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Particle methods have become indispensible in conformation dynamics to compute transition rates in protein folding, binding processes and molecular design, to mention a few. Conformation dynamics requires at a decomposition of a molecule's position space into metastable conformations. In this paper, we show how this decomposition can be obtained via the design of either ``soft'' or ``hard'' molecular conformations. We show, that the soft approach results in a larger metastabilitiy of the decomposition and is thus more advantegous. This is illustrated by a simulation of Alanine Dipeptide.
This paper deals with the computation of regular coderivatives of
solution maps associated with a frequently arising class of generalized equations.
The constraint sets are given by (not necessarily convex) inequalities,
and we do not assume linear independence of gradients to active constraints.
The achieved results enable us to state several versions of sharp necessary optimality
conditions in optimization problems with equilibria governed by such
generalized equations. The advantages are illustrated by means of examples.
The article investigates the relation between global solutions of hyperbolic balance laws and viscous balance laws on the circle. It is thematically located at the crossroads of hyperbolic and parabolic partial differential equations with one-dimensional space variable and periodic boundary conditions. The two equations are given by:
u_t+f(u)_x=g(u)
and
u_t+f(u)_x=e u_{xx}+g(u).
The main result of the paper corrects a result on the persistence of heteroclinic connections by Fan and Hale from 1995 when viscosity vanishes: The "Connection Lemma" states that a connection can only persist if the zero number of the source state is a multiple of the zero number of the target state. The "Cascading Theorem" then yields convergence of heteroclinic connections to a sequence of heteroclinic connections and stationary solutions in case of non-persistence.
In addition a full description of the connection problem of rotating waves on the parabolic attractor is given.
A capillary surface in a negative gravitational field describes the shape of the surface of a hanging drop in a capillary tube with wetting material on the bottom. Mathematical modeling leads to the volume- and obstacle-constrained minimization of a nonconvex nonlinear energy functional of mean curvature type which is unbounded from below. In 1984 Huisken proved the existence and regularity of local minimizers of this energy under the condition on gravitation being sufficiently weak. We prove convergence of a first order finite element approximation of these minimizers. Numerical results demonstrating the theoretic convergence order are given.
Flows over time and generalized flows are two advanced network flow models of utmost importance, as they incorporate two crucial features occurring in numerous real-life networks. Flows over time feature time as a problem dimension and allow to realistically model the fact that commodities (goods, information, etc.) are routed through a network over time. Generalized flows allow for gain/loss factors on the arcs that model physical transformations of a commodity due to leakage, evaporation, breeding, theft, or interest rates. Although the latter effects are usually time-bound, generalized flow models featuring a temporal dimension have never been studied in the literature.
In this paper we introduce the problem of computing a generalized maximum flow over time in networks with both gain factors and transit times on the arcs. While generalized maximum flows and maximum flows over time can be computed efficiently, our combined problem turns out to be NP-hard and even completely non-approximable. A natural special case is given by lossy networks where the loss rate per time unit is identical on all arcs. For this case we present a (practically efficient) FPTAS that also reveals a surprising connection to so-called earliest arrival flows.
We consider a basic subproblem which arises in line planning,
and is of particular importance in the context of a high system
load or robustness: How much can be routed maximally along all possible
lines? The essence of this problem is the Path Constrained Network
Flow (PCN) problem. We explore the complexity of this problem and
its dual. In particular we show for the primal that it is as hard to
approximate as MAX CLIQUE and for the dual that it is as hard to
approximate as SET COVER. We also prove that the PCN problem is
hard for special graph classes, interesting both from a complexity and
from a practical perspective. Finally, we present a special graph class
for which there is a polynomial-time algorithm.
We consider a sorting problem from railway optimization
called train classification: incoming trains are split up into their single
cars and reassembled to form new outgoing trains. Trains are subject
to delay, which may turn a prepared sorting schedule infeasible for the
disturbed situation. The classification methods applied today deal with
this issue by completely disregarding the input order of cars, which provides
robustness against any amount of disturbance but also wastes the
potential contained in the a priori knowledge about the input.
We introduce a new method that provides a feasible sorting schedule for
the expected input and allows to
flexibly insert additional sorting steps
if the schedule has become infeasible after revealing the disturbed input.
By excluding disruptions that almost never occur from our consideration,
we obtain a classification process that is quicker than the current railway
practice but still provides robustness against realistic delays. In fact, our
algorithm allows
flexibly trading off fast classification against high degrees
of robustness depending on the respective need. We further explore
this
flexibility in experiments on real-world traffic data, underlining our
algorithm improves on the methods currently applied in practice.
The knapsack problem is one of the basic problems in combinatorial optimization. In real-world applications it is often part of a more complex problem. Examples are machine capacities in production planning or bandwidth restrictions in telecommunication network design. Due to unpredictable future settings or erroneous data, parameters of such a subproblem are subject to uncertainties.
In high risk situations a robust approach should be chosen to deal with these uncertainties.
Unfortunately, classical robust optimization outputs solutions with little profit by prohibiting any adaption of the solution when the actual realization of the uncertain parameters is known.
This ignores the fact that in most settings minor changes to a previously determined solution are possible. To overcome these drawbacks we allow a limited recovery of a previously fixed item set as soon as the data are known by deleting at most k items and adding up to l new items.
We consider the complexity status of this recoverable robust knapsack problem and extend the classical concept of cover inequalities to obtain stronger polyhedral descriptions. Finally, we present two extensive computational studies to investigate the influence of parameters k and l to the objective and evaluate the effectiveness of our new class of valid inequalities.
In this paper, we investigate the recoverable robust knapsack problem,
where the uncertainty of the item weights follows the approach of Bertsimas and
Sim. In contrast to the robust approach, a limited recovery action is allowed,
i.e., up to k items may be removed when the actual weights are known. This problem
is motivated by the assignment of traffic nodes to antennas in wireless network
planning. Starting from an exponential min-max optimization model, we derive an
integer linear programming formulation of quadratic size. In a preliminary computational
study, we evaluate the gain of recovery using realistic planning data.
In this paper we investigate two different recoverable robust models to deal with cost uncertainties in a shortest path problem. Recoverable robustness extends the classical concept of robustness to deal with uncertainties by incorporating limited recovery actions after the
full data are revealed. Our first model focuses on the case where the recovery actions are quite restricted: after a simple path is fixed in the first stage, in the second stage, after all data are revealed, any path containing at most k new arcs may be chosen.
Thus, the parameter k can be interpreted as a mediator between
robust optimization - no changes allowed - and optimization
on the fly - an arbitrary solution can be chosen. Considering three
classical scenario sets, which model uncertainties in the cost function,
we show that this new problem is strongly NP-hard in all
these cases and is not approximable, unless P=NP.
This is in contrast to the robust shortest path problem, where, for
example, an optimal solution can be computed efficiently for interval
and Gamma-scenarios. For series-parallel graphs and interval scenarios,
we present a polynomial time algorithm for this recoverable robust
setting.
In our second model the recovery set, i.e., the set of paths selectable
in the second stage is not limited, but deviating from the previous
choice comes at extra cost. Thus, a path chosen in the first stage
produces renting costs modeled as an alpha-fraction of the scenario
cost. For an arc taken in the second stage the remaining cost needs
to be paid in addition to some extra inflation cost modeled by a beta-fraction
of the scenario cost, if the arc was not reserved beforehand. The
complexity status of this problem is similar to the robust case. Yet,
for Gamma-scenarios the problem is again strongly NP-hard,
but can be approximated.