Displaying similar documents to “Discrete Groups and Internal Symmetries of Icosahedral Viral Capsids”

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...

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...

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...

Efficient fidelity control by stepwise nucleotide selection in polymerase elongation

Jin Yu (2014)

Molecular Based Mathematical Biology

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Polymerases select nucleotides according to a template before incorporating them for chemical synthesis during gene replication or transcription. Efficient selection to achieve sufficiently high fidelity and speed is essential for polymerase function. Due to multiple kinetic steps detected in a polymerase elongation cycle, there exist multiple selection checkpoints to allow different strategies of fidelity control. In our current work, we examined step-by-step selections in an elongation...

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,...

Nonlocal Electrostatics in Spherical Geometries Using Eigenfunction Expansions of Boundary-Integral Operators

Jaydeep P. Bardhan, Matthew G. Knepley, Peter Brune (2015)

Molecular Based Mathematical Biology

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In this paper, we present an exact, infinite-series solution to Lorentz nonlocal continuum electrostatics for an arbitrary charge distribution in a spherical solute. Our approach relies on two key steps: (1) re-formulating the PDE problem using boundary-integral equations, and (2) diagonalizing the boundaryintegral operators using the fact that their eigenfunctions are the surface spherical harmonics. To introduce this uncommon approach for calculations in separable geometries, we first...

A note on majorization transforms and Ryser’s algorithm

Geir Dahl (2013)

Special Matrices

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The notion of a transfer (or T -transform) is central in the theory of majorization. For instance, it lies behind the characterization of majorization in terms of doubly stochastic matrices. We introduce a new type of majorization transfer called L-transforms and prove some of its properties. Moreover, we discuss how L-transforms give a new perspective on Ryser’s algorithm for constructing (0; 1)-matrices with given row and column sums.

Factorizable matrices

Miroslav Fiedler, Frank J. Hall (2013)

Special Matrices

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We study square matrices which are products of simpler factors with the property that any ordering of the factors yields a matrix cospectral with the given matrix. The results generalize those obtained previously by the authors.