Article
Chemistry, Medicinal
Reecan J. Juarez, Yaoyukun Jiang, Matthew Tremblay, Qianzhen Shao, A. James Link, Zhongyue J. Yang
Summary: LassoHTP is a software developed for automatic construction and modeling of lasso peptide structures, enabling efficient prediction and design of lasso peptides. The software was used to construct eight known lasso peptide structures and simulate their conformational ensembles. The results show that the LassoHTP-initiated ensembles are similar to those initiated from the PDB structures. LassoHTP provides a computational platform for lasso peptide prediction and design.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Medicinal
Reecan J. Juarez, Yaoyukun Jiang, Matthew Tremblay, Qianzhen Shao, A. James Link, Zhongyue J. Yang
Summary: Lasso peptides are ribosomally synthesized and posttranslationally modified peptides with a slipknot conformation, showing great potential in bioengineering and pharmaceutical applications. To facilitate computational prediction and design of lasso peptides, we developed a software called LassoHTP, which enables automatic structure construction and modeling. LassoHTP has been successfully used to generate de novo structures and simulate conformational ensembles for known lasso peptides.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Multidisciplinary
Rafael Garcia-Meseguer, Enrique Orti, Inaki Tunon, J. Javier Ruiz-Pernia, Juan Arago
Summary: Polyethylene terephthalate (PET) is a commonly used polyester plastic in textiles and packaging, but it is also one of the most discarded after one use. The enzymatic biodegradation of PET has gained interest in recent years. The study investigated the molecular origin of the enhanced catalytic activity of FAST-PETase in PET degradation, finding that the rate-limiting reaction step for FAST-PETase is the acylation stage with a lower energy barrier compared to PETase. The enhancement is mainly attributed to the N233K mutation, inducing a chain folding that affects the catalytic triad and decreases the catalytic barrier.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Materials Science, Ceramics
Bhargav Akkinepally, I. Neelakanta Reddy, Tae Jo Ko, Kisoo Yoo, Jaesool Shim
Summary: The performance of NASICON-type LiZr2(PO4)3 solid electrolytes for Li-ion batteries relies on their ion transportation properties. Al doping was found to enhance the ionic conductivity and diffusion in LZP solid electrolytes. Computational and experimental results confirmed the improvement in ion conductivity and diffusion with Al doping, while excessive doping led to a decrease in ionic conductivity due to Li-ion trapping.
CERAMICS INTERNATIONAL
(2022)
Article
Physics, Fluids & Plasmas
Anthony Saliou, Philippe Jarry, Noel Jakse
Summary: By using large-scale computer simulations and supervised learning, the relationship between excess entropy and diffusion was analyzed for the Lennard-Jones potential. The results showed a strong correlation between excess entropy and the potential energy landscape (PEL). The exponential law in liquids was found to be linked with the landscape-influenced regime of the PEL, while the power-law behavior in fluid-like systems corresponded to the free diffusion regime.
Article
Chemistry, Multidisciplinary
Carlos A. Ramos-Guzman, Milorad Andjelkovic, Kirill Zinovjev, J. Javier Ruiz-Pernia, Inaki Tunon
Summary: In this study, the by-residue decomposition of noncovalent interactions and analysis of naturally occurring mutations were used to detect potential mutations in the 3CL protease of SARS-CoV-2 that confer resistance to nirmatrelvir. It was found that the E166V mutation reduces the binding affinity of the protease to nirmatrelvir and increases the activation free energy for the formation of the covalent enzyme-inhibitor complex, resulting in resistance to the treatment with this drug. The conclusions of this study can be useful for predicting the consequences of introducing nirmatrelvir in the virus fitness landscape and designing new inhibitors targeting possible resistance mechanisms.
Article
Chemistry, Physical
B. P. Prajwal, James M. Blackwell, Patrick Theofanis, Fernando A. Escobedo
Summary: This work introduces a computational framework to study the molecular inhomogeneities in chemically amplified photoresists. Molecular dynamics simulations were used to investigate the effect of ionic and steric interactions on the dispersibility of photoacid generators (PAGs) in polymer medium. The results show that the dispersibility of PAGs varies depending on their ionic nature and the polymer used.
CHEMISTRY OF MATERIALS
(2023)
Article
Physics, Fluids & Plasmas
Luana S. Moreira, Douglas D. de Vargas, Mateus H. Kohler
Summary: The introduction of flexibility in water force fields during molecular dynamics simulations of nanoconfined water has a significant impact on viscosity, diffusion, and dipole orientation. The level of confinement and the choice of force-field family greatly influence the behavior of water molecules in nanoconfined systems.
Article
Physics, Fluids & Plasmas
Luana S. Moreira, Douglas D. de Vargas, Mateus H. Koehler
Summary: This study investigates the effects of introducing flexibility in water force fields on molecular dynamics simulations of nanoconfined water. The results show that viscosity, diffusion, and dipole orientation are greatly influenced by the flexibility and the family of force fields used.
Article
Anesthesiology
Amir Hossein Irani, Logan Voss, Nicola Whittle, Jamie W. Sleigh
Summary: Computational molecular dynamics simulations were used to study the interaction between sugammadex and neuromuscular blocking drugs. The results confirmed the binding strength between sugammadex and other drugs, and revealed a potential weak interaction between sugammadex and propofol. Experimental validation showed that the drug encapsulation process occurred in the opposite direction than previously hypothesized.
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
Chemistry, Physical
Mohammed Guerboub, Steve Dave Wansi Wendji, Carlo Massobrio, Assil Bouzid, Mauro Boero, Guido Ori, Evelyne Martin
Summary: It is found that the thermal conductivity of amorphous systems is not sensitive to the details of the atomic structure, despite the difference in local structure between different models. The behavior is rationalized in terms of extended vibrational modes.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Construction & Building Technology
Fenghua Nie, Wei Jian, Zechuan Yu, Cheuk Lun Chow, Denvid Lau
Summary: In this study, a new coarse-grained model is developed to investigate the formation of aggregated microstructures in asphaltene. The results show that asphaltene disks gradually adjust their positions and orientations during equilibrium process, forming columnar structures containing packed asphaltene disks. The packing fraction and microstructures are influenced by the aspect ratio, temperature, and pressure of asphaltene disks. This coarse-grained model helps understand the formation mechanism of asphaltene agglomerates and provides insights for solving aggregation problems in asphaltene systems.
CONSTRUCTION AND BUILDING MATERIALS
(2023)
Article
Chemistry, Physical
Ahmad Moghimikheirabadi, Martin Kroger, Argyrios Karatrantos
Summary: In this study, conformation, entanglement, and dynamics in attractive polymer nanocomposites were investigated using coarse-grained molecular dynamics simulation. The behavior of the apparent tube diameter and the entangled polymer mobility were found to be greatly influenced by the geometric confinement length at strong confinement due to the presence of nanoparticles. Additionally, entangled polymer dynamics were hindered by the strong confinement created by the nanoparticles.
Article
Mechanics
S. M. Kazem Manzoorolajdad, Hossein Hamzehpour, Jalal Sarabadani
Summary: The electrokinetic transport in a neutral system was studied by investigating an aqueous NaCl solution confined in a nanochannel with two similar parallel phosphorene walls. Different black, blue, red, and green phosphorene allotropes were studied under the presence of an external electric field in the x and y directions. The results showed the increase in Stern layer thickness with negative electric surface charge density (ESCD) and roughness ratio, as well as the occurrence of Debye-Huckel regime, intermediate regime, and flow reversal with increasing absolute value of negative ESCD.