Processes in Space

ddd Stochas*c, Spa*al and Concurrent Biological Processes Modeling Yifei Bao, Philippe Bidinger, Eduardo Bonelli, Vishakha Sharma, Jus*n Sousa, and Peter Zafonte Advisor: Adriana B. Compagnoni Department of Computer Science, Schaefer School of Engineering and Science, Stevens Ins*tute of Technology, Hoboken, NJ 07030 Introduc*on We define and implement a language for the stochas*c simula*on of biological processes with spa*al informa*on, which is an extension of the SPiM (Stochas*c Pi Machine) language. Simula*ons in SPiM assume that all processes are uniformly distributed in space, and interac*ons between processes are scheduled randomly based on concentra*ons and reac*on rates. Consequently, it cannot accurately model reac*ons that do not occur in a homogeneous mixture. In order to address this limita*on, our new language places mobile processes in 3D space, where processes can interact only if they are within communica*on distance. We apply our language to modeling a drug delivery nanosystem in collabora*on with Prof. Libera and Prof. Sukhishvili From CCBBME. Drug Delivery System Modeling 1. Drug Delivery System 2. Our Language Simula*on Background Stochas*c Pi Machine (SPiM) Our Language New Spa*al Features • Process state includes spa*al informa*on – Each process has a posi*on and three vectors that define its local system of coordinates • This state can be modified by applica*on of affine maps (transla*on, rota*on..) – Simula*on of movement (transla*on, rota*ons) • Interac*ons may be condi*oned by the distance between two molecules Graduate Student Research Conference October 6, 2010 Ongoing work 1. New features (shapes) 2. Valida*on (correctness of simula*on) 3. Improved performance of simula*on algorithm 4. Drug delivery system modeling (controlled experiments)

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Transcript of Processes in Space

ddd

Stochas*c, Spa*al and Concurrent Biological Processes Modeling Yifei Bao, Philippe Bidinger, Eduardo Bonelli, Vishakha Sharma,

Jus*n Sousa, and Peter Zafonte Advisor: Adriana B. Compagnoni

Department of Computer Science, Schaefer School of Engineering and Science, Stevens Ins*tute of Technology, Hoboken, NJ 07030

Introduc*on We define and implement a language for the

stochas*c simula*on of biological processes with

spa*al informa*on, which is an extension of the

SPiM (Stochas*c Pi Machine) language. Simula*ons

in SPiM assume that all processes are uniformly

distributed in space, and interac*ons between

processes are scheduled randomly based on

concentra*ons and reac*on rates. Consequently, it

cannot accurately model reac*ons that do not occur

in a homogeneous mixture. In order to address this

limita*on, our new language places mobile processes

in 3D space, where processes can interact only if they

are within communica*on distance. We apply our

language to modeling a drug delivery nano-‐system in

collabora*on with Prof. Libera and Prof. Sukhishvili

From CCBBME.

Drug Delivery System Modeling 1. Drug Delivery System

2. Our Language -‐-‐ Simula*on

Background Stochas*c Pi Machine (SPiM)

Our Language New Spa*al Features • Process state includes spa*al informa*on – Each process has a posi*on and three vectors that define its local system of coordinates

• This state can be modified by applica*on of affine maps (transla*on, rota*on..)

– Simula*on of movement (transla*on, rota*ons) • Interac*ons may be condi*oned by the distance between two molecules

Graduate Student Research Conference

October 6, 2010

Ongoing work 1. New features (shapes)

2. Valida*on (correctness of simula*on)

3. Improved performance of simula*on algorithm 4. Drug delivery system modeling (controlled experiments)