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Comparing chemical reaction networks: A categorical and algorithmic perspective

Luca Cardelli, Mirco Tribastone, Max Tschaikowski, Andrea Vandin
2017 Theoretical Computer Science  
We study chemical reaction networks (CRNs) as a kernel language for concurrency models with semantics based on ordinary differential equations.  ...  Using a categorical framework, we extend and relate model-comparison approaches based on structural (syntactic) and on dynamical (semantic) properties of a CRN, proving their equivalence.  ...  Cardelli is partially funded by a Royal Society Research Professorship.  ... 
doi:10.1016/j.tcs.2017.12.018 fatcat:3w4rqxfnujhh3nqzfm6trgo26y

The Exploration of Chemical Reaction Networks

Jan P. Unsleber, Markus Reiher
2020 Annual review of physical chemistry (Print)  
This will replace the standard approach of manually studying a selected and restricted number of molecular structures for a chemical mechanism.  ...  Modern computational chemistry has reached a stage at which massive exploration into chemical reaction space with unprecedented resolution with respect to the number of potentially relevant molecular structures  ...  ACKNOWLEDGMENTS This work was financially supported by the Deutsche Forschungsgemeinschaft (DFG) (GZ: UN 417/1-1) and by the Schweizerischer Nationalfonds (SNF) (Project 200021_182400).  ... 
doi:10.1146/annurev-physchem-071119-040123 pmid:32105566 fatcat:eeyb7b5w7badpm7bakd5x6a4hy

Computation in Complex Networks

Clara Pizzuti, Annalisa Socievole
2021 Entropy  
The Special Issue on "Computation in Complex Networks" focused on gathering highly original papers in the field of current complex network research [...]  ...  Acknowledgments: We express our thanks to the authors of the above contributions, and to the journal Entropy and MDPI for their support during this work.  ...  Due to their ability to model a wide variety of daily-life systems-including the Internet, communication, chemical, neural, social, political and financial networks-complex network systems and their behavior  ... 
doi:10.3390/e23020192 pmid:33562478 fatcat:g2ad4eiupnaydp653k7hvzeqyu

Mechanism Deduction from Noisy Chemical Reaction Networks [article]

Jonny Proppe, Markus Reiher
2018 arXiv   pre-print
We introduce KiNetX, a fully automated meta-algorithm for the kinetic analysis of complex chemical reaction networks derived from semi-accurate but efficient electronic structure calculations.  ...  Second, KiNetX identifies and eliminates all kinetically irrelevant species and elementary reactions to reduce a complex network graph to a comprehensible mechanism.  ...  Theoretical and Algorithmic Details Kinetic Modeling from a Network Perspective We describe the structure of a chemical reaction network by a graph of N vertices and L bidirectional edges.  ... 
arXiv:1803.09346v2 fatcat:e2nov66msjevlmjta3rioz4mhu

Snazer: the simulations and networks analyzer

Tommaso Mazza, Gennaro Iaccarino, Corrado Priami
2010 BMC Systems Biology  
From a pure dynamical perspective, simulation represents a relevant way-out.  ...  Conclusions: Snazer is a solid prototype that integrates biological network and simulation time-course data analysis techniques.  ...  Acknowledgements The authors thank Alida Palmisano and Alessandro Romanel for their precious suggestions and the CoSBi team.  ... 
doi:10.1186/1752-0509-4-1 pmid:20056001 pmcid:PMC2880970 fatcat:3aohjf6dlbhljdfb2dlopwmiti

Algorithms for Various Biological Networks

Bharti Talukdar
2014 IOSR Journal of Computer Engineering  
This paper present a novel algorithm to visualize different biological networks and network analysis results in meaningful ways depending on network types and analysis outcome.  ...  The presented approach provides a generic, universal algorithm for layout of biological networks: 1.  ...  Types of Networks There are many ways of categorizing the network.  ... 
doi:10.9790/0661-16364555 fatcat:53op2kmeyba6jbrkdyfefvzdqu

Metabolic Robustness and Network Modularity: A Model Study

Petter Holme, Matej Oresic
2011 PLoS ONE  
[Methodology/Principal Findings] By using a model for generating chemical reaction systems where one can tune the network modularity, we find that robustness increases with modularity for changes in the  ...  In this paper we measure the relation between network modularity and several aspects of robustness directly in a model system of metabolism.  ...  Author Contributions Conceived and designed the experiments: PH. Performed the experiments: PH. Analyzed the data: PH. Contributed reagents/materials/analysis tools: PH. Wrote the paper: PH.  ... 
doi:10.1371/journal.pone.0016605 pmid:21311770 pmcid:PMC3032788 fatcat:3v34p6v3tfeirdftz7ctkde3o4

Drug Combinations: Mathematical Modeling and Networking Methods

Vahideh Vakil, Wade Trappe
2019 Pharmaceutics  
This comprehensive investigation of the mathematical methods includes models that employ pharmacodynamics equations, those that rely on signaling and how the underlying chemical networks are affected by  ...  Additionally, this article reviews computational methods including mathematical algorithms, machine learning, and search algorithms that can identify promising combinations of drug compounds.  ...  The figure also shows a basic reaction graph that includes the immediate receptor, ligand and inhibitor, and its corresponding chemical reaction network.  ... 
doi:10.3390/pharmaceutics11050208 pmid:31052580 pmcid:PMC6571786 fatcat:p2tsu6ju75hylkkh5dzh46cbaa

Biological network analyses: computational genomics and systems approaches

S.P. Walton, Z. Li, C. Chan
2006 Molecular Simulation  
The integration of such data for the computational elucidation and analysis of cellular pathways and networks is an area of considerable current interest.  ...  This commentary describes some of the recent contributions of chemical engineering researchers to the computational analysis of highthroughput, multi-source data as described in recent publications and  ...  Acknowledgements The authors gratefully acknowledge support from the National Science Foundation (BES 0222747, BES 0331297, and BES 0425821), the Environmental  ... 
doi:10.1080/08927020600647052 fatcat:rluf4kjvubd4xphayjg5brozta

Artefacts in statistical analyses of network motifs: general framework and application to metabolic networks

M. E. Beber, C. Fretter, S. Jain, N. Sonnenschein, M. Muller-Hannemann, M.-T. Hutt
2012 Journal of the Royal Society Interface  
As a case study, we explore the metabolic network of Escherichia coli and show that only by excluding ever more artefacts from the motif signature a strong and plausible correlation with the essentiality  ...  profile of metabolic reactions emerges.  ...  Any study that employs the perspective of network motifs to relate the function to the topology of a network must have strong evidence for the following: (i) the subgraph composition is non-random (compared  ... 
doi:10.1098/rsif.2012.0490 pmid:22896565 pmcid:PMC3481585 fatcat:47zooay6x5ditmdpicelghyrzy

Mathematical optimization applications in metabolic networks

Ali R. Zomorrodi, Patrick F. Suthers, Sridhar Ranganathan, Costas D. Maranas
2012 Metabolic Engineering  
This has spurred the development of a wide array of computational tools, and in particular, mathematical optimization approaches, to assist in fundamental metabolic network analyses and redesign efforts  ...  This review highlights a number of optimization-based frameworks developed towards addressing challenges in the analysis and engineering of metabolic networks.  ...  genome-scale metabolic network leading to the overproduction of a desired chemical.  ... 
doi:10.1016/j.ymben.2012.09.005 pmid:23026121 fatcat:b4l4kokjczakvo6gzerjn6xifu

Open networks from within: input or output betweenness centrality of nodes in directed networks

Taichi Haruna
2018 Applied Network Science  
We also compare them with the existing centrality measures that reflect asymmetry of links in directed networks: out-and in-degrees and Hub and Authority scores.  ...  New betweenness centralities of nodes in a directed network are proposed based on the idea that nodes in a network are processes rather than things.  ...  Availability of data and materials The data set used in this article is available from the cited reference. The result of analysis is available as an Additional file 1.  ... 
doi:10.1007/s41109-018-0076-1 fatcat:2qcjwqvvkzf2jgsn32u5idklsu

A Neural Network-Inspired Matrix Formulation of Chemical Kinetics for Acceleration on GPUs

Shivam Barwey, Venkat Raman
2021 Energies  
The goal of this paper is to recast Arrhenius kinetics as a neural network using matrix-based formulations.  ...  of highly optimized libraries for artificial neural networks used in machine learning, provides a unique pathway for acceleration.  ...  Acknowledgments: This research used resources of the Oak Ridge Leadership Computing Facility, which is a DOE Office of Science User Facility, supported under Contract DE-AC05-00OR22725.  ... 
doi:10.3390/en14092710 fatcat:iuo75twc25cr3d7ma6jwzjmuqe

Challenges and Limitations of Biological Network Analysis

Marianna Milano, Giuseppe Agapito, Mario Cannataro
2022 BioTech  
databases in which they are stored and the alignment algorithms for the comparison of pathways and PPI networks of different organisms.  ...  Otherwise, biological networks such as Protein–Protein Interaction (PPI) Networks, represent the biochemical interactions among proteins by using nodes that model the proteins from a given organism, and  ...  Both LNA and GNA may also be categorized on the basis of the input networks in Pairwise Alignment Algorithms, i.e., algorithms that align two input networks, and Multiple Alignment Algorithms, i.e., algorithms  ... 
doi:10.3390/biotech11030024 pmid:35892929 pmcid:PMC9326688 fatcat:7f5zp3sczzfclbbz6ty3nyremu

A survey on bio-inspired networking

Falko Dressler, Ozgur B. Akan
2010 Computer Networks  
The existing bio-inspired networking and communication protocols and algorithms devised by looking at biology as a source of inspiration, and by mimicking the laws and dynamics governing these systems  ...  to further explore this timely and exciting topic. result will be a pervasive and, in fact, living network extending the current Internet capabilities.  ...  Depicted is the information exchange within a cell, between cells, within the human body, among people, and around the globe Table 1: Categorization of biological phenomena and networking algorithms  ... 
doi:10.1016/j.comnet.2009.10.024 fatcat:hkc3vn42pfdfddkwxff7ojwrzu
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