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Raymond Devillers
Antti Valmari (Eds.)
Application and Theory

LNCS 9115
of Petri Nets
and Concurrency
36th International Conference, PETRI NETS 2015
Brussels, Belgium, June 21–26, 2015
Proceedings
123
Lecture Notes in Computer Science 9115
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Raymond Devillers · Antti Valmari (Eds.)
Application and Theory

of Petri Nets
and Concurrency
36th International Conference, PETRI NETS 2015
Brussels, Belgium, June 21–26, 2015
Proceedings
ABC
Editors
Raymond Devillers Antti Valmari
Université Libre de Bruxelles Tampere University of Technology
Brussels Tampere
Belgium Finland
ISSN 0302-9743 ISSN 1611-3349 (electronic)

Lecture Notes in Computer Science
ISBN 978-3-319-19487-5 ISBN 978-3-319-19488-2 (eBook)
DOI 10.1007/978-3-319-19488-2
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Preface
This volume constitutes the proceedings of the 36th International Conference on Ap-
plication and Theory of Petri Nets and Concurrency (Petri Nets 2015). This series of
conferences serves as an annual meeting place to discuss progress in the field of Petri
nets and related models of concurrency. These conferences provide a forum for re-
searchers to present and discuss both applications and theoretical developments in this
area. Novel tools and substantial enhancements to existing tools can also be presented.
This year, the satellite program of the conference comprised four workshops, two Petri
net courses, two advanced tutorials, and a model checking contest.
Petri Nets 2015 was co-located with the Application of Concurrency to Sys-
tem Design Conference (ACSD 2015). Both were organized by the Département
d’Informatique (Science Faculty) of the Université Libre de Bruxelles (ULB) and took
place in Brussels, Belgium, June 21–26, 2015. We would like to express our deepest
thanks to the Organizing Committee chaired by Gilles Geeraerts for the time and effort
invested in the local organization of the conference.
This year, 30 regular papers and four tool papers were submitted to Petri Nets 2015.
The authors of the submitted papers represented 21 different countries. We thank all the
authors. Each paper was reviewed by at least three reviewers. The Program Committee
(PC) meeting took place electronically, using the EasyChair conference system for the
paper selection process. The PC selected 12 regular papers and two tool papers for
presentation. After the conference, some authors were invited to submit an extended
version of their contribution for consideration in a special issue of the Fundamenta
Informaticae journal.
We thank the PC members and other reviewers for their careful and timely eval-
uation of the submissions before the meeting, and the fruitful discussions during the
electronic meeting. The Springer LNCS team and the EasyChair system provided ex-
cellent support in the preparation of this volume.
We are also grateful to the invited speakers for their contribution:
Robert Lorenz (Modeling Quantitative Aspects of Concurrent Systems using
Weighted Petri Net Transducers)
Marlon Dumas (Process Mining Reloaded: Event Structures as a Unified Represen-
tation of Process Models and Event Logs)
Marta Kwiatkowska (On Quantitative Modelling and Verification of DNA Walker
Circuits Using Stochastic Petri nets)
June 2015 Raymond Devillers

Antti Valmari
Organization
Steering Committee
W. van der Aalst,
L.M. Kristensen, Norway
The Netherlands
C. Lin, China
G. Ciardo, USA
W. Penczek, Poland
J. Desel, Germany
L. Pomello, Italy
S. Donatelli, Italy
W. Reisig, Germany
S. Haddad, France
G. Rozenberg, The Netherlands
K. Hiraishi, Japan
M. Silva, Spain
J. Kleijn, The Netherlands
A. Valmari, Finland
F. Kordon, France
A. Yakovlev, UK
M. Koutny, UK (Chair)
Program Committee
Kamel Barkaoui Conservatoire National des Arts et Métiers,
France
Marco Beccuti Università degli Studi di Torino, Italy
Robin Bergenthum FernUniversität in Hagen, Germany
Luca Bernardinello Università di Milano-Bicocca, Italy
Hanifa Boucheneb Polytechnique Montréal, Canada
Didier Buchs University of Geneva, Switzerland
Josep Carmona Universitat Polytècnica de Catalunya, Spain
Piotr Chrzastowski-Wachtel Warsaw University, Poland
Gianfranco Ciardo Iowa State University, USA
David de Frutos Escrig Complutense University of Madrid, Spain
Raymond Devillers (Co-chair) Université Libre de Bruxelles, Belgium
João M. Fernandes Universidade do Minho, Portugal
Henri Hansen Tampere University of Technology, Finland
Monika Heiner Brandenburg University of Technology, Germany
Joost-Pieter Katoen Aachen University, Germany
Ekkart Kindler Technical University of Denmark, Denmark
Hanna Klaudel Université d’ Evry-Val d’ Essonne, France
Lars Michael Kristensen Bergen University College of Applied Sciences,
Norway
Ranko Lazic University of Warwick, UK
Irina Lomazova Higher School of Economics, Moscow, Russia
Hiroshi Matsuno Yamaguchi University, Japan
Daniel Moldt Universität Hamburg, Germany
Madhavan Mukund Chennai Mathematical Institute, India
VIII Organization
Artem Polyvyanyy Queensland University of Technology, Australia

Riadh Robbana Carthage University, Tunisia
Stefan Schwoon ENS Cachan and Inria, France
Carla Seatzu Università di Cagliari, Italy
Natalia Sidorova Technische Universiteit Eindhoven,
The Netherlands
Yann Thierry-Mieg Laboratoire d’Informatique de Paris 6, France
Antti Valmari (Co-chair) Tampere University of Technology, Finland
Michael Westergaard Technische Universiteit Eindhoven,
The Netherlands
Mengchu Zhou New Jersey Institute of Technology, USA
Organizing Committee
Romain Brenguier Axel Haddad Guillermo A. Pérez
Ami Kumar Dhar Ismaël Jecker Jean-François Raskin
Emmanual Filiot Stéphane Le Roux Ocan Sankur
Gilles Geeraerts (Chair) Benjamin Monmege
Workshops and Tutorials Chairs

Jörg Desel FernUniversität in Hagen, Germany
Jetty Kleijn Universiteit Leiden, The Netherlands
Tools Exhibition Chair

Thomas Brihaye University of Mons, Belgium
Publicity Chair
Thierry Massart ULB, Belgium
Additional Reviewers
Amparore, Elvio Gilberto Kılınç, Görkem Ribeiro, Óscar R.
Bashkin, Vladimir Langar, Mahjoub Rohr, Christian
Cabac, Lawrence Ma, Ziyue Rosa-Velardo, Fernando
Chaouiya, Claudine Macià, Hermenegilda Schwarick, Martin
Colange, Maximilien Mosteller, David Sfaxi, Lilia
Costa, Aniko Munoz-Gama, Jorge Slaats, Tijs
Gabarro, Joaquim Nakamura, Morikazu Valero, Valentin
Gomes, Luis Noll, Thomas Wagner, Thomas
Göller, Stefan Pinna, G. Michele Wu, Hao
Haustermann, Michael Racordon, Dimitri Yamaguchi, Shingo
Herajy, Mostafa Rataj, Artur
Contents
On Quantitative Modelling and Verification of DNA Walker Circuits

Using Stochastic Petri Nets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
Benoît Barbot and Marta Kwiatkowska
Process Mining Reloaded: Event Structures as a Unified Representation

of Process Models and Event Logs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
Marlon Dumas and Luciano García-Bañuelos
Modeling Quantitative Aspects of Concurrent Systems Using Weighted

Petri Net Transducers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
Robert Lorenz
On Interval Process Semantics of Petri Nets with Inhibitor Arcs . . . . . . . . . 77

Mohammed Alqarni and Ryszard Janicki
An SRN-Based Resiliency Quantification Approach . . . . . . . . . . . . . . . . . . 98

Dario Bruneo, Francesco Longo, Marco Scarpa, Antonio Puliafito,
Rahul Ghosh, and Kishor S. Trivedi
Non-atomic Transition Firing in Contextual Nets . . . . . . . . . . . . . . . . . . . . 117

Thomas Chatain, Stefan Haar, Maciej Koutny, and Stefan Schwoon
Discrete Parameters in Petri Nets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137

Nicolas David, Claude Jard, Didier Lime, and Olivier H. Roux
Negotiation Programs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 157

Javier Esparza and Jörg Desel
Nested-Unit Petri Nets: A Structural Means to Increase Efficiency

and Scalability of Verification on Elementary Nets. . . . . . . . . . . . . . . . . . . 179
Hubert Garavel
Charlie – An Extensible Petri Net Analysis Tool (Tool Paper) . . . . . . . . . . . 200

Monika Heiner, Martin Schwarick, and Jan-Thierry Wegener
Petri Nets with Structured Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 212

Eric Badouel, Loïc Hélouët, and Christophe Morvan
On the Reversibility of Live Equal-Conflict Petri Nets . . . . . . . . . . . . . . . . 234

Thomas Hujsa, Jean-Marc Delosme, and Alix Munier-Kordon
SNAKES: A Flexible High-Level Petri Nets Library (Tool Paper) . . . . . . . . 254

Franck Pommereau
X Contents
Characterizing Stable Inequalities of Petri Nets . . . . . . . . . . . . . . . . . . . . . 266

Marvin Triebel and Jan Sürmeli
Process Discovery Using Localized Events . . . . . . . . . . . . . . . . . . . . . . . . 287

Wil M.P. van der Aalst, Anna Kalenkova, Vladimir Rubin,
and Eric Verbeek
New Search Strategies for the Petri Net CEGAR Approach . . . . . . . . . . . . . 309
Ákos Hajdu, András Vörös, and Tamás Bartha
Workflow Management Principles for Interactions Between Petri

Net-Based Agents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 329
Thomas Wagner and Daniel Moldt
Author Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 351

On Quantitative Modelling and Verification
of DNA Walker Circuits Using
Stochastic Petri Nets
Benoı̂t Barbot(B) and Marta Kwiatkowska(B)
Department of Computer Science, University of Oxford,

Wolfson Building, Parks Road, Oxford OX1 3QD, UK
{benoit.barbot,marta.kwiatkowska}@cs.ox.ac.uk
Abstract. Molecular programming is an emerging field concerned with

building synthetic biomolecular computing devices at the nanoscale, for
example from DNA or RNA molecules. Many promising applications
have been proposed, ranging from diagnostic biosensors and nanorobots
to synthetic biology, but prohibitive complexity and imprecision of exper-
imental observations makes reliability of molecular programs difficult to
achieve. This paper advocates the development of design automation
methodologies for molecular programming, highlighting the role of quan-
titative verification in this context. We focus on DNA ‘walker’ circuits, in
which molecules can be programmed to traverse tracks placed on a DNA
origami tile, taking appropriate decisions at junctions and reporting the
outcome when reaching the end of the track. The behaviour of molecular
walkers is inherently probabilistic and thus probabilistic model check-
ing methods are needed for their analysis. We demonstrate how DNA
walkers can be modelled using stochastic Petri nets, and apply statisti-
cal model checking using the tool Cosmos to analyse the reliability and
performance characteristics of the designs. The results are compared and
contrasted with those obtained for the PRISM model checker. The paper
ends by summarising future research challenges in the field.
1 Introduction
Molecular programming is an emerging field concerned with building synthetic
biomolecular computing devices at the nanoscale, for example from DNA or
RNA molecules. Several nanotechnologies have been developed, of which DNA
strand displacement (DSD) [55,56] is particularly popular, since it uses only
DNA molecules, is enzyme-free, and easy to synthesize chemically. DSD has
ben used to implement logic circuits [41,44], diagnostic biosensors [29] and con-
trollers programmed in DNA [11]. Further, DNA self-assembly technologies such
as origami folding [43] have enabled novel designs, including DNA walker systems
that can traverse tracks ‘printed’ on origami tiles and deliver cargo [51,54].
Molecular computing devices built from DNA are autonomous – they can
interact with the biochemical environment, process information, make deci-
sions and act on them – and programmable, that is, they can be systematically

c Springer International Publishing Switzerland 2015
R. Devillers and A. Valmari (Eds.): PETRI NETS 2015, LNCS 9115, pp. 1–32, 2015.
DOI: 10.1007/978-3-319-19488-2 1
2 B. Barbot and M. Kwiatkowska
configured to perform specific computational or mechanical tasks. The com-

putational power of such systems has been shown to be equivalent to Turing
computability [45]. The future potential of these developments is tremendous,
particularly for smart therapeutics, point-of-care diagnostics and synthetic biol-
ogy. For example, biosensing involves a decision process that aims to detect
various input biomarkers in an environment, such as strands of messenger RNA
within a cell, and take action based on the detected input.
Since such systems can perform information processing within living cells,
their use is envisaged in healthcare applications, where safety is paramount.
As argued in [32], this paper advocates the development of design automa-
tion methodologies for molecular programming. There are similarities to existing
work in design automation for silicon circuits and hardware verification, but we
must consider inherent stochasticity of the underlying molecular interactions, the
need to state requirements in quantitative form, and the importance to consider
control of molecular systems. Therefore, probabilistic modelling and automated,
quantitative verification and synthesis techniques are needed [31,33,34].
In this paper, we focus on DNA walker circuits introduced in [8,50,51]. The
behaviour of molecular walkers is inherently probabilistic and we have studied
their performance and reliability in [14–16]. In [38], we have developed tech-
niques to automatically synthesise rates so that a given quantitative require-
ment is guaranteed to be satisfied. The models of DNA walkers were developed
in PRISM’s modelling language, a notation based on reactive modules [34].
DNA walkers, however, perform spatially localised computation by following
programmable tracks. Therefore, graphical notations such as Petri nets are par-
ticularly well suited to their modelling and analysis. We demonstrate how DNA
walker circuits can be modelled using stochastic Petri nets, matching the lay-
out of the original circuit designs, and analyse the reliability and performance
characteristics of the designs. In view of state-space explosion observed in the
original study [15,16], we focus on evaluating the potential of statistical model
checking using the tool Cosmos. We develop a family of models, some designed
by biochemist and some artificial schemes aimed to exhibit design challenges,
and a range of quantitative requirements. The results are compared and con-
trasted with those obtained for the PRISM model checker using state-of-the-art
numerical techniques (uniformisation and fast adaptive uniformisation [14,21])
and PRISM’s statistical model checking implementation known as approximate
model checking [34]. We conclude that statistical model checking significantly
benefits from parallelisation and enables efficient analysis of much larger models
at no great loss of accuracy compared to numerical methods. The paper ends by
summarising future research challenges in the field.
2 Background on Molecular Walkers
DNA computing has so far mainly focused on designing logic circuits that per-
form computation in vitro, by transforming DNA strands using strand displace-
ment systems as e.g. demonstrated experimentally in [41,44]. However, this
On Quantitative Modelling and Verification 3
approach has limitations, in that the strands are cascaded through a series of
logic gates in solution, which may lead to unintended interference [36] and conse-
quently incorrect outcomes. An alternative approach is to design localised com-
putation by ‘printing’ circuits on origami tiles as proposed in [9,41]. In this paper
we focus on DNA walker systems [8,50,51], and particularly the programmable
walkers of [48].
A DNA walker system consists of a track of strands, called anchorages, that
are tethered to a DNA origami tile and traversed by a walker strand [48]. Origami
tiles [43] are long circular single-stranded DNA scaffolds that can be folded into
the tile shape with complementary short DNA strands that hybridize with the
scaffold. The tracks can fork at junctions, and the walkers can be programmed
to take a left or the right branch by selectively unblocking the anchorages that
the walker can follow. Fig. 1 shows an example of a double-junction circuit that
we will study later, where the two directions at the first junction are respectively
labelled X and ¬X.
The stepping process is shown in Fig. 2. The walker, which carries a quencher
(Q), is initially bound (hybridized) to the initial anchorage. The target anchor-
ages at the end of the tracks have fluorophores (F) attached to them. After some
initial preparation, the walker is able to autonomously step from one anchorage
to another, eventually reaching the target anchorages and quenching the fluo-
rophores. The programming of the tracks is achieved as follows. Initially, the
anchorages are hybridized to the tile, and are either unblocked, meaning that the
walker can bind to them, or blocking, that is, initially bound to a blocking strand
that will prevent the walker from binding to them. Sections of the track can be
reprogrammed by selectively unblocking them through the addition of strands
that are complementary to the blocking strand; see Fig. 2 (Pane 2), where ¬X
is unblocked but X remains blocked.
After the walker is placed at the initial anchorage, a nicking enzyme is added
to the solution. It binds to the walker-anchorage complex, melting the top of
the anchorage away, which frees the top of the walker. This enables the walker
strand to bind to the next anchorage through a displacement reaction (Panes 3
and 4 of Fig. 2). The process repeats, and the walker thus continues along the
unblocked section of the track, through junctions, towards the final anchorage,
where it reports the outcome by quenching the fluorophore.
Formally, the system can be viewed as a planar graph, composed from undi-
rected tracks (consecutive anchorages) and gates (track junction points) that
connect at most three tracks. [48] experimentally demonstrated that a walker
can be directed to any leaf in a complete two-level binary tree by selectively
unblocking the anchorages. In [15,16], we have studied the expressive power of
DNA walker circuits implemented by this technology and showed that the cir-
cuits can compute any Boolean function through reduction to 3-CNF. Compared
to DNA strand displacement systems in solution, an advantage of this technol-
ogy is its spatial locality, but we have found that the undirected nature of the
tracks imposes limitations on the use of parallelism. Other walker technologies
that work with directed tracks have been demonstrated, so this limitation does
not apply to all walker systems.
Fig. 1. A double-junction DNA walker circuit ([16])
Fig. 2. The stepping action of the walker ([16])
Computing Boolean functions using nanotechnologies such as the DNA

walker systems has application in biosensing, for example to detect the presence
of certain molecules. However, experiments have shown that the computation is
quite unreliable, in the sense that walkers may release from a track, jump over
two anchorages, or a blockade can fail to block an anchorage, delaying or divert-
ing the walker to a different anchorage, thus returning wrong result. To study
the reliability and performance of such systems, in [15,16] we also developed a
stochastic model of DNA walker systems based on [8,48,50]. Note that, since
we are considering localised computation, standard mass action kinetics which
applies to well-mixed solution cannot be used, and we instead derive a model
from experimental observations.
The model can be configured to a specific circuit layout, where we can vary
the topology of the circuit, the number of anchorages in each section, and their
physical spacing. We also model the different modes of anchorages, such as
blocked, unblocked, empty or bound to the walker. The stepping process of Fig. 2
has been abstracted into a single walker step transition, taking the walker from
one anchorage to the next. The rate of the stepping transition is dependent on
the distance between anchorages, and was derived using rate constants estimated
in [50]. Maximum interaction distance was observed to be dM = 24 nm. Taking

into account the average distance between anchorages in the experiment of 6.2
nm, we have defined the walker stepping rate k to be a function of the distance
da and the base rate ks given by:
⎧
⎪
⎪ ks = 0.009s−1 when d ≤ 1.5da
⎪
⎨ ks /50 when 1.5da < d ≤ 2.5da
k= (1)
⎪
⎪ ks /100 when 2.5da < d ≤ dM
⎪
⎩
0 otherwise
This determines a sphere of reach of up to dM around the walker-anchorage

complex, within which the walker may step onto an uncut anchorage. We note
that this abstraction of the stepping rate makes certain simplifying assumptions,
such as we do not consider walker moving between intact anchorages or stepping
backwards; these aspects have been experimentally observed and the model can
be refined further in future.
One aspect that we do consider, however, and which also has been observed
experimentally, is the failure of the blocking mechanism. We can allow the
anchorages to spontaneously unblock and assume that the unblocking is uniform.
If this happens, the walker may step onto such an unblocked anchorage and fol-
low an incorrect track. The failure rate of 30% was estimated based on [48]. We
have not modelled the failure of other mechanisms, such as missing anchorages
or the failure of the reporting mechanisms, but these could again be added to
the model.
In [15,16], we have constructed a family of models for a variety of circuits,
fitting the rates from the single-junction circuit experiments [48], and then eval-
uating the quality of the model on the double-junction circuits. We found good
alignment of model predictions with the experimental data, in particular also
observing the effect of leakage transitions, that is, when the walker unintention-
ally transfers to the neighbouring track because of its proximity. In addition, we
have considered a range of circuit designs and analysed their performance and
reliability using the probabilistic model checker PRISM [34].
3 Stochastic Models and Analysis Techniques

As discussed in the previous section, stochasticity is an important aspect that we
need to consider when designing molecular circuits, particularly localised compu-
tation such as DNA walkers placed on origami tiles. In this section we introduce
the background notation and briefly overview existing stochastic models and
analysis methods applicable to molecular systems.
3.1 Continuous-Time Markov Chains (CTMC)

The evolution of molecular systems is naturally modelled as a stochastic pro-
cess tracking the probability of molecular populations over time. This process,
under the assumption of constant volume and temperature, is a (homogeneous)

continuous-time Markov chain (CTMC).
Formally, a CTMC C is a tuple (S, s0 , R), where S is a set of states, s0 ∈ [0, 1]S
is the initial distribution over states, and R is the rate transition matrix with
∀s, s ∈ S, R(s, s ) ≥ 0, R(s, s) = 0.
Each CTMC can be unfolded into execution paths from the start state as
follows.
The residence time in state s is exponentially distributed with exit rate
λs = s ∈S R(s, s ). Once the residence time expires, the probability to move

to state s from s is R(s,s )
λs . We refer to the discrete-time Markov chain encoding
the discrete transition probabilities for each state as the embedded DTMC.
Alternatively, for a CTMC the probability over time (transient probability
distribution) is given by the Chemical Master Equation (CME) [23] dt d
πt = πt ·Q,
where Q is the infinitesimal generator matrix, defined as Q(s, s ) = R(s, s ) if

s = s , and 1 − s =s R(s, s ) otherwise, and π0 = s0 .

A CTMC can be extended with a reward structure (ρ, ι), where ρ and ι are
respectively a vector and matrix of non-negative reals. ρ(s) is a state reward,
and defines the rate at which the reward is acquired when C remains in state
s for t time units. The function ι(s, s ), s, s ∈ S, defines the transition reward
acquired each time the transition (s, s ) occurs.
All Markov processes with countable state spaces and continuous distribu-
tions of time may be described as CTMCs, since the exponential distribution
is the only continuous distribution with the Markov property. We usually work
with finite state CTMCs, though some of the analysis techniques generalise to
countable CTMCs.
In the context of verification CTMCs are enriched with atomic propositions
that label states. Formally, a labelled CTMC is a tuple (AP, L, S, s0 , R) such
that (S, s0 , R) is a CTMC, AP is a set of atomic propositions and L : S → 2AP
is a labelling function that assigns atomic propositions to the states. When
considering molecular systems, the set of atomic propositions usually includes
inequalities over the number of each molecule type, for example, “there are at
least 5 molecules x” (written x ≥ 5).
3.2 Quantitative Verification for CTMCs

To specify quantitative properties of CTMCs, a number of formalisms can be
used. These are divided into two families, linear time and branching time. Linear
time formalisms specify accepting paths, and contain a single outer probabilistic
operator. They include:
– temporal logics LTL (linear-time temporal logic) [40] and BLTL (bounded
linear-time temporal logic) [28];
– deterministic timed automata specifications [6,19], where timed paths are
accepted only if they are in the language of the automaton;
– deterministic linear hybrid automata specifications [5], an extension of timed
automata with clocks evolving at different speed;
– temporal logic MTL (metric temporal logic) [10]which is an extension of

BLTL with real-time constraints on the until operator.
Branching-time formalisms, on the other hand, contain nested probabilistic oper-
ators, and include:
– temporal logics PCTL [24] and PCTL* (probabilistic computation tree
logic) [1], based on CTL/CTL* with the probabilistic operator added (for
untimed properties);
– temporal logic CSL (continuous stochastic logic) [2], an extension of PCTL
where temporal operators are equipped with real-time constraints and with
an additional operator to specify steady state distribution.
These formalism can be extends with rewards. In this paper we will work with
linear-time properties that we introduce using random variables. The key prop-
erties of interest are P=? [Xφ ], the probability of the path formula φ being sat-
isfied from a given state over time (Xφ is a random variable defined over paths
from s equal to 1 if the path satisfies φ and 0 otherwise); and E=? [X(ρ,ι) ], the
expected cumulative reward in a given state over time (X(ρ,ι) is a random vari-
able defined over paths annotated with rewards (ρ, ι) that computes the total
reward cumulated up to t). Path formulas φ include the temporal operators
‘until’ and ‘future’, both unbounded and time-bounded variants; for example,
(x ≥ 1)U(x = 0) denotes a path along which molecules x eventually degrade,
and F≤100 (x ≥ 1) ∧ (y = 0) a path which reaches a state where there is at least
one x molecule and no y molecules within 100 time units.
A number of techniques are available to analyse CTMCs. Since precise solu-
tion of the CME is in general intractable, the prevailing method is stochastic
simulation, e.g. using the Gillespie algorithm [23], which generates forward tra-
jectories from the initial state or distribution. Quantitative verification aims to
compute the probability or expectations of certain events specified using the
above temporal logic or automata formalisms. For CSL formulas, the computa-
tion of probability over time reduces to transient analysis on a modified model.
Given an automaton representation of the property (which can be derived from
LTL formulas or provided directly, e.g. as a timed automaton), it is necessary
first to build the product of the automaton and the model, and then compute
transient probability distributions on the product. Quantitative verification of
expected reward properties is similar.
Transient analysis usually proceeds through numerical methods or
simulation-based analysis known as statistical model checking, which we describe
next.
3.3 Numerical Verification Methods for CTMCs

Numerical methods require that the state space and rate matrix of the CTMC
be constructed. Typically, the numerical computation of transient distribution
proceeds through discretisation of the CTMC, resulting in approximate proba-
bility values. These methods are more efficient on branching-time formalisms,
in particular for CSL, where they take advantage of the strict alternation of
probabilistic and temporal operators. On linear-time properties one first has to
build an automaton from the specification, and then build the product of the
automaton and the CTMC, which increases the state space. Two methods have
been developed for transient analysis, uniformisation and its variant fast adap-
tive uniformisation that neglects states with insignificant probability mass, thus
improving performance of the computation.
Uniformisation. Uniformisation (see e.g. [35] translates the problem of com-

puting transient distribution of a CTMC to the computation of transient distribu-
tion of its discretisation, called the uniformised DTMC, and can be summarised
as follows.
– For any CTMCs where there exists a bound on the maximal exit rate, the
uniformised DTMC can be computed over the same state space, where each
step in the DTMC corresponds to one exponentially distributed delay in the
CTMC with rate equal to the maximal exit rate.
– Transient probability of the CTMC at time t can be computed as an infi-
nite summation of i jumps in the uniformised DTMC weighted by Poisson
probabilities.
– The Poisson weights of the infinite summation are derived using the Fox &
Glynn algorithm [22], which also determines the upper bound on the number
of summation terms needed to meet a given error bound.
Uniformisation involves operations on the stochastic matrix of the uni-
formised DTMC, and thus can suffer from state-space explosion.
Fast Adaptive Uniformisation (FAU). Fast adaptive uniformisation

(FAU) [18,39] can reduce the size of the explored state space by neglecting states
with insignificant probability mass. It is an approximate method for computing
the transient distribution of a CTMC and can be summarised as follows:
– Transient probability distributions are computed forward from the initial
state in the embedded DTMC. States with low probability of occurrence
(below a threshold δ) are discarded. Therefore, FAU only explores a subset
of the state space.
– The maximal exit rate of the CTMC is approximated and computed on the
fly on the set of states that have not been discarded. The upper bound on
the infinite summation is also computed on the fly.
The FAU method can greatly improve the time and memory consumption
of the transient probability computation when the state space is large and exit
rates of states span several orders of magnitude. It has also been extended to
the computation of rewards [14].
Numerical model checking for CTMCs against CSL probability and reward
formulas has been implemented in PRISM [34] using uniformisation (symbolic,
hybrid, sparse and explicit engine) and FAU (explicit engine).
3.4 Statistical Model Checking

Instead of constructing the rate matrix of the CTMC, an alternative when deal-
ing with large state spaces is to use statistical methods. The statistical model
checking approach relies on Monte Carlo simulation algorithm to estimate the
probability of interest. These methods are better suited to linear-time proper-
ties due to the difficulty of dealing with nested probabilistic operators. In [53] an
algorithm for nested probabilistic operators is provided, but the simulation time
greatly increases with the depth of the nesting. More precisely, statistical meth-
ods are applied as follows: for a path formula φ, a Bernoulli random variable X
is defined which takes 1 as value on a path that satisfies φ and 0 otherwise. The
probability estimate is thus obtained as the ratio of the number of paths satisfy-
ing φ to the total number of paths, where the Monte Carlo algorithm simulates
a large number, say N , of paths. The random variable Z is defined as the mean
of N independent copies of X:
1
N
Z= Xi
N i=1
An advantage of statistical model checking is that it can be parallelised very

easily: it suffices to run several simulators of the system on different processors
and take the mean result of paths from all simulators. Particular attention needs
to be paid to the random number generator to ensure that all generated paths
are independent, but otherwise the overhead of parallelisation is low. Statistical
model checking can be naturally extended to computing expected rewards, that
is, the expected value of a random variable whose values depend on rewards
cumulated over simulated paths.
Confidence Intervals. When one computes a probability estimate for some

random variable X, and the exact value cannot be computed, it is important to
know how far this estimate is from the actual value. Statistical methods cannot
guarantee that the numerical value we obtain is at a given distance to the actual
value. This is because using a fixed number of samples the simulation may avoid
certain parts of the system with non-zero probability, thus biasing the estimation.
Nevertheless, probabilistic guarantees on the obtained result can be given in the
form of confidence interval, namely, confidence in the fact that the actual value
is close enough to the realisation, defined as follows.
Let (Xi )N
1 be independent random variables following a common distribution
including a parameter θ. Let 0 < γ < 1 be a confidence level. Then a confidence
interval for θ with level at least γ is given by two random variables l(X1 , . . . , XN )
and u(X1 , . . . , XN ) such that for all θ:
P [l(X1 , . . . , XN ) ≤ θ ≤ u(X1 , . . . , XN )] ≥ γ
Classical statistical inequality can be used to derive confidence intervals from

a set of realisations of a random variable. As a general rule, these inequalities
link together the confidence level, the number of samples and the width of the
confidence interval, such that the user specifies two of them and the third is
derived from the inequality.
The simplest approach is Gaussian analysis, which uses central limit theorem
to approximate the distribution of the mean value of the observations of the ran-
dom variable. When a random variable follows normal distribution, confidence
interval can be computed using Gaussian error function.
A variant of this approach is to approximate the distribution of the random
variable to a normal distribution and use the cumulative distribution function
of the student-t distribution to compute confidence intervals. This confidence
interval is more conservative than the one of the normal distribution when the
number of samples is small, but as the number of samples increases they converge
to each other.
When more conservative results are required and bounds on the value taken
by the random variable are known, then Chernoff-Hoeffding inequality can be
used to produce confidence intervals.
Sequential Estimation. Using additional hypotheses, the required number of

samples can be computed on the fly; the simulation is then stopped as soon as the
number of samples is sufficient. These methods are called sequential estimation.
Given a confidence level and a confidence interval width, the Chow and Rob-
bin algorithm [12] requires the same hypothesis as Gaussian analysis and that
the width of the confidence interval tends to zero. The algorithm provides the
optimal stopping rules for the simulation and returns a confidence interval with
expected width and variance.
When one is not interested in the actual expected value of a random variable
but rather in deciding whether this value is above or below a threshold, then
hypothesis testing can be used. Given a confidence level, a threshold and an open
interval around this threshold called indifference region, the Sequential Proba-
bility Ratio Test (SPRT) [46,53] returns whether the value is above or below
the threshold. If the true expected value is in the indifference region the test
result has no probabilistic guarantee. Otherwise, the test result is correct with
a probability equal to the confidence level. Two different confidence levels may
be used for values above and below the threshold to make the test asymmetric
(type I and type II errors).
Rare Events. One of the main limitations of statistical model checking is the
rare event problem. When the probability that we want to compute is very
small (usually smaller than 10−6 , statistical model checking becomes inefficient.
Recently, several methods have addressed this limitation using importance sam-
pling [7,26,42] or splitting [27], summarised below.
– Importance sampling relies on biasing the model such that the satisfaction
of the formula is no longer a rare event. During simulation an the overall
bias is estimated to produce an accurate estimation of the rare event. The
difficulty lies in the choice of bias.
– Splitting relies on defining a sequence of successive embeddedings of subsets

of the state space. The smallest subset only contains states satisfying the
property of interest, while the largest contains all states. During simulation,
each time a path reaches the next subset it is split into several copies. The
probability that one path reaches the smaller subset is higher than the initial
probability. Appropriately choosing the subsets is crucial to obtain precise
results.
Statistical model checking for CTMCs has been implemented in a number of

tools, to mention PRISM and Cosmos. In particular, PRISM [34] implements
the confidence interval and SPRT methods for time-bounded CSL properties
(also known as approximate probabilistic model checking), whereas Cosmos [3,4]
provides a range of statistical model checking methods, including importance
sampling, for a more expressive specification language.
3.5 Stochastic Petri Nets
CTMC models of molecular systems are complex, and high-level modelling lan-
guages facilitate their construction. Such languages include stochastic extensions
of process algebras (cf PEPA [13]), reactive modules (cf PRISM [34]) or Petri
nets (cf Cosmos [3,4]). We focus here on stochastic Petri nets (SPNs), a graph
of places connected by transitions, where the time for a transition to fire is dis-
tributed according to exponential distributions. SPNs are naturally interpreted
as CTMCs whose state space is the set of reachable marking. They have been
widely studied, for example in [17].
Formally, an SPN is a tuple N = (P, T, W − , W + , m0 , Λ), where P is a finite
set of places, T is a finite set of transitions, W − : P × T → N is the pre incidence
matrix, W + : P × T → N is the post incidence matrix, m0 ∈ NP is the initial
marking, and Λ : NP × T → R is the rate function which associates a rate to
each marking and transition.
SPNs can be endowed with CTMC semantics, which for N =
(P, T, W − , W + , m0 , Λ) is given as the CTMC C = (S, s0 , R) defined by:
– S = Reach(N , m0 ), the set of reachable markings
∀s ∈ S\{m0 }, s0 (s) = 0
– s0 (m0 ) = 1,
– R(m, m ) = t Λ(m, t).
t∈T, s.t. m−
→m
A common extension of SPNs are generalized stochastic Petri nets (GSPN),
which additionally use immediate transitions with Dirac distributions. Weights
are added to resolve concurrent firing of immediate transitions. As immediate
transitions are memoryless, the semantics of a GSPN is still Markovian as long
as there is no cycle of immediate transitions [20]. Such cycles can be detected
by an analysis of the structure of the net. Adding such immediate transitions is
convenient for modelling stochastic systems and may reduce the size of the set
of reachable markings [30].
GSPNs are supported by a number of tools, including Cosmos and Marcie [25].
4 Modelling DNA Walkers

In [15,16], DNA walkers were modelled in the native language of PRISM, which
represents each walker circuit as a synchronised parallel composition of reactive
modules, each specified using guarded commands whose updates are annotated
with rates. Since DNA walker circuits are planar, GSPNs are well suited to their
modelling, with the layout of the GSPN closely corresponding to the layout of
the original circuit: the state of each anchorage is modelled using an indepen-
dent place, while the steps of the walker are modelled with transitions that are
exponentially distributed.
The blocking mechanism used to steer the movement of the walker may fail
with some probability; this failure occurs before the walker is released and thus
before any walker movement. In PRISM, this is modelled with transitions with
very high rates (a billion times larger than walker movement rates), which makes
the computation intractable when uniformisation is used. In GSPN this blocking
mechanism is modelled using instantaneous transitions.
More precisely, each DNA walker circuit comprises several tracks (sequences
of anchorages) and transitions correspond to walker taking a step from one
anchorage to another nearby. The states of each anchorage are modelled as
follows:
– Each anchorage is modelled with a single place, to preserve the layout of the
original circuit placement. The relative placement of each place corresponds
to that of the corresponding anchorage on the origami.
– Intact anchorages are modelled with places containing one token.
– Anchorages where the top has melted away are modelled by empty places.
– The anchorage to which the walker is attached is modelled by a place with
two tokens.
– Blocked anchorages are modelled like anchorages where the top has melted
away, with empty places.
Fig. 3 illustrates a transition encoding a displacement reaction between two
anchorages a and b. Place a encodes the anchorage to which to walker is cur-
rently bound. Place b encodes an intact, unblocked anchorage. The transition
consumes two tokens in the place corresponding to a and one token in the place
corresponding to b, and produces two tokens in the place corresponding to b.
Indeed, after the transition is fired the place corresponding to a is left empty,
which models the anchorage where the top has melted away.
The walker may move between two anchorages that are sufficiently close.
Each such movement is modelled with independent transitions. The rate of each
transition depends on the distance between the two anchorages as specified on
page 5.
Blocked anchorages do not initially contain tokens. In order to model the
possibility of failure of the blocking mechanism, a place with initially one token
and two immediate concurrent transitions are added to each blocked anchorage.
Fig. 4 illustrates this. With failure probability f = 0.3, a token is added to the
place for anchorage a. In this case the anchorage is no longer blocked.
2
a 2 b
Fig. 3. Transition modelling movement of the walker from anchorage a to anchorage b
1−f f
a
Fig. 4. Two transition model of the failure of the blocking mechanism of anchorage a
Our modelling approach ensures modularity of the design and that the layout
of the Petri net closely resembles that of the original walker system. Different
circuits can be composed together easily by merging together initial and final
anchorages and by adding transitions between places encoding nearby transi-
tions. Additional behaviours of the circuit, such as a missing anchorage, may
be added easily by adding or removing tokens. An alternative modelling app-
roach would have been to use colour to model the position of the walker, sim-
ilarly to works in [37], but this would not preserve the layout of the original
walker.
The walker models that we study are complex and have large number of
transitions, but can nevertheless be viewed on screen and zoomed in. As an
example, Fig. 5 shows one of the smallest models. In the following, for the sake
of clarity we will hide most of the transitions when displaying a Petri net.
The state space of the walker systems increases exponentially with the num-
ber of anchorages. Table 1 shows the number of places and transitions, together
with the size of the state space for models of DNA walkers that we studied. For
the larger models it was not possible to build the state space due to memory
limits.
The size of the state space makes the analysis of these models difficult. Qual-
itative analysis is still possible using symbolic representation of the state space
for the smaller examples. For quantitative analysis, numerical computation of
transient probability via uniformisation requires the storage of a vector of prob-
abilities (one floating point number per state). Currently, the maximal amount
of memory in a computer is in the order of 100 GByte using single precision,
namely, at most 100 · 1024 · 1024 · 1024/4 ≈ 27 · 109 states. This neglects the
amount of memory required to store the transition matrix, let alone the time to
compute with such a large vector. Unfortunately, the state space of some of the
models of DNA walkers that we consider exceeds this limit. This problem can
be partially alleviated using FAU. However, when the state space is too large to
be constructed the only viable alternative is to use statistical model checking for
the analysis.
Fig. 5. A single junction circuit. The walker is initially in the upper anchorage. The
anchorage on the left of the junction is blocked. Gray-scale used for the transitions
indicate the tree possible rates (ks , ks /50, ks /100). Black transitions correspond to
immediate transitions.
5 Experiments and Results

In this paper, we model a variety of DNA walker circuits using stochastic Petri
nets and analyse their reliability and performance. We focus on the application
of statistical model checking, which we compare to numerical solution methods
implemented in PRISM. We first briefly describe the tools used, followed by an
overview of the results and analysis of the advantages of each method and the
corresponding trade offs that can serve as guidelines when selecting software
tools for quantitative modelling and verification of similar systems.
5.1 Tools
We use three modelling and analysis tools to perform computational experi-
ments, namely Marcie [25], PRISM [34] and Cosmos [3,4]. We also use Graphviz
for the visualisation of Petri nets.
Marcie supports qualitative and quantitative analysis of generalised stochas-
tic Petri nets. The tool has been developed for the study of chemical reaction
networks and thus facilitates the modelling of such systems. It employs Inter-
val Decision Diagrams (IDD) to symbolically represent the state space of the
Table 1. Size of the state space of DNA walker models studied
Model Places Transitions States Model Places Transitions States

control 8 34 172 ringLL 27 260 27,950,678
controlMissing1 7 22 50 ringRL 27 260 27,950,678
controlMissing2 6 13 13 ringLR 27 260 28,209,796
controlMissing7 7 27 82 ringRR 27 260 28,209,796
track12Block1 13 82 3,795 ringLLLarge 33 312 1,885,372,776
track12Block2 14 84 5,459 ringRLLarge 33 312 1,885,372,776
track12BlockBoth 14 84 5,248 ringLRLarge 33 312 1,860,879,029
track28LL 34 250 432,884,827 ringRRLarge 33 312 1,860,879,029
track28LR 34 250 435,340,831 redundantChoiceL 43 490 -
track28RL 34 250 435,340,831 redundantChoiceR 43 490 -
track28RR 34 250 432,884,827
Petri net. The implementation of IDD is mostly parallel, taking advantage of

multicore architectures. The tool has recently been extended with a simulation
engine for model checking of PLTL (propositional linear-time temporal logic)
formulas. Marcie can deal with unbounded until properties as long as the user
guarantees termination. We use Marcie to compute the size of the state space in
our experiments.
PRISM is a probabilistic model checker that supports a variety of probabilis-
tic models and probabilistic temporal logics, including CTMCs and temporal
logic CSL. A CTMC model is provided in the PRISM modelling language as a
synchronised parallel composition of reactive modules, but model imports, e.g.
via SBML, are also supported. Verification of CSL properties can proceed via
numerical methods (uniformisation or fast adaptive uniformisation) or statistical
model checking (confidence interval and SPRT), known as approximate proba-
bilistic model checking. We use PRISM to perform quantitative verification using
numerical methods and approximate model checking.
Cosmos is a statistical model checker for generalised stochastic Petri nets with
general distributions. It takes Hybrid Automata Stochastic Logic (HASL), based
on linear hybrid automata, as a specification language. Efficient simulation is
obtained using code generation that generates lightweight optimised C++ code.
The generated code implements a simulator for the product of the model with
the automaton underlying the specification. We use Cosmos for the evaluation
of the models using statistical model checking.
5.2 The Setting

We perform experiments with Cosmos and PRISM on several circuit designs
that have either been experimentally studied by biochemists or present design
challenges. To ensure that the model given to each tool encodes the same system,
the following workflow is used:
1. Each circuit defines a set of anchorages; for each anchorage, the position is
specified as well as whether it is an initial or final anchorage. Additionally,
the correct final anchorage is specified.
2. From this description of the circuit a GSPN is built.

3. The GSPN is exported in the GrML (Graph Markup Language) file format
for Cosmos; the ANDL (Abstract Net Description Language) for Marcie;
and the DOT language for Graphviz and the PRISM language. All these
exports are simple except for PRISM, for which the GSPN is transformed
into a single module, where each place is transformed into one variable and
each transition into one guarded command. The property that the GSPN is
2-safe is used to bound variables.
4. From the GSPN and the initial description of the circuit, properties are
provided as logical formulas for PRISM and as automata for Cosmos.
On each model we define atomic propositions of the form Ax = y, with Ax
indicating an anchorage name, x either a place name or a PRISM variable, and
y an integer. Labels and reward structures on states are also added to express
certain properties, as described below.
For each model we perform the following initial analysis. The first four for-
mulas are simple bounded reachability properties that can be expressed in many
logics, for example BLTL or CSL with rewards. For the two remaining ones, we
give the specification. We compute after 200 min the following properties:
1. The probability of reaching a deadlock state, where we assume an atomic
proposition deadlock labelling deadlock states:
Deadlock := P=? F≤12000 deadlock
2. The probability of reaching a final anchorage, define using a state label

(final):
Finish := P=? F≤12000 final
3. The average time spent in an anchorage that was supposed to be blocked
but the failure mechanism failed; this is defined using reward structure block
that increases linearly with the time spent in a blocked anchorage:
Blockade := R{block}=? C <=12000
4. The expected number of steps of the walker, defined using reward structure
steps that is increased by one for each firing of a transition:
Steps := R{steps}=? C<=12000
5. The reliability of the walker computation, written as an algebraic expression

over (quantitative) CSL or BLTL formulas:
P=? F≤12000 finalCorrect

Reliability :=
P=? F≤12000 final
6. The probability that a path reaches the correct final anchorage while visiting
a blocked anchorage, defined in BLTL using state label blockAnchorage:
uB := P=? ((F≤12000 blockAnchorage) ∧ (F≤12000 finalCorrect))

The first five properties were already studied in [15] for some of the models.
The tool Cosmos takes deterministic Linear Hybrid Automata (LHA) as
a specification formalism. Compared to timed automata, in LHA clocks are
replaced by piecewise linear variables. Cosmos implements the synchronisation
of a GSPN with an LHA. The main features of a property automaton are illus-
trated in Fig. 6. The locations of the automaton are labelled with invariants,
which are atomic propositions of the GSPN. Locations are labelled with the rate
of each variable; for clarity only rates different from 0 are labelled in the figure
except for variable t, whose rate is always equal to 1. Accepting locations of the
automaton are labelled with a name (in Fig. 6 names are sl,fc,fnc). The tran-
sitions of the automaton are of two types: synchronized transitions are labelled
with a set of GSPN transition names, or the symbol A for any transition, and
are synchronised with the firing of the GSPN transition. They can be labelled
with a time guard; autonomous transitions, indicated with symbol #, are not
synchronised and occur as soon as the time guard is satisfied. More detail on the
synchronisation of GSPN and LHA can be found in [3].
In addition to the property automata, Cosmos relies on several HASL expres-
sions that specify which value to estimate from the automaton. For our properties
the expressions are as follows:
– The probability of reaching a deadlock state is expressed as follows:
P=? dl
and is interpreted as the probability for an accepting trajectory of the GSPN

to end in location dl;
– The probability of reaching a final anchorage is expressed as follows:
P=? fc ∨ fnc
– The average time spent in an anchorage that was supposed to be blocked,

but the failure mechanism failed, is expressed as follows:
E=? bt
and is interpreted as the average value of variable bt in accepting states;

– The reliability property is expressed as:
P=? fc
P=? fc ∨ fnc
– The probability that a path reaches the correct final anchorage while visiting
a blocked anchorage is defined as:
P=? (ub = 1) ∧ fc
P=? fc
The sixth property is expressed with a slightly more involved automaton, which is
not reported here for reasons of space. In this automaton a variable s is added to
count the number of steps of the walker; it is increased by 1 on each synchronised
transition except the one that loops over the initial state. The HASL expression
is E=? s. More details and formal specification of HASL expressions can be found
in [3].
fc
block ∧ ¬finish A
˙ =1 finishCorrect
bt A
dl A #,t=12000
A, t = 0
deadlock A A,ub:=1
#,t=12000
A
¬block A finish∧

t := 0 A, t > 0 ∧¬finish A ¬finishCorrect
bt := 0 fnc
ub := 0
Fig. 6. LHA for the first four of the properties. This LHA contains two variables: t is
a clock which is never reset, and bt is a piecewise linear variable with respect to time
whose derivative is equal to 0 everywhere except in states where block holds. Symbol
A indicates that the automaton reads any action of the model.
In the remainder of this section we describe the models and report on the
results of verifying the above properties using statistical model checking meth-
ods. In Section 6 we compare and contrast the outcomes produced by the differ-
ent tools and methods on each model, as well as the time and memory require-
ments.
5.3 Control Model
We begin by analysing the experimental designs of DNA walker models intro-

duced in [47,52], which were modelled and analysed in [15,16]. These circuits
comprise several anchorages in a straight line, where some anchorages have been
removed. Fig. 7 depicts the control model where, for clarity, the transitions of
the Petri net have been omitted except for the self-loops on final anchorages.
The positioning of places corresponding to each anchorage is consistent with the
positioning of the anchorage on the circuit layout. The initial position of the
walker is in the upper left corner and is encoded with two tokens. The final posi-
tion is in the lower right corner. There are three variants of this model. In the
first, the anchorage 4 is omitted. In the second, anchorages 4 and 5 are omitted.
In the third anchorage, 7 is omitted.
control controlMissing1 controlMissing2 controlMissing7
Fig. 7. Simplified Petri nets of control models
The results for this control model are reported in Table 2. We compute the
average number of steps (Steps), the probability of deadlock (Deadlock) and the
probability to reach the final anchorage in 200 minutes (Finish).
Table 2. Experimental results for the control model
Model Steps Deadlock Finish

control 6.8756 0.0033 0.9618
controlMissing1 5.5141 0.0002 0.8528
controlMissing2 3.8529 0.0194 0.5909
controlMissing7 5.1453 0.0305 0.1755
We observe that the number of steps is directly proportional to the number

of anchorages, and the probability to reach the final anchorage within the time
bound greatly decreases when an anchorage is missing. From these two obser-
vations, we can deduce that the predominant path in these models is the one
that successively visits each anchorage, which is consistent with wetlab experi-
ments [47] (Fig. 2).
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§. 11. Of the Worms of the Spindle.
I promised at the latter end of Numb. 2. to give a more copious
account than there I did of making Worms, when I came to exercise
upon Printing-Press Spindles; and being now arrived to it, I shall
here make good my promise.
¶. 1. The Worms for Printing-Press Spindles must be projected

with such a declivity, as that they may come down at an
assigned progress of the Bar.
The assigned progress may be various, and yet the Spindle do its
office: For if the Cheeks of the Press stand wide assunder, the
sweep or progress of the same Bar will be greater than if they stand
nearer together.
It is confirm’d upon good consideration and Reason as well as
constant experience, that in a whole Revolution of the Spindle, in the
Nut, the Toe does and ought to come down two Inches and an half;
but the Spindle in work seldom makes above one quarter of a
Revolution at one Pull, in which sweep it comes down but half an
Inch and half a quarter of an Inch; and the reason to be given for this
coming down, is the squeezing of the several parts in the Press,
subject to squeeze between the Mortesses of the Winter and the
Mortesses the Head works in; and every Joynt between these are
subject to squeeze by the force of a Pull. As first, The Winter may
squeeze down into its Mortess one third part of the thickness of a
Scabbord. (Allowing a Scabbord to be half a Nomparel thick.)
Secondly, The Ribs squeeze closer to the Winter one Scabbord.
Thirdly, The Iron-Ribs to the Wooden Ribs one Scabbord. Fourthly,
The Cramp-Irons to the Planck of the Coffin one Scabbord. Fifthly,
The Planck it self half a Scabbord. Sixthly, The Stone to the Planck
one Scabbord. Seventhly, The Form to the Stone half a Scabbord.
Eighthly, The Justifyers in the Mortess of the Head three Scabbords.
Ninthly, The Nut in the Head one Scabbord. Tenthly, The Paper,
Tympans and Blankets two Scabbords. Eleventhly, Play for the Irons
of the Tympans four Scabbords. Altogether make fifteen Scabbords
and one third part of a Scabbord thick, which (as aforesaid) by
allowing two Scabbords to make a Nomparel, and as I shewed in
Vol. 2. Numb. 2. §. 2. One hundred and fifty Nomparels to make one
Foot, gives twelve and an half Nomparels for an Inch, and
consequently twenty five Scabbords for an Inch; so by proportion,
fifteen Scabbords and one third part of a Scabbord, gives five eighth
parts of an Inch, and a very small matter more, which is just so much
as the Toe of the Spindle comes down in a quarter of a Revolution.
This is the Reason that the coming down of the Toe ought to be just
thus much; for should it be less, the natural Spring that all these
Joynts have, when they are unsqueez’d, would mount the Irons of
the Tympans so high, that it would be troublesom and tedious for the
Press-man to Run them under the Plattin, unless the Cheeks stood
wider assunder, and consequently every sweep of the Bar in a Pull
exceed a quarter of a Revolution, which would be both laborious for
the Press-man, and would hinder his usual riddance of Work.
I shew’d in Numb. 2. fol. 31, 32, 33, 34, 35. the manner of making a
Screw in general; but assigned it no particular Rise; which for the
aforesaid reason, these Printing-Press Screws are strictly bound to
have: Therefore its assigned Rise being two Inches and an half in a
Revolution, This measure must be set off upon the Cilindrick Shank,
from the top towards the Cube of the Spindle, on any part of the
Cilinder, and there make a small mark with a fine Prick-Punch, and
in an exact Perpendicular to this mark make another small mark on
the top of the Cilinder, and laying a straight Ruler on these two
marks, draw a straight line through them, and continue that line
almost as low as the Cube of the Spindle. Then devide that portion
of the straight line contained between the two marks into eight equal
parts, and set off those equal parts from the two Inch and half mark
upwards, and then downwards in the line so oft as you can: Devide
also the Circumference of the Shank of the Cilinder into eight equal
parts, and draw straight lines through each devision, parallel to the
first upright line; and describe the Screw as you were directed in the
afore-quoted place; so will you find that the revolution of every line
so carried on about the Shank of the Cilinder, will be just two Inches
and an half off the top of the Shank: which measure and manner of
working may be continued downward to within an Inch and an half of
the Cube of the Spindle. This is the Rule and Measure that ought to
be observ’d for ordinary Presses: But if for some by-reasons the
aforesaid Measure of two Inches and an half must be varied, then
the varied Measure must be set off from the top of the Cilinder, and
working with that varied Measure as hath been directed, the Toe of
the Spindle will come down lower in a revolution if the varied
Measure be longer, or not so low if the varied Measure be shorter.
There is a Notion vulgarly accepted among Workmen, that the
Spindle will Rise more or less for the number of Worms winding
about the Cilinder; for they think, or at least by tradition are taught to
say, that a Three-Worm’d Spindle comes faster and lower down than
a four-Worm’d Spindle: But the opinion is false; for if a Spindle were
made but with a Single-Worm, and should have this Measure, viz.
Two Inches and an half set off from the top, and a Worm cut to make
a Revolution to this Measure, it would come down just as fast, and
as low, as if there were two, three, four, five or six Worms, &c. cut in
the same Measure: For indeed, the numbers of Worms are only
made to preserve the Worms of the Spindle and Nut from wearing
each other out the faster; for if the whole stress of a Pull should bear
against the Sholder of a single Worm, it would wear and shake in the
Nut sooner by half than if the stress should be borne by the Sholders
of two Worms; and so proportionably for three, four, five Worms, &c.
But the reason why four Worms are generally made upon the
Spindle, is because the Diameters of the Spindle are generally of
this propos’d size; and therefore a convenient strength of Mettal may
be had on this size for four Worms; But should the Diameter of the
Spindle be smaller, as they sometimes are when the Press is
designed for small Work, only three Worms will be a properer
number than four; because when the Diameter is small, the
thickness of the Worms would also prove small, and by the stress of
a Pull would be more subject to break or tear the Worms either of the
Spindle or Nut.
And thus I hope I have performed the promise here I made at the
latter end of Numb. 2. Whither I refer you for the breadth, and reason
of the breadth of the Worm.
¶. 13. Of the Bar marked B in Plate 8.
This Bar is Iron, containing in length about two Foot eight Inches and
an half, from a to b, and its greatest thickness, except the Sholder,
an Inch and a quarter; The end a hath a Male-Screw about an Inch
Diameter and an Inch long, to which a Nut with a Female-Screw in it
as at C is fitted. The Iron Nut in which this Female-Screw is made,
must be very strong, viz. at least an Inch thick, and an Inch and three
quarters in Diameter; in two opposite sides of it is made two Ears,
which must also be very strong, because they must with heavy blows
be knock’t upon to draw the Sholder of the square shank on the Bar,
when the square Pin is in the Eye of the Spindle close and steddy up
to the Cube on the Spindle. The square Pin of the Bar marked c is
made to fit just into the Eye, through the middle of the Cube of the
Spindle, on the hither end of this square Pin is made a Sholder or
stop to this square Pin, as at d. This Sholder must be Filed exactly
Flat on all its four insides, that they may be drawn close and tight up
to any flat side of the Cube on the Spindle; It is two Inches square,
that it may be drawn the firmer, and stop the steddyer against any of
the flat sides of the said Cube, when it is hard drawn by the strength
of the Female-Screw in the aforesaid Nut at C. The thickness from d
to e of this Sholder is about three quarters of an Inch, and is Bevil’d
off towards the Handle of the Bar with a small Molding.
The substance of this Bar, as aforesaid, is about an Inch and a
quarter; but its Corners are all the way slatted down till within five
Inches of the end: And from these five Inches to the end, it is taper’d
away, that the Wooden-Handle may be the stronger forced and
fastned upon it.
About four Inches off the Sholder, the Bar is bowed beyond a right
Angle, yet not with an Angle, but a Bow, which therefore lies ready to
the Press-man’s Hand, that he may Catch at it to draw the Wooden-
Handle of the Bar within his reach.
This Wooden-Handle with long Working grows oft loose; but then it is
with hard blows on the end of it forced on again, which oft splits the
Wooden-Handle and loosens the square Pin at the other end of the
Bar, in the Eye of the Spindle: To remedy which inconvenience, I
used this Help, viz. To weld a piece of a Curtain-Rod as long as the
Wooden-Handle of the Bar, to the end of the Iron Bar, and made a
Male-screw at the other end with a Female-screw to fit it; Then I
bored an hole quite through the Wooden-Handle, and Turn’d the
very end of the Wooden-Handle with a small hollow in it flat at the
bottom, and deep enough to bury the Iron-Nut on the end of the
Curtain-Rod, and when this Curtain-Rod was put through the Hollow
in the Wooden-Handle and Screwed fast to it at the end, it kept the
Wooden-Handle, from flying off; Or if it loosened, by twisting the Nut
once or twice more about, it was fastned again.
¶. 14. Of the Hose, Garter, and Hose-Hooks.
The Hose are the upright Irons in Plate 8. at a a, They are about
three quarters of an Inch square, both their ends have Male-screws
on them; The lower end is fitted into a square Hole made at the
parting of the Hose-Hooks, which by a square Nut with a Female-
screw in it, is Screwed tight up to them; Their upper ends are let into
square Holes made at the ends of the Garter, and by Nuts with
Female-Screws in them, and Ears to turn them about as at l l are
drawn up higher, if the Plattin-Cords are too loose; or else let down
lower if they are too tight: These upper Screws are called the Hose-
Screws.
The Garter (but more properly the Coller) marked b b, is the round
Hoop incompassing the flat Groove or Neck in the Shank of the
Spindle at e e; This round Hoop is made of two half-round Hoops,
having in a Diametrical-line without the Hoop square Irons of the
same piece proceeding from them, and standing out as far as g g,
These Irons are so let into each other, that they comply and run
Range with the square Sholders at both ends, wherein square Holes
are made at the ends of the Hose. They are Screwed together with
two small Screws, as at h h.
The four Hose-Hooks are marked i i i i, They proceed from two
Branches of an Iron Hoop at k encompassing the lower end of the
Spindle, on either Corner of the Branch, and have notches filled in
their outer-sides as in the Figure, which notches are to contain
several Turns of Whip-cord in each notch, which Whip-cord being
also fastned to the Hooks on the Plattin, holds the Plattin tight to the
Hooks of the Hose.
¶. 15. Of the Ribs, and Cramp-Irons.
The Ribs are delineated in Plate 8. at E, they are made of four

square Irons the length of the Wooden-Ribs and End-Rails, viz. four
Foot five Inches long, and three quarters of an Inch square, only one
end is batter’d to about a quarter of an Inch thick, and about two
Inches and an half broad, in which battering four or five holes are
Punch’t for the nailing it down to the Hind-Rail of the Wooden-Ribs.
The Fore-end is also batter’d down as the Hind-end, but bound
downwards to a square, that it may be nailed down on the outer-side
of the Fore-Rail of the Wooden-Ribs.
Into the bottom of these Ribs, within nine Inches of the middle, on
either side is made two Female-Duftails about three quarters of an
Inch broad, and half a quarter of an Inch thick, which Female-Duftails
have Male-Duftails as at a a a a fitted stiff into them, about an Inch
and three quarters long; and these Male-Duftails have an hole
punched at either end, that when they are fitted into the Female-
Duftails in the Ribs, they may in these Holes be Nailed down the
firmer to the Wooden-Ribs.
Plate 9.
These Ribs are to be between the upper and the under-side exactly
of an equal thickness, and both to lye exactly Horizontal in straight
lines; For irregularities will both Mount and Sink the Cramp-Irons,
and make them Run rumbling upon the Ribs.
The upper-sides of these Ribs must be purely Smooth-fil’d and
Pollish’d, and the edges a little Bevil’d roundish away, that they may
be somewhat Arching at the top; because then the Cramp-Irons Run
more easily and ticklishly over them.
The Cramp-Irons are marked F in Plate 8. They are an Inch and an
half long besides the Battering down at both ends as the Ribs were;
They have three holes Punched in each Battering down, to Nail them
to the Planck of the Coffin; They are about half an Inch deep, and
one quarter and an half thick; their upper-sides are smoothed and
rounded away as the Ribs.
¶. 16. Of the Spindle for the Rounce, described in Plate 9. at a.
The Axis or Spindle is a straight Bar of Iron about three quarters of

an Inch square, and is about three Inches longer than the whole
breadth of the Frame of the Ribs, viz. two Foot two Inches: The
farther end of it is Filed to a round Pin (as at a) three quarters of an
Inch long, and three quarters of an Inch in Diameter; the hither end is
filed away to such another round Pin, but is two Inches and a quarter
long (as at b); at an Inch and a quarter from this end is Filed a
Square Pin three quarters of an Inch long, and within half an Inch of
the end is Filed another round Pin, which hath another Male-Screw
on it, to which is fitted a square Iron Nut with a Female-Screw in it.
On the Square Pin is fitted a Winch somewhat in form like a Jack-
winch, but much stronger; the Eye of which is fitted upon the Square
aforesaid, and Screwed up tight with a Female-Screw. On the
straight Shank of this Winch is fitted the Rounce, marked e.
The round ends of this Axis are hung up in two Iron-Sockets (as at c
c) fastned with Nails (but more properly with Screws) on the outside
the Wooden Frame of the Ribs.
The Girt-Barrel marked d is Turned of a Piece of Maple or Alder-
wood, of such a length, that it may play easily between the two
Wooden Ribs; and of such a diameter, that in one revolution of it,
such a length of Girt may wind about it as shall be equal to half the
length contained between the fore-end Iron of the Tympan, and the
inside of the Rail of the Inner-Tympan; because two Revolutions of
this Barrel must move the Carriage this length of space.
This Barrel is fitted and fastned upon the Iron Axis, at such a
distance from either end, that it may move round between the
Wooden Ribs aforesaid.
¶. 17. Of the Press-Stone.
The Press-Stone should be Marble, though sometimes Master

Printers make shift with Purbeck, either because they can buy them
cheaper, or else because they can neither distinguish them by their
appearance, or know their different worths.
Its thickness must be all the way throughout equal, and ought to be
within one half quarter of an Inch the depth of the inside of the
Coffin; because the matter it is Bedded in will raise it high enough.
Its length and breadth must be about half an Inch less than the
length and breadth of the inside of the Coffin: Because Justifiers of
Wood, the length of every side, and almost the depth of the Stone,
must be thrust between the insides of the Coffin and the outsides of
the Stone, to Wedge it tight and steddy in its place, after the Press-
man has Bedded it. Its upper-side, or Face must be exactly straight
and smooth.
I have given you this description of the Press-Stone, because they
are thus generally used in all Printing-Houses: But I have had so
much trouble, charge and vexation with the often breaking of Stones,
either through the carelesness or unskilfulness (or both) of Press-
men, that necessity compell’d me to consider how I might leave them
off; and now by long experience I have found, that a piece of
Lignum-vitæ of the same size, and truly wrought, performs the office
of a Stone in all respects as well as a Stone, and eases my mind, of
the trouble, charge and vexation aforesaid, though the first cost of it
be greater.
¶. 18. Of the Plattin marked d in Plate 9.
The Plattin is commonly made of Beechen-Planck, two Inches and

an half thick, its length about fourteen Inches, and its breadth about
nine Inches. Its sides are Tryed Square, and the Face or under-side
of the Plattin Plained exactly straight and smooth. Near the four
Corners on the upper-side, it hath four Iron Hooks as at a a a a,
whose Shanks are Wormed in.
In the middle of the upper-side is let in and fastned an Iron Plate
called the Plattin-Plate, as b b b b, a quarter of an Inch thick, six
Inches long, and four Inches broad; in the middle of this Plate is
made a square Iron Frame about half an Inch high, and half an Inch
broad, as at c. Into this square Frame is fitted the Stud of the Plattin
Pan, so as it may stand steddy, and yet to be taken out and put in as
occasion may require.
The Stud marked d, is about an Inch thick, and then spreads wider
and wider to the top (at e e e e) of it, till it becomes about two Inches
and an half wide; and the sides of this spreading being but about half
a quarter of an Inch thick makes the Pan. In the middle of the bottom
of this Pan is a small Center hole Punch’d for the Toe of the Spindle
to work in.
¶. 19. Of the Points and Point-Screws.
The Points are made of Iron Plates about the thickness of a Queen
Elizabeth Shilling: It is delineated at e in Plate 9. which is sufficient to
shew the shape of it, at the end of this Plate, as at a, stands upright
the Point. This Point is made of a piece of small Wyer about a
quarter and half quarter of an Inch high, and hath its lower end Filed
away to a small Shank about twice the length of the thickness of the
Plate; so that a Sholder may remain. This small Shank is fitted into a
small Hole made near the end of the Plate, and Revetted on the
other side, as was taught Numb. 2. Fol. 24. At the other end of the
Plate is filed a long square notch in the Plate as at b c quarter and
half quarter Inch wide, to receive the square shank of the Point-
Screws.
The Point-Screw marked f is made of Iron; It hath a thin Head about
an Inch square, And a square Shank just under the Head, an Inch
deep, and almost quarter and half quarter Inch square, that the
square Notch in the hinder end of the Plate may slide on it from end
to end of the Notch; Under this square Shank is a round Pin filed
with a Male-Screw upon it, to which is fitted a Nut with a Female-
Screw in it, and Ears on its outside to twist about, and draw the Head
of the Shank close down to the Tympan, and so hold the Point-Plate
fast in its Place.
¶. 20. Of the Hammer, described at h, and Sheeps-Foot

described at i in Plate 9.
The Hammer is a common Hammer about a quarter of a Pound

weight; It hath no Claws but a Pen, which stands the Press-man
instead when the Chase proves so big, that he is forced to use small
Quoins.
The Figure of the Sheeps-Foot is description sufficient. Its use is to
nail and un-nail the Balls.
The Sheeps-Foot is all made of Iron, with an Hammer-head at one
end, to drive the Ball-Nails into the Ball-Stocks, and a Claw at the
other end, to draw the Ball-Nails out of the Ball-Stocks.
¶. 21. Of the Foot-step, Girts, Stay of the Carriage, Stay of the
Frisket, Ball-Stocks,
Paper-Bench, Lye-Trough, Lye-Brush, Lye-Kettle, Tray to wet
Paper
in, Weights to Press Paper, Pelts, or Leather, Wool or Hair, Ball-
Nails or Pumping-Nails.
The Foot-Step is an Inch-Board about a Foot broad, and sixteen

Inches long. This Board is nailed upon a piece of Timber about
seven or eight Inches high, and is Bevil’d away on its upper-side, as
is also the Board on its under-side at its hither end, that the Board
may stand aslope upon the Floor. It is placed fast on the Floor under
the Carriage of the Press. Its Office shall be shewed when we come
to treat of Exercise of the Press-man.
Girts are Thongs of Leather, cut out of the Back of an Horse-hide, or
a Bulls hide, sometimes an Hogs-hide. They are about an Inch and
an half, or an Inch and three quarters broad. Two of them are used
to carry the Carriage out and in. These two have each of them one of
their ends nailed to the Barrel on the Spindle of the Rounce, and the
other ends nailed to the Barrel behind the Carriage in the Planck of
the Coffin, and to the Barrel on the fore-end of the Frame of the
Coffin.
The Stay of the Carriage is sometimes a piece of the same Girt
fastned to the outside of the further Cheek, and to the further hinder
side of the Frame of the Carriage. It is fastned at such a length by
the Press-man, that the Carriage may ride so far out, as that the
Irons of the Tympan may just rise free and clear off the fore-side of
the Plattin.
Another way to stay the Carriage is to let an Iron Pin into the upper-
side of the further Rail of the Frame of the Ribs, just in the place
where the further hinder Rail of the Carriage stands projecting over
the Rib-Rail, when the Iron of the Tympan may just rise free from the
Fore-side of the Plattin; for then that projecting will stop against the
Iron Pin.
The Stay of the Frisket is made by fastning a Batten upon the middle
of the Top-side of the Cap, and by fastning a Batten to the former
Batten perpendicularly downwards, just at such a distance, that the
upper-side of the Frisket may stop against it when it is turned up just
a little beyond a Perpendicular. When a Press stands at a convenient
distance from a Wall, that Wall performs the office of the aforesaid
Stay.
Ball-Stocks are Turn’d of Alder or Maple. Their Shape is delineated
in Plate 9. at g: They are about seven Inches in Diameter, and have
their under-side Turned hollow, to contain the greater quantity of
Wool or Hair, to keep the Ball-Leathers plump the longer.
The Lye-Trough (delineated in Plate 9. at k) is a Square Trough
made of Inch-Boards, about four Inches deep, two Foot four Inches
long, and one Foot nine Inches broad, and flat in the Bottom. Its
inside is Leaded with Sheet-Lead, which reaches up over the upper
Edges of the Trough. In the middle of the two ends (for so I call the
shortest sides) on the outer-sides as a a, is fastned a round Iron Pin,
which moves in a round hole made in an Iron Stud with a square
Sprig under it, to be drove and fastned into a Wooden Horse, which
Horse I need not describe, because in Plate aforesaid I have given
you the Figure of it.
The Paper-Bench is only a common Bench about three Foot eight
Inches long, one Foot eight Inches broad, and three Foot four Inches
high.
The Lye-Brush is made of Hogs-Bristles fastned into a Board with
Brass-Wyer, for durance sake: Its Board is commonly about nine
Inches long, and four and an half Inches broad; and the length of the
Bristles about three Inches.
To perform the Office of a Lye-Kettle (which commonly holds about
three Gallons) the old-fashion’d Chafers are most commodious, as
well because they are more handy and manageable than Kettles
with Bails, as also because they keep Lye longer hot.
The Tray to Wet Paper in is only a common Butchers Tray, large
enough to Wet the largest Paper in.
The Weight to Press Paper with, is either Mettal, or Stone, flat on the
Bottom, to ly steddy on the Paper-Board: It must be about 50 or 60
pound weight.
For Pelts or Leather, Ball-Nails or Pumping-Nails, Wool or Hair,
Vellom or Parchment or Forrel, the Press-man generally eases the
Master-Printer of the trouble of choosing, though not the charge of
paying for them: And for Paste, Sallad Oyl, and such accidental
Requisites as the Press-man in his work may want, the Devil
commonly fetches for him.
¶. 22. Of Racks to Hang Paper on, and of the Peel.
Our Master-Printer must provide Racks to hang Paper on to Dry.

They are made of Deal-board Battens, square, an Inch thick, and an
Inch and an half deep, and the length the whole length of the Deal,
which is commonly about ten or eleven Foot long, or else so long as
the convenience of the Room will allow: The two upper corners of
these Rails are rounded off that they may not mark the Paper.
These Racks are Hung over Head, either in the Printing-House, or
Ware-house, or both, or any other Room that is most convenient to
Dry Paper in; they are hung athwart two Rails an Inch thick, and
about three or four Inches deep, which Rails are fastned to some
Joysts or other Timber in the Ceiling by Stiles perpendicular to the
Ceiling; These Rails stand so wide assunder, that each end of the
Racks may hang beyond them about the distance of two Foot, and
have on their upper edge at ten Inches distance from one another,
so many square Notches cut into them as the whole length of the
Rail will bear; Into these square notches the Racks are laid parallel
to each other with the flat side downwards, and the Rounded off side
upwards.
The Peel is described in Plate 9. at l, which Figure sufficiently shews
what it is; And therefore I shall need say no more to it, only its
Handle may be longer or shorter according as the height of the
Room it is to be used in may require.
¶. 23. Of Inck.
The providing of good Inck, or rather good Varnish for Inck, is none
of the least incumbent cares upon our Master-Printer, though
Custom has almost made it so here in England; for the process of
making Inck being as well laborious to the Body, as noysom and
ungrateful to the Sence, and by several odd accidents dangerous of
Firing the Place it is made in, Our English Master-Printers do
generally discharge themselves of that trouble; and instead of having
good Inck, content themselves that they pay an Inck-maker for good
Inck, which may yet be better or worse according to the Conscience
of the Inck-maker.
That our Neighbours the Hollanders who exhibit Patterns of good
Printing to all the World, are careful and industrious in all the
circumstances of good Printing, is very notorious to all Book-men;
yet should they content themselves with such Inck as we do, their
Work would appear notwithstanding the other circumstances they
observe, far less graceful than it does, as well as ours would appear
more beautiful if we used such Inck as they do: for there is many
Reasons, considering how the Inck is made with us and with them,
why their Inck must needs be better than ours. As First, They make
theirs all of good old Linseed-Oyl alone, and perhaps a little Rosin in
it sometimes, when as our Inck-makers to save charges mingle
many times Trane-Oyl among theirs, and a great deal of Rosin;
which Trane-Oyl by its grossness, Furs and Choaks up a Form, and
by its fatness hinders the Inck from drying; so that when the Work
comes to the Binders, it Sets off; and besides is dull, smeary and
unpleasant to the Eye. And the Rosin if too great a quantity be put in,
and the Form be not very Lean Beaten, makes the Inck turn yellow:
And the same does New Linseed-Oyl.
Secondly, They seldom Boyl or Burn it to that consistence the
Hollanders do, because they not only save labour and Fewel, but
have a greater weight of Inck out of the same quantity of Oyl when
less Burnt away than when more Burnt away; which want of Burning
makes the Inck also, though made of good old Linseed-Oyl Fat and
Smeary, and hinders its Drying; so that when it comes to the Binders
it also Sets off.
Thirdly, They do not use that way of clearing their Inck the
Hollanders do, or indeed any other way than meer Burning it,
whereby the Inck remains more Oyly and Greasie than if it were well
clarified.
Fourthly, They to save the Press-man the labour of Rubbing the
Blacking into Varnish on the Inck-Block, Boyl the Blacking in the
Varnish, or at least put the Blacking in whilst the Varnish is yet
Boyling-hot, which so Burns and Rubifies the Blacking, that it loses
much of its brisk and vivid black complexion.
Fifthly, Because Blacking is dear, and adds little to the weight of
Inck, they stint themselves to a quantity which they exceed not; so
that sometimes the Inck proves so unsufferable Pale, that the Press-
man is forc’d to Rub in more Blacking upon the Block; yet this he is
often so loth to do, that he will rather hazard the content the Colour
shall give, than take the pains to amend it: satisfying himself that he
can lay the blame upon the Inck-maker.
Having thus hinted at the difference between the Dutch and English
Inck, I shall now give you the Receipt and manner of making the
Dutch-Varnish.
They provide a Kettle or a Caldron, but a Caldron is more proper,
such an one as is described in Plate 9. at m. This Vessel should hold
twice so much Oyl as they intend to Boyl, that the Scum may be
some considerable time a Rising from the top of the Oyl to the top of
the Vessel to prevent danger. This Caldron hath a Copper Cover to
fit the Mouth of it, and this Cover hath an Handle at the top of it to
take it off and put it on by. This Caldron is set upon a good strong
Iron Trevet, and fill’d half full of old Linseed-Oyl, the older the better,
and hath a good Fire made under it of solid matter, either Sea Coal,
Charcoal or pretty big Chumps of Wood that will burn well without
much Flame; for should the Flame rise too high, and the Oyl be very
hot at the taking off the Cover of the Caldron, the fume of the Oyl
might be apt to take Fire at the Flame, and endanger the loss of the
Oyl and Firing the House: Thus they let Oyl heat in the Caldron till
they think it is Boyling-hot; which to know, they peel the outer Films
of an Oynion off it, and prick the Oynion fast upon the end of a small
long Stick, and so put it into the heating Oyl: If it be Boyling-hot, or
almost Boyling-hot, the Oynion will put the Oyl into a Fermentation,
so that a Scum will gather on the top of the Oyl, and rise by degrees,
and that more or less according as it is more or less Hot: But if it be
so very Hot that the Scum rises apace, they quickly take the Oynion
out, and by degrees the Scum will fall. But if the Oyl be Hot enough,
and they intend to put any Rosin in, the quantity is to every Gallon of
Oyl half a Pound, or rarely a whole Pound. The Rosin they beat
small in a Mortar, and with an Iron Ladle, or else by an Handful at a
time strew it in gently into the Oyl lest it make the Scum rise too fast;
but every Ladle-full or Handful they put in so leasurely after one
another, that the first must be wholly dissolv’d before they put any
more in; for else the Scum will Rise too fast, as aforesaid: So that
you may perceive a great care is to keep the Scum down: For if it
Boyl over into the Fire never so little, the whole Body of Oyl will take
Fire immediately.
If the Oyl be Hot enough to Burn, they Burn it, and that so often till it
be Hard enough, which sometimes is six, seven, eight times, or
more.
To Burn it they take a long small Stick, or double up half a Sheet of
Paper, and light one end to set Fire to the Oyl; It will presently Take if
the Oyl be Hot enough, if not, they Boyl it longer, till it be.
To try if it be Hard enough, they put the end of a Stick into the Oyl,
which will lick up about three or four drops, which they put upon an
Oyster-shell, or some such thing, and set it by to cool, and when it is
cold they touch it with their Fore or Middle-Finger and Thumb, and
try its consistence by sticking together of their Finger and Thumb; for
if it draw stiff like strong Turpentine it is Hard enough, if not, they
Boyl it longer, or Burn it again till it be so consolidated.
When it is well Boyled they throw in an Ounce of Letharge of Silver
to every four Gallons of Oyl to Clarifie it, and Boyl it gently once
again, and then take it off the Fire to stand and cool, and when it is
cool enough to put their Hand in, they Strain it through a Linnen
Cloath, and with their Hands wring all the Varnish out into a Leaded
Stone Pot or Pan, and keeping it covered, set it by for their use; The
longer it stands by the better, because it is less subject to turn Yellow
on the Paper that is Printed with it.
This is the Dutch way of making Varnish, and the way the English
Inck-makers ought to use.
Note, First, That the Varnish may be made without Burning the Oyl,
viz. only with well and long Boyling it; for Burning is but a violent way
of Boyling, to consolidate it the sooner.
Secondly, That an Apple or a Crust of Bread, &c. stuck upon the end
of a Stick instead of an Oynion will also make the Scum of the Oyl
rise: For it is only the Air contained in the Pores of the Apple, Crust
or Oynion, &c. pressed or forced out by the violent heat of the Oyl,
that raises the many Bubbles on the top of the Oyl: And the
connection of those Bubbles are vulgarly called Scum.
Thirdly, The English Inck-makers that often make Inck, and that in
great quantities, because one Man may serve all England, instead of
setting a Caldron on a Trevet, build a Furnace under a great
Caldron, and Trim it about so with Brick, that it Boyls far sooner and
more securely than on a Trevet; because if the Oyl should chance to
Boyl over, yet can it not run into the Fire, being Fenced round about
with Brick as aforesaid, and the Stoking-hole lying far under the
Caldron.
Fourthly, When for want of a Caldron the Master-Printer makes
Varnish in a Kettle, He provides a great piece of thick Canvass, big
enough when three or four double to cover the Kettle, and also to
hang half round the sides of the Kettle: This Canvass (to make it
more soluble) is wet in Water, and the Water well wrung out again,
so that the Canvass remains only moist: Its use is to throw flat over
the Mouth of the Kettle when the Oyl is Burning, to keep the smoak
in, that it may stifle the Flame when they see cause to put it out. But
the Water as was said before, must be very well wrung out of the
Canvass, for should but a drop or two fall from the sides of it into the
Oyl when it is Burning, it will so enrage the Oyl, and raise the Scum,
that it might endanger the working over
the top of the
Kettle
.
Having shewn you the Master-Printers Office, I account it suitable to

proper Method, to let you know how the Letter-Founder Cuts the
Punches, how the Molds are made, the Matrices Sunck, and the
Letter Cast and Drest, for all these Operations precede the
Compositers Trade, as the Compositers does the Press-mans;
wherefore the next Exercises shall be (God willing) upon Cutting of
the Steel-Punches.
MECHANICK EXERCISES:
Or, the Doctrine of
Handy-works.
Applied to the Art of
Letter-Cutting.
PREFACE.
LEtter-Cutting is a Handy-Work hitherto kept so conceal’d among the

Artificers of it, that I cannot learn any one hath taught it any other;
But every one that has used it, Learnt it of his own Genuine
Inclination. Therefore, though I cannot (as in other Trades) describe
the general Practice of Work-men, yet the Rules I follow I shall shew
here, and have as good an Opinion of these Rules, as those have
that are shyest of discovering theirs. For, indeed, by the appearance
of some Work done, a judicious Eye may doubt whether they go by
any Rule at all, though Geometrick Rules, in no Practice whatever,
ought to be more nicely or exactly observed than in this.
§. 12. ¶. 1. Of Letter-Cutters Tools.

The making of Steel-Punches is a Branch of the Smith’s Trade: For,
as I told you in the Preface to Numb. 1. The Black-Smith’s Trade
comprehends all Trades that use either Forge or File, from the
Anchor-Smith, to the Watch-maker: They all working by the same
Rules, though not with equal exactness; and all using the same
Tools, though of different Sizes from those the Common Black-Smith

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Application and Theory of Petri Nets

and Concurrency 36th International

Application and Theory of Petri Nets and Concurrency

Application and Theory of Petri Nets and Concurrency

Formal Concept Analysis 13th International Conference

Artificial Intelligence in Education 17th International

Intelligent Mechanisms for Network Configuration and

Analytical and Stochastic Modelling Techniques and

Mathematics of Program Construction 12th International

Advanced Information Systems Engineering 27th

Application and Theory

Application and Theory

ISSN 0302-9743 ISSN 1611-3349 (electronic)

Library of Congress Control Number: 2015939435

LNCS Sublibrary: SL1 – Theoretical Computer Science and General Issues

Springer Cham Heidelberg New York Dordrecht London

Printed on acid-free paper

Springer International Publishing AG Switzerland is part of Springer Science+Business Media

June 2015 Raymond Devillers

Artem Polyvyanyy Queensland University of Technology, Australia

Workshops and Tutorials Chairs

Tools Exhibition Chair

On Quantitative Modelling and Verification of DNA Walker Circuits

Process Mining Reloaded: Event Structures as a Unified Representation

Modeling Quantitative Aspects of Concurrent Systems Using Weighted

On Interval Process Semantics of Petri Nets with Inhibitor Arcs . . . . . . . . . 77

An SRN-Based Resiliency Quantification Approach . . . . . . . . . . . . . . . . . . 98

Non-atomic Transition Firing in Contextual Nets . . . . . . . . . . . . . . . . . . . . 117

Discrete Parameters in Petri Nets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137

Negotiation Programs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 157

Nested-Unit Petri Nets: A Structural Means to Increase Efficiency

Charlie – An Extensible Petri Net Analysis Tool (Tool Paper) . . . . . . . . . . . 200

Petri Nets with Structured Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 212

On the Reversibility of Live Equal-Conflict Petri Nets . . . . . . . . . . . . . . . . 234

SNAKES: A Flexible High-Level Petri Nets Library (Tool Paper) . . . . . . . . 254

Characterizing Stable Inequalities of Petri Nets . . . . . . . . . . . . . . . . . . . . . 266

Process Discovery Using Localized Events . . . . . . . . . . . . . . . . . . . . . . . . 287

Workflow Management Principles for Interactions Between Petri

Author Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 351

Benoı̂t Barbot(B) and Marta Kwiatkowska(B)

Department of Computer Science, University of Oxford,

Abstract. Molecular programming is an emerging ﬁeld concerned with

conﬁgured to perform speciﬁc computational or mechanical tasks. The com-

2 Background on Molecular Walkers

Fig. 1. A double-junction DNA walker circuit ([16])

Fig. 2. The stepping action of the walker ([16])

Computing Boolean functions using nanotechnologies such as the DNA

in [50]. Maximum interaction distance was observed to be dM = 24 nm. Taking

This determines a sphere of reach of up to dM around the walker-anchorage

3 Stochastic Models and Analysis Techniques

3.1 Continuous-Time Markov Chains (CTMC)

under the assumption of constant volume and temperature, is a (homogeneous)

s = s , and 1 − s =s R(s, s ) otherwise, and π0 = s0 .

3.2 Quantitative Verification for CTMCs

– temporal logic MTL (metric temporal logic) [10]which is an extension of

3.3 Numerical Verification Methods for CTMCs

Uniformisation. Uniformisation (see e.g. [35] translates the problem of com-

Fast Adaptive Uniformisation (FAU). Fast adaptive uniformisation

3.4 Statistical Model Checking

An advantage of statistical model checking is that it can be parallelised very

Confidence Intervals. When one computes a probability estimate for some

Classical statistical inequality can be used to derive conﬁdence intervals from

Sequential Estimation. Using additional hypotheses, the required number of

– Splitting relies on deﬁning a sequence of successive embeddedings of subsets

s = s , and 1 − s =s R(s, s ) otherwise, and π0 = s0 .