We study by computer simulations the interaction between two similarly charged colloidal particles confined between parallel planes, in salt free conditions. Both the colloids and ions are simulated explicitly, in a fine-mesh lattice, and the electrostatic interaction is calculated using Ewald summation in two dimensions. The internal energy is measured by setting the colloidal particles at a given position and equilibrating the ions, whereas the free energy is obtained introducing a bias (attractive) potential between the colloids. Our results show that upon confining the system, the internal energy decreases, resulting in an attractive contribution to the interaction potential for large charges and strong confinement. However, the loss of entropy of the ions is the dominant mechanism in the interaction, irrespective of the confinement of the system. The interaction potential is therefore repulsive in all cases, and is well described by the DLVO functional form, but effective values have to be used for the interaction strength and Debye length.
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http://dx.doi.org/10.1016/j.jcis.2014.10.044 | DOI Listing |
J Chem Phys
January 2025
Department of Computer Science, Stanford University, Stanford, California 94305, USA.
Atomic-level simulations are widely used to study biomolecules and their dynamics. A common goal in such studies is to compare simulations of a molecular system under several conditions-for example, with various mutations or bound ligands-in order to identify differences between the molecular conformations adopted under these conditions. However, the large amount of data produced by simulations of ever larger and more complex systems often renders it difficult to identify the structural features that are relevant to a particular biochemical phenomenon.
View Article and Find Full Text PDFJ Chem Phys
January 2025
Dipartimento di Fisica, Università degli Studi di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, 80126 Naples, Italy.
In the last years, it has been proved that some viruses are able to re-structure chromatin organization and alter the epigenomic landscape of the host genome. In addition, they are able to affect the physical mechanisms shaping chromatin 3D structure, with a consequent impact on gene activity. Here, we investigate with polymer physics genome re-organization of the host genome upon SARS-CoV-2 viral infection and how it can impact structural variability within the population of single-cell chromatin configurations.
View Article and Find Full Text PDFEnviron Sci Process Impacts
January 2025
College of Environment, Zhejiang University of Technology, Hangzhou, 310014, P. R. China.
The nano-self-assembly of natural organic matter (NOM) profoundly influences the occurrence and fate of NOM and pollutants in large-scale complex environments. Machine learning (ML) offers a promising and robust tool for interpreting and predicting the processes, structures and environmental effects of NOM self-assembly. This review seeks to provide a tutorial-like compilation of data source determination, algorithm selection, model construction, interpretability analyses, applications and challenges for big-data-based ML aiming at elucidating NOM self-assembly mechanisms in environments.
View Article and Find Full Text PDFLangmuir
January 2025
Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, Műegyetem rkp. 3, 1111 Budapest, Hungary.
During the experimental formation of sol-gel coatings, the colloid dispersions go through a drying process, and the structure of the coatings is formed as a result of complex chemical, colloidal, and capillary interactions. While computer simulations provide guidelines to tune and even design the nanomaterials synthesis, simulations of coating structure formation are hitherto unknown in the literature. Based on real experiments, we establish here a ReaxFF reactive force field-based molecular dynamics simulation protocol in order to investigate and determine the role of the experimental conditions on the pore structure formation in the coatings.
View Article and Find Full Text PDFInt J Med Robot
February 2025
Department of Mechanical, Energy, Management and Transportation Engineering, University of Genova, Genova, Italy.
Background: Medical simulation is relevant for training medical personnel in the delivery of medical and trauma care, with benefits including quantitative evaluation and increased patient safety through reduced need to train on patients.
Methods: This paper presents a prototype medical simulator focusing on ocular and craniofacial trauma (OCF), for training in management of facial and upper airway injuries. It consists of a physical, electromechanical representation of head and neck structures, including the mandible, maxillary region, neck, orbit and peri-orbital regions to replicate different craniofacial traumas.
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