0 Up votes0 Down votes

1 views15 pagespresentation FOI 2015

Feb 24, 2016

© © All Rights Reserved

PDF, TXT or read online from Scribd

presentation FOI 2015

© All Rights Reserved

1 views

presentation FOI 2015

© All Rights Reserved

- Steve Jobs
- The Woman Who Smashed Codes: A True Story of Love, Spies, and the Unlikely Heroine who Outwitted America's Enemies
- NIV, Holy Bible, eBook
- NIV, Holy Bible, eBook, Red Letter Edition
- Cryptonomicon
- Hidden Figures Young Readers' Edition
- Everybody Lies: Big Data, New Data, and What the Internet Can Tell Us About Who We Really Are
- Make Your Mind Up: My Guide to Finding Your Own Style, Life, and Motavation!
- Console Wars: Sega, Nintendo, and the Battle that Defined a Generation
- The Golden Notebook: A Novel
- Alibaba: The House That Jack Ma Built
- Life After Google: The Fall of Big Data and the Rise of the Blockchain Economy
- Hit Refresh: The Quest to Rediscover Microsoft's Soul and Imagine a Better Future for Everyone
- Hit Refresh: The Quest to Rediscover Microsoft's Soul and Imagine a Better Future for Everyone
- The Innovators: How a Group of Hackers, Geniuses, and Geeks Created the Digital Revolution
- The 10X Rule: The Only Difference Between Success and Failure
- Autonomous: A Novel

You are on page 1of 15

Bogdan Aman

Gabriel Ciobanu

Bld. Carol I, no.8, 700505, Iasi, Rom

ania

FOI 2015

24-29 August 2015

B.Aman; G.Ciobanu

1 / 15

Outline

Introduction

Safety Automata

Conclusion

B.Aman; G.Ciobanu

2 / 15

Introduction

A fundamental mechanism in most of the living cells is the Na+ /K + ATPase that is essential for the maintenance of Na+ and K + concentrations across the membrane by transporting Na+ out of the cell and

K + back into the cell.

In this paper we model the movement of ions and the conformational transformations of ion transporters (NaK ion pumps, Na and

K ion channels) using a very simple but powerful new formalism called

BioMaxP .

BioMaxP allows to work with multisets of ions, explicit interpretation of

the transportation (from inside to outside, and from outside to inside)

based on the number of existing ions, and a maximal parallel execution

of the involved pumps.

B.Aman; G.Ciobanu

3 / 15

BioMaxP Syntax

Processes

P, Q ::=

amax ?(f (u : T )) then P p

id (v ) p

P|Q

(sending)

(receiving)

(recursion)

(parallel)

makes the channel a available for sending z units/ions of type T only

if the total available quantity of ions of type T is greater than min.

A constraint max associated to a receiving action amax ?(x : T ) then P

along a channel a is activated only if the number of ions of the type T

available is less than max.

B.Aman; G.Ciobanu

4 / 15

BioMaxP Syntax

Processes

P, Q ::=

amax ?(f (u : T )) then P p

id (v ) p

P|Q

(sending)

(receiving)

(recursion)

(parallel)

Remark

In order to focus on the local interaction aspects of BioMaxP , we abstract from arithmetical operations (using the function f ), considering by

default that the simple ones (comparing, addition, subtraction) are included

in the language.

B.Aman; G.Ciobanu

5 / 15

(Com)

v :T

min |T | max

and

{v /u}

and |T | = |T | v if f = id or |T | = |T | + v if f = add

id

{v /u}Pid

Pid

(Call)

id

id (v )

(Par1)

1

P1

P1

P 6

1

P1 | P

P1 | P

B.Aman; G.Ciobanu

Pid

def

where id (v : T ) = Pid

(Par2)

1

P1

P1

2

P2

P2

2

P1 | P2 1

P1 | P2

6 / 15

Example

Consider a system formed from n1 NaK pumps, n2 Na channels and

n3 K channels.

Each pump i is modelled by three processes:

one that models the interaction of the pump with the environment,

one modelling the interaction with the cell and

one that models the transport of ions through the membrane.

channel (one end for input, and another for output), while the molecular

interaction coincides with communication on channels.

NaKPumpEnv (id ) = site2[id ]160 ?(add(yna : NaEnv ))

then site2[id ]2 !h2K i

then p[id ]6 ?(add(yp : P))

then NaKPumpEnv (id )

B.Aman; G.Ciobanu

7 / 15

Safety Automata

Definition

A Safety Automata

where

N is a finite set of nodes;

start

y<=20

10<=y

enter

x:=0, y:=0

E N B(C) NC N is

the set of edges.

x==10

work

x:=0

loop

y<=50

10<=y

y:=0

g ,a,r

hn, g , a, r , n i E . r denotes fresh assignments to variables after the transition is performed.

40<=y

leave

y:=0

end

y<=20

B.Aman; G.Ciobanu

8 / 15

Safety Automata

Is the parallel composition A1 | . . . | An of a set of safety automata

A1 , . . . , An combined into a single system.

Synchronous communication inside the network is by handshake synchronisation of input and output actions.

In this case, the action alphabet consists of

a! symbols (for output actions),

symbols (for internal actions).

B.Aman; G.Ciobanu

9 / 15

Safety Automata

A network state is a pair hn, ui, where n denotes a vector of current nodes

of the network (one for each automaton), and u is an assignment storing

the current values of all network integer variables.

Definition

The operational semantics of a automaton is a transition system where

states are pairs hn, ui and transitions are defined by the rules:

g ,,r

hn, ui

hn[ni /ni ], u i if ni ni , g |= u and u = r [u];

hn, ui

hn[ni /ni ][nj /nj ], u i if there exist i 6= j such that

1

2

gi ,a?,ri

gj ,a!,rj

ni ni , nj nj , gi gj |= u,

u = ri [rj [u]].

B.Aman; G.Ciobanu

10 / 15

Construction

Given a process P without the parallel operator at the top level, we associate

to it an automaton A = hN, n0 , E i, where n0 = l0 , N = {l0 }, E = . The

components N and E are updated depending on the structure of process P:

for P = amin !hv i then P1 we have

E = E {n, min |T |, a!, , li +1}.

N =(

N {li +1} where i = max{j | lj N};

E {li , |T | max, a!, |T | = |T | |u|, li +1 }, if f = id;

E=

E {li , |T | max, a!, |T | = |T | + |u|, li +1 }, if f = add.

B.Aman; G.Ciobanu

11 / 15

Building an automaton for each process leads to the next result about the

equivalence between a BioMaxP process P and its corresponding automaton

AP in state hnP , uP i (i.e., (AP , hnP , uP i). Their transition systems differ

not only in transitions, but also in states; thus, we adapt the notion of

bisimilarity:

Definition

A symmetric relation between BioMaxP processes and their corresponding

P ,

then hnP , uP i

hnP , uP i and (P , (AP , hnP , uP i)) for some P .

B.Aman; G.Ciobanu

12 / 15

Theorem

Given a BioMaxP process P, there exists an automata AP with a bisimilar

behaviour. Formally, P AP .

Corollary

For a BioMaxP process, the reachability problem is decidable.

B.Aman; G.Ciobanu

13 / 15

Conclusion

In this paper we try to unify and extend our previous attempts to model

the movement of ions using the sodium-potassium pump by introducing

a simple, elegant and powerful new formalism called BioMaxP .

BioMaxP is able to:

abstract conditions associated with evolution (e.g., the number of ions

is between certain thresholds).

This approach facilitates a better understanding of the processes happening in a cell viewed as a complex system of ion pumps working in

parallel.

As future work we plan to use Uppaal to verify some properties of the

systems modelled in BioMaxP .

B.Aman; G.Ciobanu

14 / 15

Thank you!

B.Aman; G.Ciobanu

15 / 15

- project rubric-19-1Uploaded byapi-261139685
- Math Quiz Bee ProposalUploaded byGeraldine Madrigal
- Automata LecturesUploaded byranaateeq
- UML2SAN_TOWARD_A_NEW_SOFTWARE_PERFORMANC.pdfUploaded byRai Gulzar
- aboriginal water lessonUploaded byapi-272315026
- 2 september 27 2019Uploaded byapi-262810562
- AI_Lect_12Uploaded byapi-3696125
- Toc Project ReportUploaded byKrishna Reddy
- newsletter decemberUploaded byapi-235411487
- goal planUploaded byapi-241633936
- Final236_236Uploaded byUsman Tariq
- Su Jits Maths TalksUploaded byolaydyosa
- FractionSenseUploaded bytututi22
- homework 25-05 - 29- 05Uploaded byapi-239483488
- productFlyer_978-3-540-22551-5Uploaded byTeferi
- c - Subtracting Two Numbers Without Using '-' Operator - Stack OverflowUploaded byPoovannanManivannan
- 8th Math Solved Exercises Unit 7 NotesUploaded byAmjed Iqbal
- Title DefenseUploaded byMauro Ubungen
- 021811gilmartinUploaded bypambowman
- 3-25-13Uploaded bymacoffey
- proj_infoUploaded bythiren ukarde
- Grade 4 maths worksheetsUploaded byleenaap
- Second Grade WebsitesUploaded byDana Williams
- summer parent meetingUploaded byapi-318231449
- term letterUploaded byapi-419699524
- Time Table.pdfUploaded byPeter Sakalah
- week 6 newsletter 2017Uploaded byapi-296339827
- ANSWER SHEET.docxUploaded byKenneth Salivio
- Sonnets Math 1Uploaded bySapere Aude
- weekly agendaUploaded byapi-401785334

- 15 Physics.pdfUploaded byPrakash Kothare
- p Week II Kinematics ViiiUploaded bySesha Sai Kumar
- 2010 Haiti EarthquakeUploaded byAdam Tang
- R-pramarketingliteraturemanuals20544482 Cyl-tel3tank-Tel3 User Manual - Rev 2Uploaded byaLeXiN
- MIL-STD-1628 Fillet Weld Size, Strength, and EfficiencyUploaded byGarthSanders
- Fouling of Heat exchangersUploaded byOdalis Alcantara
- SmokeTreatmentinWolloOpalUploaded byRobyn Hawk
- Fractal Analysis of Shoreline Patterns for Crenulate-bay Beaches, Southern ChinaUploaded byJavier Enríquez
- W2-303E_SectionBillet_Mills.pdfUploaded byfonsekapdl
- radars WitH loW probabilitY oF interceptionUploaded bySally
- Knotting of Optical VorticesUploaded by拳醉
- 2.12 Mass Spectra and IRUploaded bySandyDavid
- CTAB-Bentonit Untuk Adsorpsi Zat Warna Supranol Yellow 4GLUploaded byedywiyono2013
- A Practical Guide to Wig ModelsUploaded bydogbreath27
- Cxhapter 10Uploaded bysdrtfg
- Guided Inquiry Why is Sticky Tape StickyUploaded by신재호
- Materials_ch01.pptUploaded bysaezh1
- Microwave Assignment 2_Nkamwesiga NicholasUploaded byNkamwesiga Nicholas
- Nitronic60 MainUploaded byAnonymous IpqcBB
- Application of gates in industryUploaded bySaad Ahmed
- Causes and Costs of Gasket FailureUploaded bysachinumarye
- 2004-10-27 Work Problems-Solutions.docUploaded byvirkarash
- 2007 Energy InternationalUploaded byklavdaki3823
- Rudiments of Io AnalysisUploaded byJay-ar Mira
- ASAP2020 Operator's ManualUploaded byNJ QP
- 3A978-3-319-27460-7Uploaded by沈益
- Anderson Distribution of the Correlation CoefficientUploaded bydauren_pc
- Endeavor Analysis and Predictive Engineering Fatigue EssentialsUploaded byN.g. Nagaraj
- HW2Uploaded byCameron O'Neal
- Different Types of Rudder #SafkatUploaded bySafkat Jubaer Shuvo

## Much more than documents.

Discover everything Scribd has to offer, including books and audiobooks from major publishers.

Cancel anytime.