We numerically study Turing patterns (TPs) on two-dimensional surfaces with a square boundary in using a surface model for polymerized membranes. The variables used to describe the membranes correspond to two distinct degrees of freedom: an internal degree of freedom for the polymer directions in addition to the positional degree of freedom. This generalised surface model enables us to identify non-trivial interference between the TP system and the membranes. To this end, we employ a hybrid numerical technique, utilising Monte Carlo updates for membrane configurations and discrete time iterations for the FitzHugh-Nagumo type Turing equation. The simulation results clearly show that anisotropies in the mechanical deformation properties, particularly the easy axes associated with the stretching and bending of the membranes, determine the direction of the TPs to be perpendicular or parallel to the easy axes. Additionally, by calculating the dependence of the maximum entropy on the internal degree of freedom, we can obtain information on the relaxation with respect to the polymer structure. This crucial information serves to remind us that non-equilibrium configurations can be captured within the canonical Monte Carlo simulations.
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J Chem Theory Comput
March 2025
School of Science, Constructor University, Campus Ring 1, 28759 Bremen, Germany.
The estimation of accurate free energies for antibiotic permeation via the bacterial outer-membrane porins has proven to be challenging. Atomistic simulations of the process suffer from sampling issues that are typical of systems with complex and slow dynamics, even with the application of advanced sampling methods. Ultimately, the objective is to obtain accurate potential of mean force (PMF) for a large set of antibiotics and to predict permeation rates.
View Article and Find Full Text PDFJ Chem Theory Comput
March 2025
Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States.
We show that following the standard mantra of quantum chemistry and diagonalizing the Born-Oppenheimer (BO) Hamiltonian () is not the optimal means to construct potential energy surfaces. A better approach is to diagonalize a phase-space electronic Hamiltonian, (, ), which is parameterized by both nuclear position and nuclear momentum . Such a nonperturbative phase-space electronic Hamiltonian can be constructed using a partial Wigner transform and the method has exactly the same cost as BO for a semiclassical calculation (and only a slight increase in cost for a quantum nuclear calculation).
View Article and Find Full Text PDFNanomaterials (Basel)
February 2025
Department of Physics, Changzhi University, Changzhi 046011, China.
Metasurface-based longitudinal modulation introduces the propagation distance as a new degree of freedom, extending the light modulation with metasurfaces from 2D to 3D space. However, relevant longitudinal studies have been constrained to designing the metasurface of half-wave plate (HWP) meta-atoms and generating either non-focused or two-channel vortex and vector beams. In this study, we propose a metasurface composed of quarter-wave plate (QWP) meta-atoms to generate the longitudinal multi-channel focused vortex and vector beams.
View Article and Find Full Text PDFPhys Chem Chem Phys
March 2025
Department of Chemistry, Lehigh University, 6 E. Packer Ave., Bethlehem, Pennsylvania 18015, USA.
Despite their wide use as molecular photoswitches, the mechanistic photophysics of azo dyes are complex and nuanced, and therefore under-explored. To understand the complex electronic interactions that govern the photoisomerization and thermal reversion of two phenyl-azo-indole dyes that differ by R-sterics near the azo bond, potential energy surfaces that combine the dihedral rotation of the azo bond and the aryl inversion on each side of the azo bond were calculated with density functional theory and time-dependent density functional theory. These multidimensional singlet surfaces provide insights into the correlated rotation and inversion pathways allowing for detailed understanding of both photoisomerization, governed by the excited-state surfaces, and thermal reversion, governed by the ground-state surface, mechanisms to be developed.
View Article and Find Full Text PDFWearable Technol
February 2025
Department of Information Physics and Computing, The University of Tokyo, 113-8656, Tokyo, Japan.
Machine - human interaction systems have been proposed to improve motion learning efficiency. We developed a pneumatic-driven motion teaching system that provides feedback to the learner by simultaneously presenting visual and torque information. We achieved a lightweight, soft, and user-safety haptic system using a pneumatic artificial muscle (PAM).
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