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Register a new userEstimation of the infinitesimal generator by square-root approximation
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For the analysis of molecular processes, the estimation of time-scales, i.e., transition rates, is very important. Estimating the transition rates between molecular conformations is -- from a mathematical point of view -- an invariant subspace projection problem. A certain infinitesimal generator acting on function space is projected to a low-dimensional rate matrix. This projection can be performed in two steps. First, the infinitesimal generator is discretized, then the invariant subspace is approxi-mated and used for the subspace projection. In our approach, the discretization will be based on a Voronoi tessellation of the conformational space. We will show that the discretized infinitesimal generator can simply be approximated by the geometric average of the Boltzmann weights of the Voronoi cells. Thus, there is a direct correla-tion between the potential energy surface of molecular structures and the transition rates of conformational changes. We present results for a 2d-diffusion process and Alanine dipeptide.
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Let Q_0 denote the rational numbers expanded to a meadow by totalizing inversion such that 0^{-1}=0. Q_0 can be expanded by a total sign function s that extracts the sign of a rational number. In this paper we discuss an extension Q_0(s ,sqrt) of the signed rationals in which every number has a unique square root.
Molecular dynamics are extremely complex, yet understanding the slow components of their dynamics is essential to understanding their macroscopic properties. To achieve this, one models the molecular dynamics as a stochastic process and analyses the dominant eigenfunctions of the associated Fokker-Planck operator, or of closely related transfer operators. So far, the calculation of the discretized operators requires extensive molecular dynamics simulations. The Square-root approximation of the Fokker-Planck equation is a method to calculate transition rates as a ratio of the Boltzmann densities of neighboring grid cells times a flux, and can in principle be calculated without a simulation. In a previous work we still used molecular dynamics simulations to determine the flux. Here, we propose several methods to calculate the exact or approximate flux for various grid types, and thus estimate the rate matrix without a simulation. Using model potentials we test computational efficiency of the methods, and the accuracy with which they reproduce the dominant eigenfunctions and eigenvalues. For these model potentials, rate matrices with up to $mathcal{O}(10^6)$ states can be obtained within seconds on a single high-performance compute server if regular grids are used.
We describe the software package FELIX that solves the equations of the time-dependent generator coordinate method (TDGCM) in N-dimensions (N $geq$ 1) under the Gaussian overlap approximation. The numerical resolution is based on the Galerkin finite element discretization of the collective space and the Crank-Nicolson scheme for time integration. The TDGCM solver is implemented entirely in C++. Several additional tools written in C++, Python or bash scripting language are also included for convenience. In this paper, the solver is tested with a series of benchmarks calculations. We also demonstrate the ability of our code to handle a realistic calculation of fission dynamics.
Square-root topological states are new topological phases, whose topological property is inherited from the square of the Hamiltonian. We realize the first-order and second-order square-root topological insulators in phononic crystals, by putting additional cavities on connecting tubes in the acoustic Su-Schrieffer-Heeger model and the honeycomb lattice, respectively. Because of the square-root procedure, the bulk gap of the squared Hamiltonian is doubled. In both two bulk gaps, the square-root topological insulators possess multiple localized modes, i.e., the end and corner states, which are evidently confirmed by our calculations and experimental observations. We further propose a second-order square-root topological semimetal by stacking the decorated honeycomb lattice to three dimensions.
We introduce the notions of infinitesimal extension and square-zero extension in the context of simplicial commutatie algebras. We next investigate their mutual relationship and we show that the Postnikov tower of a simplicial commutative algebra is built out of square-zero extensions. We conclude the notes with two applications: we give connectivity estimates for the cotangent complex and we show how obstructions can be seen as deformations over simplicial rings.
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