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In this paper, we construct the metric tensor and volume for the manifold of purifications associated with an arbitrary reduced density operator ρS. We also define a quantum coarse-graining (CG) to study the volume where macrostates are the manifolds of purifications, which we call surfaces of ignorance (SOI), and microstates are the purifications of ρS. In this context, the volume functions as a multiplicity of the macrostates that quantifies the amount of information missing from ρS. Using examples where the SOI are generated using representations of SU(2), SO(3), and SO(N), we show two features of the CG: (1) A system beginning in an atypical macrostate of smaller volume evolves to macrostates of greater volume until it reaches the equilibrium macrostate in a process in which the system and environment become strictly more entangled, and (2) the equilibrium macrostate takes up the vast majority of the coarse-grained space especially as the dimension of the total system becomes large. Here, the equilibrium macrostate corresponds to a maximum entanglement between the system and the environment. To demonstrate feature (1) for the examples considered, we show that the volume behaves like the von Neumann entropy in that it is zero for pure states, maximal for maximally mixed states, and is a concave function with respect to the purity of ρS. These two features are essential to typicality arguments regarding thermalization and Boltzmann's original CG.
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http://dx.doi.org/10.3390/e25050788 | DOI Listing |
J Phys Chem B
August 2025
Department of Physics, Emory University, Atlanta, Georgia 30322, United States.
The activity of the intrinsically disordered protein, α-synuclein, in human brain neurons is associated with neurotransmitter storage, trafficking, and release, and its dysfunctional aggregation is linked to Parkinsons's disease. To describe the as-yet unknown molecular function of α-synuclein, we address physical and mechanical properties of the isolated, monomeric human protein, by measuring the protein-coupled solvent dynamics detected by the electron paramagnetic resonance (EPR) spin probe, TEMPOL, colocalized in solvent regions around the protein, under temperature-controlled (200-265 K) ice-boundary confinement. The spin probe rotational correlation time at all temperatures is characterized by two components that are assigned to protein hydration water regions around nominally stable protein structure (slow motion; distal N-terminal and central domains) and to dynamically disordered regions (fast motion; C-terminal and proximal N-terminal domains).
View Article and Find Full Text PDFInt J Mol Sci
June 2025
College of Agriculture and Biological Science, Dali University, Dali 671000, China.
Activating mutations in the epidermal growth factor receptor (EGFR) are key oncogenic drivers across multiple cancers, yet the structural mechanisms by which these mutations promote persistent receptor activation remain elusive. Here, we investigate how three clinically relevant mutations-T790M, L858R, and the T790M_L858R double mutant-reshape EGFR's conformational ensemble and regulatory network architecture. Using multiscale molecular simulations and kinetic modeling, we show that these mutations, particularly in combination, enhance flexibility in the αC-helix and A-loop, favoring activation-competent states.
View Article and Find Full Text PDFSci Rep
March 2024
Graduate School of Education, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
Prompted by the ubiquity of empirical observations of critical phenomena, often in non-equilibrium macrostates, we developed a modelling approach in which several critical phenomena coexist. Instead of a single critical point, many coexisting critical points in the system are identified, forming a one-dimensional critical manifold. Identified within our game-of-life-like heterogeneous agent-based simulation model, where agents can be created and annihilated in the presence of a catalyst, each critical point belonging to the critical manifold is associated with a multi-spectrum of critical exponents.
View Article and Find Full Text PDFThe chaperonin GroEL is a multisubunit molecular machine that assists in protein folding in the cytosol. Past studies have shown that GroEL undergoes large allosteric conformational changes during its reaction cycle. Here, we report single-molecule Förster resonance energy transfer measurements that directly probe the conformational transitions of one subunit within GroEL and its single-ring variant under equilibrium conditions.
View Article and Find Full Text PDFEntropy (Basel)
May 2023
Air Force Research Laboratory, Rome, NY 13441, USA.
In this paper, we construct the metric tensor and volume for the manifold of purifications associated with an arbitrary reduced density operator ρS. We also define a quantum coarse-graining (CG) to study the volume where macrostates are the manifolds of purifications, which we call surfaces of ignorance (SOI), and microstates are the purifications of ρS. In this context, the volume functions as a multiplicity of the macrostates that quantifies the amount of information missing from ρS.
View Article and Find Full Text PDF