96 research outputs found
Automated Calculation of Thermal Rate Coefficients using Ring Polymer Molecular Dynamics and Machine-Learning Interatomic Potentials with Active Learning
We propose a methodology for fully automated calculation of thermal rate
coefficients of gas phase chemical reactions, which is based on combining the
ring polymer molecular dynamics (RPMD) with the machine-learning interatomic
potentials actively learning on-the-fly. Based on the original computational
procedure implemented in the RPMDrate code, our methodology gradually and
automatically constructs the potential energy surfaces (PESs) from scratch with
the data set points being selected and accumulated during the RPMDrate
simulation. Such an approach ensures that our final machine-learning model
provides reliable description of the PES which avoids artifacts during
exploration of the phase space by RPMD trajectories. We tested our methodology
on two representative thermally activated chemical reactions studied recently
by RPMDrate at temperatures within the interval of 300--1000~K. The
corresponding PESs were generated by fitting to only a few thousands
automatically generated structures (less than 5000) while the RPMD rate
coefficients retained the deviation from the reference values within the
typical convergence error of RPMDrate. In future, we plan to apply our
methodology to chemical reactions which proceed via complex-formation thus
providing a completely general tool for calculating RPMD thermal rate
coefficients for any polyatomic gas phase chemical reaction
Exploring van der Waals materials with high anisotropy: geometrical and optical approaches
The emergence of van der Waals (vdW) materials resulted in the discovery of
their giant optical, mechanical, and electronic anisotropic properties,
immediately enabling countless novel phenomena and applications. Such success
inspired an intensive search for the highest possible anisotropic properties
among vdW materials. Furthermore, the identification of the most promising
among the huge family of vdW materials is a challenging quest requiring
innovative approaches. Here, we suggest an easy-to-use method for such a survey
based on the crystallographic geometrical perspective of vdW materials followed
by their optical characterization. Using our approach, we found As2S3 as a
highly anisotropic vdW material. It demonstrates rare giant in-plane optical
anisotropy, high refractive index and transparency in the visible range,
overcoming the century-long record set by rutile. Given these benefits, As2S3
opens a pathway towards next-generation nanophotonics as demonstrated by an
ultrathin true zero-order quarter-waveplate that combines classical and the
Fabry-Perot optical phase accumulations. Hence, our approach provides an
effective and easy-to-use method to find vdW materials with the utmost
anisotropic properties.Comment: 11 pages, 5 figure
Nanostructure-specific X-ray tomography reveals myelin levels, integrity and axon orientations in mouse and human nervous tissue
Myelin insulates neuronal axons and enables fast signal transmission, constituting a key component of brain development, aging and disease. Yet, myelin-specific imaging of macroscopic samples remains a challenge. Here, we exploit myelin’s nanostructural periodicity, and use small-angle X-ray scattering tensor tomography (SAXS-TT) to simultaneously quantify myelin levels, nanostructural integrity and axon orientations in nervous tissue. Proof-of-principle is demonstrated in whole mouse brain, mouse spinal cord and human white and gray matter samples. Outcomes are validated by 2D/3D histology and compared to MRI measurements sensitive to myelin and axon orientations. Specificity to nanostructure is exemplified by concomitantly imaging different myelin types with distinct periodicities. Finally, we illustrate the method’s sensitivity towards myelin-related diseases by quantifying myelin alterations in dysmyelinated mouse brain. This non-destructive, stain-free molecular imaging approach enables quantitative studies of myelination within and across samples during development, aging, disease and treatment, and is applicable to other ordered biomolecules or nanostructures
- …