Article
Multidisciplinary Sciences
Chen Zhang, Fujia Tian, Ying Lu, Bing Yuan, Zhi-Jie Tan, Xing-Hua Zhang, Liang Dai
Summary: DNA deformations can occur upon environmental changes, and an increase in salt concentration leads to DNA overwinding. Our magnetic tweezers experiments and simulations demonstrate that the twist change induced by salt can be quantitatively explained by the screening of electrostatic repulsion and the coupling between twist and DNA diameter. We determine the coupling constant and predict the temperature dependence of DNA twist, finding that the twist-diameter coupling is a common driving force for salt- and temperature-induced DNA twist changes.
Article
Engineering, Electrical & Electronic
Yuyao Lu, Geng Yang, Shenqiang Wang, Yuqi Zhang, Yihui Jian, Long He, Ting Yu, Huayu Luo, Depeng Kong, Yunlei Xianyu, Bo Liang, Tao Liu, Xiaoping Ouyang, Jicheng Yu, Xinyang Hu, Huayong Yang, Zhen Gu, Wei Huang, Kaichen Xu
Summary: A thin elastic conductive nanocomposite formed by cryogenically transferring laser-induced graphene to a hydrogel film can be used to create multifunctional sensors for on-skin monitoring and cardiac patches for in vivo detection.
NATURE ELECTRONICS
(2023)
Article
Multidisciplinary Sciences
Poutoum P. Samire, Bo Zhuang, Bertrand Legeret, Angel Baca-Porcel, Gilles Peltier, Damien Sorigue, Alexey Aleksandrov, Frederic Beisson, Pavel Mueller
Summary: Ongoing climate change is driving the search for renewable and carbon-neutral alternatives to fossil fuels. Pho-tocatalytic conversion of fatty acids to hydrocarbons by fatty acid photodecarboxylase (FAP) represents a promising route to green fuels. Chlorella variabilis FAP (CvFAP) has higher catalytic activity on n-octanoic acid, in part, due to an autocatalytic effect of its n-heptane product.
Article
Chemistry, Physical
Akhilesh Paspureddi, Zidan Zhang, Venkat Ganesan, Mukul M. M. Sharma, Lynn E. E. Katz
Summary: In this study, atomistic molecular dynamics simulations were used to investigate the molecular mechanisms that control the mobility of cations with different valences in Nafion membranes. The results showed that monovalent and divalent cations have structural differences, leading to differences in ion diffusion in Nafion. Monovalent cations are territorially bound while partially hydrated to the fixed charge groups, whereas divalent cations are site bound while fully dehydrated to the charge groups on the polymer. This difference in binding structure results in differences in the transport characteristics of cations in Nafion.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Anirban Chandra, Troy Loeffler, Henry Chan, Xiaoyu Wang, G. B. Stephenson, Michael J. Servis, Subramanian K. R. S. Sankaranarayanan
Summary: Exploring mesoscopic physical phenomena remains challenging for all-atom molecular dynamics simulations. Coarse-graining of all-atom models provides a solution to study mesoscale physics but without sacrificing desired structural features. In this study, a hybrid bond-order coarse-grained forcefield (HyCG) is proposed to model mesoscale aggregation in liquid-liquid mixtures. The potential is parameterized using a reinforcement learning algorithm and accurately captures critical fluctuations in binary extraction systems. This approach could be applied to explore inaccessible mesoscale phenomena with the developed potential model and training workflow.
JOURNAL OF CHEMICAL PHYSICS
(2023)
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
Chemistry, Multidisciplinary
Hanna Baltrukevich, Piia Bartos
Summary: This study investigates the differences in force fields when simulating RNA-protein complexes using molecular dynamics simulations. The results show that non-polarizable force fields lead to compact and stable complexes, while polarizable force fields allow for more movement but can result in complex disintegration.
FRONTIERS IN CHEMISTRY
(2023)
Article
Chemistry, Physical
Asante Obed Frimpong, Xiao Xu, Xu Jia, Yuejun Zhang
Summary: This study investigates the interaction between divalent cations (DCs) and lipopolysaccharides (LPSs) through molecular dynamics simulations. The results show that initial addition of DCs promotes the aggregation of LPSs, while further addition of DCs leads to the dissolution of LPSs. With increasing DC concentration, the DCs replace monovalent cations as counterions on the LPS, resulting in a change in LPS effective charge and solubility. This interaction change affects the structure of LPS assemblies.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Energy & Fuels
Zhongze Bai, Xi Zhuo Jiang, Kai H. Luo
Summary: This study investigates the effects of electric field on fuel-NOx formation during pyridine combustion and fills the knowledge gaps regarding the influence of electric field on fuel-NOx emissions.
Article
Multidisciplinary Sciences
Nabih A. Baeshen, Abdulaziz O. Albeshri, Naseebh N. Baeshen, Roba Attar, Alaa Karkashan, Basma Abbas, Thamer A. Bouback, Abdullah A. Aljaddawi, Mohammed Y. Refai, Hayam S. Abdelkader, Abdullah Al Tamim, Abdullah Alowaifeer, Firoz Ahmed, Mohammed N. Baeshen
Summary: This study computationally investigated the antiviral activity of five nonalkaloid compounds from Rhazya stricta against SARS-CoV-2. The compounds showed strong binding affinities and potential as a treatment strategy to control viral entry.
SCIENTIFIC REPORTS
(2022)
Article
Chemistry, Multidisciplinary
Chisa Higuchi, Kazunari Yoshizawa
Summary: The study highlights the importance of synergistic effects of dispersion and electrostatic interactions at the interface between an epoxy resin and a silica surface. The ratio of dispersion energies to total interaction energies in the layer model correlates well with experimental values, showing that dispersion plays a significant role in adhesion between the two materials. Individual analysis of 20 epoxy molecules in the layer model reveals that bonding and interactions within 3.6 angstrom from the silica surface account for more than 99% of total interaction energies.
Article
Chemistry, Medicinal
Zhixiong Lin, Junjie Zou, Shuai Liu, Chunwang Peng, Zhipeng Li, Xiao Wan, Dong Fang, Jian Yin, Gianpaolo Gobbo, Yongpan Chen, Jian Ma, Shuhao Wen, Peiyu Zhang, Mingjun Yang
Summary: XFEP is a scalable cloud computing platform developed to address the limitations of FEP applications in drug discovery, such as high cost, long waiting time, and limited scalability. By combining artificial intelligence techniques, XFEP can also assist in structure exploration in a larger chemical space, enabling evaluation and comparison of unrelated molecules, providing more opportunities for drug discovery projects.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)
Article
Chemistry, Physical
Midas Segers, Aderik Voorspoels, Takahiro Sakaue, Enrico Carlon
Summary: The mechanical properties of nucleic acids are crucial in biological processes, with different behaviors at various length scales. This paper discusses the origin of the coupling between distal sites in DNA and RNA double helices and introduces a ladder model to explain this universal coupling behavior.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Hyeonjun Kim, Changwon Yang, Youngshang Pak
Summary: This study computationally investigated the transition of G·C base pair from Watson-Crick to Hoogsteen base pair under different pH conditions. A classical molecular dynamics simulation protocol was proposed and successfully produced free-energy surfaces that closely matched experimental results. This simulation is expected to provide valuable insights into DNA base pair transition events.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Biochemical Research Methods
Krzysztof M. Ocetkiewicz, Cezary Czaplewski, Henryk Krawczyk, Agnieszka G. Lipska, Adam Liwo, Jerzy Proficz, Adam K. Sieradzan, Pawel Czarnul
Summary: The UNRES-GPU package has been implemented on GPUs and achieved significant speed-up for large protein systems. It is capable of simulating large protein systems at the millisecond time scale.