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Register a new userA robust approach to estimating rates from time-correlation functions
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While seemingly straightforward in principle, the reliable estimation of rate constants is seldom easy in practice. Numerous issues, such as the complication of poor reaction coordinates, cause obvious approaches to yield unreliable estimates. When a reliable order parameter is available, the reactive flux theory of Chandler allows the rate constant to be extracted from the plateau region of an appropriate reactive flux function. However, when applied to real data from single-molecule experiments or molecular dynamics simulations, the rate can sometimes be difficult to extract due to the numerical differentiation of a noisy empirical correlation function or difficulty in locating the plateau region at low sampling frequencies. We present a modified version of this theory which does not require numerical derivatives, allowing rate constants to be robustly estimated from the time-correlation function directly. We compare these approaches using single-molecule force spectroscopy measurements of an RNA hairpin.
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The problem of calculating real-time correlation functions is formulated in terms of an imaginary-time partial differential equation. The latter is solved analytically for the perturbed harmonic oscillator and compared with the known exact result. The first order approximation for the short-time propagator is derived and used for numerical solution of the equation by a Monte Carlo integration. In general, the method provides a reformulation of the dynamic sign problem, and is applicable to any two-time correlation function including single-particle, density-density, current-current, spin-spin, and others. The prospects of extending the technique onto multi-dimensional problems are discussed.
We study the impact of DNA coiling on the search rate of proteins moving along the DNA contour interspersed by three-dimensional (3D) bulk excursions. When the DNA is coiled proteins performing short 3D hops along a DNA segment can be captured by foreign DNA segments that have looped back close to the original segment. These intersegmental jumps are shown to enhance the search rate for a specific site on the DNA by lowering the tendency to resample previously visited sites on the DNA. The model developed here offers a quantitative description of recent single molecule experiments on facilitated diffusion of restriction enzymes EcoRV.
We show that the dynamics resulting from preparing a one-dimensional quantum system in the ground state of two decoupled parts, then joined together and left to evolve unitarily with a translational invariant Hamiltonian (a local quench), can be described by means of quantum field theory. In the case when the corresponding theory is conformal, we study the evolution of the entanglement entropy for different bi-partitions of the line. We also consider the behavior of one- and two-point correlation functions. All our findings may be explained in terms of a picture, that we believe to be valid more generally, whereby quasiparticles emitted from the joining point at the initial time propagate semiclassically through the system.
We present a new approach to the static finite temperature correlation functions of the Heisenberg chain based on functional equations. An inhomogeneous generalization of the n-site density operator is considered. The lattice path integral formulation with a finite but arbitrary Trotter number allows to derive a set of discrete functional equations with respect to the spectral parameters. We show that these equations yield a unique characterization of the density operator. Our functional equations are a discrete version of the reduced q-Knizhnik-Zamolodchikov equations which played a central role in the study of the zero temperature case. As a natural result, and independent of the arguments given by Jimbo, Miwa, and Smirnov (2009) we prove that the inhomogeneous finite temperature correlation functions have the same remarkable structure as for zero temperature: they are a sum of products of nearest-neighbor correlators.
Reaction coordinates are widely used throughout chemical physics to model and understand complex chemical transformations. We introduce a definition of the natural reaction coordinate, suitable for condensed phase and biomolecular systems, as a maximally predictive one-dimensional projection. We then show this criterion is uniquely satisfied by a dominant eigenfunction of an integral operator associated with the ensemble dynamics. We present a new sparse estimator for these eigenfunctions which can search through a large candidate pool of structural order parameters and build simple, interpretable approximations that employ only a small number of these order parameters. Example applications with a small molecules rotational dynamics and simulations of protein conformational change and folding show that this approach can filter through statistical noise to identify simple reaction coordinates from complex dynamics.
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