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TCS
2008
14 years 10 days ago
On process rate semantics
We provide translations between process algebra and systems of chemical reactions. We show that the translations preserve discrete-state (stochastic) and continuous-state (concent...
Luca Cardelli
JCC
2006
103views more  JCC 2006»
14 years 12 days ago
Flooding in GROMACS: Accelerated barrier crossings in molecular dynamics
: The major bottleneck of today's atomistic molecular dynamics (MD) simulations is that because of the enormous computational effort involved, only processes at nanoseconds to...
Oliver F. Lange, Lars V. Schäfer, Helmut Grub...
BMCBI
2007
128views more  BMCBI 2007»
14 years 17 days ago
Absolute estimation of initial concentrations of amplicon in a real-time RT-PCR process
Background: Since real time PCR was first developed, several approaches to estimating the initial quantity of template in an RT-PCR reaction have been tried. While initially only ...
Marjo V. Smith, Chris R. Miller, Michael Kohn, Nig...
ALIFE
2007
14 years 17 days ago
Life Cycle of a Minimal Protocell - A Dissipative Particle Dynamics Study
Cross-reactions and other systematic difficulties generated by the coupling of functional chemical subsystems pose the largest challenge for assembling a viable protocell in the la...
Harold Fellermann, Steen Rasmussen, Hans-Joachim Z...
JBI
2004
163views Bioinformatics» more  JBI 2004»
14 years 1 months ago
Artificial Chemistries and Metabolic Pathways
Metabolism can be regarded as a network of biochemical reactions, connected via their substrates and products. A metabolic pathway is thus a coordinated series of reactions, and i...
Liliana Félix, Francesc Rosselló, Ga...
GG
2004
Springer
14 years 5 months ago
Analysis of Metabolic Pathways by Graph Transformation
Biochemical pathways, such as metabolic, regulatory, and signal transduction pathways, constitute complex networks of functional and physical interactions between molecular species...
Francesc Rosselló, Gabriel Valiente