Article
Chemistry, Physical
Taichi Inagaki, Shinji Saito
Summary: In this paper, a new hybrid method called potential scaling HMC (PS-HMC) is introduced to study complex chemical processes. By modulating the trajectory and gradually flattening the potential energy surface, the PS-HMC method is capable of constructing the canonical ensemble with a multimodal distribution. Applications to different molecular processes demonstrate the feasibility and features of this new method.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Physics, Fluids & Plasmas
Hirakjyoti Sarma, Ritupan Sarmah, Nilakshi Das
Summary: The dynamics of a harmonically trapped three-dimensional Yukawa ball of charged dust particles immersed in plasma is investigated as a function of external magnetic field and Coulomb coupling parameter using molecular dynamics simulation. It is shown that the trapped dust particles self-organize into nested spherical shells. The particles start rotating in a coherent order as the magnetic field reaches a critical value corresponding to the coupling parameter of the system of dust particles. The magnetically controlled charged dust cluster of finite size undergoes a first-order phase transition from disordered to ordered phase. At sufficiently high coupling and strong magnetic field, the vibrational mode of this finite-sized charged dust cluster freezes, and the system retains only rotational motion.
Article
Polymer Science
Khloe Shuk-Ying Kwan, Ying-Ying Lui, Takashi Kajitani, Franco King-Chi Leung
Summary: This study demonstrates the fabrication of macroscopic functional soft materials through supramolecular assembly without the use of inorganic salts. Anionic and cationic nanotubes of stiff stilbene amphiphiles (SAs) can co-assemble into nanoribbons, which can be further prepared into macroscopic soft materials using inorganic salt solutions or deionized water. These macroscopic soft materials exhibit stability at low concentrations and retain their photoresponsiveness to undergo morphological changes upon photoirradiation.
MACROMOLECULAR RAPID COMMUNICATIONS
(2022)
Article
Chemistry, Physical
Jessica Bowles, Sascha Jahnigen, Rodolphe Vuilleumier, Florent Calvo, Carine Clavaguera, Federica Agostini
Summary: The vibrational spectrum of alanine amino acid was computationally determined in different environments and phases using molecular dynamics trajectories and an optimized polarizable force field. The analysis revealed significant differences between the spectra of neutral and zwitterionic forms of alanine in the gas phase, and provided insights into the molecular origins of vibrational bands in condensed phases.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Jiuyang Liang, Pan Tan, Liang Hong, Shi Jin, Zhenli Xu, Lei Li
Summary: We have developed a new RBE method for molecular dynamics simulations of charged particles in a periodic box. This method is accurate, highly efficient, and scalable, allowing for efficient computation in large-scale systems and achieving satisfactory results.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Multidisciplinary
Amita Mahapatra, Unmesh Dutta Chowdhury, Sahadev Barik, Subhakanta Parida, B. L. Bhargava, Moloy Sarkar
Summary: This study investigates the role of anions in stabilizing nucleic acids in ionic liquids (ILs). The results demonstrate that, in addition to cations, the chemical nature of anions plays a significant role in the interaction between ILs and DNA.
Article
Chemistry, Physical
Min Li, WenCai Lu, John ZengHui Zhang
Summary: The study successfully extended the coarse-graining strategy to ultra-coarse-grained models and effectively parameterized liquid water, accurately predicting some important properties of liquid water. Additionally, two polarizable states of UCG molecules were observed after system equilibration. The results demonstrate that the proposed UCG models can accelerate liquid water simulation effectively.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Biochemistry & Molecular Biology
Lavi S. Bigman, Yaakov Levy
Summary: Many proteins have disordered regions with high fractions of charged residues, either mixed charge or uniform charge. Previous research found that negatively charged D/E repeats are longer and more common in eukaryotes compared to positively charged K/R repeats. The conformational preferences and dynamics of these charged polypeptides change with salt concentration, with D/E repeats being more sensitive to salt and tending to adsorb more divalent cations. The greater prevalence of D/E repeats and the higher abundance of E and K can be explained by biophysical factors.
Article
Chemistry, Multidisciplinary
Olgun Guvench, Elizabeth K. Whitmore
Summary: The effects of sulfation and calcium cations on the conformation of chondroitin carbohydrate polymers in aqueous solutions were studied using molecular dynamics simulations. The results showed that sulfation and Ca2+ led to more compact polymer conformations, and differences in force-field parametrization influenced Ca2+ binding to chondroitin functional groups. The study highlights the importance of accurate force-field parametrization in balancing ion-water and ion-chondroitin interactions.
Article
Chemistry, Physical
Karishma Jain, Aleksandar Y. Mehandzhiyski, Igor Zozoulenko, Lars Wagberg
Summary: The study focuses on the particle morphology, size, charge density, and zeta potential of PEDOT:PSS dispersion, showing significant changes with pH levels and ionic strengths. The molecular model developed accurately represents the characteristics of PEDOT:PSS nanoparticles in aqueous dispersion. The results provide new insights and a deep understanding of the morphology and zeta potential evolution in PEDOT:PSS dispersion.
JOURNAL OF COLLOID AND INTERFACE SCIENCE
(2021)
Article
Chemistry, Physical
Mohammad Soroush Barhaghi, Brad Crawford, Gregory Schwing, David J. Hardy, John E. Stone, Loren Schwiebert, Jeffrey Potoff, Emad Tajkhorshid
Summary: py-MCMD is an open-source Python software that manages and generates thermodynamic properties and trajectories. The MC/MD simulations show close agreement with reference MC simulations and have higher computational efficiency. The CD-CBMC algorithm greatly improves sampling efficiency in water simulations.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Multidisciplinary
Danh Nguyen, James Wu, Patrick Corrigan, Ying Li
Summary: This study investigates the mechanisms of lipid bilayer disruption by Janus nanoparticles (NPs) through computational simulations. The results reveal that the Janus balance and the concentration of charged phospholipids play significant roles in the interactions between Janus NPs and lipid bilayers. The study provides molecular insights into the selectivity of Janus NPs for negatively charged lipid membranes and highlights the importance of the anisotropic properties of Janus NPs in membrane disruption.
Article
Multidisciplinary Sciences
Hao Chen, Valery Levitas, Dmitry Popov, Nenad Velisavljevic
Summary: The unexpected nanostructure evolution during Si-I -> Si-II phase transformation is revealed by combining molecular dynamics, crystallographic theory, and in situ real-time Laue X-ray diffraction. This phase transformation results in twinned Si-II and unexpected nanobands, which form specific interfaces with Si-I and create self-accommodated nanostructure.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Multidisciplinary
Qing-Hai Hao, Jie Cheng, Fan Yang, Hong-Ge Tan
Summary: The self-assembled morphologies of polyelectrolyte sparsely grafted nanoparticles can be predicted by studying the impact of different matrix chain lengths and rigidness, as well as electrostatic interactions. Understanding the mechanisms of self-assembled structure formation is crucial for designing smart polymer nanocomposites based on PE coated nanoparticles.
Article
Chemistry, Physical
Fabrizio Lo Celso, Giampaolo Barone, Loredana Maiuolo, Vincenzo Algieri, Carmen Cretu, Pietro Calandra
Summary: This study investigates the solubility and molecular dynamics of two newly synthesized oxindole nitrones with proven antiproliferative and antioxidant activity in liquid amphiphile solvents using a combination of experimental and computational methods. The different chemical structures of the solvents provide different chemical environments for the nitrones, and the study highlights the intermolecular interactions involved in the stabilization of nitrones in the solvents, providing valuable information for the design of specific carriers for nitrones delivery.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Biochemistry & Molecular Biology
Helen V. Thorbjornsrud, Luca Bressan, Tamjidmaa Khatanbaatar, Manuel Carrer, Kathrin Wurth-Roderer, Gabriele Cordara, Peter Kast, Michele Cascella, Ute Krengel
Summary: Unlike typical chorismate mutases, the enzyme from Mycobacterium tuberculosis (MtCM) has low activity, but its catalytic efficiency can be significantly increased by forming a complex with a partner enzyme. Through molecular dynamics simulations and kinetic investigations, we have studied the structure and functional changes of this enzyme. Our findings show that key residues in artificially evolved enzyme variants contribute to enhancing catalysis by preorganizing and stabilizing the active site loop.
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
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, Medicinal
Samiran Sen, Morten Ledum, Sigbjorn Loland Bore, Michele Cascella
Summary: Hamiltonian hybrid particle-field molecular dynamics is an efficient method for studying large soft matter systems. In this work, the method is extended to constant-pressure simulations and the calculation of internal pressure is reformulated to account for particle distribution. The resulting model accurately describes the physics of systems under pressure and successfully reproduces experimental results.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Physical
Morten Ledum, Samiran Sen, Sigbjorn Loland Bore, Michele Cascella
Summary: Hybrid particle-field molecular dynamics is a molecular simulation strategy that couples particles to a density field. The Hamiltonian hybrid particle-field method has been expanded and generalized to establish compatibility with any local soft pair potential. The mean-field regime observed in hybrid particle-field simulations is determined by the systems considered, and the Hamiltonian hybrid particle-field model has been shown to effectively capture all properties of the Gaussian Core model.
JOURNAL OF CHEMICAL PHYSICS
(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
Morten Ledum, Samiran Sen, Xinmeng Li, Manuel Carrer, Yu Feng, Michele Cascella, Sigbjorn Loland Bore
Summary: We present HylleraasMD (HyMD), a comprehensive implementation of a recently proposed Hamiltonian formulation of hybrid particle-field molecular dynamics. The methodology utilizes a grid-independent length-scale of coarse-graining that allows for systematic convergence of energies and forces by grid refinement, while eliminating nonphysical force aliasing. By separating the time integration of fast modes and slow modes, HyMD enables the first time-reversible, energy-conserving hybrid particle-field simulations. The ability of HyMD to perform simulations in various ensembles is demonstrated through test cases and compared to established literature.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Biology
Dario Segura-Pena, Oda Hovet, Hemanga Gogoi, Jennine Dawicki-McKenna, Stine Malene Hansen Woien, Manuel Carrer, Ben E. Black, Michele Cascella, Nikolina Sekulic
Summary: This study investigates the effects of phosphorylation on the molecular dynamics and structure of the Aurora B/IN-box enzymatic complex. The dynamics of Aurora and IN-box are found to be interconnected, and IN-box plays both positive and negative regulatory roles depending on the phosphorylation status. Phosphorylation in the activation loop of Aurora B and synergistic phosphorylation at two sites are crucial for full enzyme activity.
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
Manuel Carrer, Josefine Eilso Nielsen, Henrique Musseli Cezar, Reidar Lund, Michele Cascella, Thereza A. Soares
Summary: We investigate the lipid transport properties of model lipid membranes in the presence of antimicrobial peptide indolicidin. Experimental techniques are used to compare with fully atomistic molecular dynamics simulations. The results show that lipid flip-flop dynamics is greatly accelerated upon peripheral binding of the peptides, even at low concentrations. Computer modeling explains the interplay between structural changes and lipid dynamics induced by peptides and proposes a universal mechanism for the mode of action of antimicrobial peptides.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Chemistry, Multidisciplinary
Marinella de Giovanetti, Sondre Hopen H. Eliasson, Abril C. Castro, Odile Eisenstein, Michele Cascella
Summary: Ab initio molecular dynamics simulations are performed to study THF solutions containing LiCl and LiCl with CH3MgCl, as model compounds of the turbo Grignard reagent. LiCl aggregates as compact cubane-like Li4Cl4 structures, with an open-edge pseudotetrahedral frame promoted by solvent-assisted Li-Cl bond cleavage. LiCl prefers to coordinate MgCl2 through μ(2)-Cl bridges. The study identifies the role of LiCl in the determination of compounds present in turbo Grignard solutions.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
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.