4.5 Article

Modeling microtubule cytoskeleton via an active liquid crystal elastomer model

Journal

COMPUTATIONAL MATERIALS SCIENCE
Volume 96, Issue -, Pages 559-566

Publisher

ELSEVIER
DOI: 10.1016/j.commatsci.2014.04.041

Keywords

Biopolymer; Cytoskeleton; Liquid crystal elastomer; Microtubule; Soft matter

Funding

  1. Microsoft Corporation
  2. National Science Foundation (CMMI), United States [0800744]
  3. Chinese Scholarship Council (CSC), China
  4. Directorate For Engineering [0800744] Funding Source: National Science Foundation
  5. Div Of Civil, Mechanical, & Manufact Inn [0800744] Funding Source: National Science Foundation

Ask authors/readers for more resources

In this work, a three-dimensional (3D) liquid crystal polymer model is developed to model the microtubule cytoskeleton aggregate and to study its interaction with the extracellular matrix. In the proposed microtubule cytoskeleton model, the cytoskeleton aggregate is treated as a homogenized liquid crystal elastomer medium, with an extra active stress term included to account for the effect of the active process of Guanosine Triphosphate (GTP) hydrolysis. The cell extracellular matrix (ECM) is modeled as a hyperelastic material. The specific and non-specific interactions between the cell and its ECM are modeled by a Coarse-Grained Contact Model. Surface tension effects are incorporated into the simulation, through a Multiscale Dynamic Wetting Model, to account for the interface conditions between the cell and its surrounding environment. The cell model is implemented in a Lagrange type Galerkin formulation. The numerical results show that the cell can sense and move under the gradient of matrix elasticity. (C) 2014 Elsevier B. V. All rights reserved.

Authors

I am an author on this paper
Click your name to claim this paper and add it to your profile.

Reviews

Primary Rating

4.5
Not enough ratings

Secondary Ratings

Novelty
-
Significance
-
Scientific rigor
-
Rate this paper

Recommended

Article Computer Science, Interdisciplinary Applications

Peridynamic modeling and simulation of thermo-mechanical fracture in inhomogeneous ice

Ying Song, Shaofan Li, Yunbo Li

Summary: In this work, a peridynamics approach is used to develop an inhomogeneous sea ice model and simulate crack propagation in a thermo-mechanical field of ice sheet. The proposed model not only provides an efficient tool to simulate the complex deformation pattern in ice failure process, but also reveals the mechanical mechanism of fracture in ice.

ENGINEERING WITH COMPUTERS (2023)

Article Mathematics, Interdisciplinary Applications

A machine-learning aided multiscale homogenization model for crystal plasticity: application for face-centered cubic single crystals

Dana Bishara, Shaofan Li

Summary: In this study, a machine learning-assisted multiscale method is proposed to efficiently eliminate the effects of loading rate and mesh size, leading to improved accuracy in homogenization results while maintaining consistency at the atomic level.

COMPUTATIONAL MECHANICS (2023)

Article Engineering, Multidisciplinary

A coupling approach of the isogeometric-meshfree method and peridynamics for static and dynamic crack propagation

Qi Zhang, Nhon Nguyen-Thanh, Weidong Li, A-Man Zhang, Shaofan Li, Kun Zhou

Summary: A coupling approach of the isogeometric-meshfree method and the peridynamic method is developed for static and dynamic crack propagation. The approach allows for flexible modeling of cracks while maintaining exact geometry representation. By using the balanced force principle, the isogeometric-meshfree nodes are directly coupled with peridynamic points, effectively eliminating surface effects and enforcing boundary conditions. The coupling approach achieves adaptive coupling with the same convergence rate as the isogeometric-meshfree method and is extended to crack problems with contact loading.

COMPUTER METHODS IN APPLIED MECHANICS AND ENGINEERING (2023)

Article Mechanics

A three-dimensional (3D) micro-potential-based peridynamics model for deformation and fracture in solid materials

Renwei Liu, Yanzhuo Xue, Shaofan Li

Summary: In this study, a novel three-dimensional micro-potential-based peridynamics model is developed for simulating deformation and fracture of solid materials. The model considers bond deformation with a square measure and constructs a 3D nonlocal strain tensor that includes nonlocal shear strain and nonlocal volumetric strain. The micro-potential energy generated by particle deformation follows the Xu-Needleman potential function, leading to the establishment of a micro-potential-based peridynamics constitutive model. The model's bond failure criterion based on energy release rate is derived and the numerical implementation of the model is provided. Mode I, II, and III cracks are used to verify the model's performance in simulating deformation, fracture, and nonlocal strain, crack nucleation, and propagation characteristics.

ENGINEERING FRACTURE MECHANICS (2023)

Article Mechanics

A multiscale two-dimensional finite element incorporating the second-order Cauchy-Born rule for cohesive zone modeling: Simulation of fracture in polycrystalline materials

Dana Bishara, Shaofan Li

Summary: In this paper, a multiscale cohesive zone model is developed to simulate crack growth in polycrystalline solids by elaborating the second-order Cauchy-Born rule. The model discretizes a two-dimensional domain with bulk elements and finite width cohesive zone interphase, allowing crack propagation through both grain boundaries and grains. The correlation between micro and macroscale material properties is specified using the CB rule, and extensive numerical studies are conducted to investigate various factors and compare with other methods. The model shows the ability to predict both brittle and ductile fractures and maintains consistency in constitutive relations.

ENGINEERING FRACTURE MECHANICS (2023)

Article Computer Science, Interdisciplinary Applications

A general finite deformation hypoelastic-plasticity non-ordinary state-based peridynamics model and its applications

Renwei Liu, Yanzhuo Xue, Shaofan Li

Summary: In this study, a general approach is presented to incorporate the rate form finite elastoplasticity theory into the state-based peridynamics framework. The developed state-based peridynamics model includes isotropic hardening behaviors in mechanical response and is validated through convergence studies against finite element method. Additionally, a meshfree particle contact force model is incorporated to simulate impact problems. This work provides a systematic procedure to incorporate general inelastic constitutive models into the state-based peridynamics and establishes a foundation for further development of hyper-elastoplastic peridynamics material models.

ENGINEERING WITH COMPUTERS (2023)

Article Acoustics

Study on the dynamic characteristics of the suspender with additional dampers and a frequency-based multiple parameter identification method for the system

L. Ma, C. S. Cai, L. H. Wu, S. F. Li

Summary: The measurement of tensile forces in suspenders is crucial for safety inspection and monitoring in large structural engineering projects. The frequency-based method is commonly used, but affected by factors such as additional damping and boundary conditions. This study derives the equation of damped motion for a suspender-damper system, develops a numerical solution method based on finite difference scheme, and proposes a frequency-based multiple parameter identification method. The research demonstrates that the position and damping coefficient of the damper significantly affect the frequency and mode of the suspender-damper system, and discusses the influencing mechanism. Numerical examples show that the proposed algorithm can accurately identify multiple system parameters of the suspender, with a maximum error of 1%. The study also discusses the influence of frequency errors.

JOURNAL OF SOUND AND VIBRATION (2023)

Article Engineering, Environmental

Carbonation dynamics of hydrated alite revealed by electron microscopy

Qi Zheng, Chengyao Liang, Jinyang Jiang, Shaofan Li

Summary: In this study, the carbonation dynamics of alite hydrates were explored using electron microscopy. It was found that calcite is the dominant phase of carbonate crystals in the alite system throughout the carbonation process. The shape evolution of calcite crystals, from spindle carbonates to rhombohedrons, was observed, along with intermediate states such as polyhedral particles and layered rhomboids. The growth rate of calcite particles was determined to be approximately 0.2 μm/day, which may be influenced by the relative concentration of calcium ions and CO2 source. Atomic force microscopy was used to uncover the relationship between the microstructure and mechanical properties of calcite. Additionally, the morphology development of calcite crystals during carbonation was explained by the variation in surface energy of different facets. This work provides a unique approach to study carbonation kinetics and sheds light on underlying carbonation mechanisms at the nanoscale.

CHEMICAL ENGINEERING JOURNAL (2023)

Article Mathematics, Interdisciplinary Applications

A meshfree orthotropic laminated shell model for geometrically nonlinear static and dynamic analysis

Bing Xue, A-Man Zhang, Yu-Xiang Peng, Qi Zhang, Shaofan Li

Summary: A meshfree orthotropic laminated shell model based on the reproducing kernel particle method (RKPM) and the Mindlin-Reissner shell theory is proposed for dealing with finite deformation of composite shell structures, suitable for arbitrary geometry in engineering. The model is validated through static and dynamic benchmarks, demonstrating its accuracy and convergence in solving nonlinear responses of composite structures.

COMPUTATIONAL MECHANICS (2023)

Article Engineering, Multidisciplinary

A bond-based peridynamics modeling of polymeric material fracture under finite deformation

Caglar Tamur, Shaofan Li

Summary: We have developed a bond-based peridynamics model that can accurately capture the fracture of polymer networks under finite deformation. Through numerical examples, we have demonstrated that this model is robust, efficient, and able to simulate crack growth in polymeric materials with good accuracy. Compared to existing continuum models, our approach is theoretically simple, rigorous, and computationally fast, making it a convenient simulation tool for modeling polymer failure processes.

COMPUTER METHODS IN APPLIED MECHANICS AND ENGINEERING (2023)

Article Engineering, Multidisciplinary

Higher-order nonlocal operator theory for phase-field modeling of ductile fracture in elasto-plastic materials

Nhon Nguyen-Thanh, Qi Zhang, Weidong Li, Mao See Wu, Shaofan Li, Kun Zhou

Summary: In this work, a novel approach based on the higher-order nonlocal operator is proposed for the phase-field modeling of ductile fracture in elasto-plastic materials. The method introduces a total energy function consisting of elastic, plastic, and fracture terms. Plasticity is coupled with fracture through a degradation function applied to the tensile part of elastic strain energy. The proposed higher-order nonlocal operator method provides advantages over the original method by not requiring direct computation of kernel function or moment matrix derivatives, improving computational efficiency and simplifying implementation. The accuracy and effectiveness of the proposed method are demonstrated through various numerical examples, detecting complex patterns of ductile fracture such as crack propagation and plastic localization.

COMPUTER METHODS IN APPLIED MECHANICS AND ENGINEERING (2023)

Article Computer Science, Interdisciplinary Applications

A novel peridynamic solution for modelling saturated soil-pore fluid interaction in liquefaction analysis

Quan Gu, Zhe Lin, Lei Wang, Zhijian Qiu, Surong Huang, Shaofan Li

Summary: Saturated soil-pore fluid interaction under earthquake shaking can cause extensive damages to critical infrastructure systems. Accurate modeling of this interaction is important for liquefaction analysis. The authors propose a novel solution strategy for modeling soil-pore fluid interaction, based on a hybrid Peridynamics (HPD) method. The method is validated and shown to be effective for solving the soil-pore fluid equations and applicable to a broad range of geotechnical earthquake engineering problems associated with liquefaction.

COMPUTERS AND GEOTECHNICS (2023)

Article Materials Science, Multidisciplinary

On Peierls-Rice-Beltz nonlocal continuum model and simulations of mesoscale dislocations (slips) and shear cracks

Xuan Hu, Shaofan Li

Summary: In this work, a cohesive Peierls-Rice-Beltz nonlocal continuum theory is developed and applied to model mesoscale dislocation motions and shear cracks in crystal solids. The main novelties of this work are the development of a bond-based peridynamics model and the ability to simulate different types of fractures. The proposed method is shown to be effective in modeling inelastic fracture in nonlocal cohesive media.

JOURNAL OF THE MECHANICS AND PHYSICS OF SOLIDS (2023)

Article Engineering, Marine

A Multi-Yield-Surface Plasticity State-Based Peridynamics Model and its Applications to Simulations of Ice-Structure Interactions

Ying Song, Luwen Zhang, Shaofan Li, Yunbo Li

Summary: Building an accurate ice constitutive model to predict ice loads during ship-ice collision is challenging due to the complex mesoscopic and macroscopic characteristics of ice. In this study, we combine a conventional plasticity model with state-based peridynamics and consider the effects of temperature distribution, strain rate, and pressure sensitivity. The proposed model successfully predicts material failure of different types of ice and is validated through benchmark tests.

JOURNAL OF MARINE SCIENCE AND APPLICATION (2023)

Article Mathematics, Interdisciplinary Applications

A multigrid coupling approach of the extended isogeometric-meshfree method and peridynamics for brittle fracture

Weidong Li, Nguyen-Thanh Nhon, Qi Zhang, Hejun Du, Shaofan Li, Kun Zhou

Summary: A multigrid coupling approach of the extended isogeometric-meshfree method and bond-based peridynamics is developed for static and dynamic fracture problems. The approach divides the problem domain into two subdomains and connects them with interface meshes to capture fracture patterns.

COMPUTATIONAL MECHANICS (2023)

Correction Materials Science, Multidisciplinary

Efficiency and accuracy of GPU-parallelized Fourier spectral methods for solving phase-field models (vol 228, ,112313, 2023)

A. D. Boccardo, M. Tong, S. B. Leen, D. Tourret, J. Segurado

COMPUTATIONAL MATERIALS SCIENCE (2024)

Article Materials Science, Multidisciplinary

Deep learning interatomic potential for thermal and defect behaviour of aluminum nitride with quantum accuracy

Tao Li, Qing Hou, Jie-chao Cui, Jia-hui Yang, Ben Xu, Min Li, Jun Wang, Bao-qin Fu

Summary: This study investigates the thermal and defect properties of AlN using molecular dynamics simulation, and proposes a new method for selecting interatomic potentials, developing a new model. The developed model demonstrates high computational accuracy, providing an important tool for modeling thermal transport and defect evolution in AlN-based devices.

COMPUTATIONAL MATERIALS SCIENCE (2024)

Article Materials Science, Multidisciplinary

Illuminating the mechanical responses of amorphous boron nitride through deep learning: A molecular dynamics study

Shin-Pon Ju, Chao-Chuan Huang, Hsing-Yin Chen

Summary: Amorphous boron nitride (a-BN) is a promising ultralow-dielectric-constant material for interconnect isolation in integrated circuits. This study establishes a deep learning potential (DLP) for different forms of boron nitride and uses molecular dynamics simulations to investigate the mechanical behaviors of a-BN. The results reveal the structure-property relationships of a-BN, providing useful insights for integrating it in device applications.

COMPUTATIONAL MATERIALS SCIENCE (2024)

Article Materials Science, Multidisciplinary

Multiscale modeling of shape memory polymers foams nanocomposites

M. Salman, S. Schmauder

Summary: Shape memory polymer foams (SMPFs) are lightweight cellular materials that can recover their undeformed shape through external stimulation. Reinforcing the material with nano-clay filler improves its physical properties. Multiscale modeling techniques can be used to study the thermomechanical response of SMPFs and show good agreement with experimental results.

COMPUTATIONAL MATERIALS SCIENCE (2024)

Article Materials Science, Multidisciplinary

DFT study on zeolites' intrinsic Brønsted acidity: The case of BEA

Laura Gueci, Francesco Ferrante, Marco Bertini, Chiara Nania, Dario Duca

Summary: This study investigates the acidity of 30 Bronsted sites in the beta-zeolite framework and compares three computational methods. The results show a wide range of deprotonation energy values, and the proposed best method provides accurate calculations.

COMPUTATIONAL MATERIALS SCIENCE (2024)

Article Materials Science, Multidisciplinary

Unveiling the CO2 adsorption capabilities of biphenylene network monolayers through DFT calculations

K. A. Lopes Lima, L. A. Ribeiro Junior

Summary: Advancements in nanomaterial synthesis and characterization have led to the discovery of new carbon allotropes, including biphenylene network (BPN). The study finds that BPN lattices with a single-atom vacancy exhibit higher CO2 adsorption energies than pristine BPN. Unlike other 2D carbon allotropes, BPN does not exhibit precise CO2 sensing and selectivity by altering its band structure configuration.

COMPUTATIONAL MATERIALS SCIENCE (2024)

Article Materials Science, Multidisciplinary

Ab-initio study of quaternary Heusler alloys LiAEFeSb (AE = Be, Mg, Ca, Sr or Ba) and prediction of half-metallicity in LiSrFeSb and LiBaFeSb

Jay Kumar Sharma, Arpita Dhamija, Anand Pal, Jagdish Kumar

Summary: In this study, the quaternary Heusler alloys LiAEFeSb were investigated for their crystal structure, electronic properties, and magnetic behavior. Density functional theory calculations revealed that LiSrFeSb and LiBaFeSb exhibit half-metallic band structure and 100% spin polarization, making them excellent choices for spintronic applications.

COMPUTATIONAL MATERIALS SCIENCE (2024)

Article Materials Science, Multidisciplinary

Graph neural networks for predicting structural stability of Cd- and Zn-doped-CsPbI3

Roman A. Eremin, Innokentiy S. Humonen, Alexey A. Kazakov, Vladimir D. Lazarev, Anatoly P. Pushkarev, Semen A. Budennyy

Summary: Computational modeling of disordered crystal structures is essential for studying composition-structure-property relations. In this work, the effects of Cd and Zn substitutions on the structural stability of CsPbI3 were investigated using DFT calculations and GNN models. The study achieved accurate energy predictions for structures with high substitution contents, and the impact of data subsampling on prediction quality was comprehensively studied. Transfer learning routines were also tested, providing new perspectives for data-driven research of disordered materials.

COMPUTATIONAL MATERIALS SCIENCE (2024)

Article Materials Science, Multidisciplinary

Insight into effect of high pressure on the structural, electronic, and optical properties of KH2PO4

Zhixin Sun, Hang Dong, Yaohui Yin, Ai Wang, Zhen Fan, Guangyong Jin, Chao Xin

Summary: In this study, the crystal structure, electronic structure, and optical properties of KH2PO4: KDP crystals under different pressures were investigated using the generalized gradient approximate. It was found that high pressure caused a phase transition in KDP and greatly increased the band gap. The results suggest that high pressure enhances the compactness of KDP and improves the laser damage threshold.

COMPUTATIONAL MATERIALS SCIENCE (2024)

Article Materials Science, Multidisciplinary

Phenomenon of anti-driving force during grain boundary migration

Tingting Yu

Summary: This study presents atomistic simulations revealing that an increase in driving force may result in slower grain boundary movement and switches in the mode of grain boundary shear coupling migration. Shear coupling behavior is found to effectively alleviate stress and holds potential for stress relaxation and microstructure manipulation in materials.

COMPUTATIONAL MATERIALS SCIENCE (2024)

Article Materials Science, Multidisciplinary

The electronic properties of C2N/antimonene heterostructure regulated by the horizontal and vertical strain, external electric field and interlayer twist

Y. Zhang, X. Q. Deng, Q. Jing, Z. S. Zhang

Summary: The electronic properties of C2N/antimonene van der Waals heterostructure are investigated using density functional theory. The results show that by applying horizontal strain, vertical strain, electric field, and interlayer twist, the electronic structure can be adjusted. Additionally, the band alignment and energy states of the heterostructure can be significantly changed by applying vertical strain on the twisted structure. These findings are important for controlling the electronic properties of heterostructures.

COMPUTATIONAL MATERIALS SCIENCE (2024)

Article Materials Science, Multidisciplinary

Functionalized carbophenes as high-capacity versatile gas adsorbents: An ab initio study

Chad E. Junkermeier, Evan Larmand, Jean-Charles Morais, Jedediah Kobebel, Kat Lavarez, R. Martin Adra, Jirui Yang, Valeria Aparicio Diaz, Ricardo Paupitz, George Psofogiannakis

Summary: This study investigates the adsorption properties of carbon dioxide (CO2), methane (CH4), and dihydrogen (H2) in carbophenes functionalized with different groups. The results show that carbophenes can be promising adsorbents for these gases, with high adsorption energies and low desorption temperatures. The design and combination of functional groups can further enhance their adsorption performance.

COMPUTATIONAL MATERIALS SCIENCE (2024)

Article Materials Science, Multidisciplinary

Insights from symmetry: Improving machine-learned models for grain boundary segregation

Y. Borges, L. Huber, H. Zapolsky, R. Patte, G. Demange

Summary: Grain boundary structure is closely related to solute atom segregation, and machine learning can predict the segregation energy density. The study provides a fresh perspective on the relationship between grain boundary structure and segregation properties.

COMPUTATIONAL MATERIALS SCIENCE (2024)

Article Materials Science, Multidisciplinary

Phase-field dislocation dynamics simulations of temperature-dependent glide mechanisms in niobium

M. R. Jones, L. T. W. Fey, I. J. Beyerlein

Summary: In this work, a three-dimensional ab-initio informed phase-field-dislocation dynamics model combined with Langevin dynamics is used to investigate glide mechanisms of edge and screw dislocations in Nb at finite temperatures. It is found that the screw dislocation changes its mode of glide at two distinct temperatures, which coincides with the thermal insensitivity and athermal behavior of Nb yield strengths.

COMPUTATIONAL MATERIALS SCIENCE (2024)

Article Materials Science, Multidisciplinary

Spline-based neural network interatomic potentials: Blending classical and machine learning models

Joshua A. Vita, Dallas R. Trinkle

Summary: This study introduces a new machine learning model framework that combines the simplicity of spline-based potentials with the flexibility of neural network architectures. The simplified version of the neural network potential can efficiently describe complex datasets and explore the boundary between classical and machine learning models. Using spline filters for encoding atomic environments results in interpretable embedding layers that can incorporate expected physical behaviors and improve interpretability through neural network modifications.

COMPUTATIONAL MATERIALS SCIENCE (2024)