Current Past Me Papers Talks Artifacts Extra HotPage

Highlights

Morphisms of Reaction Networks that Couple Structure to Function (BMC Systems Biology'14)
Lineage Grammars: Describing, Simulating and Analyzing Population Dynamics. (BMC Bioinformatics'14)
Programmable chemical controllers made from DNA (Nature Nanotech'13)
The Cell Cycle Switch Computes Approximate Majority (Scientific Reports'12)
Programming Chemistry in DNA Addressable Bioreactors (Interface '14)
Two-Domain DNA Strand Displacement (MSCS'13)

Molecular Programming


The goal of molecular programming is the systematic manipulation of matter at the molecular scale, for applications in engineering + technology and biology + medicine.
Structural DNA/RNA nanotechnology currently provides the only fabrication pipeline for truly programmable molecular structures, in the form of static and dynamic nucleic acid assemblies. But through it we can organize also other forms of matter.

 Papers
Programmable chemical controllers made from DNA (Nature Nanotech'13)
Two-Domain DNA Strand Displacement (MSCS'13)
Design and Analysis of DNA Strand Displacement Devices using Probabilistic Model Checking (J.R.S. Interface)
Strand Algebras for DNA Computing (Natural Computing)
A Programming Language for Composable DNA Circuits (J.R.S.Interface)
 Edited Proceedings
DNA 17
 Talks
info Molecular Programming (ECOOP'14)
info Computing with Molecules (DCM'12)
info Two-Domain DNA Strand Displacement (DCM'10)
info Strand Algebras for DNA Computing (DNA '09)
 Tools
info DSD - DNA Strand Displacement Simulator
 Links
Correctness of DNA encodings of chemical reaction networks
DNA Computing and Molecular Programming Conferences
NYUCaltechUWDukeOxfordAarhusMicrosoft

 Outreach
Inner Life of A Cell - Movie
Powering the Cell: Mitochondria - Movie
DNA Strand Displacement - Movies
Nanocrafter - Game
EteRNA - Game

Quantitative Semantics


The semantics of programming languages is based on states and state transitions, through which one can study for example termination, nodeterminism, and concurrency. Adding rates to transitions induces quantitative meanings that can be related to stochastic and even continuous dynamical systems.

 Papers
Morphisms of Reaction Networks that Couple Structure to Function (BMC Systems Biology'14)
On Process Rate Semantics (TCS'08)
A Process Algebra Master Equation (QEST'07)
From Processes to ODEs by Chemistry (IFIP TCS'08)
A Correct Abstract Machine for the Stochastic Pi-calculus (BioConcur'04)
Efficient, Correct Simulation of Biological Processes in Stochastic Pi-calculus (CMSB'07)
A Graphical Representation for Biological Processes in Stochastic Pi-calculus (TCSB)
 Lectures
info On Process Rate Semantics PDF (Warsaw Lectures Extract, March'09)
info Molecules as Automata - Open Lectures PDF PDF PDF PDF (Warsaw, March&May'09)
info Molecules as Automata - Summer School on Natural Computation PDF PDF (BNC'08)
info Process Rate Semantics - Computational and Systems Biology Course (Trento 2008)
 Talks
info Morphisms of Reaction Networks (VEMDP'14)
info Molecules as Automata (DNA'08, ECS'09)
info From Processes to ODEs by Chemistry (TCS'08)
info On Process Rate Semantics (MFPS'08)
info A Graphical Representation for Stochastic π-Calculus (BioConcur '05)
info A Correct Abstract Machine for the Stochastic pi-calculus (BioConcur '04)

Cell Cycle Switch


At the core of the biochemical networks that regulates the cell cycle there is a switch that triggers an irreversible transition from one critical stage of cell division to the next. Its dynamical system behavior is fairly well understood, and could be achieved by many different networks. But in nature, from yeast to us, we find a specific universal structure of the network: what is special about this structure, beyond its required function? To answer this question we shift our perspective from dynamical systems to computing systems. We ask: what does the cell cycle switch compute, and how does it compute it?

 Papers
The Cell Cycle Switch Computes Approximate Majority (Scientific Reports'12)
Transcriptional Regulation is a Major Controller of Cell Cycle Transition Dynamics (PLoS ONE)
 Talks
info The Cell Cycle Switch Computes Approximate Majority  Robert Stewart Distinguished Lecture (Iowa State 2014)

Phosphorelays


Organisms employ a variety of signalling systems to sense and react to their environment. Among the most basic, commonly found in bacteria, lower eukaryotes and plants, are the so-called phosphorelays. These systems transfer sensor information (typically from the cellular membrane) very economically through a chain of chemical reactions.
Despite their widespread use and simple architecture, we are still far from a full understanding of the signal-processing capabilities of phosphorelays.

 Papers
Phosphorelays provide tunable signal processing capabilities for the cell (PLOS CompBio)
Response Dynamics of Phosphorelays Suggest Their Potential Utility in Cell Signaling (J.R.S. Interface)

Immune System


Major Histocompatibility Complex (MHC) class I molecules are a key component of the innate immune system. They continuously select a signature of the cell contents (fragments of any protein present) and present it to the cell surface, where it can be inspected by cytotoxic T lymphocytes that destroy virus-infected and cancerous cells based on such signature. In this mechanism there is a trade-off between speed and accuracy of presentation: we study how various molecular components contribute to optimizing this process.

 Papers
A Peptide Filtering Relation Quantifies MHC Class I Peptide Optimization (PLoS Computational Biology)
 Projects
A Stochastic π-Calculus Models of MHC Class I Antigen Presentation (Computational Biology MPhil Project)
 Links
Computational Modeling of Immune System Processes

Biological Network Modeling


We use stochastic pi-calculus to represent and then simulate interactions within protein networks. The pi-calculus approach allows a biological system to be programmed in a scalable manner, by allowing models of individual proteins to be directly composed to form subsystems, which can in turn be composed together to form larger systems. This allows new components to be added incrementally without having to re-wire the existing model, which also improves the usability of models. Furthermore, the modular structure of the biological system and the pi-calculus model are in direct correspondence.

 Papers
Computational Modeling of the EGFR Network Elucidates Control Mechanisms Regulating Signal Dynamics (BMC Systems Biology)
A Process Model of Rho GTP-binding Proteins (FBTC'07) (TCS)
A Process Model of Actin Polymerisation (FBTC'08) (ENTCS)
 Lectures
info Biochemical Systems as Reactive Systems - Bioinformatics Master Course (Cabridge '12)
 Talks
info Biological Networks in Stochastic Pi-Calculus (Imperial College London 2005)

Systems Biology


An abstract machine is a fictional information-processing device that can, in principle, have a number of different physical realizations (mechanical, electronic, biological, or software). Biochemical toolkits in cellular biology (nucleotides, amino acids, and phospholipids) can be seen as abstract machines with appropriate sets of states and operations, corresponding respectively to genes, proteins, and membranes. To understand the functioning of a cell, one must understand (at least) how the various machines interact. This involves considerable difficulties in modeling and simulations because of the drastic differences in the "programming model" of each machine, and in the time and size scales involved.

 Papers
Lineage Grammars: Describing, Simulating and Analyzing Population Dynamics. (BMC Bioinformatics'14)
An Intuitive Modelling Interface for Systems Biology (DCM'09) (IJSI'13)
Abstract Machines of Systems Biology (TCSB)
Artificial Biochemistry (Algorithmic Bioprocesses)
Can a Systems Biologist Fix a Tamagotchi? (Gilles Kahn Colloquium)
 Visualization in Process Algebra Models of Biological Systems (The Fourth Paradigm)
 Lectures
info Artificial Biochemistry - Graduate Course (Trento, May 22-26 '06)
 Talks
info Speaking the Language of Molecules (CDE Distinguished Lacture, U.Washington)
info Living Software (L'INRIA a Quarante Ans)
info Artificial Biochemistry (Longo Symposium 2007)
info Can a Systems Biologist Fix a Tamagotchi? (Kahn Colloquium 2007)
info Abstract Machines of Systems Biology (Dagstuhl 2006)
info Languages and Notations for Systems Biology (UPP'04 Invited Talk)

Continuous Markov Processes


We introduce stochastic extensions of process algebras endowed with structural operational semantics expressed in terms of measure theory. The set of processes is organised as a measurable space by the sigma-algebra generated by structural congruence. The structural operational semantics associates to each process a set of measures over the space of processes. The measures encode the rates of the transitions from a process (state of a system) to a measurable set of processes. We prove that stochastic bisimulation is a congruence that extends structural congruence. In addition to an elegant operational semantics, our approach provides a canonic way to define metrics on processes that measure how similar two processes are in terms of behaviour.

 Papers on
 Logic
Continuous Markovian Logic Axiomatization and Quantified Metatheory (LMCS'12)
Modular Markovian Logic (ICALP'11)
Continuous Markovian Logic (CLS'11)
 Papers on
 Algebra
Stochastic Pi-Calculus Revisited (ICTAC'13)
The Measurable Space of Stochastic Processes (QEST'10, Fundamenta Informaticae)
 Talks
info Stochastic Pi-Calculus Revisited (ICTAC'13)
info Continuous Markovian Logic (CSL'11)
info Modular Markovian Logic (ICALP'11)
info The Measurable Space of Stochastic Processes  (QEST'10)

Membrane Computing


The basic physical operations on membranes are local fusion (two patches merging) and local fission (one patch splitting in two). When seen at the global scale of whole membranes, these local operations induce four transformations: in addition to the obvious splitting (Mito) and merging (Mate) of membranes, there are also operation, quite common in reality, that cause a membrane to eat (Endo) or spit (Exo) another subsystem. Although this is an unusual computational model, the membrane operations supports the execution of real algorithms, some of which occur in nature. Some sets of operations are Turing-complete, and can encode the other membrane operations.

 Papers on
 Brane Calculi
Programming Chemistry in DNA Addressable Bioreactors (Interface '14)
Brane Calculi (ENTCS, CMSB'04)
Bitonal Membrane Systems (TCS)
Where Membranes Meet Complexes (BioConcur '05)
A Universality Result for a (Mem)Brane Calculus Based on Mate/Drip Operations (IJFCS)
 Papers on
 BioAmbients
BioAmbients: An Abstraction for Biological Compartments (TCS)
Bioware Languages (Computing Systems - A Tribute to Roger Needham)
 Lectures
info Membrane Interactions PDF PDF  (CSSB School Rovereto, April'04)
 Talks
info Bitonal Membrane Systems  (MeCBIC'06)
info WhereMembranesMeetComplexes (BioConcur'05)
info Biological Systems as Reactive Systems (ECCS'05)

Natural Computability


We investigate the question of whether basic chemical kinetics (kinetics of unar yand binary chemical reactions), formulated as a process algebra, is capable of general computation. In particular, we investigate nondeterministic and probabilistic termination problems. The answers to those problems reveal a surprisingly rich picture of what is decidable and undecidable in basic chemistry.
We introduce an algebra for massive concurrent systems, called reversible structures, where terms retain bits of causal dependencies that allow one to reverse computation histories. These bits permit to trace effects of interactions, but not to the point of being able to identify the precise molecule that caused an effect. The algebra and the causal hints match a particular form of DNA computation.

 Papers on
 Termination
Turing Universality of the Biochemical Ground Form (MSCS)
On the Computational Power of Biochemistry (AB'08)
Termination Problems in Chemical Kinetics (CONCUR'08)
 Papers on
 Reversibility
Reversibility in Massive Concurrent Systems (SACS)
Reversible Structures (CMSB '11)
 Talks
info Termination Problems in Chemical Kinetics (CONCUR'08)
info On The Computational Power of Biochemistry (AB'08)
info Reversible Structures (CMSB'11)

Stochastic Gene Networks


We propose a compositional approach to the dynamics of gene regulatory networks based on the stochastic p-calculus, and develop a representation of gene network elements which can be used to build complex circuits in a transparent and efficient way. To demonstrate the power of the approach we apply it to several artificial networks, such as the repressilator and combinatorial gene circuits. We point out how the topology of the circuits and the interplay of the stochastic gate interactions influence the circuit behavior. Our approach may be useful for the testing of biological mechanisms proposed to explain the experimentally observed circuit dynamics.

 Papers
A Compositional Approach to the Stochastic Dynamics of Gene Networks (TCSB)
Compositionality, Stochasticity and Cooperativity in Dynamic Models of Gene Regulation (HFSP Journal)
 Talks
info A Compositional Approach to the Stochastic Dynamics of Gene Networks (Concur '05)

Geometric Process Algebra


We introduce a geometric process algebra based on affine geometry, with the aim of describing the concurrent evolution of geometric structures in 3D space. We prove a relativity theorem stating that algebraic equations are invariant under rigid body transformations.

 Papers
Processes in Space (CiE'10, TCS 2012)
 Talks
info Processes in Space(CiE'10)
info Pi in the Sky: Spatial Process Algebra for Developmental Biology (MeCBIC'09)
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