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We investigate a nonstandard phase field
model of Cahn-Hilliard type. The model, which was introduced in
[16], describes two-species phase segregation and consists of a
system of two highly nonlinearly coupled PDEs. It has been studied
recently in
[5], [6] for the case of homogeneous Neumann
boundary conditions. In this paper, we investigate the case that the
boundary condition for one of the unknowns of the system is of third
kind and nonhomogeneous. For the resulting system, we show
well-posedness, and we study optimal boundary control
problems. Existence of optimal controls is shown, and the first-order
necessary optimality conditions are derived. Owing to the strong
nonlinear couplings in the PDE system, standard arguments of optimal
control theory do not apply directly, although the control constraints
and the cost functional will be of standard type.
This paper is concerned with a diffusion model of phase-field type, consisting
of a {parabolic} system of two partial differential equations{,} interpreted as balances
of microforces and microenergy{, for two unknowns: the problem's order parameter $\rho$}
and the chemical potential $\mu$; each equation includes a viscosity term -- respectively, $\varepsilon \,\partial_t\mu$ and $\delta\,\partial_t\rho$ -- with $\varepsilon$ and $\delta$ two positive parameters; the field equations are complemented by Neumann homogeneous boundary conditions and suitable initial conditions. In a recent paper \cite{CGPS3}, we proved that this problem is \wepo\ and investigated the \loti\ \bhv\ of its $(\varepsilon,\delta)-$solutions. Here we discuss the asymptotic limit of the system as $\eps$
tends to $0$. We prove convergence of
$(\varepsilon,\delta)-$solutions to the corresponding solutions for
the case $\eps =0$, whose long-time behavior we characterize; in the
proofs, we employ compactness and monotonicity arguments.
We study the expansion of the eigenfunctions of Schrödinger operators with smooth confinement potentials in Hermite functions; confinement potentials are potentials that become unbounded at infinity. The key result is that such eigenfunctions and all their derivatives decay more rapidly than any exponential function under some mild growth
conditions to the potential and its derivatives. Their expansion in Hermite functions converges therefore very fast, super-algebraically.
The mixed regularity of electronic wave functions in fractional order and weighted Sobolev spaces
(2012)
The paper continues the study of the regularity of electronic wave functions in Hilbert spaces of mixed derivatives. It is shown that the eigenfunctions of electronic Schr\"odinger operators and their
exponentially weighted counterparts possess, roughly speaking, square integrable mixed weak derivatives of fractional order $\vartheta$ for $\vartheta<3/4$. The bound $3/4$ is best possible and can neither be reached nor surpassed. Such results are important for the study
of sparse grid-like expansions of the wave functions and show that their asymptotic convergence rate measured in terms of the number of ansatz functions involved does not deteriorate with the number of electrons.
We present Undercover, a primal heuristic for nonconvex mixed-integer nonlinear programming (MINLP) that explores a mixed-integer linear subproblem (sub-MIP) of a given MINLP. We solve a vertex covering problem to identify a minimal set of variables that need to be fixed in order to linearize each constraint, a so-called cover. Subsequently, these variables are fixed to values obtained from a reference point, e.g., an optimal solution of a linear relaxation. We apply domain propagation and conflict analysis to try to avoid infeasibilities and learn from them, respectively. Each feasible solution of the sub-MIP corresponds to a feasible solution of the original problem.
We present computational results on a test set of mixed-integer quadratically constrained programs (MIQCPs) and general MINLPs from MINLPLib. It turns out that the majority of these instances allow for small covers. Although general in nature, the heuristic appears most promising for MIQCPs, and complements nicely with existing root node heuristics in different state-of-the-art solvers.
The slow processes of metastable stochastic dynamical systems are difficult to access by direct numerical simulation due the sampling problem. Here, we suggest an approach for modeling the slow parts of Markov processes by approximating the dominant eigenfunctions and eigenvalues of the propagator. To this end, a variational principle is derived that is based on the maximization of a Raleigh coefficient. It is shown that this Raleigh coefficient can be estimated from statistical observables that can be obtained from short distributed simulations starting from different parts of state space. The approach forms a basis for the development of adaptive and efficient computational algorithms for simulating and analyzing metastable Markov processes while avoiding the sampling problem. Since any stochastic process with finite memory can be transformed into a Markov process, the approach is applicable to a wide range of processes relevant for modeling complex real-world phenomena.
Folding and conformational changes of macromolecules often require the generation of large amounts of simulation data that are difficult to ana- lyze. Markov state models (MSMs) address this challenge by providing a systematic way to decompose the state space of the molecular system into substates and to estimate a transition matrix containing the transi- tion probabilities between these substates. This transition matrix can be analyzed to reveal the metastable, i.e. long-living, states of the system, its slowest relaxation timescales and transition pathways and rates e.g. from unfolded to folded, or from dissociated to bound states. To reduce the technical burden of constructing such MSMs we provide the software framework EMMA (available at https://simtk.org/home/emma) to con- struct, validate and analyse such Markov State Models.
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.
Single-molecule force spectroscopy has proven to be a powerful tool for studying the kinetic be- havior of biomolecules. Through application of an external force, conformational states with small or transient populations can be stabilized, allowing them to be characterized and the statistics of in- dividual trajectories studied to provide insight into biomolecular folding and function. Because the observed quantity (force or extension) is not necessarily an ideal reaction coordinate, individual ob- servations cannot be uniquely associated with kinetically distinct conformations. While maximum- likelihood schemes such as hidden Markov models have solved this problem for other classes of single-molecule experiments by using temporal information to aid in the inference of a sequence of distinct conformational states, these methods do not give a clear picture of how precisely the model parameters are determined by the data due to instrument noise and finite-sample statistics, both sig- nificant problems in force spectroscopy. We solve this problem through a Bayesian extension that allows the experimental uncertainties to be directly quantified, and build in detailed balance to fur- ther reduce uncertainty through physical constraints. We illustrate the utility of this approach in characterizing the three-state kinetic behavior of an RNA hairpin in a stationary optical trap.