Filtering high quality text for display on raster scan devices

Recently several investigators have studied the problem of displaying text characters on grey level raster scan displays. Despite arguments suggesting that grey level displays are equivalent to very high resolution bitmaps, the performance of grey level displays has been disappointing. this paper will show that much of the problem can be traced to inappropriate antialiasing procedures. Instead of the classical (sin x)/x filter, the situation calls for a filter with characteristics matched both to the nature of display on CRTs and to the human visual system. We give examples to illustrate the problems of the existing methods and the advantages of the new methods. Although the techniques are described in terms of text, the results have application to the general antialiasing problem--at least in theory if not practice

The Electrostatic Persistence Length Calculated from Monte Carlo, Variational and Perturbation Methods

Monte Carlo simulations and variational calculations using a Gaussian ansatz are applied to a model consisting of a flexible linear polyelectrolyte chain as well as to an intrinsically stiff chain with up to 1000 charged monomers. Addition of salt is treated implicitly through a screened Coulomb potential for the electrostatic interactions. For the flexible model the electrostatic persistence length shows roughly three regimes in its dependence on the Debye-H\"{u}ckel screening length, $\kappa^{-1}$.As long as the salt content is low and $\kappa^{-1}$ is longer than the end-to-end distance, the electrostatic persistence length varies only slowly with $\kappa^{-1}$. Decreasing the screening length, a controversial region is entered. We find that the electrostatic persistence length scales as $sqrt{\xi_p}/\kappa$, in agreement with experiment on flexible polyelectrolytes, where $\xi_p$ is a strength parameter measuring the electrostatic interactions within the polyelectrolyte. For screening lengths much shorter than the bond length, the $\kappa^{-1}$ dependence becomes quadratic in the variational calculation. The simulations suffer from numerical problems in this regime, but seem to give a relationship half-way between linear and quadratic. A low temperature expansion only reproduces the first regime and a high temperature expansion, which treats the electrostatic interactions as a perturbation to a Gaussian chain, gives a quadratic dependence on the Debye length. For a sufficiently stiff chain, the persistence length varies quadratically with $\kappa^{-1}$ in agreement with earlier theories.Comment: 20 pages LaTeX, 9 postscript figure

Persistence length of a polyelectrolyte in salty water: a Monte-Carlo study

We address the long standing problem of the dependence of the electrostatic persistence length $l_e$ of a flexible polyelectrolyte (PE) on the screening length $r_s$ of the solution within the linear Debye-Huckel theory. The standard Odijk, Skolnick and Fixman (OSF) theory suggests $l_e \propto r_s^2$, while some variational theories and computer simulations suggest $l_e \propto r_s$. In this paper, we use Monte-Carlo simulations to study the conformation of a simple polyelectrolyte. Using four times longer PEs than in previous simulations and refined methods for the treatment of the simulation data, we show that the results are consistent with the OSF dependence $l_e \propto r_s^2$. The linear charge density of the PE which enters in the coefficient of this dependence is properly renormalized to take into account local fluctuations.Comment: 7 pages, 6 figures. Various corrections in text and reference

Variational theory for a single polyelectrolyte chain revisited

We reconsider the electrostatic contribution to the persistence length, $\ell_e$, of a single, infinitely long charged polymer in the presence of screening. A Gaussian variational method is employed, taking $\ell_e$ as the only variational parameter. For weakly charged and flexible chains, crumpling occurs at small length scales because conformational fluctuations overcome electrostatic repulsion. The electrostatic persistence length depends on the square of the screening length, $\ell_e\sim\kappa^{-2}$, as first argued by Khokhlov and Khachaturian by applying the Odijk-Skolnick-Fixman (OSF) theory to a string of crumpled blobs. We compare our approach to previous theoretical works (including variational formulations) and show that the result $\ell_e\sim\kappa^{-1}$ found by several authors comes from the improper use of a cutoff at small length scales. For highly charged and stiff chains, crumpling does not occur; here we recover the OSF result and validate the perturbative calculation for slightly bent rods.Comment: 11 pages, 6 figure

An Electronic Analog of Synthetic Genetic Networks

An electronic analog of a synthetic genetic network known as the repressilator is proposed. The repressilator is a synthetic biological clock consisting of a cyclic inhibitory network of three negative regulatory genes which produces oscillations in the expressed protein concentrations. Compared to previous circuit analogs of the repressilator, the circuit here takes into account more accurately the kinetics of gene expression, inhibition, and protein degradation. A good agreement between circuit measurements and numerical prediction is observed. The circuit allows for easy control of the kinetic parameters thereby aiding investigations of large varieties of potential dynamics

Complex and unexpected dynamics in simple genetic regulatory networks

Peer reviewedPublisher PD

The transition between stochastic and deterministic behavior in an excitable gene circuit

We explore the connection between a stochastic simulation model and an ordinary differential equations (ODEs) model of the dynamics of an excitable gene circuit that exhibits noise-induced oscillations. Near a bifurcation point in the ODE model, the stochastic simulation model yields behavior dramatically different from that predicted by the ODE model. We analyze how that behavior depends on the gene copy number and find very slow convergence to the large number limit near the bifurcation point. The implications for understanding the dynamics of gene circuits and other birth-death dynamical systems with small numbers of constituents are discussed.Comment: PLoS ONE: Research Article, published 11 Apr 201

The Human Body as a Super Network: Digital Methods to Analyze the Propagation of Aging

Biological aging is a complex process involving multiple biological processes. These can be understood theoretically though considering them as individual networks—e.g., epigenetic networks, cell-cell networks (such as astroglial networks), and population genetics. Mathematical modeling allows the combination of such networks so that they may be studied in unison, to better understand how the so-called “seven pillars of aging” combine and to generate hypothesis for treating aging as a condition at relatively early biological ages. In this review, we consider how recent progression in mathematical modeling can be utilized to investigate aging, particularly in, but not exclusive to, the context of degenerative neuronal disease. We also consider how the latest techniques for generating biomarker models for disease prediction, such as longitudinal analysis and parenclitic analysis can be applied to as both biomarker platforms for aging, as well as to better understand the inescapable condition. This review is written by a highly diverse and multi-disciplinary team of scientists from across the globe and calls for greater collaboration between diverse fields of research

The Human Body as a Super Network: Digital Methods to Analyze the Propagation of Aging

Biological aging is a complex process involving multiple biological processes. These can be understood theoretically though considering them as individual networks—e.g., epigenetic networks, cell-cell networks (such as astroglial networks), and population genetics. Mathematical modeling allows the combination of such networks so that they may be studied in unison, to better understand how the so-called “seven pillars of aging” combine and to generate hypothesis for treating aging as a condition at relatively early biological ages. In this review, we consider how recent progression in mathematical modeling can be utilized to investigate aging, particularly in, but not exclusive to, the context of degenerative neuronal disease. We also consider how the latest techniques for generating biomarker models for disease prediction, such as longitudinal analysis and parenclitic analysis can be applied to as both biomarker platforms for aging, as well as to better understand the inescapable condition. This review is written by a highly diverse and multi-disciplinary team of scientists from across the globe and calls for greater collaboration between diverse fields of research

Optimizing end-labeled free-solution electrophoresis by increasing the hydrodynamic friction of the drag-tag

We study the electrophoretic separation of polyelectrolytes of varying lengths by means of end-labeled free-solution electrophoresis (ELFSE). A coarse-grained molecular dynamics simulation model, using full electrostatic interactions and a mesoscopic Lattice Boltzmann fluid to account for hydrodynamic interactions, is used to characterize the drag coefficients of different label types: linear and branched polymeric labels, as well as transiently bound micelles. It is specifically shown that the label's drag coefficient is determined by its hydrodynamic size, and that the drag per label monomer is largest for linear labels. However, the addition of side chains to a linear label offers the possibility to increase the hydrodynamic size, and therefore the label efficiency, without having to increase the linear length of the label, thereby simplifying synthesis. The third class of labels investigated, transiently bound micelles, seems very promising for the usage in ELFSE, as they provide a significant higher hydrodynamic drag than the other label types. The results are compared to theoretical predictions, and we investigate how the efficiency of the ELFSE method can be improved by using smartly designed drag-tags.Comment: 32 pages, 11 figures, submitted to Macromolecule