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Graph Theoretical Description of Phase Transitions in Complex Multiscale Phases with Supramolecular Assemblies.
Adv Sci (Weinh)
September 2024
Department of Chemistry, Federal University of São Carlos, São Carlos, SP, 13565-905, Brazil.
Phase transitions are typically quantified using order parameters, such as crystal lattice distances and radial distribution functions, which can identify subtle changes in crystalline materials or high-contrast phases with large structural differences. However, the identification of phases with high complexity, multiscale organization and of complex patterns during the structural fluctuations preceding phase transitions, which are essential for understanding the system pathways between phases, is challenging for those traditional analyses. Here, it is shown that for two model systems- thermotropic liquid crystals and a lyotropic water/surfactant mixtures-graph theoretical (GT) descriptors can successfully identify complex phases combining molecular and nanoscale levels of organization that are hard to characterize with traditional methodologies.
View Article and Find Full Text PDFNucleosome spacing controls chromatin spatial structure and accessibility.
Biophys J
April 2024
Competence Center Bioinformatics, Institute for Applied Computer Science, Hochschule Stralsund, Stralsund, Germany. Electronic address:
Recent research highlights the significance of the three-dimensional structure of chromatin in regulating various cellular processes, particularly transcription. This is achieved through dynamic chromatin structures that facilitate long-range contacts and control spatial accessibility. Chromatin consists of DNA and a variety of proteins, of which histones play an essential structural role by forming nucleosomes.
View Article and Find Full Text PDFMapping out the glassy landscape of a mesoscopic elastoplastic model.
J Chem Phys
November 2022
Institute of Applied Mathematics, University of Bonn, Endenicher Allee 60, Bonn, Germany.
We develop a mesoscopic model to study the plastic behavior of an amorphous material under cyclic loading. The model is depinning-like and driven by a disordered thresholds dynamics that is coupled by long-range elastic interactions. We propose a simple protocol of "glass preparation" that allows us to mimic thermalization at high temperatures as well as aging at vanishing temperature.
View Article and Find Full Text PDFBrownian dynamics simulations of shear-induced aggregation of charged colloidal particles in the presence of hydrodynamic interactions.
J Colloid Interface Sci
October 2022
University of Fribourg, Department of Chemistry, Chemin du Musée 9, CH-1700 Fribourg, Switzerland. Electronic address:
Hypothesis: In spite of the abundant literature on Brownian simulations of the aggregation behavior of colloidal suspensions both under quiescent conditions and in the presence of shear, few works performed simulations including the effect of hydrodynamic interactions. Even fewer works have investigated the effects of shear on the aggregation of electrostatically-stabilized colloidal suspensions.
Simulations: In this work, we employed Brownian dynamics simulations implementing the Rotne-Prager-Yamakawa approximation to account for hydrodynamic interactions and investigated the aggregation kinetics of electrostatically-stabilized colloidal suspensions exposed to simple shear, for various Péclet number values, particle volume fractions and surface potential values.
Making Sense of Coulomb Explosion Imaging.
J Phys Chem Lett
March 2019
Institute of Chemistry , The Hebrew University of Jerusalem, Jerusalem 91904 , Israel.
A multifaceted agreement between ab initio theoretical predictions and experimental measurements, including branching ratios, channel-specific kinetic energy release, and three-body momentum correlation spectra, leads to the identification of new mechanisms in Coulomb-explosion (CE) induced two- and three-body breakup processes in methanol. These identified mechanisms include direct nonadiabatic Coulomb explosion responsible for CO bond-breaking, a long-range " inverse harpooning" dominating the production of H + HCOH, a transient proton migration leading to surprising energy partitioning in three-body fragmentation and other complex dynamics forming products such as HO and H. These mechanisms provide general concepts that should be useful for analyzing future time-resolved Coulomb explosion imaging of methanol as well as other molecular systems.
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