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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 correlation function. However, when applied to real data from single- molecule experiments or molecular dynamics simulations, the reactive flux correlation function requires the numerical differentiation of a noisy empirical correlation function, which can result in an unacceptably poor estimate of the rate and pathological dependence on the sampling interval. 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 illustrate the approach using single-molecule passive force spectroscopy measurements of an RNA hairpin.
In this paper we propose and analyze a new Multiscale Method for solving semi-linear elliptic problems with heterogeneous and highly variable coeffcient functions. For this purpose we construct a generalized finite element basis that spans a low dimensional multiscale space. The basis is assembled by performing localized linear finescale computations in small patches that have a diameter of order H |log(H)| where H is the coarse mesh size. Without any assumptions on the type of the oscillations in the coeffcients, we give a rigorous proof for a linear convergence of the H1-error with respect to the coarse mesh
size. To solve the arising equations, we propose an algorithm that is based on a damped Newton scheme in the multiscale space.
In this review article we discuss different techniques to solve numerically the
time-dependent Schrödinger equation on unbounded domains.
We present in detail the most recent approaches and describe briefly alternative ideas pointing out the relations between these works.
We conclude with several numerical examples from
different application areas to compare the presented techniques. We mainly focus on the one-dimensional problem but also touch upon the situation in two space dimensions and the cubic nonlinear case.
A Lavrentiev type regularization technique for
solving elliptic boundary control problems with pointwise state
constraints is considered. The main concept behind this
regularization is to look for controls in the range of the adjoint
control-to-state mapping. After investigating the analysis of the
method, a semismooth Newton method based on the optimality
conditions is presented. The theoretical results are confirmed by
numerical tests. Moreover, they are validated by comparing the
regularization technique with standard numerical codes based on the
discretize-then-optimize concept.
This note addresses a three-dimensional model for isothermal stress-induced transformation in shape-memory polycrystalline materials. We treat the problem within the framework of the energetic formulation of rate-independent processes and investigate existence and continuous dependence issues at both the constitutive relation and quasi-static evolution level. Moreover, we focus on time and space approximation as well as on regularization and parameter asymptotics.
This paper focuses on
rate-independent damage in elastic bodies. Since the driving energy is nonconvex,
solutions may have jumps as a function of time, and in this situation it is known that the classical concept
of energetic solutions for rate-independent systems
may fail to accurately describe the
behavior of the system at jumps.
Therefore, we resort to the (by now well-established) vanishing viscosity approach to rate-independent modeling
and approximate the model by its viscous regularization.
In fact, the analysis of the latter PDE system presents
remarkable difficulties, due to its highly nonlinear character.
We tackle it by combining a variational approach to a class of abstract doubly nonlinear evolution equations, with
careful regularity estimates tailored to this specific system relying on a q-Laplacian type gradient regularization of the damage variable.
Hence, for the viscous problem we conclude the existence of weak solutions satisfying a
suitable energy-dissipation inequality that is the starting point for the vanishing viscosity analysis.
The latter leads to the notion of (weak) parameterized
solution to our rate-independent system,
which encompasses the influence of viscosity in the description of the jump regime.
Quasi-Newton methods based on least change secant updating
formulas that solve linear equations $Ax=b$ in $n=\dim(x)=\dim(b)$ steps
can be expected to solve corresponding smooth nonlinear
systems $n$-step quadratically, i.e. with an $r$-order
of $\rho = 2^{1/n} = 1 + 1/n +O(1/n^2)$. The best rate one can
possibly expect on general problems is given by the positive root
$\rho_n$ of $\rho^n(\rho -1)=1$, for which
$\rho_n-1 = \ln(n)/n + O(1/n^2)$. To show that this upper bound is
actually achieved one usually has to impose a priori some kind of
linear independence condition on the sequence of steps taken by the
quasi-Newton iteration in question. Without any such assumptions we
establish in this paper the convergence order $\rho_n$ for the
two-sided rank one formula proposed by Schlenkrich et al in \cite{SGW06}.
It requires the evaluation of adjoint vectors, is invariant with respect
to linear transformations on the variable domain and combines the
properties of bounded deterioration and heredity.
We study a stationary Schrödinger-Poisson system on a bounded interval of the real axis. The Schrödinger operator is defined on the bounded domain with transparent boundary conditions. This allows us to model a non-zero current through the boundary of the interval. We prove that the system always admits a solution and give explicit a priori estimates for the solutions.
In this paper we develop a QR-like algorithm for the palindromic eigenvalue problem $Ax=\lambda A^\adj x$.
We will discuss the two cases that $A^\adj$ denotes the transpose or the conjugate transpose of $A\in\C^{n,n}$.
It is shown that this so-called palindromic QR iteration is equivalent to applying the standard QR algorithm to $A^{-\adj}A$.
Also the concepts of deflation, shifting, and exploiting the invariance of a Hessenberg-type form are adapted.
Moreover, we analyze the problem of reducing a general square matrix to the mentioned Hessenberg-type form
and establish analogies to the Hamiltonian eigenvalue problem.
Finally, we present concrete Hessenberg-type reduction algorithms for special cases.