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Conformational dynamics is essential to biomolecular processes. Markov State Models (MSMs) are widely used to elucidate dynamic properties of molecular systems from unbiased Molecular Dynamics (MD). However, the implementation of reweighting schemes for MSMs to analyze biased simulations is still at an early stage of development. Several dynamical reweighing approaches have been proposed, which can be classified as approaches based on (i) Kramers rate theory, (ii) rescaling of the probability density flux, (iii) reweighting by formulating a likelihood function, (iv) path reweighting. We present the state-of-the-art and discuss the methodological differences of these methods, their limitations and recent applications.
BEAM-ME: Accelerating Linear Energy Systems Models by a Massively Parallel Interior Point Method
(2020)
UG is a generic framework to parallelize branch-and-bound based solvers (e.g., MIP, MINLP, ExactIP) in a distributed or shared memory computing environment. It exploits the powerful performance of state-of-the-art "base solvers", such as SCIP, CPLEX, etc. without the need for base solver parallelization.
UG framework, ParaSCIP(ug[SCIP,MPI]) and FiberSCIP (ug[SCIP,Pthreads]) are available as a beta version. For MIP solving, ParaSCIP and FiberSCIP are well debugged and should be stable. For MINLP solving, they are relatively stable, but not as thoroughly debugged. This release version should handle branch-and-cut approaches where subproblems are defined by variable bounds and also by constrains for ug[SCIP,*] ParaSCIP and FiberSCIP). Therefore, problem classes other than MIP or MINLP can be handled, but they have not been tested yet.
v0.9.1: Update orbitope cip files.
Stand-alone quantum dot-based single-photon source operating at telecommunication wavelengths
(2020)
Von Graphen zu Hypergraphen
(2020)
In graphical representations of public transportation networks, there is often some degree of uncertainty in the arc values, due to delays or transfer times. This uncertainty can be expressed as a parameterized weight on the transfer arcs. Classical shortest path algorithms often have difficulty handling parameterized arc weights and a tropical geometry approach has been shown as a possible solution. The connection between the classical shortest path problem and tropical geometry is well establish: Tropically multiplying the n × n adjacency matrix of a graph with itself n − 1 times results in the so-called Kleene star, and is a matrix-form solution to the all-pairs shortest path problem. Michael Joswig and Benjamin Schröter showed in their paper The Tropical Geometry of Shortest Paths that the same method can be used to find the solution to the all-pairs shortest path problem even in the case of variable arc weights and they proposed an algorithm to solve the single-target shortest path problem in such a case. The solution takes the form of a polyhedral subdivision of the parameter space. As the number of variable arc weights grows, the time needed to execute an implementation of this algorithm grows exponentially. As the size of a public transportation network grows, the number of variable arc weights grows exponentially as well. However, it has been observed that in public transportation networks, there are usually only a few possible shortest routes. Geometrically, this means that there should be few polyhedra in the polyhedral subdivision. This algorithm is used on an example of a real-world public transportation network and an analysis of the polyhedral subdivision is made. Then a geometrical approach is used to analyze the impact of limiting the number of transfers, and thereby limiting the number of parameterized arcs used, as an estimation of the solution to the all-pairs shortest path problem
One of the fundamental steps in the optimization of public transport is line planning. It involves determining lines and assigning frequencies of service such that costs are minimized while also maximizing passenger comfort and satisfying travel demands. We formulate the problem as a mixed integer linear program that considers all circuit-like lines in a graph and allows free passenger routing. Traveler and operator costs are included in a linear scalarization in the objective. We apply said programming problem to the Parametric City, which is a graph model introduced by Fielbaum, Jara-Díaz and Gschwender that exibly represents different cities. In his dissertation, Fielbaum solved the line planning problem for various parameter choices in the Parametric City. In a first step, we therefore review his results and make comparative computations. Unlike Fielbaum we arrive at the conclusion that the optimal line plan for this model indeed depends on the demand. Consequently, we analyze the line planning problem in-depth: We find equivalent, but easier to compute formulations and provide a lower bound by LP-relaxation, which we show to be equivalent to a multi-commodity flow problem. Further, we examine what impact symmetry has on the solutions. Supported both by computational results as well as by theoretical analysis, we reach the conclusion that symmetric line plans are optimal or near-optimal in the Parametric City. Restricting the model to symmetric line plans allows for a \kappa-factor approximation algorithm for the line planning problem in the Parametric City.
Constrained second-order convex optimization algorithms are the method of choice when a high accuracy solution to a problem is needed, due to their local quadratic convergence. These algorithms require the solution of a constrained quadratic subproblem at every iteration. We present the \emph{Second-Order Conditional Gradient Sliding} (SOCGS) algorithm, which uses a projection-free algorithm to solve the constrained quadratic subproblems inexactly. When the feasible region is a polytope the algorithm converges quadratically in primal gap after a finite number of linearly convergent iterations. Once in the quadratic regime the SOCGS algorithm requires O(log(log1/ε)) first-order and Hessian oracle calls and O(log(1/ε)log(log1/ε)) linear minimization oracle calls to achieve an ε-optimal solution. This algorithm is useful when the feasible region can only be accessed efficiently through a linear optimization oracle, and computing first-order information of the function, although possible, is costly.
Demand Side Management (DSM) is usually considered as a process of energy consumption shifting from peak hours to off-peak times. DSM does not always reduce total energy consumption, but it helps to meet energy demand and supply. For example, it balances variable generation from renewables (such as solar and wind) when energy demand differs from renewable generation.