@article{1477,
  abstract     = {We consider partially observable Markov decision processes (POMDPs) with ω-regular conditions specified as parity objectives. The class of ω-regular languages provides a robust specification language to express properties in verification, and parity objectives are canonical forms to express them. The qualitative analysis problem given a POMDP and a parity objective asks whether there is a strategy to ensure that the objective is satisfied with probability 1 (resp. positive probability). While the qualitative analysis problems are undecidable even for special cases of parity objectives, we establish decidability (with optimal complexity) for POMDPs with all parity objectives under finite-memory strategies. We establish optimal (exponential) memory bounds and EXPTIME-completeness of the qualitative analysis problems under finite-memory strategies for POMDPs with parity objectives. We also present a practical approach, where we design heuristics to deal with the exponential complexity, and have applied our implementation on a number of POMDP examples.},
  author       = {Chatterjee, Krishnendu and Chmelik, Martin and Tracol, Mathieu},
  journal      = {Journal of Computer and System Sciences},
  number       = {5},
  pages        = {878 -- 911},
  publisher    = {Elsevier},
  title        = {{What is decidable about partially observable Markov decision processes with ω-regular objectives}},
  doi          = {10.1016/j.jcss.2016.02.009},
  volume       = {82},
  year         = {2016},
}

@article{1478,
  abstract     = {We consider the Tonks-Girardeau gas subject to a random external potential. If the disorder is such that the underlying one-particle Hamiltonian displays localization (which is known to be generically the case), we show that there is exponential decay of correlations in the many-body eigenstates. Moreover, there is no Bose-Einstein condensation and no superfluidity, even at zero temperature.},
  author       = {Seiringer, Robert and Warzel, Simone},
  journal      = {New Journal of Physics},
  number       = {3},
  publisher    = {IOP Publishing Ltd.},
  title        = {{Decay of correlations and absence of superfluidity in the disordered Tonks-Girardeau gas}},
  doi          = {10.1088/1367-2630/18/3/035002},
  volume       = {18},
  year         = {2016},
}

@article{1479,
  abstract     = {Most entropy notions H(.) like Shannon or min-entropy satisfy a chain rule stating that for random variables X,Z, and A we have H(X|Z,A)≥H(X|Z)−|A|. That is, by conditioning on A the entropy of X can decrease by at most the bitlength |A| of A. Such chain rules are known to hold for some computational entropy notions like Yao’s and unpredictability-entropy. For HILL entropy, the computational analogue of min-entropy, the chain rule is of special interest and has found many applications, including leakage-resilient cryptography, deterministic encryption, and memory delegation. These applications rely on restricted special cases of the chain rule. Whether the chain rule for conditional HILL entropy holds in general was an open problem for which we give a strong negative answer: we construct joint distributions (X,Z,A), where A is a distribution over a single bit, such that the HILL entropy H HILL (X|Z) is large but H HILL (X|Z,A) is basically zero.

Our counterexample just makes the minimal assumption that NP⊈P/poly. Under the stronger assumption that injective one-way function exist, we can make all the distributions efficiently samplable.

Finally, we show that some more sophisticated cryptographic objects like lossy functions can be used to sample a distribution constituting a counterexample to the chain rule making only a single invocation to the underlying object.},
  author       = {Krenn, Stephan and Pietrzak, Krzysztof Z and Wadia, Akshay and Wichs, Daniel},
  journal      = {Computational Complexity},
  number       = {3},
  pages        = {567 -- 605},
  publisher    = {Springer},
  title        = {{A counterexample to the chain rule for conditional HILL entropy}},
  doi          = {10.1007/s00037-015-0120-9},
  volume       = {25},
  year         = {2016},
}

@article{1480,
  abstract     = {Exponential varieties arise from exponential families in statistics. These real algebraic varieties have strong positivity and convexity properties, familiar from toric varieties and their moment maps. Among them are varieties of inverses of symmetric matrices satisfying linear constraints. This class includes Gaussian graphical models. We develop a general theory of exponential varieties. These are derived from hyperbolic polynomials and their integral representations. We compare the multidegrees and ML degrees of the gradient map for hyperbolic polynomials. },
  author       = {Michałek, Mateusz and Sturmfels, Bernd and Uhler, Caroline and Zwiernik, Piotr},
  journal      = {Proceedings of the London Mathematical Society},
  number       = {1},
  pages        = {27 -- 56},
  publisher    = {Oxford University Press},
  title        = {{Exponential varieties}},
  doi          = {10.1112/plms/pdv066},
  volume       = {112},
  year         = {2016},
}

@article{1482,
  abstract     = {Plants have the ability to continously generate new organs by maintaining populations of stem cells throught their lives. The shoot apical meristem (SAM) provides a stable environment for the maintenance of stem cells. All cells inside the SAM divide, yet boundaries and patterns are maintained. Experimental evidence indicates that patterning is independent of cell lineage, thus a dynamic self-regulatory mechanism is required. A pivotal role in the organization of the SAM is played by the WUSCHEL gene (WUS). An important question in this regard is that how WUS expression is positioned in the SAM via a cell-lineage independent signaling mechanism. In this study we demonstrate via mathematical modeling that a combination of an inhibitor of the Cytokinin (CK) receptor, Arabidopsis histidine kinase 4 (AHK4) and two morphogens originating from the top cell layer, can plausibly account for the cell lineage-independent centering of WUS expression within SAM. Furthermore, our laser ablation and microsurgical experiments support the hypothesis that patterning in SAM occurs at the level of CK reception and signaling. The model suggests that the interplay between CK signaling, WUS/CLV feedback loop and boundary signals can account for positioning of the WUS expression, and provides directions for further experimental investigation.},
  author       = {Adibi, Milad and Yoshida, Saiko and Weijers, Dolf and Fleck, Christian},
  journal      = {PLoS One},
  number       = {2},
  publisher    = {Public Library of Science},
  title        = {{Centering the organizing center in the Arabidopsis thaliana shoot apical meristem by a combination of cytokinin signaling and self-organization}},
  doi          = {10.1371/journal.pone.0147830},
  volume       = {11},
  year         = {2016},
}

@article{1484,
  author       = {Chen, Xu and Wu, Shuang and Liu, Zengyu and Friml, Jiřĺ},
  journal      = {Trends in Cell Biology},
  number       = {6},
  pages        = {409 -- 419},
  publisher    = {Cell Press},
  title        = {{Environmental and endogenous control of cortical microtubule orientation}},
  doi          = {10.1016/j.tcb.2016.02.003},
  volume       = {26},
  year         = {2016},
}

@article{1485,
  abstract     = {In this article the notion of metabolic turnover is revisited in the light of recent results of out-of-equilibrium thermodynamics. By means of Monte Carlo methods we perform an exact sampling of the enzymatic fluxes in a genome scale metabolic network of E. Coli in stationary growth conditions from which we infer the metabolites turnover times. However the latter are inferred from net fluxes, and we argue that this approximation is not valid for enzymes working nearby thermodynamic equilibrium. We recalculate turnover times from total fluxes by performing an energy balance analysis of the network and recurring to the fluctuation theorem. We find in many cases values one of order of magnitude lower, implying a faster picture of intermediate metabolism.},
  author       = {De Martino, Daniele},
  journal      = {Physical Biology},
  number       = {1},
  publisher    = {IOP Publishing Ltd.},
  title        = {{Genome-scale estimate of the metabolic turnover of E. Coli from the energy balance analysis}},
  doi          = {10.1088/1478-3975/13/1/016003},
  volume       = {13},
  year         = {2016},
}

@article{1486,
  abstract     = {We review recent results concerning the mathematical properties of the Bardeen-Cooper-Schrieffer (BCS) functional of superconductivity, which were obtained in a series of papers, partly in collaboration with R. Frank, E. Hamza, S. Naboko, and J. P. Solovej. Our discussion includes, in particular, an investigation of the critical temperature for a general class of interaction potentials, as well as a study of its dependence on external fields. We shall explain how the Ginzburg-Landau model can be derived from the BCS theory in a suitable parameter regime.},
  author       = {Hainzl, Christian and Seiringer, Robert},
  journal      = {Journal of Mathematical Physics},
  number       = {2},
  publisher    = {American Institute of Physics},
  title        = {{The Bardeen–Cooper–Schrieffer functional of superconductivity and its mathematical properties}},
  doi          = {10.1063/1.4941723},
  volume       = {57},
  year         = {2016},
}

@article{1487,
  abstract     = {Rhythms with time scales of multiple cycles per second permeate the mammalian brain, yet neuroscientists are not certain of their functional roles. One leading idea is that coherent oscillation between two brain regions facilitates the exchange of information between them. In rats, the hippocampus and the vibrissal sensorimotor system both are characterized by rhythmic oscillation in the theta range, 5–12 Hz. Previous work has been divided as to whether the two rhythms are independent or coherent. To resolve this question, we acquired three measures from rats—whisker motion, hippocampal local field potential (LFP), and barrel cortex unit firing—during a whisker-mediated texture discrimination task and during control conditions (not engaged in a whisker-mediated memory task). Compared to control conditions, the theta band of hippocampal LFP showed a marked increase in power as the rats approached and then palpated the texture. Phase synchronization between whisking and hippocampal LFP increased by almost 50% during approach and texture palpation. In addition, a greater proportion of barrel cortex neurons showed firing that was phase-locked to hippocampal theta while rats were engaged in the discrimination task. Consistent with a behavioral consequence of phase synchronization, the rats identified the texture more rapidly and with lower error likelihood on trials in which there was an increase in theta-whisking coherence at the moment of texture palpation. These results suggest that coherence between the whisking rhythm, barrel cortex firing, and hippocampal LFP is augmented selectively during epochs in which the rat collects sensory information and that such coherence enhances the efficiency of integration of stimulus information into memory and decision-making centers.},
  author       = {Grion, Natalia and Akrami, Athena and Zuo, Yangfang and Stella, Federico and Diamond, Mathew},
  journal      = {PLoS Biology},
  number       = {2},
  publisher    = {Public Library of Science},
  title        = {{Coherence between rat sensorimotor system and hippocampus is enhanced during tactile discrimination}},
  doi          = {10.1371/journal.pbio.1002384},
  volume       = {14},
  year         = {2016},
}

@article{1488,
  abstract     = {Branching morphogenesis of the epithelial ureteric bud forms the renal collecting duct system and is critical for normal nephron number, while low nephron number is implicated in hypertension and renal disease. Ureteric bud growth and branching requires GDNF signaling from the surrounding mesenchyme to cells at the ureteric bud tips, via the Ret receptor tyrosine kinase and coreceptor Gfrα1; Ret signaling up-regulates transcription factors Etv4 and Etv5, which are also critical for branching. Despite extensive knowledge of the genetic control of these events, it is not understood, at the cellular level, how renal branching morphogenesis is achieved or how Ret signaling influences epithelial cell behaviors to promote this process. Analysis of chimeric embryos previously suggested a role for Ret signaling in promoting cell rearrangements in the nephric duct, but this method was unsuited to study individual cell behaviors during ureteric bud branching. Here, we use Mosaic Analysis with Double Markers (MADM), combined with organ culture and time-lapse imaging, to trace the movements and divisions of individual ureteric bud tip cells. We first examine wild-type clones and then Ret or Etv4 mutant/wild-type clones in which the mutant and wild-type sister cells are differentially and heritably marked by green and red fluorescent proteins. We find that, in normal kidneys, most individual tip cells behave as self-renewing progenitors, some of whose progeny remain at the tips while others populate the growing UB trunks. In Ret or Etv4 MADM clones, the wild-type cells generated at a UB tip are much more likely to remain at, or move to, the new tips during branching and elongation, while their Ret−/− or Etv4−/− sister cells tend to lag behind and contribute only to the trunks. By tracking successive mitoses in a cell lineage, we find that Ret signaling has little effect on proliferation, in contrast to its effects on cell movement. Our results show that Ret/Etv4 signaling promotes directed cell movements in the ureteric bud tips, and suggest a model in which these cell movements mediate branching morphogenesis.},
  author       = {Riccio, Paul and Cebrián, Cristina and Zong, Hui and Hippenmeyer, Simon and Costantini, Frank},
  journal      = {PLoS Biology},
  number       = {2},
  publisher    = {Public Library of Science},
  title        = {{Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis}},
  doi          = {10.1371/journal.pbio.1002382},
  volume       = {14},
  year         = {2016},
}

@article{1489,
  abstract     = {We prove optimal local law, bulk universality and non-trivial decay for the off-diagonal elements of the resolvent for a class of translation invariant Gaussian random matrix ensembles with correlated entries. },
  author       = {Ajanki, Oskari H and Erdös, László and Krüger, Torben H},
  journal      = {Journal of Statistical Physics},
  number       = {2},
  pages        = {280 -- 302},
  publisher    = {Springer},
  title        = {{Local spectral statistics of Gaussian matrices with correlated entries}},
  doi          = {10.1007/s10955-016-1479-y},
  volume       = {163},
  year         = {2016},
}

@article{1490,
  abstract     = {To induce adaptive immunity, dendritic cells (DCs) migrate through afferent lymphatic vessels (LVs) to draining lymph nodes (dLNs). This process occurs in several consecutive steps. Upon entry into lymphatic capillaries, DCs first actively crawl into downstream collecting vessels. From there, they are next passively and rapidly transported to the dLN by lymph flow. Here, we describe a role for the chemokine CCL21 in intralymphatic DC crawling. Performing time-lapse imaging in murine skin, we found that blockade of CCL21-but not the absence of lymph flow-completely abolished DC migration from capillaries toward collecting vessels and reduced the ability of intralymphatic DCs to emigrate from skin. Moreover, we found that in vitro low laminar flow established a CCL21 gradient along lymphatic endothelial monolayers, thereby inducing downstream-directed DC migration. These findings reveal a role for intralymphatic CCL21 in promoting DC trafficking to dLNs, through the formation of a flow-induced gradient.},
  author       = {Russo, Erica and Teijeira, Alvaro and Vaahtomeri, Kari and Willrodt, Ann and Bloch, Joël and Nitschké, Maximilian and Santambrogio, Laura and Kerjaschki, Dontscho and Sixt, Michael K and Halin, Cornelia},
  journal      = {Cell Reports},
  number       = {7},
  pages        = {1723 -- 1734},
  publisher    = {Cell Press},
  title        = {{Intralymphatic CCL21 promotes tissue egress of dendritic cells through afferent lymphatic vessels}},
  doi          = {10.1016/j.celrep.2016.01.048},
  volume       = {14},
  year         = {2016},
}

@article{1491,
  abstract     = {We study the ground state of a trapped Bose gas, starting from the full many-body Schrödinger Hamiltonian, and derive the non-linear Schrödinger energy functional in the limit of a large particle number, when the interaction potential converges slowly to a Dirac delta function. Our method is based on quantitative estimates on the discrepancy between the full many-body energy and its mean-field approximation using Hartree states. These are proved using finite dimensional localization and a quantitative version of the quantum de Finetti theorem. Our approach covers the case of attractive interactions in the regime of stability. In particular, our main new result is a derivation of the 2D attractive non-linear Schrödinger ground state.},
  author       = {Lewin, Mathieu and Nam, Phan and Rougerie, Nicolas},
  journal      = {Transactions of the American Mathematical Society},
  number       = {9},
  pages        = {6131 -- 6157},
  publisher    = {American Mathematical Society},
  title        = {{The mean-field approximation and the non-linear Schrödinger functional for trapped Bose gases}},
  doi          = {10.1090/tran/6537},
  volume       = {368},
  year         = {2016},
}

@article{1492,
  abstract     = {To sustain a lifelong ability to initiate organs, plants retain pools of undifferentiated cells with a preserved prolif eration capacity. The root pericycle represents a unique tissue with conditional meristematic activity, and its tight control determines initiation of lateral organs. Here we show that the meristematic activity of the pericycle is constrained by the interaction with the adjacent endodermis. Release of these restraints by elimination of endo dermal cells by single-cell ablation triggers the pericycle to re-enter the cell cycle. We found that endodermis removal substitutes for the phytohormone auxin-dependent initiation of the pericycle meristematic activity. However, auxin is indispensable to steer the cell division plane orientation of new organ-defining divisions. We propose a dual, spatiotemporally distinct role for auxin during lateral root initiation. In the endodermis, auxin releases constraints arising from cell-to-cell interactions that compromise the pericycle meristematic activity, whereas, in the pericycle, auxin defines the orientation of the cell division plane to initiate lateral roots.},
  author       = {Marhavy, Peter and Montesinos López, Juan C and Abuzeineh, Anas and Van Damme, Daniël and Vermeer, Joop and Duclercq, Jérôme and Rakusova, Hana and Marhavá, Petra and Friml, Jirí and Geldner, Niko and Benková, Eva},
  journal      = {Genes and Development},
  number       = {4},
  pages        = {471 -- 483},
  publisher    = {Cold Spring Harbor Laboratory Press},
  title        = {{Targeted cell elimination reveals an auxin-guided biphasic mode of lateral root initiation}},
  doi          = {10.1101/gad.276964.115},
  volume       = {30},
  year         = {2016},
}

@article{1493,
  abstract     = {We introduce a new method for deriving the time-dependent Hartree or Hartree-Fock equations as an effective mean-field dynamics from the microscopic Schrödinger equation for fermionic many-particle systems in quantum mechanics. The method is an adaption of the method used in Pickl (Lett. Math. Phys. 97 (2) 151–164 2011) for bosonic systems to fermionic systems. It is based on a Gronwall type estimate for a suitable measure of distance between the microscopic solution and an antisymmetrized product state. We use this method to treat a new mean-field limit for fermions with long-range interactions in a large volume. Some of our results hold for singular attractive or repulsive interactions. We can also treat Coulomb interaction assuming either a mild singularity cutoff or certain regularity conditions on the solutions to the Hartree(-Fock) equations. In the considered limit, the kinetic and interaction energy are of the same order, while the average force is subleading. For some interactions, we prove that the Hartree(-Fock) dynamics is a more accurate approximation than a simpler dynamics that one would expect from the subleading force. With our method we also treat the mean-field limit coupled to a semiclassical limit, which was discussed in the literature before, and we recover some of the previous results. All results hold for initial data close (but not necessarily equal) to antisymmetrized product states and we always provide explicit rates of convergence.},
  author       = {Petrat, Sören P and Pickl, Peter},
  journal      = {Mathematical Physics, Analysis and Geometry},
  number       = {1},
  publisher    = {Springer},
  title        = {{A new method and a new scaling for deriving fermionic mean-field dynamics}},
  doi          = {10.1007/s11040-016-9204-2},
  volume       = {19},
  year         = {2016},
}

@article{1496,
  abstract     = {The two-photon 1s2 2s 2p 3P0 1s22s2 1S0 transition in berylliumlike ions is theoretically investigated within a fully relativistic framework and a second-order perturbation theory. We focus our analysis on how electron correlation, as well as the negative-energy spectrum, can affect the forbidden E1M1 decay rate. For this purpose, we include the electronic correlation via an effective local potential and within a single configuration-state model. Due to its experimental interest, evaluations of decay rates are performed for berylliumlike xenon and uranium. We find that the negative-energy contribution can be neglected at the present level of accuracy in the evaluation of the decay rate. On the other hand, if contributions of electronic correlation are not carefully taken into account, it may change the lifetime of the metastable state by up to 20%. By performing a full-relativistic jj-coupling calculation, we found a decrease of the decay rate by two orders of magnitude compared to non-relativistic LS-coupling calculations, for the selected heavy ions.},
  author       = {Amaro, Pedro and Fratini, Filippo and Safari, Laleh and Machado, Jorge and Guerra, Mauro and Indelicato, Paul and Santos, José},
  journal      = {Physical Review A - Atomic, Molecular, and Optical Physics},
  number       = {3},
  publisher    = {American Physical Society},
  title        = {{Relativistic evaluation of the two-photon decay of the metastable 1s22s2p3P0 state in berylliumlike ions with an effective-potential model}},
  doi          = {10.1103/PhysRevA.93.032502},
  volume       = {93},
  year         = {2016},
}

@article{1518,
  abstract     = {The inference of demographic history from genome data is hindered by a lack of efficient computational approaches. In particular, it has proved difficult to exploit the information contained in the distribution of genealogies across the genome. We have previously shown that the generating function (GF) of genealogies can be used to analytically compute likelihoods of demographic models from configurations of mutations in short sequence blocks (Lohse et al. 2011). Although the GF has a simple, recursive form, the size of such likelihood calculations explodes quickly with the number of individuals and applications of this framework have so far been mainly limited to small samples (pairs and triplets) for which the GF can be written by hand. Here we investigate several strategies for exploiting the inherent symmetries of the coalescent. In particular, we show that the GF of genealogies can be decomposed into a set of equivalence classes that allows likelihood calculations from nontrivial samples. Using this strategy, we automated blockwise likelihood calculations for a general set of demographic scenarios in Mathematica. These histories may involve population size changes, continuous migration, discrete divergence, and admixture between multiple populations. To give a concrete example, we calculate the likelihood for a model of isolation with migration (IM), assuming two diploid samples without phase and outgroup information. We demonstrate the new inference scheme with an analysis of two individual butterfly genomes from the sister species Heliconius melpomene rosina and H. cydno.},
  author       = {Lohse, Konrad and Chmelik, Martin and Martin, Simon and Barton, Nicholas H},
  journal      = {Genetics},
  number       = {2},
  pages        = {775 -- 786},
  publisher    = {Genetics Society of America},
  title        = {{Efficient strategies for calculating blockwise likelihoods under the coalescent}},
  doi          = {10.1534/genetics.115.183814},
  volume       = {202},
  year         = {2016},
}

@article{1522,
  abstract     = {We classify smooth Brunnian (i.e., unknotted on both components) embeddings (S2 × S1) ⊔ S3 → ℝ6. Any Brunnian embedding (S2 × S1) ⊔ S3 → ℝ6 is isotopic to an explicitly constructed embedding fk,m,n for some integers k, m, n such that m ≡ n (mod 2). Two embeddings fk,m,n and fk′ ,m′,n′ are isotopic if and only if k = k′, m ≡ m′ (mod 2k) and n ≡ n′ (mod 2k). We use Haefliger’s classification of embeddings S3 ⊔ S3 → ℝ6 in our proof. The relation between the embeddings (S2 × S1) ⊔ S3 → ℝ6 and S3 ⊔ S3 → ℝ6 is not trivial, however. For example, we show that there exist embeddings f: (S2 ×S1) ⊔ S3 → ℝ6 and g, g′ : S3 ⊔ S3 → ℝ6 such that the componentwise embedded connected sum f # g is isotopic to f # g′ but g is not isotopic to g′.},
  author       = {Avvakumov, Serhii},
  issn         = {1609-4514},
  journal      = {Moscow Mathematical Journal},
  number       = {1},
  pages        = {1 -- 25},
  publisher    = {Independent University of Moscow},
  title        = {{The classification of certain linked 3-manifolds in 6-space}},
  doi          = {10.17323/1609-4514-2016-16-1-1-25},
  volume       = {16},
  year         = {2016},
}

@article{1523,
  abstract     = {For random graphs, the containment problem considers the probability that a binomial random graph G(n, p) contains a given graph as a substructure. When asking for the graph as a topological minor, i.e., for a copy of a subdivision of the given graph, it is well known that the (sharp) threshold is at p = 1/n. We consider a natural analogue of this question for higher-dimensional random complexes Xk(n, p), first studied by Cohen, Costa, Farber and Kappeler for k = 2. Improving previous results, we show that p = Θ(1/ √n) is the (coarse) threshold for containing a subdivision of any fixed complete 2-complex. For higher dimensions k > 2, we get that p = O(n−1/k) is an upper bound for the threshold probability of containing a subdivision of a fixed k-dimensional complex.},
  author       = {Gundert, Anna and Wagner, Uli},
  journal      = {Proceedings of the American Mathematical Society},
  number       = {4},
  pages        = {1815 -- 1828},
  publisher    = {American Mathematical Society},
  title        = {{On topological minors in random simplicial complexes}},
  doi          = {10.1090/proc/12824},
  volume       = {144},
  year         = {2016},
}

@inproceedings{1524,
  abstract     = {When designing genetic circuits, the typical primitives used in major existing modelling formalisms are gene interaction graphs, where edges between genes denote either an activation or inhibition relation. However, when designing experiments, it is important to be precise about the low-level mechanistic details as to how each such relation is implemented. The rule-based modelling language Kappa allows to unambiguously specify mechanistic details such as DNA binding sites, dimerisation of transcription factors, or co-operative interactions. Such a detailed description comes with complexity and computationally costly executions. We propose a general method for automatically transforming a rule-based program, by eliminating intermediate species and adjusting the rate constants accordingly. To the best of our knowledge, we show the first automated reduction of rule-based models based on equilibrium approximations.
Our algorithm is an adaptation of an existing algorithm, which was designed for reducing reaction-based programs; our version of the algorithm scans the rule-based Kappa model in search for those interaction patterns known to be amenable to equilibrium approximations (e.g. Michaelis-Menten scheme). Additional checks are then performed in order to verify if the reduction is meaningful in the context of the full model. The reduced model is efficiently obtained by static inspection over the rule-set. The tool is tested on a detailed rule-based model of a λ-phage switch, which lists 92 rules and 13 agents. The reduced model has 11 rules and 5 agents, and provides a dramatic reduction in simulation time of several orders of magnitude.},
  author       = {Beica, Andreea and Guet, Calin C and Petrov, Tatjana},
  location     = {Madrid, Spain},
  pages        = {173 -- 191},
  publisher    = {Springer},
  title        = {{Efficient reduction of kappa models by static inspection of the rule-set}},
  doi          = {10.1007/978-3-319-26916-0_10},
  volume       = {9271},
  year         = {2016},
}