Exploring the Free Energy Landscape: From Dynamics to Networks and Back

The knowledge of the Free Energy Landscape topology is the essential key to understand many biochemical processes. The determination of the conformers of a protein and their basins of attraction takes a central role for studying molecular isomerization reactions. In this work, we present a novel framework to unveil the features of a Free Energy Landscape answering questions such as how many meta-stable conformers are, how the hierarchical relationship among them is, or what the structure and kinetics of the transition paths are. Exploring the landscape by molecular dynamics simulations, the microscopic data of the trajectory are encoded into a Conformational Markov Network. The structure of this graph reveals the regions of the conformational space corresponding to the basins of attraction. In addition, handling the Conformational Markov Network, relevant kinetic magnitudes as dwell times or rate constants, and the hierarchical relationship among basins, complete the global picture of the landscape. We show the power of the analysis studying a toy model of a funnel-like potential and computing efficiently the conformers of a short peptide, the dialanine, paving the way to a systematic study of the Free Energy Landscape in large peptides.Comment: PLoS Computational Biology (in press

Genetic embedded matching approach to ground states in continuous-spin systems

Due to an extremely rugged structure of the free energy landscape, the determination of spin-glass ground states is among the hardest known optimization problems, found to be NP-hard in the most general case. Owing to the specific structure of local (free) energy minima, general-purpose optimization strategies perform relatively poorly on these problems, and a number of specially tailored optimization techniques have been developed in particular for the Ising spin glass and similar discrete systems. Here, an efficient optimization heuristic for the much less discussed case of continuous spins is introduced, based on the combination of an embedding of Ising spins into the continuous rotators and an appropriate variant of a genetic algorithm. Statistical techniques for insuring high reliability in finding (numerically) exact ground states are discussed, and the method is benchmarked against the simulated annealing approach.Comment: 17 pages, 12 figures, 1 tabl

Detecting animals in African Savanna with UAVs and the crowds

Unmanned aerial vehicles (UAVs) offer new opportunities for wildlife monitoring, with several advantages over traditional field-based methods. They have readily been used to count birds, marine mammals and large herbivores in different environments, tasks which are routinely performed through manual counting in large collections of images. In this paper, we propose a semi-automatic system able to detect large mammals in semi-arid Savanna. It relies on an animal-detection system based on machine learning, trained with crowd-sourced annotations provided by volunteers who manually interpreted sub-decimeter resolution color images. The system achieves a high recall rate and a human operator can then eliminate false detections with limited effort. Our system provides good perspectives for the development of data-driven management practices in wildlife conservation. It shows that the detection of large mammals in semi-arid Savanna can be approached by processing data provided by standard RGB cameras mounted on affordable fixed wings UAVs

Full stack development toward a trapped ion logical qubit

Quantum error correction is a key step toward the construction of a large-scale quantum computer, by preventing small infidelities in quantum gates from accumulating over the course of an algorithm. Detecting and correcting errors is achieved by using multiple physical qubits to form a smaller number of robust logical qubits. The physical implementation of a logical qubit requires multiple qubits, on which high fidelity gates can be performed. The project aims to realize a logical qubit based on ions confined on a microfabricated surface trap. Each physical qubit will be a microwave dressed state qubit based on 171Yb+ ions. Gates are intended to be realized through RF and microwave radiation in combination with magnetic field gradients. The project vertically integrates software down to hardware compilation layers in order to deliver, in the near future, a fully functional small device demonstrator. This thesis presents novel results on multiple layers of a full stack quantum computer model. On the hardware level a robust quantum gate is studied and ion displacement over the X-junction geometry is demonstrated. The experimental organization is optimized through automation and compressed waveform data transmission. A new quantum assembly language purely dedicated to trapped ion quantum computers is introduced. The demonstrator is aimed at testing implementation of quantum error correction codes while preparing for larger scale iterations.Open Acces

Genetic optimization of energy- and failure-aware continuous production scheduling in pasta manufacturing

Energy and failure are separately managed in scheduling problems despite the commonalities between these optimization problems. In this paper, an energy- and failure-aware continuous production scheduling problem (EFACPS) at the unit process level is investigated, starting from the construction of a centralized combinatorial optimization model combining energy saving and failure reduction. Traditional deterministic scheduling methods are difficult to rapidly acquire an optimal or near-optimal schedule in the face of frequent machine failures. An improved genetic algorithm (IGA) using a customized microbial genetic evolution strategy is proposed to solve the EFACPS problem. The IGA is integrated with three features: Memory search, problem-based randomization, and result evaluation. Based on real production cases from Soubry N.V., a large pasta manufacturer in Belgium, Monte Carlo simulations (MCS) are carried out to compare the performance of IGA with a conventional genetic algorithm (CGA) and a baseline random choice algorithm (RCA). Simulation results demonstrate a good performance of IGA and the feasibility to apply it to EFACPS problems. Large-scale experiments are further conducted to validate the effectiveness of IGA

Trapping ACO applied to MRI of the Heart

The research presented here supports the ongoing need for automatic heart volume calculation through the identification of the left and right ventricles in MRI images. The need for automated heart volume calculation stems from the amount of time it takes to manually processes MRI images and required esoteric skill set. There are several methods for region detection such as Deep Neural Networks, Support Vector Machines and Ant Colony Optimization. In this research Ant Colony Optimization (ACO) will be the method of choice due to its efficiency and flexibility. There are many types of ACO algorithms using a variety of heuristics that provide advantages in different environments and knowledge domains. All ACO algorithms share a foundational attribute, a heuristic that acts in conjunction with pheromones. These heuristics can work in various ways, such as dictating dispersion or the interpretation of pheromones. In this research a novel heuristic to disperse and act on pheromone is presented. Further, ants are applied to more general problem than the normal objective of finding edges, highly qualified region detection. The reliable application of heuristic oriented algorithms is difficult in a diverse environment. Although the problem space here is limited to MRI images of the heart, there are significant difference among them: the topology of the heart is different by patient, the angle of the scans changes and the location of the heart is not known. A thorough experiment is conducted to support algorithm efficacy using randomized sampling with human subjects. It will be shown during the analysis the algorithm has both prediction power and robustness

A study of data coding technology developments in the 1980-1985 time frame, volume 2

The source parameters of digitized analog data are discussed. Different data compression schemes are outlined and analysis of their implementation are presented. Finally, bandwidth compression techniques are given for video signals