Kramers problem for a dimer: Effect of noise correlations

Singh, Rajesh

doi:10.1103/physreve.95.042132

Cited by 5 publications

(2 citation statements)

References 27 publications

(24 reference statements)

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“…From the simulation trajectories, we calculated the distribution of first passage times for passage from globules to self-avoiding walks and passage from coils to globules. The probability of realizing a first passage time that is longer than a lag time t can be fit to an exponential equation of the form: (77) (Fig. 5B).…”

Section: Resultsmentioning

confidence: 99%

Competing interactions give rise to two-state behavior and switch-like transitions in charge-rich intrinsically disordered proteins

Zeng

Ruff

Pappu

2022

Preprint

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The most commonly occurring intrinsically disordered proteins (IDPs) are polyampholytes, which are defined by the duality of low net charge per residue and high fractions of charged residues. Recent experiments have uncovered surprises regarding sequence-ensemble relationships of model polyampholytic IDPs. These include differences in conformational preferences for sequences with lysine vs. arginine, and the suggestion that well-mixed sequences either form globules or conformations with ensemble averages that are reminiscent of ideal chains wherein intra-chain and chain-solvent interactions are counterbalanced. Here, we explain these observations by analyzing results from atomistic simulations. We find that polyampholytic IDPs generally sample two distinct stable states, namely globules and self-avoiding walks. Globules are favored by electrostatic attractions between oppositely charged residues, whereas self-avoiding walks are favored by favorable free energies of hydration of charged residues. We find sequence-specific temperatures of bistability at which globules and self-avoiding walks can coexist. At these temperatures, ensemble averages over coexisting states give rise to statistics that resemble ideal chains without there being an actual counterbalancing of intra-chain and chain-solvent interactions. At equivalent temperatures, arginine-rich sequences tilt the preference toward globular conformations whereas lysine-rich sequences tilt the preference toward self-avoiding walks. This stems from intrinsic differences in free energies of hydration between arginine and lysine. We also identify differences between aspartate and glutamate containing sequences, whereby the shorter aspartate sidechain engenders preferences for metastable, necklace-like conformations. Finally, although segregation of oppositely charged residues within the linear sequence maintains the overall two-state behavior, compact states are highly favored by such systems.

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Section: Resultsmentioning

confidence: 99%

Competing interactions give rise to two-state behavior and switch-like transitions in charge-rich intrinsically disordered proteins

Zeng

Ruff

Pappu

2022

Preprint

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“…Further gains may also come from gravitational wave observations, as glitch induced asymmetries can couple to the gravitational field and lead to a possibly observable signal [305][306][307][308][309][310][311][312]. Searches have been carried out in LIGO and Virgo data following glitches in the Vela and Crab [313,314], and in other pulsars that glitched during the third observational run of the detectors [315].…”

Section: Discussionmentioning

confidence: 99%

Pulsar glitches: observations and physical interpretation

Antonopoulou¹,

Haskell²,

Espinoza³

2022

Rep. Prog. Phys.

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The interpretation of pulsar rotational glitches, the sudden increase in spin frequency of neutron stars, is a half-century-old challenge. The common view is that glitches are driven by the dynamics of the stellar interior, and connect in particular to the interactions between a large-scale neutron superfluid and the other stellar components. This thesis is corroborated by observational data of glitches and the post-glitch response seen in pulsars' rotation, which often involves very long timescales, from months to years. As such, glitch observables combined with consistent models incorporating the rich physics of neutron stars -- from the lattice structure of their crust to the equation of state for matter beyond nuclear densities -- can be very powerful at placing limits on, and reduce uncertainties of, the internal properties. This review summarises glitch observations, current data, and recent analyses, and connects them to the underlying mechanisms and microphysical parameters in the context of the most advanced theoretical glitch models to date.

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Escape rate of a dimer under the influence of additive colored noise: Ornstein–Uhlenbeck process

Lyngdoh,

Reenbohn

2024

Physica A: Statistical Mechanics and its Applications

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Kramers problem for a dimer: Effect of noise correlations

Cited by 5 publications

References 27 publications

Competing interactions give rise to two-state behavior and switch-like transitions in charge-rich intrinsically disordered proteins

Competing interactions give rise to two-state behavior and switch-like transitions in charge-rich intrinsically disordered proteins

Pulsar glitches: observations and physical interpretation

Escape rate of a dimer under the influence of additive colored noise: Ornstein–Uhlenbeck process

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