Explicit Flow-Aligned Orientational Distribution Functions for Dilute Nematic Polymers in Weak Shear

2002 ◽  
Author(s):  
M. Gregory Forest ◽  
Ruhai Zhou ◽  
Qi Wang
Keyword(s):  
Kinetic Theory ◽  
Mean Field ◽  
Distribution Functions ◽  
Small Molecular Weight ◽  
Exact Probability ◽  
Exact Probability Distribution ◽  
Orientational Distribution ◽  
Alignment Angle ◽  
Nematic Polymers ◽  
Leslie Angle

Flow-alignment of sheared nematic polymers occurs in various flow-concentration regimes. Analytical descriptions of shear-aligned nematic monodomains have a long history across continuum, mesoscopic and mean-field kinetic models, sacrificing precision at each finer scale. Continuum Leslie-Ericksen theory applies to highly concentrated, weak flows of small molecular weight polymers, giving an explicit macroscopic alignment angle formula dependent only on Miesowicz viscosities. Mesoscopic tensor models apply at all concentrations and shear rates, but explicit “Leslie angle” formulas exist only in the weak shear limit (Cocchini et. al, 90; Bhave et. al, 93; Wang, 97; Rienacker and Hess, 99; Maffettone et. al, 00; Forest and Wang, 02; Forest et. al, 02c; Grecov and Rey, 02), with distinct behavior in dilute versus concentrated regimes. Exact probability distribution functions (pdf’s) of kinetic theory do not exist for highly concentrated nematic states, even without flow, although appealing flow-aligned approximations have been derived (Kuzuu and Doi, 83; Kuzuu and Doi, 84; Semenov, 83; Semenov, 86; Archer and Larson, 95; Kroger and Seller, 95), which offer a molecular theory basis for the Leslie alignment angle. A simpler problem concerns the dilute concentration regime where the unique quiescent equilibrium is isotropic, corresponding to a constant pdf, and whose weak shear deformation is robust to mesoscopic closure approximation (Forest and Wang, 02; Forest et. al, 02c): steady, flow-aligning, weakly anisotropic, and biaxial. The purpose of this paper is to explicitly construct the weakly anisotropic branch of stationary pdf’s by a weak-shear asymptotic expansion of kinetic theory. A second-moment pdf projection confirms mesoscopic model predictions, and further yields explicit Leslie angle and degree of alignment formulas in terms of molecular parameters and normalized shear rate.

scholarly journals Blinking statistics and molecular counting in direct stochastic reconstruction microscopy (dSTORM)

2021 ◽  
Author(s):  
Lekha Patel ◽  
David Williamson ◽  
Dylan M Owen ◽  
Edward A K Cohen
Keyword(s):  
Probability Distribution ◽  
Single Molecule ◽  
Immunological Synapse ◽  
Training Data ◽  
Supplementary Information ◽  
Cellular Structures ◽  
Exact Probability ◽  
Stochastic Optical Reconstruction Microscopy ◽  
Exact Probability Distribution ◽  
Optical Reconstruction

Abstract Motivation Many recent advancements in single-molecule localization microscopy exploit the stochastic photoswitching of fluorophores to reveal complex cellular structures beyond the classical diffraction limit. However, this same stochasticity makes counting the number of molecules to high precision extremely challenging, preventing key insight into the cellular structures and processes under observation. Results Modelling the photoswitching behaviour of a fluorophore as an unobserved continuous time Markov process transitioning between a single fluorescent and multiple dark states, and fully mitigating for missed blinks and false positives, we present a method for computing the exact probability distribution for the number of observed localizations from a single photoswitching fluorophore. This is then extended to provide the probability distribution for the number of localizations in a direct stochastic optical reconstruction microscopy experiment involving an arbitrary number of molecules. We demonstrate that when training data are available to estimate photoswitching rates, the unknown number of molecules can be accurately recovered from the posterior mode of the number of molecules given the number of localizations. Finally, we demonstrate the method on experimental data by quantifying the number of adapter protein linker for activation of T cells on the cell surface of the T-cell immunological synapse. Availability and implementation Software and data available at https://github.com/lp1611/mol_count_dstorm. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals On the birthday problem: some generalizations and applications

2003 ◽  
Vol 2003 (60) ◽  
pp. 3827-3840 ◽  
Author(s):  
P. N. Rathie ◽  
P. Zörnig
Keyword(s):  
Probability Distribution ◽  
Random Graph ◽  
Generating Functions ◽  
Hypergeometric Functions ◽  
Exact Probability ◽  
Confluent Hypergeometric Functions ◽  
Birthday Problem ◽  
Exact Probability Distribution

We study the birthday problem and some possible extensions. We discuss the unimodality of the corresponding exact probability distribution and express the moments and generating functions by means of confluent hypergeometric functionsU(−;−;−)which are computable using the software Mathematica. The distribution is generalized in two possible directions, one of them consists in considering a random graph with a single attracting center. Possible applications are also indicated.

scholarly journals Order Parameters, Orientational Distribution Functions and Heliconical Tilt Angles of Oligomeric Liquid Crystals

2019 ◽  
Author(s):  
Richard Mandle ◽  
John W. Goodby
Keyword(s):  
Phase Transition ◽  
Liquid Crystals ◽  
Tilt Angle ◽  
Order Parameter ◽  
Nematic Phase ◽  
Liquid Crystalline ◽  
Thermal Evolution ◽  
Order Parameters ◽  
Distribution Functions ◽  
Orientational Distribution

We compare the order parameters, orientational distribution functions (ODF) and heliconical tilt angles of the TB phase exhibited by a liquid-crystalline dimer (CB7CB) to a tetramer (O47) and hexamer (O67) by SAXS/WAXS. Following the N-TB phase transition we find that all order parameters decrease, and while 〈P2 〉 remains positive 〈P4 〉 becomes negative. For all three materials the order parameter 〈P6 〉 is near zero in both phases. The ODF is sugarloaf-like in the nematic phase and volcano-like in the TB phase, allowing us to estimate the heliconical tilt angle of each material and its thermal evolution. The heliconical tilt angle appears to be largely independent of the material studied despite the differing number of mesogenic units.

Beyond the Cahn-Hilliard Equation: a Vacancy-Based Kinetic Theory

2011 ◽  
Vol 172-174 ◽  
pp. 321-330 ◽  
Author(s):  
Maylise Nastar
Keyword(s):  
Kinetic Theory ◽  
Structure Function ◽  
Diffusion Mechanism ◽  
Kinetic Equations ◽  
Mean Field ◽  
Early Time ◽  
Present Theory ◽  
Kinetic Coupling ◽  
Amplification Rate ◽  
Cahn Hilliard Equation

A Self-Consistent Mean Field (SCMF) kinetic theory including an explicit description ofthe vacancy diffusion mechanism is developed. The present theory goes beyond the usual local equi-librium hypothesis. It is applied to the study of the early time spinodal decomposition in alloys. Theresulting analytical expression of the structure function highlights the contribution of the vacancydiffusion mechanism. Instead of the single amplification rate of the Cahn-Hillard linear theory, thelinearized SCMF kinetic equations involve three constant rates, first one describing the vacancy re-laxation kinetics, second one related to the kinetic coupling between local concentrations and paircorrelations and the third one representing the spinodal amplification rate. Starting from the same va-cancy diffusion model, we perform kineticMonte Carlo simulations of a Body Centered Cubic (BCC)demixting alloy. The resulting spherically averaged structure function is compared to the SCMF pre-dictions. Both qualitative and quantitative agreements are satisfying.

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