Displaying similar documents to “Efficient fidelity control by stepwise nucleotide selection in polymerase elongation”

Modeling and Simulating Asymmetrical Conductance Changes in Gramicidin Pores

Shixin Xu, Minxin Chen, Sheereen Majd, Xingye Yue, Chun Liu (2014)

Molecular Based Mathematical Biology

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Gramicidin A is a small and well characterized peptide that forms an ion channel in lipid membranes. An important feature of gramicidin A (gA) pore is that its conductance is affected by the electric charges near the its entrance. This property has led to the application of gramicidin A as a biochemical sensor for monitoring and quantifying a number of chemical and enzymatic reactions. Here, a mathematical model of conductance changes of gramicidin A pores in response to the presence...

Overview of Drude-Lorentz type models and their applications

Paolo Di Sia (2014)

Nanoscale Systems: Mathematical Modeling, Theory and Applications

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This paper presents an overview of mathematical models for a better understanding of mechanical processes, as well as dynamics, at the nanoscale. After a short introduction related to semi-empirical and ab initio formulations, molecular dynamics simulations, atomic-scale finite element method, multiscale computational methods, the paper focuses on the Drude-Lorentz type models for the study of dynamics, considering the results of a recently appeared generalization of them for the nanoscale...

Transmission-line laser modeling of carrier diffusion in VCSEL

Vladimir Gerasik, Jacek Miloszewski, Marek S. Wartak (2014)

Nanoscale Systems: Mathematical Modeling, Theory and Applications

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The transmission-line laser model (TLLM) is an equivalent-circuit model which provides stable and explicit matrix routines for the solution of the laser rate equations. The application of TLLM method to the analysis of a vertical-cavity surface-emitting laser (VCSEL) requires certain modifications. The theoretical basis of the model is considered, including space discretization of the inhomogeneous VCSEL cavity so that it yields the synchronization condition. The main attention is paid...

A variant of gravitational classification

Tomasz Górecki, Maciej Luczak (2014)

Biometrical Letters

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In this article there is proposed a new two-parametrical variant of the gravitational classification method. We use the general idea of objects' behavior in a gravity field. Classification depends on a test object's motion in a gravity field of training points. To solve this motion problem, we use a simulation method. This classifier is compared to the 1NN method, because our method tends towards it for some parameter values. Experimental results on different data sets demonstrate an...

Discrete Groups and Internal Symmetries of Icosahedral Viral Capsids

Richard Kerner (2014)

Molecular Based Mathematical Biology

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A classification of all possible icosahedral viral capsids is proposed. It takes into account the diversity of hexamers’ compositions, leading to definite capsid size.We showhowthe self-organization of observed capsids during their production results from definite symmetries of constituting hexamers. The division of all icosahedral capsids into four symmetry classes is given. New subclasses implementing the action of symmetry groups Z2, Z3 and S3 are found and described. They concern...

Bayesian Analysis for Robust Synthesis of Nanostructures

Nader Ebrahimi, Mahmoud Shehadeh, Kristin McCullough (2012)

Nanoscale Systems: Mathematical Modeling, Theory and Applications

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Nanomaterials, because of their unique properties such as extremely small size and increased ratio of surface area to volume, have a great potential in many industrial applications that involve electronics, sensors, solar cells, super-strong materials, coatings, drug delivery, and nanomedicine. They have the potential also to improve the environment by direct applications of these materials to detect, prevent and remove pollutants. While nanomaterials present seemingly limitless possibilities,...

Real-valued GCS classifier system

Łukasz Cielecki, Olgierd Unold (2007)

International Journal of Applied Mathematics and Computer Science

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Learning Classifier Systems (LCSs) have gained increasing interest in the genetic and evolutionary computation literature. Many real-world problems are not conveniently expressed using the ternary representation typically used by LCSs and for such problems an interval-based representation is preferable. A new model of LCSs is introduced to classify real-valued data. The approach applies the continous-valued context-free grammar-based system GCS. In order to handle data effectively, the...