Macromolecular diffusion in strongly confined geometries and crowded environments is still to a large extent an open subject in soft matter physics and biology. In this paper, we employ large-scale Langevin dynamics simulations to investigate how the diffusion of a tracer is influenced by the combined action of excluded-volume and weak attractive crowder-tracer interactions. We consider two species of tracers, standard hard-core particles described by the Weeks-Chandler-Andersen (WCA) repulsive potential and core-softened (CS) particles, which model, e.g., globular proteins, charged colloids, and nanoparticles covered by polymeric brushes. These systems are characterized by the presence of two length scales in the interaction and can show waterlike anomalies in their diffusion, stemming from the inherent competition between different length scales. Here we report a comprehensive study of both diffusion and structure of these two tracer species in an environment crowded by quenched configurations of polymers at increasing density. We analyze in detail how the tracer-polymer affinity and the system density affect transport as compared to the emergence of specific static spatial correlations. In particular, we find that, while hardly any differences emerge in the diffusion properties of WCA and CS particles, the propensity to develop structural order for large crowding is strongly frustrated for CS particles. Surprisingly, for large enough affinity for the crowding matrix, the diffusion coefficient of WCA tracers display a nonmonotonic trend as their density is increased when compared to the zero affinity scenario. This waterlike anomaly turns out to be even larger than what observed for CS particle and appears to be rooted in a similar competition between excluded-volume and affinity effects.
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http://dx.doi.org/10.1103/PhysRevE.102.032618 | DOI Listing |
Phys Rev Lett
December 2024
Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.
We measure the high-intensity laser propagation throughout meter-scale, channel-guided laser-plasma accelerators by adjusting the length of the plasma channel on a shot-by-shot basis, showing high-quality guiding of 500 TW laser pulses over 30 cm in a hydrogen plasma of density n_{0}≈1×10^{17} cm^{-3}. We observed transverse energy transport of higher-order modes in the first ≈12 cm of the plasma channel, followed by quasimatched propagation, and the gradual, dark-current-free depletion of laser energy to the wake. We quantify the laser-to-wake transfer efficiency limitations of currently available petawatt-class lasers and demonstrate via simulation how control over the laser mode can significantly improve beam parameters.
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December 2024
Center for Computational Astrophysics, Flatiron Institute, 162 5th Avenue, New York, New York 10010, USA.
High-energy extensions to general relativity modify the Einstein-Hilbert action with higher-order curvature corrections and theory-specific coupling constants. The order of these corrections imprints a universal curvature dependence on observations while the coupling constant controls the deviation strength. In this Letter, we leverage the theory-independent expectation that modifications to the action of a given order in spacetime curvature (Riemann tensor and contractions) lead to observational deviations that scale with the system length scale to a corresponding power.
View Article and Find Full Text PDFPhys Rev Lett
December 2024
Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), 50018 Zaragoza, Spain.
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January 2025
Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, United States.
Motivation: Partial order alignment is a widely used method for computing multiple sequence alignments, with applications in genome assembly and pangenomics, among many others. Current algorithms to compute the optimal, gap-affine partial order alignment do not scale well to larger graphs and sequences. While heuristic approaches exist, they do not guarantee optimal alignment and sacrifice alignment accuracy.
View Article and Find Full Text PDFChaos
January 2025
IGCE-Physics Department, São Paulo State University (UNESP), 13506-900 Rio Claro, SP, Brazil.
The dynamics of the convergence for the stationary state considering a Duffing-like equation are investigated. The driven potential for these dynamics is supplied by a damped forced oscillator that has a piecewise linear function. Fixed points and their basins of attraction were identified and measured.
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