Revealing enhanced dilution effect of conjugated polymers in partially miscible blends by Hongbo Chen, Ming Hu, Yuehua Zhao, Kaixuan Lyu, Yushuai Xu, Yuansheng Sun, Zhiyuan Xie, Jinying Huang, Dapeng Wang

“…In this work, we propose a cascade analysis by combining multiple fluorescence microscopic techniques and all‐atom molecular dynamics simulations to study the solid‐to‐solid dilution of poly[2‐methoxy‐5‐(2‐ethylhexyloxy)‐1,4‐phenylenevinylene] (MEH‐PPV) in MEH‐PPV/polystyrene (PS) blends and MEH‐PPV/poly(vinylcarbazole) (PVK) blends. …”
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Elucidation of α-glucosidase inhibitory activity and UHPLC-ESI-QTOF-MS based metabolic profiling of endophytic fungi Alternaria alternata BRN05 isolated from seeds of Swietenia mac... by Piyush Kumar, Sai Anand Kannakazhi Kantari, Ranendra Pratap Biswal, Prasanth Ghanta, Malleswara Dharanikota

“…Molecular docking analysis revealed that twelve among these exhibited greater binding energies than that of acarbose (-6.6 kcal/mol). Molecular Dynamics (MD) simulations of 3’,4’,7-trihydroxyisoflavanone (THF) and alternariol 9-methyl ether (AME) from EQS, exhibiting high binding energies (-7.5 and -7 kcal/mol, respectively), were performed to investigate their interactions with human intestinal α-glucosidase. …”
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UNet-Att: a self-supervised denoising and recovery model for two-photon microscopic image by Yuer Lu, Yongfa Ying, Chen Lin, Yan Wang, Jun Jin, Xiaoming Jiang, Jianwei Shuai, Xiang Li, Jinjin Zhong

“…Abstract Two-photon microscopy is indispensable in cell and molecular biology for its high-resolution visualization of cellular and molecular dynamics. However, the inevitable low signal-to-noise conditions significantly degrade image quality, obscuring essential details and complicating morphological analysis. …”
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Scrutinizing the evidence of anthracene toxicity on adrenergic receptor beta-2 and its bioremediation by fungal manganese peroxidase via in silico approaches by Muhammad Naveed, Khadija Khatoon, Tariq Aziz, Rida Naveed, Muhammad Nouman Majeed, Maida Salah Ud Din, Tayyab Javed, Ayaz Ali Khan, Abdullah F. Alasmari

“…Visualization using Discovery Studio elucidated the molecular interactions within the docked complex. Molecular dynamics simulations using the OpenMM engine and AMBER force field confirmed stable enzyme-ligand complexes, highlighting the potential of manganese peroxidase for sustained enzymatic activity against anthracene.…”
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A hammerhead ribozyme selects mechanically stable conformations for catalysis against viral RNA by Man Lu, Zhiqiang Cao, Luoan Xiong, Hongying Deng, Kangkang Ma, Ning Liu, Yanding Qin, Shen-Bo Chen, Jun-Hu Chen, Yao Li, Yijin Liu, Zhongbo Yu

“…Our results are supported by molecular dynamics simulations. Our understanding of the RNA catalytic mechanism will be beneficial for ribozyme’s biotechnological applications and as potential therapeutics against RNA viruses.…”
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Neuron-inspired CsPbBr3/PDMS nanospheres for multi-dimensional sensing and interactive displays by Junhu Cai, Xiang Zhang, Yu Chen, Wenzong Lai, Yun Ye, Sheng Xu, Qun Yan, Tailiang Guo, Jiajun Luo, Enguo Chen

“…The carefully engineered polydimethylsiloxane (PDMS) shell enables the reversible activity of the core CsPbBr3, serving a dual role similar to dendrites in conveying and evaluating external stimuli with high sensitivity. Molecular dynamics analysis reveals that the PDMS shell with proper pore density enhances the conductivity in water and heat, imparting CsPbBr3 with sensitive but reversible properties. …”
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AM1241 inhibits chondrocyte inflammation and ECM degradation through the Nrf2/HO-1 and NF-κB pathways and alleviates osteoarthritis in mice by Zhuan Zou, Songmu Pan, Changzheng Sun, Jiyong Wei, Yi Xu, Kaizhen Xiao, Jinmin Zhao, Ronghe Gu

“…The specific action modes and binding sites of AM1241 with NEMO/IκB kinases (IKKs) in the NF-κB pathway and Keap1 protein in the Nrf2 pathway were predicted via molecular docking and molecular dynamics simulation, and the NF-κB and Nrf2 pathways were detected using western blot and immunofluorescence. …”
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Design and fabrication of {111}-textured nanotwinned silver coating for enhancing surface wear resistance of depleted uranium by Kunming Yang, Xiaobo Wang, Shengfa Zhu, Yawen Zhao, Qingdong Xu, Yiyun Wei, Chao Lu, Zhiyuan Wen, Tongxiang Fan, Mingyu Gong, Anyi Yin, Wenhua Luo

“…Meanwhile, molecular statics (MS) and molecular dynamics (MD) simulations were carried out to understand the behaviors of Ag adatoms and the tribological performance of subsequent different textured Ag. …”
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High Catalytic Selectivity of Electron/Proton Dual‐Conductive Sulfonated Polyaniline Micropore Encased IrO2 Electrocatalyst by Screening Effect for Oxygen Evolution of Seawater Ele... by Yuhan Shen, Shengqiu Zhao, Fanglin Wu, Hao Zhang, Liyan Zhu, Mingjuan Wu, Tian Tian, Haolin Tang

“…The SPTTPAB/IrO2 presents a ‐SO3H concentration of 5.62 × 10−4 mol g−1 and micropore below 2 nm numbering 1.026 × 1016 g−1. Molecular dynamics simulations demonstrate that the conjugated organic framework blocked 98.62% of Cl− in seawater from reaching the catalyst. …”
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Domperidone inhibits dengue virus infection by targeting the viral envelope protein and nonstructural protein 1 by Nuttapong Kaewjiw, Thanawat Thaingtamtanha, Damini Mehra, Wanida Chawnawa, Tanapan Prommool, Chunya Puttikhunt, Adisak Songjaeng, Kessiri Kongmanas, Panisadee Avirutnan, Prasit Luangaram, Chatchawan Srisawat, Sittiruk Roytrakul, Stephan A. Bäurle, Sansanee Noisakran

“…Domperidone was identified by pharmacophore-based virtual screening as a small molecule that can bind to both the viral envelope (E) and the nonstructural protein 1 (NS1) of DENV. Molecular dynamics (MD) simulations and surface plasmon resonance (SPR) analysis were subsequently performed to determine specific interactions of domperidone with the DENV E and NS1 proteins and their binding affinity. …”
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Targeting necroptosis in MCF-7 breast cancer cells: In Silico insights into 8,12-dimethoxysanguinarine from Eomecon Chionantha through molecular docking, dynamics, DFT, and MEP stu... by Maram B Alhawarri, Mohammad G Al-Thiabat, Amit Dubey, Aisha Tufail, Katreen Banisalman, Ghazi A Al Jabal, Eman Alkasasbeh, Esra'a Ibrahim Al-Trad, Bilal Harieth Alrimawi

“…This study presents the first computational exploration of SG-A interactions with key necroptotic proteins-RIPK1, RIPK3, and MLKL-through molecular docking, molecular dynamics (MD), density functional theory (DFT), and molecular electrostatic potential (MEP) analyses. …”
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Systemic antihyperalgesic effect of a novel conotoxin from Californiconus californicus in an inflammatory pain model by Joaquín López-Carrillo, Johanna Bernáldez-Sarabia, Tushar J. Pawar, Samanta Jiménez, Salvador Dueñas, Andrea Figueroa-Montiel, José L. Olivares-Romero, Vinicio Granados-Soto, Alexei F. Licea-Navarro, Alexei F. Licea-Navarro, Nadia L. Caram-Salas, Nadia L. Caram-Salas

“…Structural differences between O1_cal6.4b and O1_cal6.4d were examined using in silico modeling and molecular dynamics simulations.ResultsSystemic administration of O1_cal6.4b significantly reduced thermal hyperalgesia in a dose-dependent manner without impairing motor coordination. …”
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Structural insights into the mechanism of phosphate recognition and transport by XPR1 by Wenhui Zhang, Yanke Chen, Zeyuan Guan, Yong Wang, Meng Tang, Zhangmeng Du, Jie Zhang, Meng Cheng, Jiaqi Zuo, Yan Liu, Qiang Wang, Yanjun Liu, Delin Zhang, Ping Yin, Ling Ma, Zhu Liu

“…Pathogenic mutations in two arginine residues, which line the translocation channel, disrupt Pi transport. Molecular dynamics simulations reveal that Pi ion undergoes a stepwise transition through the sequential recognition sites during the transport process. …”
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Designing multi-epitope vaccines against Echinococcus granulosus: an in-silico study using immuno-informatics by Jadoon Khan, Asma Sadiq, May M. Alrashed, Nosheen Basharat, Syed Nadeem Ul Hassan Mohani, Tawaf Ali Shah, Kotb A. Attia, Aamer Ali Shah, Hayat Khan, Ijaz Ali, Arif Ahmed Mohammed

“…The majority of the amino acids were positioned in the Ramachandran plot’s favourable area, and during the molecular dynamic simulation at 100 ns, no notable structural abnormalities were noticed. …”
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Microenvironmental modulation breaks intrinsic pH limitations of nanozymes to boost their activities by Tong Li, Xiaoyu Wang, Yuting Wang, Yihong Zhang, Sirong Li, Wanling Liu, Shujie Liu, Yufeng Liu, Hang Xing, Ken-ichi Otake, Susumu Kitagawa, Jiangjiexing Wu, Hao Dong, Hui Wei

“…Experimental investigations and molecular dynamics simulations reveal that PAA not only donates protons but also holds protons through the salt bridges between hydroniums and deprotonated carboxyl groups in neutral pH condition. …”
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Amebicidal and Antiadhesion Activities of Knema retusa Extract Against Acanthamoeba triangularis T4 Genotype on Contact Lenses and Modeling Simulation of Its Main Compound, E2N, Ag... by Watcharapong Mitsuwan, Imran Sama-ae, Suthinee Sangkanu, Dhrubo Ahmed Khan, Partha Biswas, Md. Nazmul Hasan, Julalak Chuprom, Tajudeen O. Jimoh, Christophe Wiart, Masyitah Binti Zulkipli, Nor Hayati Abdullah, Maria de Lourdes Pereira, Sonia M. Rodrigues Oliveira, Shanmuga Sundar Saravanabhavan, Polrat Wilairatana, Tooba Mahboob, Veeranoot Nissapatorn

“…E2N generated multiple connections via hydrogen, hydrophobic, ionic, and water bridge bonding and maintained these connections until the simulation finished, facilitating the creation of stable bindings with the β-tubulin protein as measured by molecular dynamics simulation. These findings suggest that Kre exhibits amebicidal and antiadhesion activities which could be used for the prevention of A. triangularis adhesion to contact lenses.…”
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Unveiling the inhibitory effect of hydrogen-decorated voids and dislocation loops on the glide of edge dislocation in tungsten by Qing-Yuan Ren, Yu-Hao Li, Yu-Chen Du, Tian-Ren Yang, Dmitry Terentyev, Wei-Zhong Han, Hong-Bo Zhou, Guang-Hong Lu

“…Hydrogen (H) can further exacerbate the hardening effect, but the underlying physical mechanisms remain unclear. Using molecular dynamics simulations, we investigate the impact of H aggregation within voids and ½ <111> dislocation loops on obstructing the glide of ½ <111> edge dislocations. …”
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Cooperative mechanisms of LexA and HtpG in the regulation of virulence gene expression in Pseudomonas plecoglossicida by Rongchao He, Yanfei Zuo, Qiu Li, Qingpi Yan, Lixing Huang

“…We employed an array of methods including molecular dynamics simulations, molecular docking, ChIP-seq, RNA-seq, mass spectrometry, gene mutagenesis, LacZ reporter assays, electrophoretic mobility shift assays, co-immunoprecipitation, and in vitro LexA degradation experiments. …”
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Lopinavir and Ritonavir have High Affinity Toward the SARS-CoV-2 S-protein Receptor-binding Domain Sequenced in Brazil by Aline Diogo Marinho, Helyson Lucas Bezerra Braz, João Alison de Moraes Silveira, Danilo Galvão Rocha, Roberta Jeane Bezerra Jorge, Geanne Matos de Andrade

“…Ritonavir showed a binding affinity of −8.9 kcal/mol, interacting with residues ARG148, ASN130, VAL23, SER81, ASN33, PHE29, TYR33, SER31, ASN132, ALA26, ALA30, ALA34, and TYR133.Molecular dynamics simulations confirmed the stability of the complexes formed between lopinavir and ritonavir and the RBD active site. …”
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Combating COVID-19 and its co-infection by Aspergillus tamarii SP73-EGY using in vitro and in silico Studies by Eman Abdelsalam, Amal Mosad Ibrahim, Ahmed A. El-Rashedy, Mohamed S. Abdel-Aziz, Omnia Kutkat, Faten K. Abd EL-Hady

“…A molecular docking study showed that hexadecanoic, Kojic, octanoic acids, and 4(4-Methylbenzylidene)cyclohexane-1,3-dione have stronger binding affinity to the SARS-CoV-2 Mpro than Remdesivir. Molecular dynamics simulations were employed to examine the structural stability and flexibility of these complexes. …”
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