group, which considers the specific chemical nature of atomic interactions.
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
Biochemistry & Molecular Biology
Makoto Isogai, Masataka Seshimo, Hirohiko Houjou
Summary: In this study, the coarse-graining method was applied to analyze intermolecular vibrations in molecular heterodimers assembled by double hydrogen bonding. The analysis provided three parameters relevant to the mechanical nature of molecular assembly, showing a good correlation with the association energies of the dimers. The reordering schemes of intramolecular vibration vectors played a crucial role in constructing the optimal coarse-grained space.
JOURNAL OF MOLECULAR MODELING
(2021)
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)
Article
Polymer Science
Chengyuan Wen, Roy Odle, Shengfeng Cheng
Summary: A coarse-grained model is developed for large-scale MD simulations of a branched polyetherimide, using systematic protocols based on chemistry-informed grouping of atoms and parameterization methods. The model has been successfully applied to explore the mechanical, structural, and rheological properties of the polymer.
Article
Computer Science, Theory & Methods
Longlong Chen, Jianfeng Zhu, Yangdong Deng, Zhaoshi Li, Jian Chen, Xiaowei Jiang, Shouyi Yin, Shaojun Wei, Leibo Liu
Summary: The article proposes an elastic task scheduling scheme that enables lightweight dynamic scheduling in CGRAs, by rescheduling tasks at runtime according to the classic tagged-token dataflow paradigm for dynamic task-level parallelism, and dynamically resizing tasks based on run-time throughputs through duplication, combination, and substitution operators for balanced multitask execution.
IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS
(2021)
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.
Article
Chemistry, Multidisciplinary
Pei Du, Meng Li, Shengyao Liang, Lin Ji, Luigi Acampora, Francesco Saverio Marra
Summary: The coarse graining idea is introduced into the analysis of detailed combustion models to identify the key reaction steps that drive macroscopic combustion characteristics. A novel method combining network community detection and parametric bifurcation techniques is proposed for this purpose. Simulation results of a perfectly stirred reactor using the proposed method validate its effectiveness and capability to identify important reactions.
REACTION CHEMISTRY & ENGINEERING
(2023)
Article
Chemistry, Medicinal
Ezequiel N. Frigini, Rodolfo D. Porasso, Tamas Beke-Somfai, Jose Javier Lopez Cascales, Ricardo D. Enriz, Sergio Pantano
Summary: In this article, the molecular level action mechanisms of short antimicrobial peptides are explored through multiscale molecular dynamics simulations. The simulations reveal that mechanical inhomogeneities appear in the membrane when the threshold concentration of peptides on the membrane is reached, leading to membrane rupture. These findings assist in the design of new small antimicrobial peptides.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Physical
Wenjun Zheng
Summary: In order to computationally identify hidden binding sites for allosteric modulators, a fast and simple conformational sampling scheme guided by coarse-grained normal modes solved from the elastic network models followed by atomistic backbone and sidechain reconstruction has been developed. This method can adequately restructure cryptic sites so they are detectable by pocket finding programs like Concavity, making it suitable for high-throughput screening of protein structures at the genome scale. Our method has been used to locate known allosteric sites and predict new promising allosteric sites, and it is both faster and more flexible compared to other sampling methods.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Debdas Dhabal, Andressa A. Bertolazzo, Valeria Molinero
Summary: Zeolites are widely used solid catalysts in the chemical industry, and their hydrothermal synthesis involves multiple steps; Researchers have developed a computationally efficient model that accurately reproduces the experimental evolution of zeolite amorphous precursors; The study suggests that zeolite formation at the amorphous-water interface is not due to the surface's ability to heterogeneously nucleate zeolites.
JOURNAL OF PHYSICAL CHEMISTRY C
(2021)
Article
Engineering, Electrical & Electronic
Xiaobing Ni, Mengke Ge, Yongjin Tao, Wendi Sun, Feixiang Duan, Xuefei Bai, Qi Xu, Song Chen, Yi Kang
Summary: Coarse-grained reconfigurable array (CGRA) is popular in compute-intensive applications due to its flexibility and energy-efficiency. In this study, a new routing mode called bus routing is proposed for complex data flow graphs (DFGs) in CGRA. The BusMap mapping method, which incorporates bus routing, solves the maximum independent set (MIS) problem to map the DFG onto CGRA. Experimental results show that BusMap achieves fewer global register file (GRF) accesses and inserted operations compared to previous methods, while maintaining the same or smaller initiation interval (II).
IEEE TRANSACTIONS ON CIRCUITS AND SYSTEMS II-EXPRESS BRIEFS
(2023)
Article
Polymer Science
Takeshi Aoyagi
Summary: This study investigated the elasticity of block copolymers through coarse-grained molecular dynamics simulation. The effects of morphology, bridge fraction, and deformation direction on stress-strain curves were studied. The results showed that glassy networks with the DG morphology had higher initial moduli compared to those with the BCC morphology. The rubber elasticity was linearly dependent on the bridge fraction in BCC morphology, but weakly dependent in DG morphology due to the contribution of loop configurations. The effect of deformation direction was insignificant in both morphologies, contrary to experimental results.
Article
Materials Science, Multidisciplinary
C. H. Wu, R. Jiang, L. C. Zhang, Y. C. Wang, Y. Chen, Y. D. Song
Summary: This study investigates the fatigue crack growth (FCG) mechanisms of Ni-based superalloy FGH4098 at temperatures ranging from 650 to 800 degrees Celsius. The results show that the FCG rate increases by 2-3 orders of magnitude with increased temperature and prolonged dwell time, which is attributed to grain boundary oxidation. Characterization of the crack tips reveals that deformation, such as dislocations and stacking faults, mainly occurs within the gamma channel, accompanied by a change in grain orientation due to severe deformation. Pre-formed oxides at uncracked grain boundaries facilitate the FCG process. A mechanism map of the interaction between deformation-assisted grain boundary oxidation and FCG is proposed.
Article
Chemistry, Multidisciplinary
Mindaugas Zakarka, Sarunas Skuodis, Neringa Dirgeliene
Summary: This study investigates the influence of density and uniformity coefficients on geogrid-reinforced sandy and gravelly soils. The results highlight the critical role of cell pressure in the reinforcement effect, with higher pressures reducing the geogrid's influence. The study also emphasizes the importance of soil type, with gravel soils consistently exhibiting higher deviatoric stress. Overall, this research provides valuable insights into the mechanical behavior of geosynthetic-reinforced soils in road construction applications.
APPLIED SCIENCES-BASEL
(2023)
Article
Chemistry, Medicinal
Mustafa Tekpinar, Ahmet Yildirim
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2018)
Article
Biochemistry & Molecular Biology
Jerome Loc'h, Christina A. Gerodimos, Sandrine Rosario, Mustafa Tekpinar, Michael R. Lieber, Marc Delarue
JOURNAL OF BIOLOGICAL CHEMISTRY
(2019)
Article
Biochemistry & Molecular Biology
Wenjun Zheng, Han Wen
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2019)
Article
Biochemistry & Molecular Biology
Wenjun Zheng, Han Wen
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2020)
Article
Multidisciplinary Sciences
Gary J. Iacobucci, Han Wen, Matthew Helou, Beiying Liu, Wenjun Zheng, Gabriela K. Popescu
Summary: NMDA receptors are excitatory channels crucial for central synapse physiology. The activation process involves a series of kinetically distinguishable, reversible steps, starting with glutamate binding and ligand-binding domain constriction, followed by transducing movement through linkers to open the gate. This study reveals a direct chemical interaction between GluN1-I642 and GluN2A-L550 as a structural change late in the activation reaction, stabilizing the receptors after opening.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Wenjun Zheng
Summary: A fast and simple conformational sampling scheme guided by normal modes can accurately predict cryptic sites for small molecules binding in target proteins. Sampling along each of the lowest 30 modes is near optimal for adequately restructuring cryptic sites to be detected by existing pocket finding programs. The method achieves high prediction accuracy comparable to existing servers but is much faster and simpler, making it suitable for high-throughput processing of large datasets of protein structures at the genome scale.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Camille Samson, Pierre Legrand, Mustafa Tekpinar, Jef Rozenski, Mikhail Abramov, Philipp Holliger, Vitor B. Pinheiro, Piet Herdewijn, Marc Delarue
Article
Biochemistry & Molecular Biology
Mustafa Tekpinar, Ahmet Yildirim
Summary: Researchers conducted molecular dynamics simulations on SARS-CoV and SARS-CoV-2 main proteases and found that dimerization causes local structural changes and ligand binding induces key local changes in the dimeric forms. They also suggested that only one protomer is active in SARS-CoV-2 due to an allosteric interaction between the active sites.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biochemistry & Molecular Biology
Wenjun Zheng, Han Wen
Summary: TRPV1 channel undergoes gating transition from closed to open state in response to physical and chemical stimuli, regulated by small-molecule ligands including lipids. Molecular dynamics simulations identified state-dependent binding sites and predicted top ligand-binding sites as important features for distinguishing closed vs open states, providing guidance for designing small-molecular drugs targeting TRPV1.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2021)
Article
Multidisciplinary Sciences
Dariusz Czernecki, Pierre Legrand, Mustafa Tekpinar, Sandrine Rosario, Pierre-Alexandre Kaminski, Marc Delarue
Summary: The cyanophage S-2L incorporates 2-aminoadenine (Z) instead of adenine (A) in its genome. The study provides an explanation for the absence of A in S-2L genome by identifying and characterising functionally and structurally both the HD phosphohydrolase (datZ) that specifically cleaves dATP, and the sole DNA primase-polymerase of S-2L, nonspecific of dATP or dZTP.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Physical
Ahmet Yildirim, Mustafa Tekpinar, Tsjerk A. Wassenaar
Summary: The study reveals that Ca2+ binding enhances the dynamics of S100A4, regulating its interaction with NMIIA. NMIIA induces asymmetric dynamics between the chains of S100A4. In the absence of Ca2+, the interaction between S100A4 and NMIIA is weak.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Correction
Chemistry, Medicinal
Mustafa Tekpinar, Bertrand Neron, Marc Delarue
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)
Article
Chemistry, Medicinal
Mustafa Tekpinar, Bertrand Neron, Marc Delarue
Summary: The Python package correlationplus is developed to extract dynamical pairwise correlations from large molecular dynamics trajectories or normal-mode analysis, identifying key residues and interactions in proteins. By combining dynamical coupling information with sequence coevolution data, it provides new insights about protein function and aids in better understanding of residues involved in allosteric regulation. The package can be easily installed with common methods like conda or pip, and docker images are also available for usage without installation.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)
Article
Chemistry, Medicinal
Ahmet Yildirim, Mustafa Tekpinar
Summary: Researchers studied the relationship between the conservation of amino acid sequences and protein dynamics in the SARS-CoV-2 main protease. They discovered a quantifiable similarity that is crucial for designing effective drugs and has larger implications for viral proteases and proteins in general.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Physical
Wenjun Zheng
Summary: In order to computationally identify hidden binding sites for allosteric modulators, a fast and simple conformational sampling scheme guided by coarse-grained normal modes solved from the elastic network models followed by atomistic backbone and sidechain reconstruction has been developed. This method can adequately restructure cryptic sites so they are detectable by pocket finding programs like Concavity, making it suitable for high-throughput screening of protein structures at the genome scale. Our method has been used to locate known allosteric sites and predict new promising allosteric sites, and it is both faster and more flexible compared to other sampling methods.
JOURNAL OF CHEMICAL PHYSICS
(2023)