Molecular Dynamics (MD) simulations of glass-forming liquids play a pivotal role in uncovering the molecular nature of the liquid vitrification process. In particular, much focus was given to elucidating the interplay between the character of intermolecular potential and molecular dynamics behaviour. This has been tried to achieve by simulating the spherical particles interacting via isotropic potential. However, when simulation and experimental data are analysed in the same way by using the density scaling approaches, serious inconsistency is revealed between them. Similar scaling exponent values are determined by analysing the relaxation times and pVT data obtained from computer simulations. In contrast, these values differ significantly when the same analysis is carried out in the case of experimental data. As discussed thoroughly herein, the coherence between results of simulation and experiment can be achieved if anisotropy of intermolecular interactions is introduced to MD simulations. In practice, it has been realized in two different ways: (1) by using the anisotropic potential of the Gay-Berne type or (2) by replacing the spherical particles with quasi-real polyatomic anisotropic molecules interacting through isotropic Lenard-Jones potential. In particular, the last strategy has the potential to be used to explore the relationship between molecular architecture and molecular dynamics behaviour. Finally, we hope that the results presented in this review will also encourage others to explore how 'anisotropy' affects remaining aspects related to liquid-glass transition, like heterogeneity, glass transition temperature, glass forming ability, etc.
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http://dx.doi.org/10.1088/1361-6633/ad569d | DOI Listing |
J Phys Chem A
January 2025
State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
The quantum transition state framework was developed to calculate the reaction path-resolved scattering matrix for atom-diatom reactions in hyperspherical (APH) coordinates. This approach allows for simply and directly calculating the reaction path-resolved scattering matrix, especially when the encircling reaction path is negligible. It could be used to determine the reactivities of specific pathways in a chemical reaction, providing insights into phenomena such as geometric phase effects.
View Article and Find Full Text PDFAppl Biochem Biotechnol
January 2025
Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia.
Diabetes affects approximately 422 million people worldwide, leading to 1.5 million deaths annually and causing severe complications such as kidney failure, neuropathy, and cardiovascular disease. Aldose reductase (AR), a key enzyme in the polyol pathway, is an important therapeutic target for managing these complications.
View Article and Find Full Text PDFSoft Matter
January 2025
Department of Chemical and Biomolecular Engineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.
In polymerization-induced phase separation, the impact of polymer-substrate interaction on the dynamics of phase separation for polymer blends is important in determining the final morphology and properties of polymer materials as the surface can act as another driving force for phase separation other than polymerization. We modify the previously-developed polymerizing Cahn-Hilliard (pCH) method by adding a surface potential to model the phase separation behavior of a mixture of two species independently undergoing linear step-growth polymerization in the presence of a surface. In our approach, we explicitly model polydispersity by separately considering different molecular-weight components with their own respective diffusion constants, and with the surface potential preferentially acting on only one species.
View Article and Find Full Text PDFJ Mater Chem B
January 2025
Department of Optical and Biophysical Systems, Institute of Physics of the Czech Academy of Sciences, Prague, 18200, Czech Republic.
DNA nanostructures (DNs) have gained popularity in various biomedical applications due to their unique properties, including structural programmability, ease of synthesis and functionalization, and low cytotoxicity. Effective utilization of DNs in biomedical applications requires a fundamental understanding of their interactions with living cells and the mechanics of cellular uptake. Current knowledge primarily focuses on how the physicochemical properties of DNs, such as mass, shape, size, and surface functionalization, affect uptake efficacy.
View Article and Find Full Text PDFOncotarget
January 2025
Laboratory of Molecular Pathology of Cancer, Faculty of Healthy Sciences, University of Brasília, Federal District, Brasília, Brazil.
Approximately two-thirds of patients with colorectal cancer (CRC) undergo resection with curative intent; however, 30% to 50% of these patients experience recurrence. The concentration of cell-free DNA (cfDNA) before and after surgery may be related to the prognosis of patients with CRC, but there is limited information regarding cfDNA levels at the time of surgery. Here, we analyzed surgical cfDNA release using plasma samples from 30 colorectal cancer patients at three key points during surgery: preoperative (immediately before surgery), intraoperative (during surgery), and postoperative (at the end of surgery).
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