Papers:
Simulation of Viral Gene Delivery
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 [...]
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 [...]
Examining Tissue Differentiation Stability through Large Scale, Multi-Cellular Pathway Modeling
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 [...]
Continuous Optimization Method for the Sequence Design of Protein Models Consisting of Multiple Monomer Types
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 [...]
Applications of Parameterized Computation in Computational Biology
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 [...]
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 [...]
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 and Simulation of Carbohydrate Metabolism using Petri Net
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 [...]
Interaction of Coupled Particles Based on Lennard-Jones and Spring Forces in Brownian Ratchet Devices
Electrophoresis is a technique used to separate polyelectrolyte strands of different lengths. One of its fields of application in nanotechnology is in the separation of DNA. Chains of particles can undergo net transport on a [...]
Application of Grid Focusing Methodology to Transport Monte Carlo Model for Ion Channel Simulations
Simulation of Ion Channels has long been an outstanding research problem in the biophysical community. Our transport Monte Carlo model BioMOCA is a particle based approach where we treat water implicitly. It has been used [...]
A Multi-scale, Integrative Model of Cellular Electrophysiological Response Incorporating Intra/Extra-cellular Transport & Dynamics
Spurred by the growing confluence of nano and bio technologies, several novel micro/nano platforms (see for example, whole cell patch clamp devices [1]) are emerging for the high-throughput and/or high-fidelity study of the electrophysiological response [...]
Systems Biology Conceptual Modeling by Means of Discrete-event Simulation (DNA-RNA-Protein)
In this paper discrete-event simulation modeling technique is used to model and simulate biological processes. In particular, we study application of discrete-event simulation to model processes taking place in Glycolosis and capture dynamic behavior of [...]
Ion Channel Simulations by the TR-PNP Model and the Excess Chemical Potential Approach
We describe a new method referred to as TR-PNP model to study general types of nanostructure ion channels. Our method extends the common continuum methods to include particle like properties, such as the ion trapping [...]
Johnson-Kendall-Roberts Theory Applied to Living Cells
Chu Y-S, Dufour S., Thiery J.-P., Perez E., Pincet F., Laboratoire de Physique Statistique de l'ENS, FR
Cell adhesion is involved in a number of biological processes ranging from transport to the defenses of organisms. A quantitative understanding of the adhesion of cells is not often possible owing to their complexity in [...]
Bioinspired Miniaturization – Stretching Information from Coherence to Dissipation for Nano-to-Micro Integrated Intelligent Systems
From previous results attained on the basis of thermodynamics, statistical physics and nanobiology it is shown that Artificial Intelligence (AI) concepts and their hard-wired implementations cannot satisfy the physical conditions for mimicking biological intelligence and [...]
Journal: TechConnect Briefs
Volume: 1, Technical Proceedings of the 2005 NSTI Nanotechnology Conference and Trade Show, Volume 1
Published: May 8, 2005
Industry sectors: Advanced Materials & Manufacturing | Medical & Biotech
Topics: Biomaterials, Informatics, Modeling & Simulation
ISBN: 0-9767985-0-6