Informatics, Modeling & Simulation – Page 55

Modeling and Simulation of Carbohydrate Metabolism using Petri Net

Barjis I., Barjis J., Yoel J.W, Barjis I., Barjis J., Berri S., Ru Y.S., Polytechnic University, US

In this paper Petri net modeling technique is used to model and simulate biological processes. In particular, we study application of Petri nets to model processes taking place in Glycolosis and capture dynamic behavior of [...]

Computational Principles of Primer Design for Site Directed Mutagenesis

Novoradovsky A., Zhang V., Ghosh M., Hogrefe H., Sorge J.A., Gaasterland T., The Rockefeller University, US

Site directed mutagenesis (SDM) is the process of altering a target DNA sequence by creating mutated copies of the original sequence where changes are intentionally designed. In the first step of an SDM experiment, an [...]

Modeling of Cellular Communication by Means of Petrinets

Barjis I., Barjis J., Berri S., Barjis I., Barjis J., New York City College of Technology, The City University of New Tork, US

This paper introduces application of Petri nets to molecular biology. In particular, it illustrates how by means of Petri nets the process of cellular communication can be modeled, and analyzed, where the model could be [...]

Applications of Parameterized Computation in Computational Biology

Huang X., Arkansas State University, US

According to the theory of NP-completeness, many problems that have important real-world applications in life science are NP-hard. This excludes the possibility of solving them in polynomial time unless P=NP. A number of approaches have [...]

Continuous Optimization Method for the Sequence Design of Protein Models Consisting of Multiple Monomer Types

Koh S.K., Ananthasuresh G.K., Yang X., Saven J., Indian Institute of Science, IN

In our earlier work, we had introduced continuous modeling of two discrete states (H: Hydrophobic; P: Polar) of the amino acid monomers and presented a deterministic continuous optimization method to design the sequence that minimizes [...]

Examining Tissue Differentiation Stability through Large Scale, Multi-Cellular Pathway Modeling

Schiek R.L., May E.M., Sandia National Laboratories, US

Using a multi-cellular, pathway model approach, we investigate the Drosophila sp. segmental differentiation network's stability as a function of initial conditions. While this network's functionality has been investigated in the absence of noise, this is [...]

A Curved Panel Integration Technique for Molecular Surfaces

Bardhan J.P., Altman M.D., Lippow S.M., Tidor B., White J.K., Massachusetts Institute of Technology, US

A key step in computational drug design is the calculation of binding free energies between drug candidates and their target; one important component of these binding free energies is the van der Waals interactions that [...]

Simulation of Viral Gene Delivery

Dinh A.T., Mitragotri S., Theofanous T., university of california, santa barbara, US

Here we develop an integrative computational framework to model biophysical processes involved in viral gene delivery. The model uses reaction-diffusion-advection equations that describe intracellular trafficking in combination with kinetic equations that describe transcription and translation [...]

Computational Biology

A Study of the Threshold Voltage Variations for Ultra-thin Body Double Gate SOI MOSFETs

Tang C-S, Lo S-C, Lee J.W., Tsai J-H, Li Y., Natl Nano Device Labs & Natl Chiao Tung Univ, TW

Double gate silicon on insulator (SOI) devices are more and more attractive for sub-50 nm ultra-large scaled integrated (ULSI) circuits manufacturing. The double gate SOI devices, owing to a difficulty of manufacturing uniformity, suffer fluctuations [...]