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Collective motion and its connection to the energy landscape in 2D soft crystals.
Soft Matter
January 2025
Physics Department, Wesleyan University, Middletown, CT 06459, USA.
We examine the collective motion in computational models of a two-dimensional dusty plasma crystal and a charged colloidal suspension as they approach their respective melting transitions. To unambiguously identify rearrangement events in the crystal, we map the trajectory of configurations from an equilibrium molecular dynamics simulation to the corresponding sequence of configurations of local potential energy minima ("inherent structures"). This inherent structure (IS) trajectory eliminates the ambiguity that arises from localized vibrational motion.
View Article and Find Full Text PDFThe 2025 Motile Active Matter Roadmap.
J Phys Condens Matter
January 2025
Biozentrum, University of Basel, Spitalstrasse 41, Basel, Basel-Stadt, 4056, SWITZERLAND.
Activity and autonomous motion are fundamental aspects of many living and engineering systems. Here, the scale of biological agents covers a wide range, from nanomotors, cytoskeleton, and cells, to insects, fish, birds, and people. Inspired by biological active systems, various types of autonomous synthetic nano- and micromachines have been designed, which provide the basis for multifunctional, highly responsive, intelligent active materials.
View Article and Find Full Text PDFQuantum Dynamics Simulations of Exciton Polariton Transport.
Nano Lett
January 2025
Department of Chemistry, University of Rochester, Rochester, New York 14627, United States.
Recent experiments have shown that exciton transport can be significantly enhanced through hybridization with confined photonic modes in a cavity. The light-matter hybridization generates exciton-polariton (EP) bands, whose group velocity is significantly larger than the excitons. Dissipative mechanisms that affect the constituent states of EPs, such as exciton-phonon coupling and cavity loss, have been observed to reduce the group velocities in experiments.
View Article and Find Full Text PDFEnhanced sampling of protein conformational changes via true reaction coordinates from energy relaxation.
Nat Commun
January 2025
Center for Bioinformatics and Quantitative Biology, Richard and Loan Hill Department of Biomedical Engineering, The University of Illinois Chicago, 851 South Morgan Street, Chicago, IL, 60607, USA.
The bottleneck in enhanced sampling lies in finding collective variables that effectively accelerate protein conformational changes; true reaction coordinates that accurately predict the committor are the well-recognized optimal choice. However, identifying them requires unbiased natural reactive trajectories, which, paradoxically, require effective enhanced sampling. Using the generalized work functional method, we uncover that true reaction coordinates control both conformational changes and energy relaxation, enabling us to compute them from energy relaxation simulations.
View Article and Find Full Text PDFExploring the complex interplay of Blastocystis, morbid obesity, and bariatric surgery on gut microbial dynamics.
Microb Pathog
January 2025
Department of Nutrition and Dietetics, Faculty of Health Sciences, Hacettepe University, Ankara, Türkiye.
This study examines Blastocystis dynamics in 15 individuals undergoing sleeve gastrectomy. Molecular detection involved DNA extraction, RT-PCR, and sequencing, while 16S rRNA sequencing via Illumina MiSeq analyzed the intestinal microbiome. Statistical analysis through SPSS considered a significance level of p < 0.
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