scholarly journals Interpreting Mass Spectra Differing from Their Peptide Models by Several Modifications

2021 ◽  
Author(s):  
Albane Lysiak ◽  
Guillaume Fertin ◽  
Géraldine Jean ◽  
Dominique Tessier
Keyword(s):  
Mass Spectra ◽  
A Priori ◽  
Dynamic Programming Algorithm ◽  
Programming Algorithm ◽  
Large Collection ◽  
Score System ◽  
Extensive Analysis ◽  
Interpretation Errors ◽  
Peptide Models ◽  
Insight Into

Abstract Background: In proteomics, mass spectra representing peptides carrying multiple unknown modifications are particularly difficult to interpret. This issue results in a large number of unidentified spectra.Methods: We developed SpecGlob, a dynamic programming algorithm that aligns pairs of spectra – each pair given by a Peptide-Spectrum Match (PSM) – provided by any Open Modification Search (OMS) method. For each PSM, SpecGlob computes the best alignment according to a given score system, interpreting the mass delta within the PSM as one or several unspecified modification(s). All the alignments are provided in a file, using a specific syntax. These alignments are then post-processed by an additional algorithm, which aims at interpreting the detected modifications.Results: Using a large collection of theoretical spectra generated from the human proteome, we demonstrate that running SpecGlob as a post-analysis of an OMS method can significantly increase the number of correctly interpreted spectra, since SpecGlob is able to infer several, and possibly many, modifications. The post-processing algorithm is able to interpret unambiguously most of the modifications detected by SpecGlob in PSMs. In addition, we performed an extensive analysis to provide insight into the potential reasons for incomplete or erroneous interpretations that may remain after alignments of PSMs.Conclusion: SpecGlob is able to correctly align spectra that differ by one or more modification(s) without any a priori. Since SpecGlob explores all possible alignments that may explain the mass delta within a PSM, it reduces interpretation errors generated by incorrect assumptions about the modifications present in the sample or the number and the specificity of modifications carried by peptides. Our results demonstrate that SpecGlob should be relevant to align experimental spectra, even if this consists in a more challenging task.

Model Predictive Control as an Energy Management Strategy for Hybrid Electric Vehicles

2009 ◽  
Author(s):  
Balaji Sampathnarayanan ◽  
Lorenzo Serrao ◽  
Simona Onori ◽  
Giorgio Rizzoni ◽  
Steve Yurkovich
Keyword(s):  
Dynamic Programming ◽  
Electric Vehicle ◽  
Energy Management ◽  
Management Strategy ◽  
Hybrid Electric Vehicle ◽  
A Priori ◽  
Dynamic Programming Algorithm ◽  
Programming Algorithm ◽  
Energy Management Strategy ◽  
Hybrid Electric

The energy management strategy in a hybrid electric vehicle is viewed as an optimal control problem and is solved using Model Predictve Control (MPC). The method is applied to a series hybrid electric vehicle, using a linearized model in state space formulation and a linear MPC algorithm, based on quadratic programming, to find a feasible suboptimal solution. The significance of the results lies in obtaining a real-time implementable control law. The MPC algorithm is applied using a quasi-static simulator developed in the MATLAB environment. The MPC solution is compared with the dynamic programming solution (offline optimization). The dynamic programming algorithm, which requires the entire driving cycle to be known a-priori, guarantees the optimality and is used here as the benchmark solution. The effect of the parameters of the MPC (length of prediction horizon, type of prediction) is also investigated.

scholarly journals Formulation and Analysis of Patterns in a Score Matrix for Global Sequence Alignment

2020 ◽  
Vol 2020 ◽  
pp. 1-9
Author(s):  
James Owusu Asare ◽  
Justice Kwame Appati ◽  
Kwaku Darkwah
Keyword(s):  
Dynamic Programming ◽  
Molecular Biology ◽  
Sequence Alignment ◽  
A Priori ◽  
Dynamic Programming Algorithm ◽  
Evolutionary Relationship ◽  
Programming Algorithm ◽  
Pairwise Sequence Alignment ◽  
Score Matrix ◽  
Unequal Length

Global sequence alignment is one of the most basic pairwise sequence alignment procedures used in molecular biology to understand the similarity that arises among the structure, function, or evolutionary relationship between two nucleotide sequences. The general algorithm associated with global sequence alignment is the dynamic programming algorithm of Needleman and Wunsch. In this paper, patterns are exploited in the score matrix of the Needleman–Wunsch algorithm. With the help of some examples, the general patterns realized are formulated as new a priori propositions and corollaries that are established for both equal and unequal length comparisons of any two arbitrary sequences.

Cooperative Multi-Vehicle Search and Coverage Problem in an Uncertain Environment

2015 ◽  
Vol 03 (01) ◽  
pp. 35-47 ◽  
Author(s):  
Farid Sharifi ◽  
Mostafa Mirzaei ◽  
Youmin Zhang ◽  
Brandon W. Gordon
Keyword(s):  
Forest Fires ◽  
A Priori ◽  
Dynamic Programming Algorithm ◽  
Programming Algorithm ◽  
Coverage Problem ◽  
Uncertain Environment ◽  
Distributed Approach ◽  
Probability Maps ◽  
Look Ahead ◽  
Service Vehicles

A distributed approach is proposed in this paper to address a cooperative multi-vehicle search and coverage problem in an uncertain environment such as forest fires monitoring and detection. Two different types of vehicles are used for search and coverage tasks: search and service vehicles. The search vehicles have a priori probability maps of targets in the environment. These vehicles update the probability maps based on their sensors measurements during the search mission. The search vehicles use a limited look-ahead dynamic programming algorithm to find their own path individually while their objective is to maximize the amount of information gathered by the whole team. The task of the service vehicles is to optimally spread out over the environment to cover the interested area for a mission. A Voronoi-based coverage control strategy is proposed to modify the configuration of service vehicles in such a way that a prescribed coverage cost function is minimized using the updated probability maps which are provided by the search vehicles. The improved performance of the proposed approach compared to conventional coverage methods is demonstrated by numerical simulation and experimental results.

Optimization for speed regulation strategy of compound coupled hydro-mechanical transmission

2020 ◽  
pp. 095440702098056
Author(s):  
Jin Yu ◽  
Pengfei Shen ◽  
Zhao Wang ◽  
Yurun Song ◽  
Xiaohan Dong
Keyword(s):  
Fuel Consumption ◽  
Dynamic Programming Algorithm ◽  
Operating Conditions ◽  
Programming Algorithm ◽  
Speed Ratio ◽  
Mechanical Transmission ◽  
Speed Regulation ◽  
Ratio Change ◽  
Low Efficiency ◽  
Wheel Loaders

Heavy duty vehicles, especially special vehicles, including wheel loaders and sprinklers, generally work with drastic changes in load. With the usage of a conventional hydraulic mechanical transmission, they face with these problems such as low efficiency, high fuel consumption and so forth. Some scholars focus on the research to solve these issues. However, few of them take into optimal strategies the fluctuation of speed ratio change, which can also cause a lot of problems. In this study, a novel speed regulation is proposed which cannot only solve problems above but also overcome impact caused by speed ratio change. Initially, based on the former research of the Compound Coupled Hydro-mechanical Transmission (CCHMT), the basic characteristics of CCHMT are analyzed. Besides, to solve these problems, dynamic programming algorithm is utilized to formulate basic speed regulation strategy under specific operating condition. In order to reduce the problem caused by speed ratio change, a new optimization is applied. The results indicate that the proposed DP optimal speed regulation strategy has better performance on reducing fuel consumption by up to 1.16% and 6.66% in driving cycle JN1015 and in ECE R15 working condition individually, as well as smoothing the fluctuation of speed ratio by up to 12.65% and 19.01% in those two driving cycles respectively. The processes determining the speed regulation strategy can provide a new method to formulate the control strategies of CCHMT under different operating conditions particularlly under real-world conditions.

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