Andreas Karrenbauer

Computing H/D-Exchange rates of single residues from data of proteolytic fragments

BackgroundProtein conformation and protein/protein interaction can be elucidated by solution-phase Hydrogen/Deuterium exchange (sHDX) coupled to high-resolution mass analysis of the digested protein or protein complex. In sHDX experiments mutant proteins are compared to wild-type proteins or a ligand is added to the protein and compared to the wild-type protein (or mutant). The number of deuteriums incorporated into the polypeptides generated from the protease digest of the protein is related to the solvent accessibility of amide protons within the original protein construct.ResultsIn this work, sHDX data was collected on a 14.5 T FT-ICR MS. An algorithm was developed based on combinatorial optimization that predicts deuterium exchange with high spatial resolution based on the sHDX data of overlapping proteolytic fragments. Often the algorithm assigns deuterium exchange with single residue resolution.ConclusionsWith our new method it is possible to automatically determine deuterium exchange with higher spatial resolution than the level of digested fragments.

Computing H/D-exchange speeds of single residues from data of peptic fragments

Determining the hydrogen-deuterium exchange speeds of single residues from data for peptic fragments obtained by FT-ICS MS is currently mainly done by manual interpretation. We provide an automated method based on combinatorial optimization. More precisely, we present an algorithm that enumerates all possible exchange speeds for single residues that explain the observed data of the peptic fragments.

Packing a trunk: now with a twist!

In an industry project with a German car manufacturer we are faced with the challenge of placing a maximum number of uniform rigid rectangular boxes in the interior of a car trunk. The problem is of practical importance due to a European industry norm which requires car manufacturers to state the trunk volume according to this measure.No really satisfactory automated solution for this problem has been known in the past. In spite of its NP hardness, combinatorial optimization techniques, which consider only grid-aligned placements, produce solutions which are very close to the one achievable by a human expert in several hours of tedious work. The remaining gap is mostly due to the constraints imposed by the chosen grid.In this paper we present a new approach which combines the grid-based combinatorial method with Simulated Annealing on a continuous model. This allows us to explore arbitrary orientations and placements of boxes, hence closing the gap even further, and - in some cases - even surpass the manual expert solution.The implemented software system allows our industrial partner to incorporate the trunk volume in a very early stage of the car design process without relying on a repeated and cumbersome manual evaluation of the volume.

Physarum can compute shortest paths: convergence proofs and complexity bounds

Physarum polycephalum is a slime mold that is apparently able to solve shortest path problems. A mathematical model for the slimes behavior in the form of a coupled system of differential equations was proposed by Tero, Kobayashi and Nakagaki [TKN07]. We prove that a discretization of the model (Euler integration) computes a (1+e)-approximation of the shortest path in O( mL (logn+logL)/e3) iterations, with arithmetic on numbers of O(log(nL/e)) bits; here, n and m are the number of nodes and edges of the graph, respectively, and L is the largest length of an edge. We also obtain two results for a directed Physarum model proposed by Ito et al. [IJNT11]: convergence in the general, nonuniform case and convergence and complexity bounds for the discretization of the uniform case.

Approximating the Interval Constrained Coloring Problem

We consider the interval constrained coloringproblem, which appears in the interpretation of experimental data in biochemistry. Monitoring hydrogen-deuterium exchange rates via mass spectroscopy experiments is a method used to obtain information about protein tertiary structure. The output of these experiments provides data about the exchange rate of residues in overlapping segments of the protein backbone. These segments must be re-assembled in order to obtain a global picture of the protein structure. The interval constrained coloringproblem is the mathematical abstraction of this re-assembly process. The objective of the interval constrained coloring problem is to assign a color (exchange rate) to a set of integers (protein residues) such that a set of constraints is satisfied. Each constraint is made up of a closed interval (protein segment) and requirements on the number of elements that belong to each color class (exchange rates observed in the experiments). We show that the problem is NP-complete for arbitrary number of colors and we provide algorithms that given a feasible instance find a coloring that satisfies all the coloring requirements within ±1 of the prescribed value. In light of our first result, this is essentially the best one can hope for. Our approach is based on polyhedral theory and randomized rounding techniques. Furthermore, we develop a quasi-polynomial-time approximation scheme for a variant of our problem where we are asked to find a coloring satisfying as many fragments as possible.

50.3: A Video‐Capable Algorithm for Local Dimming RGB Backlight

We present an algorithm for efficient calculation of local dimming RGB LED-Backlight to save power consumption. The algorithm was implemented in hardware to support Full-HD resolution at a low HW- cost. It showed clipping-free and video-capable results.

Recovering missing coefficients in DCT-transformed images

A general method for recovering missing DCT coefficients in DCT-transformed images is presented in this work. We model the DCT coefficients recovery problem as an optimization problem and recover all missing DCT coefficients via linear programming. The visual quality of the recovered image gradually decreases as the number of missing DCT coefficients increases. For some images, the quality is surprisingly good even when more than 10 most significant DCT coefficients are missing. When only the DC coefficient is missing, the proposed algorithm outperforms existing methods according to experimental results conducted on 200 test images. The proposed recovery method can be used for cryptanalysis of DCT based selective encryption schemes and other applications.

A New Addressing Scheme for PM OLED Display

This paper presents a new addressing scheme for PM OLED displays by using Consecutive Multiline Addressing, which decomposes the image information into multiline matrices and efficiently reduces the driving current amplitude of OLED pixels. As a result, the lifetime and/or resolution of PM OLED displays can substantially be extended.

Multiline addressing by network flow

We consider an optimization problem arising in the design of controllers for OLED displays. Our objective is to minimize amplitude of the electrical current through the diodes which has a direct impact on the lifetime of such a display. Modeling the problem in mathematical terms yields a class of network flow problems where we group the arcs and pay in each group only for the arc carrying the maximum flow. We develop (fully) combinatorial approximation heuristics suitable for being implemented in the hardware of a control device that drives an OLED display.

Accelerated bend minimization

We present an