Time-freeness and Clock-freeness and Related Concepts in P Systems

In the majority of models of P systems, rules are applied at the ticks of a global clock and their products are introduced into the system for the following step. In timed P systems, di erent integer durations are statically assigned to rules; time-free P systems are P systems yielding the same languages independently of these durations. In clock-free P systems, durations are real and are assigned to individual rule applications; thus, different applications of the same rule may last for a different amount of time. In this paper, we formalise timed, time-free, and clock-free P system within a framework for generalised parallel rewriting. We then explore the relationship between these variants of semantics. We show that clock-free P systems cannot effi ciently solve intractable problems. Moreover, we consider un-timed systems where we collect the results using arbitrary timing functions as well as un-clocked P systems where we take the union over all possible per-instance rule durations. Finally, we also introduce and study mode-free P systems, whose results do not depend on the choice of a mode within a fixed family of modes, and compare mode-freeness with clock-freeness

P Systems with Active Membranes and Two Polarizations

P systems with active membranes using only two electrical charges and only rules of types (a) and (c) assigned to at most two membranes are shown to be computationally complete { thus improving the previous result of this type from the point of view of the number of polarizations as well as with respect to the number of membranes. Allowing a special variant of rules of type (c) to delete symbols by sending them out, even only one membrane is needed. Moreover, we present an algorithm for deterministically deciding SAT in linear time using only two polarizations and global rules of types (a) ; (c), and (e)

Scaling properties of a ferromagnetic thin film model at the depinning transition

In this paper, we perform a detailed study of the scaling properties of a ferromagnetic thin film model. Recently, interest has increased in the scaling properties of the magnetic domain wall (MDW) motion in disordered media when an external driving field is present. We consider a (1+1)-dimensional model, based on evolution rules, able to describe the MDW avalanches. The global interface width of this model shows Family-Vicsek scaling with roughness exponent $\zeta\simeq 1.585$ and growth exponent $\beta\simeq 0.975$. In contrast, this model shows scaling anomalies in the interface local properties characteristic of other systems with depinning transition of the MDW, e.g. quenched Edwards-Wilkinson (QEW) equation and random-field Ising model (RFIM) with driving. We show that, at the depinning transition, the saturated average velocity $v_\mathrm{sat}\sim f^\theta$ vanished very slowly (with $\theta\simeq 0.037$) when the reduced force $f=p/p_\mathrm{c}-1\to 0^{+}$. The simulation results show that this model verifies all accepted scaling relations which relate the global exponents and the correlation length (or time) exponents, valid in systems with depinning transition. Using the interface tilting method, we show that the model, close to the depinning transition, exhibits a nonlinearity similar to the one included in the Kardar-Parisi-Zhang (KPZ) equation. The nonlinear coefficient $\lambda\sim f^{-\phi}$ with $\phi\simeq -1.118$, which implies that $\lambda\to 0$ as the depinning transition is approached, a similar qualitatively behaviour to the driven RFIM. We conclude this work by discussing the main features of the model and the prospects opened by it.Comment: 10 pages, 5 figures, 1 tabl

RuleMonkey: software for stochastic simulation of rule-based models

<p>Abstract</p> <p>Background</p> <p>The system-level dynamics of many molecular interactions, particularly protein-protein interactions, can be conveniently represented using reaction rules, which can be specified using model-specification languages, such as the BioNetGen language (BNGL). A set of rules implicitly defines a (bio)chemical reaction network. The reaction network implied by a set of rules is often very large, and as a result, generation of the network implied by rules tends to be computationally expensive. Moreover, the cost of many commonly used methods for simulating network dynamics is a function of network size. Together these factors have limited application of the rule-based modeling approach. Recently, several methods for simulating rule-based models have been developed that avoid the expensive step of network generation. The cost of these "network-free" simulation methods is independent of the number of reactions implied by rules. Software implementing such methods is now needed for the simulation and analysis of rule-based models of biochemical systems.</p> <p>Results</p> <p>Here, we present a software tool called RuleMonkey, which implements a network-free method for simulation of rule-based models that is similar to Gillespie's method. The method is suitable for rule-based models that can be encoded in BNGL, including models with rules that have global application conditions, such as rules for intramolecular association reactions. In addition, the method is rejection free, unlike other network-free methods that introduce null events, i.e., steps in the simulation procedure that do not change the state of the reaction system being simulated. We verify that RuleMonkey produces correct simulation results, and we compare its performance against DYNSTOC, another BNGL-compliant tool for network-free simulation of rule-based models. We also compare RuleMonkey against problem-specific codes implementing network-free simulation methods.</p> <p>Conclusions</p> <p>RuleMonkey enables the simulation of rule-based models for which the underlying reaction networks are large. It is typically faster than DYNSTOC for benchmark problems that we have examined. RuleMonkey is freely available as a stand-alone application <url>http://public.tgen.org/rulemonkey</url>. It is also available as a simulation engine within GetBonNie, a web-based environment for building, analyzing and sharing rule-based models.</p

Logic of the Powers:Towards an Impact-driven Practice of Futurist Statecraft

What global future would ensure hope, justice and peace to the human mankind? In view of a fast evolving post-Covid world order, this volume explores a novel Christian post-colonial approach to global affairs. It examines the existing 'sociology of the powers' theoretical scheme, the debate between Christian realism and Christian pacifism, the method and practice of prophetic witnessing, to elaborate a new Christian approach to statecraft and futurology in terms of theory, methodology and ontology. This book: Uses the COVID-19 pandemic as the background to examine why and how the pandemic has accelerated the US's decline, and to identify the tacit game rules that contributed to the UK government's mishandling of the pandemic; Compares the political systems between China and the West, and engages with selected theoretical narratives from the Global South to envision an alternative 'shared globalisation' project; Argues why it is important for post-colonial Christian individuals and communities to get involved in this global discussion for a new world order of complex realist interdependencies grounded on hope, social justice and peace. A fresh take on global politics and international relations, this volume will be of great interest to scholars and researchers of political science, religious studies, peace studies, theology and future studies.</p

Resolution with Symmetry Rule Applied to Linear Equations

This paper considers the length of resolution proofs when using Krishnamurthy's classic symmetry rules. We show that inconsistent linear equation systems of bounded width over a fixed finite field $\mathbb{F}_p$ with $p$ a prime have, in their standard encoding as CNFs, polynomial length resolutions when using the local symmetry rule (SRC-II). As a consequence it follows that the multipede instances for the graph isomorphism problem encoded as CNF formula have polynomial length resolution proofs. This contrasts exponential lower bounds for individualization-refinement algorithms on these graphs. For the Cai-F\"urer-Immerman graphs, for which Tor\'an showed exponential lower bounds for resolution proofs (SAT 2013), we also show that already the global symmetry rule (SRC-I) suffices to allow for polynomial length proofs.Comment: 18 pages, to be published in STACS 202

A Model of Antibiotic Resistance Evolution Dynamics Through P Systems with Active Membranes and Communication Rules

Baquero, F.; Campos Frances, M.; Llorens, C.; Sempere Luna, JM. (2018). A Model of Antibiotic Resistance Evolution Dynamics Through P Systems with Active Membranes and Communication Rules. Lecture Notes in Computer Science. 11270:33-44. https://doi.org/10.1007/978-3-030-00265-7_3S334411270Barbacari, N., Profir, A., Zelinschi, C.: Gene regulatory network modeling by means of membrane computing. In: Proceedings of the 7th International Workshop on Membrane Computing WMC 2006. LNCS, vol. 4361, pp. 162–178 (2006)Besozzi, D., Cazzaniga, P., Cocolo, S., Mauri, G., Pescini, D.: Modeling diffusion in a signal transduction pathway: the use of virtual volumes in P systems. Int. J. Found. Comput. Sci. 22(1), 89–96 (2011)Campos, M.: A membrane computing simulator of trans-hierarchical antibiotic resistance evolution dynamics in nested ecological compartments (ARES). Biol. Direct 10(1), 41 (2015)Ciobanu, G., Păun, Gh., Pérez-Jiménez, M.J.: Applications of Membrane Computing. Springer, Heidelberg (2006). https://doi.org/10.1007/3-540-29937-8Colomer, M.A., Margalida, A., Sanuy, D., Pérez-Jiménez, M.J.: A bio-inspired model as a new tool for modeling ecosystems: the avian scavengeras a case study. Ecol. Model. 222(1), 33–47 (2011)Colomer, M.A., Martínez-del-Amor, M.A., Pérez-Hurtado, I., Pérez-Jiménez, M.J., Riscos-Núñez, A.: A uniform framework for modeling based on P systems. In: Li, K., Nagar, A.K., Thamburaj, R. (eds.) IEEE Fifth International Conference on Bio-Inspired Computing: Theories and Applications (BIC-TA 2010), vol. 1, pp. 616–621 (2010)Dassow, J., Păun, Gh.: On the power of membrane computing. TUCS Technical Report No. 217 (1998)Frisco, P., Gheorghe, M., Pérez-Jiménez, M.J. (eds.): Applications of Membrane Computing in Systems and Synthetic Biology. ECC, vol. 7. Springer, Cham (2014). https://doi.org/10.1007/978-3-319-03191-0Păun, Gh.: Computing with membranes. J. Comput. Syst. Sci. 61(1), 108–143 (2000)Păun, Gh.: Membrane Computing: An Introduction. Springer, Heidelberg (2002). https://doi.org/10.1007/978-3-642-56196-2Păun, Gh., Rozenberg, G., Salomaa, A. (eds.): The Oxford Handbook of Membrane Computing. Oxford University Press, Oxford (2010)World Health Organization: Antimicrobial Resistance: Global Report on Surveillance (2014

Geometric and harmonic means based priority dispatching rules for single machine scheduling problems

[EN] This work proposes two new prority dispatching rules (PDRs) for solving single machine scheduling problems. These rules are based on the geometric mean (GM) and harmonic mean (HM) of the processing time (PT) and the due date (DD) and they are referred to as GMPD and HMPD respectively. Performance of the proposed PDRs is evaluated on the basis of five measures/criteria i.e. Total Flow Time (TFT), Total Lateness (TL), Number of Late Jobs (TNL), Total Earliness (TE) and Number of Early Parts (TNE). It is found that GMPD performs better than other PDRs in achieving optimal values of multiple performance measures. Further, effect of variation in the weight assigned to PT and DD on the combined performance of TFT and TL is also examined which reveals that for deriving optimal values of TFT and TL, weighted harmonic mean (WHMPD) rule with a weight of 0.105 outperforms other PDRs. The weighted geometric mean (WGMPD) rule with a weight of 0.37 is found to be the next after WHMPD followed by the weighted PDT i.e. WPDT rule with a weight of 0.76.Ahmad, S.; Khan, ZA.; Ali, M.; Asjad, M. (2021). Geometric and harmonic means based priority dispatching rules for single machine scheduling problems. International Journal of Production Management and Engineering. 9(2):93-102. https://doi.org/10.4995/ijpme.2021.15217OJS9310292Baharom, M. Z., Nazdah, W., &Hussin, W. (2015). Scheduling Analysis for Job Sequencing in Veneer Lamination Line. Journal of Industrial and Intelligent Information, 3(3). https://doi.org/10.12720/jiii.3.3.181-185Chan, F. T. S., Chan, H. K., Lau, H. C. W., & Ip, R. W. L. (2003). Analysis of dynamic dispatching rules for a flexible manufacturing system. Journal of Materials Processing Technology, 138(1), 325-331. https://doi.org/10.1016/S0924-0136(03)00093-1Cheng, T. C. E., &Kahlbacher, H. G. (1993). Single-machine scheduling to minimize earliness and number of tardy jobs. Journal of Optimization Theory and Applications, 77(3), 563-573. https://doi.org/10.1007/BF00940450da Silva, N. C. O., Scarpin, C. T., Pécora, J. E., & Ruiz, A. (2019). Online single machine scheduling with setup times depending on the jobs sequence. Computers & Industrial Engineering, 129, 251-258. https://doi.org/10.1016/j.cie.2019.01.038Doh, H.H., Yu, J.M., Kim, J.S., Lee, D.H., & Nam, S.H. (2013). A priority scheduling approach for flexible job shops with multiple process plans. International Journal of Production Research, 51(12), 3748-3764. https://doi.org/10.1080/00207543.2013.765074Dominic, Panneer D. D., Kaliyamoorthy, S., & Kumar, M. S. (2004). Efficient dispatching rules for dynamic job shop scheduling. The International Journal of Advanced Manufacturing Technology, 24(1), 70-75.Ðurasević, M., &Jakobović, D. (2018). A survey of dispatching rules for the dynamic unrelated machines environment. 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Global Journal of Flexible Systems Management, 20(3), 267-290. https://doi.org/10.1007/s40171-019-00214-9Jayamohan, M. S., & Rajendran, C. (2000). New dispatching rules for shop scheduling: A step forward. International Journal of Production Research, 38(3), 563-586. https://doi.org/10.1080/002075400189301Kadipasaoglu, S. N., Xiang, W., &Khumawala, B. M. (1997). A comparison of sequencing rules in static and dynamic hybrid flow systems. International Journal of Production Research, 35(5), 1359-1384. https://doi.org/10.1080/002075497195371Kanet, J. J., & Li, X. (2004). A Weighted Modified Due Date Rule for Sequencing to Minimize Weighted Tardiness. Journal of Scheduling, 7(4), 261-276. https://doi.org/10.1023/B:JOSH.0000031421.64487.95Lee, D.K., Shin, J.H., & Lee, D.H. (2020). Operations scheduling for an advanced flexible manufacturing system with multi-fixturing pallets. 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Planning and Scheduling in Manufacturing and Services (2nd ed.). Springer-Verlag. https://doi.org/10.1007/978-1-4419-0910-7Prakash, A., Chan, F. T. S., & Deshmukh, S. G. (2011). FMS scheduling with knowledge based genetic algorithm approach. Expert Systems with Applications, 38(4), 3161-3171. https://doi.org/10.1016/j.eswa.2010.09.002Rafsanjani, M. K., &Bardsiri, A. K. (2012). A New Heuristic Approach for Scheduling Independent Tasks on Heterogeneous Computing Systems. International Journal of Machine Learning and Computing, 371-376. https://doi.org/10.7763/IJMLC.2012.V2.147Tyagi, N., Tripathi, R. P., &Chandramouli, A. B. (2016). Single Machine Scheduling Model with Total Tardiness Problem. Indian Journal of Science and Technology, 9(37). https://doi.org/10.17485/ijst/2016/v9i37/97527Vinod, V., & Sridharan, R. (2008). Dynamic job-shop scheduling with sequence-dependent setup times: Simulation modeling and analysis. 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A Calculus of Looping Sequences with Local Rules

In this paper we present a variant of the Calculus of Looping Sequences (CLS for short) with global and local rewrite rules. While global rules, as in CLS, are applied anywhere in a given term, local rules can only be applied in the compartment on which they are defined. Local rules are dynamic: they can be added, moved and erased. We enrich the new calculus with a parallel semantics where a reduction step is lead by any number of global and local rules that could be performed in parallel. A type system is developed to enforce the property that a compartment must contain only local rules with specific features. As a running example we model some interactions happening in a cell starting from its nucleus and moving towards its mitochondria.Comment: In Proceedings DCM 2011, arXiv:1207.682