More Like this

1. Protein misfolding involving entanglements provides a structural explanation for the origin of stretched-exponential refolding kinetics

   https://doi.org/10.1126/sciadv.ads7379  

   Jiang, Yang; Xia, Yingzi; Sitarik, Ian; Sharma, Piyoosh; Song, Hyebin; Fried, Stephen D; O’Brien, Edward P (March 2025, Science Advances)

   Stretched-exponential protein refolding kinetics, first observed decades ago, were attributed to a nonnative ensemble of structures with parallel, non-interconverting folding pathways. However, the structural origin of the large energy barriers preventing interconversion between these folding pathways is unknown. Here, we combine simulations with limited proteolysis (LiP) and cross-linking (XL) mass spectrometry (MS) to study the protein phosphoglycerate kinase (PGK). Simulations recapitulate its stretched-exponential folding kinetics and reveal that misfolded states involving changes of entanglement underlie this behavior: either formation of a nonnative, noncovalent lasso entanglement or failure to form a native entanglement. These misfolded states act as kinetic traps, requiring extensive unfolding to escape, which results in a distribution of free energy barriers and pathway partitioning. Using LiP-MS and XL-MS, we propose heterogeneous structural ensembles consistent with these data that represent the potential long-lived misfolded states PGK populates. This structural and energetic heterogeneity creates a hierarchy of refolding timescales, explaining stretched-exponential kinetics. 

   more » « less
2. Stability of invertible, frustration-free ground states against large perturbations

   https://doi.org/10.22331/q-2022-09-08-793  

   Bachmann, Sven; De Roeck, Wojciech; Donvil, Brecht; Fraas, Martin (September 2022, Quantum)

   A gapped ground state of a quantum spin system has a natural length scale set by the gap. This length scale governs the decay of correlations. A common intuition is that this length scale also controls the spatial relaxation towards the ground state away from impurities or boundaries. The aim of this article is to take a step towards a proof of this intuition. We assume that the ground state is frustration-free and invertible, i.e. it has no long-range entanglement. Moreover, we assume the property that we are aiming to prove for one specific kind of boundary condition; namely open boundary conditions. This assumption is also known as the "local topological quantum order" (LTQO) condition. With these assumptions we can prove stretched exponential decay away from boundaries or impurities, for any of the ground states of the perturbed system. In contrast to most earlier results, we do not assume that the perturbations at the boundary or the impurity are small. In particular, the perturbed system itself can have long-range entanglement. 

   more » « less
3. Electrochemistry of Protein Electron Transfer

   https://doi.org/10.1149/1945-7111/ac60f1  

   Matyushov, Dmitry V. (June 2022, Journal of The Electrochemical Society)

   Protein fold and slow relaxation times impose constraints on configurations sampled by the protein. Incomplete sampling leads to the violation of fluctuation-dissipation relations underlying the traditional theories of electron transfer. The effective reorganization energy of electron transfer is strongly reduced thus leading to lower barriers and faster rates (catalytic effect). Electrochemical kinetic measurements support low activation barriers for protein electron transfer. The distance dependence of the rate constant displays a crossover from a plateau at short distances to a long-distance exponential decay. The transition between these two regimes is controlled by the protein dynamics. 

   more » « less
4. Probing Nonexponential Decay in Floquet–Bloch Bands

   https://doi.org/10.1515/zna-2020-0020  

   Cao, Alec; Fujiwara, Cora J.; Sajjad, Roshan; Simmons, Ethan Q.; Lindroth, Eva; Weld, David (May 2020, Zeitschrift für Naturforschung A)

   Abstract Exponential decay laws describe systems ranging from unstable nuclei to fluorescent molecules, in which the probability of jumping to a lower-energy state in any given time interval is static and history-independent. These decays, involving only a metastable state and fluctuations of the quantum vacuum, are the most fundamental nonequilibrium process and provide a microscopic model for the origins of irreversibility. Despite the fact that the apparently universal exponential decay law has been precisely tested in a variety of physical systems, it is a surprising truth that quantum mechanics requires that spontaneous decay processes have nonexponential time dependence at both very short and very long times. Cold-atom experiments have proven to be powerful probes of fundamental decay processes; in this article, we propose the use of Bose condensates in Floquet–Bloch bands as a probe of long-time nonexponential decay in single isolated emitters. We identify a range of parameters that should enable observation of long-time deviations and experimentally demonstrate a key element of the scheme: tunable decay between quasi-energy bands in a driven optical lattice. 

   more » « less
5. Spectral Gaps and Incompressibility in a $${\varvec{\nu }}$$ = 1/3 Fractional Quantum Hall System

   https://doi.org/10.1007/s00220-021-03997-0  

   Nachtergaele, Bruno; Warzel, Simone; Young, Amanda (April 2021, Communications in Mathematical Physics)

   null (Ed.)

   Abstract We study an effective Hamiltonian for the standard $$\nu =1/3$$ ν = 1 / 3 fractional quantum Hall system in the thin cylinder regime. We give a complete description of its ground state space in terms of what we call Fragmented Matrix Product States, which are labeled by a certain family of tilings of the one-dimensional lattice. We then prove that the model has a spectral gap above the ground states for a range of coupling constants that includes physical values. As a consequence of the gap we establish the incompressibility of the fractional quantum Hall states. We also show that all the ground states labeled by a tiling have a finite correlation length, for which we give an upper bound. We demonstrate by example, however, that not all superpositions of tiling states have exponential decay of correlations. 

   more » « less