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
Biochemistry & Molecular Biology
Andrew Jewett, David Stelter, Jason Lambert, Shyam M. Saladi, Otello M. Roscioni, Matteo Ricci, Ludovic Autin, Martina Maritan, Saeed M. Bashusqeh, Tom Keyes, Remus T. Dame, Joan-Emma Shea, Grant J. Jensen, David S. Goodsell
Summary: Coarse-grained models are crucial in studying biomolecular dynamics and assembly, but simulating them can be challenging due to unconventional force fields and particle attributes, as well as systems not being in thermal equilibrium. Moltemplate is a file format for storing coarse-grained molecular models and forces, with broad scope and popularity in computational chemistry, materials science, and structural biology. It accommodates new forces developed for LAMMPS, making it a useful tool with thousands of users.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Materials Science, Multidisciplinary
Nils M. Denda, Peter Behrens, Andreas M. Schneider
Summary: Atomistic molecular modelling has become increasingly important for studying polymeric hybrid materials. The choice of mapping scheme for coarse-grained models is crucial for successful development, and different schemes have varying effects on simulation speed and model representation quality. The selection of mapping scheme becomes more critical as monomer complexity increases.
MATERIALS TODAY COMMUNICATIONS
(2023)
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)
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
Chemistry, Physical
Lisa Sappl, Christos N. Likos, Andreas Zoettl
Summary: The simulation of polymer solutions requires the development of methods that accurately include hydrodynamic interactions and improve computational efficiency. This research explores a new model for simulating ring polymers and discovers a method that yields satisfying diffusion behavior by regulating the interaction intensity with the solvent.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Biochemistry & Molecular Biology
Adam Liwo, Maciej Pyrka, Cezary Czaplewski, Xubiao Peng, Antti J. Niemi
Summary: In this study, the long-term dynamics of three molecular motors were investigated using molecular dynamics simulations. The results show that rotational motion can occur with zero total angular momentum in both the microcanonical and canonical ensembles, and thermal motions can be converted into net rotation. These findings highlight the importance of molecular motors in facilitating movement and transportation within living organisms.
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
Materials Science, Multidisciplinary
A. A. Madadi, A. R. Khoei
Summary: In this paper, a multi-scale method is proposed to couple atomistic and coarse-grained systems for modeling the mechanical properties of materials with defects and heterogeneity. By combining Molecular Dynamics analysis with a coarse-grained approach, the method reduces computational costs and allows for the effective study of material behavior and properties.
COMPUTATIONAL MATERIALS SCIENCE
(2021)
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)
Article
Chemistry, Multidisciplinary
Riccardo Alessandri, Fabian Grunewald, Siewert J. Marrink
Summary: The Martini model, originally designed for biomolecular simulations, has been increasingly utilized in the field of soft materials science. Its building block principle can be applied beyond biomolecular systems. The future development of the Martini model in materials science, particularly with the release of Martini 3, holds great potential.
ADVANCED MATERIALS
(2021)
Article
Chemistry, Multidisciplinary
Adam K. Sieradzan, Jordi Sans-Duno, Emilia A. Lubecka, Cezary Czaplewski, Agnieszka G. Lipska, Krzysztof M. Ocetkiewicz, Jerzy Proficz, Pawel Czarnul, Henryk Krawczyk, Adam Liwo, Henryk Leszczyfiski
Summary: The UNRES package for coarse-grained simulations of proteins has been significantly improved with algorithmic advancements, including optimized computations, reduced memory requirements, improved parallel performance, and capability to simulate large protein systems with high efficiency.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2023)
Article
Crystallography
Mark R. Wilson, Gary Yu
Summary: In recent years, achiral liquid crystal dimer molecules have been found to exhibit nematic-nematic phase transitions, with the lower temperature phase showing emergent chirality. Atomistic simulations of CB7CB dimer molecule have provided insights into the molecular-level order of the N-TB-N-I phase sequence. This paper presents a coarse-grained model of CB7CB in the NTB phase, developed using both force matching and iterative Boltzmann inversion methods.
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
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
Chemistry, Multidisciplinary
Xingfu Tao, Yang Li, Linxiuzi Yu, Yinshu Zhang, Chenglong Han, Yang Yang, Hujun Qian, Zhongyuan Lu, Kun Liu
Summary: In this study, a high-curvature 2D polymerization method is proposed to form highly cross-linked amphiphilic Gemini monomer networks on the surfaces of nanoparticles. Selective etching of core-shell nanoparticles allows for the formation of 2D polymers as non-contacting ligands on yolk-shell structures with excellent shape retention and high surface accessibility. Furthermore, the 2D polymer ligands can be covalently linked to other functional molecules through copolymerization.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Multidisciplinary
Ni An, Youliang Zhu, Xiaohan Wang, Yixuan Li, Junjun Liu, Xu Fang, Zhongyuan Lu, Bai Yang, Junqi Sun
Summary: Noncovalently cross-linked polymer materials with super-strong mechanical strength are fabricated by incorporating carbonized polymer dots (CPDs) into poly acrylic acid (PAA) and polyvinylpyrrolidone (PVPON) composites (denoted as PAA-PVPON-CPDs). The CPDs establish strong interactions with the polymers, resulting in unprecedented tensile strength and Young's modulus in the composites. The composites also exhibit excellent impact resistance and damage tolerance, and can be healed to restore their original mechanical strength.
Article
Chemistry, Multidisciplinary
Song Zhang, Zhe Li, Yu Bao, Song Lu, Zheng Gong, Hu-jun Qian, Zhong-yuan Lu, Shuxun Cui
Summary: As the initially discovered allotrope of boron, amorphouselementaryboron (AE-B) has been reported for more than two centuries. Severalpossible structures of AE-B have been proposed during the past decades. However, the noncrystalline nature of AE-B has made it difficult to determine its structure. By analyzing the surface adsorption and using techniques such as atomic force microscopy and high-resolution transmission electron microscopy, researchers have been able to characterize the molecular structure of AE-B at the single-molecule and nanoscopic level.
Article
Chemistry, Multidisciplinary
Songlin Zhang, Yibing Deng, Alberto Libanori, Yihao Zhou, Jiachen Yang, Trinny Tat, Lin Yang, Wanxin Sun, Peng Zheng, You-Liang Zhu, Jun Chen, Swee Ching Tan
Summary: This article reports a method of creating a single homogeneous material platform using a silver-polymer framework, thus achieving seamless sensing-actuation unification. The SPF-based pneumatic actuator has multimodal sensing capability, enabling self-sensing deformations and perception of external stimuli.
ADVANCED MATERIALS
(2023)
Article
Chemistry, Physical
Zi-Qin Chen, Yu-Wei Sun, Xiao-Jie Zhang, You-Liang Zhu, Zhan-Wei Li, Zhao-Yan Sun
Summary: In this study, defects in small aspect ratio liquid crystals confined in a circular cavity were investigated using molecular dynamics simulation. Two types of defects (inside the circle and at the boundary) were found under static conditions, but four types of defects could be observed when an external field was introduced. The position of the defects could be adjusted by changing the strength of the external field, providing a feasible way to modulate liquid crystal defects and investigate the transformation between different defects.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Han-Wen Pei, You-Liang Zhu, Zhong-Yuan Lu, Jun-Peng Li, Zhao-Yan Sun
Summary: An automatic method is proposed to generate the initial configuration and input file for multiscale molecular dynamics (MD) simulation of cross-linked polymer reaction systems using SMILES. This method accurately predicts the volume shrinkage, glass transition, and all-atom structure of cross-linked polymers, and is suitable for high-throughput computations.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Polymer Science
Zehao Li, Hui Li, Muxi Wang, Zhongyan Zhang, Liting Yang, Lijun Ma, Hong Liu
Summary: By adding nano-silica, the tensile strength of poly(butylene adipate-co-terephthalate)/thermoplastic hydroxypropyl starch (PBAT/TPHSg-SiO2) composite films is significantly improved, with a 35% increase in horizontal tensile strength and a 21% increase in vertical tensile strength after adding 4 phr of nano-silica. When the content of TPHSg-4SiO2 is 40%, the composite films have horizontal and vertical tensile strengths of 9.82 and 12.09 MPa, respectively, and the elongation at break exceeds 500%. Electron micrographs show that TPHSg-4SiO2 is well dispersed in PBAT and exhibits a bi-continuous phase structure at a TPHSg-4SiO2 content of 40%. The blowing PBAT/TPHSg-4SiO2 composite films effectively reduce the cost and still show better mechanical properties, suitable for packaging applications.
Article
Chemistry, Physical
Ming Zhou, Yu-Wei Sun, Zhan-Wei Li, You-Liang Zhu, Bing Li, Zhao-Yan Sun
Summary: This study investigates the behavior of achiral smectic-B liquid crystals (LCs) confined in narrow cylindrical cavities using molecular dynamics simulations. The study reveals the presence of helical and layered structures and the effects of the arrangement of cylindrical wall particles and anchoring strength on the LC structure.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Zhao Qian, Rui Shi, Zhong-Yuan Lu, Hu-Jun Qian
Summary: In this study, a solvent evaporation strategy was reported to spontaneously generate perpendicularly oriented domains (PODs) in drying DBC films through interface segregation of SCNPs. This strategy could be useful in regulating the PODs of DBC films in practical applications.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Multidisciplinary
Siqi Zhang, You-Liang Zhu, Siyuan Ren, Chunguang Li, Xiao-Bo Chen, Zhenjiang Li, Yu Han, Zhan Shi, Shouhua Feng
Summary: In this study, a nitrogen-rich covalent organic framework (TB-COF) was designed as an aqueous anode for calcium ion batteries, addressing the challenges of organic materials' solubility and low electronic conductivity. TB-COF demonstrated a high reversible capacity and long cycle life, with a validated redox mechanism and identification of a novel active site for calcium ion storage.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Physical
Yu-Ting Sun, Can Zhao, You-Liang Zhu, Jun-Lei Guan, Li-Li Zhang, Lai Wei, Zhao-Yan Sun, Yi-Neng Huang
Summary: Highly conductive and stretchable polymer conductors with low-load nanoparticles are proposed in this study, which are achieved by the self-assembly of surface-modified nanoparticles. The conductive pathways formed by the self-assembled nanoparticles retain high percolation probability even at low NP loading and high tensile strain.
Article
Chemistry, Physical
Ming Zhou, Yu-Wei Sun, Zhan-Wei Li, Han-Wen Pei, Bing Li, You-Liang Zhu, Zhao-Yan Sun
Summary: The formation and transformation of defects in confined liquid crystals are studied using molecular dynamics simulations. The liquid-crystal droplet undergoes an isotropic to smectic-B phase transition through the smectic-A phase as the number density of the LC molecules increases. The change of LC structure from bipolar to watermelon-striped during the phase transition is observed. The results reveal the transition from bipolar defects to inhomogeneous structures with the coexistence of nematic and smectic phases in smectic liquid-crystal droplets.
Article
Chemistry, Multidisciplinary
Antonio De Nicola, Costanza Montis, Greta Donati, Antonio Molinaro, Alba Silipo, Arianna Balestri, Debora Berti, Flaviana Di Lorenzo, You-Liang Zhu, Giuseppe Milano
Summary: By combining simulations and experiments, the complex supramolecular structures of lipopolysaccharides (LPS) and lipid A at low hydration levels were revealed, uncovering the presence of a nano-compartmentalized phase composed of liposomes of variable size and shape, which can be utilized in synthetic biological applications.
Article
Chemistry, Physical
Haoxiang Sun, Xu Fang, Youliang Zhu, Zhuochen Yu, Xingyuan Lu, Junqi Sun
Summary: In this study, high-performance degradable plastics with high mechanical strength, satisfactory water resistance, and rapid degradation characteristics were fabricated through the complexation of regenerated cellulose and tannic acid. The resulting plastic, called C-TA, exhibited ultrahigh fracture strength and toughness. Molecular dynamics simulations showed that the introduction of dendritic tannic acid molecules enhanced the toughness of the plastic. The C-TA plastic also displayed excellent water resistance and could be fully degraded in soil within 35 days.
JOURNAL OF MATERIALS CHEMISTRY A
(2023)
Article
Chemistry, Multidisciplinary
Lu Cheng, Ruiyuan Tian, Yifan Zhao, Zhixuan Wei, Xin Pu, You-Liang Zhu, Dong Zhang, Fei Du
Summary: A new binder was synthesized by cross-linking sodium alginate with MXene materials, which shows improved adhesion, mechanical properties, and electronic conductivity. The binder enables the fabrication of high-capacity and high-quality electrodes and shows feasibility in different battery systems.