scholarly journals Trains, tails and loops of partially adsorbed semi-flexible filaments

Soft Matter ◽  
2015 ◽  
Vol 11 (38) ◽  
pp. 7507-7514 ◽  
Author(s):  
David Welch ◽  
M. P. Lettinga ◽  
Marisol Ripoll ◽  
Zvonimir Dogic ◽  
Gerard A. Vliegenthart
Keyword(s):  
Computer Simulations ◽  
Hard Wall ◽  
Flexible Polymers ◽  
P Depletion ◽  
Induced Adsorption

Depletion induced adsorption of semi-flexible polymers onto a hard-wall is investigated by a combination of microscopy and computer simulations. In contrast to long flexible filaments which primarily desorb by the formation of loops, the desorption of stiff, finite-sized filaments is largely driven by fluctuating filament tails.

Contact Value Formulae for the Density Profiles of the Electric Double Layer

2008 ◽  
Vol 73 (4) ◽  
pp. 558-574 ◽  
Author(s):  
Douglas J. Henderson ◽  
Lutful B. Bhuiyan
Keyword(s):  
Computer Simulations ◽  
Density Profile ◽  
Physical Interpretation ◽  
Electric Double Layer ◽  
Reasonable Agreement ◽  
Hard Wall ◽  
Density Profiles ◽  
Sum Rule ◽  
Recent Computer ◽  
Local Expression

An exact sum rule, due to Henderson, Blum, and Lebowitz, for the contact value of the density profile of ions in a primitive model electrolyte next to a planar, nonpolarizable charged hard wall, has been known for some years. This result has a pleasing physical interpretation and is local. It has been useful in assessing the accuracy of theoretical approximations. However, a sum rule for the contact value of the charge profile for the same system has, until recently, not been known. A few years ago, Boda and Henderson proposed what they thought might be a useful, but approximate, local expression for the contact value of the charge profile at a weakly charged electrode. Very recent computer simulations indicate that this expression may well be exact at low electrode charge. Recently, Holovko, Badiali, and di Caprio have obtained a more general, but nonlocal, sum rule for the contact value of the charge profile that is valid for all electrode charge. In this paper, we develop an alternative, nonlocal, but nonrigorous expression for this quantity. Both the expression of Holovko et al. and our new expression are examined by means of computer simulations. The Holovko et al. expression is exact and, within numerical uncertainties, seems supported by our simulations. Although admittedly nonrigorous, our simpler expression is in seemingly reasonable agreement with simulation and thus appears to be useful. The relation between the two expressions has not been established.

Structure of chemically reacting particles near a hard wall from integral equations and computer simulations

1996 ◽  
Vol 74 (1-2) ◽  
pp. 65-76 ◽  
Author(s):  
A. Trokhymchuk ◽  
D. Henderson ◽  
S. Sokołowski
Keyword(s):  
Monte Carlo ◽  
Computer Simulations ◽  
Hard Spheres ◽  
Total Density ◽  
Hard Wall ◽  
Monte Carlo Data ◽  
Density Profiles ◽  
Interparticle Potential ◽  
Theoretical Predictions ◽  
Chemically Reacting

We performed Monte-Carlo computer simulations of a fluid of chemically reacting, or overlapping, hard spheres near a hard wall. The model of the interparticle potential is that introduced by Cummings and Stell. This investigation is directed to the determination of the structure of the fluid at the wall, and the orientation of the dimers in particular. In addition, we applied the singlet Percus–Yevick, hypernetted chain and Born–Green–Yvon equations to calculate the total density profiles of the particles. A comparison with the Monte-Carlo data indicates that the singlet Percus–Yevick theory is superior and leads to results that are in reasonable agreement with simulations for all the parameters investigated. We also calculated the average numbers of dimers formed in the bulk part of the system and the results are compared with different theoretical predictions.

Elasticity of flexible polymers under cylindrical confinement: appreciating the blob scaling regime in computer simulations

Soft Matter ◽  
2013 ◽  
Vol 9 (26) ◽  
pp. 6142 ◽  
Author(s):  
Juin Kim ◽  
Chanil Jeon ◽  
Hawoong Jeong ◽  
Youngkyun Jung ◽  
Bae-Yeun Ha
Keyword(s):  
Computer Simulations ◽  
Flexible Polymers

scholarly journals Self-assembly and crystallisation of indented colloids at a planar wall

Soft Matter ◽  
2015 ◽  
Vol 11 (30) ◽  
pp. 6089-6098 ◽  
Author(s):  
Douglas J. Ashton ◽  
Samantha J. Ivell ◽  
Roel P. A. Dullens ◽  
Robert L. Jack ◽  
Nigel B. Wilding ◽  
...  
Keyword(s):  
Spherical Particle ◽  
Computer Simulations ◽  
Self Assembly ◽  
Particle Shape ◽  
Hard Wall ◽  
Planar Wall

Experiments and computer simulations of indented colloids near a hard wall demonstrate the suppression of crystallisation, due to the non-spherical particle shape.

scholarly journals Adsorption of semiflexible polymers in crowded environments

2021 ◽  
Author(s):  
Gaurav Chauhan ◽  
Michael L. Simpson ◽  
Steven M. Abel
Keyword(s):  
Computer Simulations ◽  
Spatial Organization ◽  
Volume Fraction ◽  
Bending Stiffness ◽  
Radius Of Gyration ◽  
Semiflexible Polymers ◽  
Size And Shape ◽  
Crowded Environments ◽  
Shed Light ◽  
Induced Adsorption

Macromolecular crowding is a feature of cellular and cell-free systems that, through depletion effects, can impact the interactions of semiflexible biopolymers with surfaces. In this work, we use computer simulations to study crowding-induced adsorption of semiflexible polymers on otherwise repulsive surfaces. Crowding particles are modeled explicitly, and we investigate the interplay between the bending stiffness of the polymer and the volume fraction and size of crowding particles. Adsorption is promoted by stiffer polymers, smaller crowding particles, and larger volume fractions of crowders. We characterize transitions from non-adsorbed to partially and strongly adsorbed states as a function of the bending stiffness. The crowding-induced transitions occur at smaller values of the bending stiffness as the volume fraction of crowders increases. Concomitant effects on the size and shape of the polymer are reflected by crowding- and stiffness-dependent changes to the radius of gyration. We also demonstrate that curvature of the confining surface can induce desorption when the bending stiffness is sufficiently large. The results of our simulations shed light on the interplay of crowding and bending stiffness on the spatial organization of biopolymers in encapsulated cellular and cell-free systems.

A High Resolution Study of G.P. Zones in Aluminum - 4.2 at % Silver

1982 ◽  
Vol 40 ◽  
pp. 722-723 ◽  
Author(s):  
R. Gronsky
Keyword(s):  
Electron Microscopy ◽  
Transmission Electron Microscopy ◽  
High Resolution ◽  
Computer Simulations ◽  
Structural Characteristics ◽  
X Ray Diffraction ◽  
X Ray ◽  
Transmission Electron ◽  
Resolution Study

The phenomenon of clustering in Al-Ag alloys has been extensively studied since the early work of Guinierl, wherein the pre-precipitation state was characterized as an assembly of spherical, ordered, silver-rich G.P. zones. Subsequent x-ray and TEM investigations yielded results in general agreement with this model. However, serious discrepancies were later revealed by the detailed x-ray diffraction - based computer simulations of Gragg and Cohen, i.e., the silver-rich clusters were instead octahedral in shape and fully disordered, atleast below 170°C. The object of the present investigation is to examine directly the structural characteristics of G.P. zones in Al-Ag by high resolution transmission electron microscopy.

Multislice calculations for quasi-periodic and non-periodic objects

1990 ◽  
Vol 48 (4) ◽  
pp. 138-139
Author(s):  
R. Herrera ◽  
A. Gómez
Keyword(s):  
Electron Diffraction ◽  
Computer Simulations ◽  
Periodic Table ◽  
Amorphous Materials ◽  
Space Group ◽  
Essential Step ◽  
Shape Effects ◽  
Atomic Scattering ◽  
Diffraction Patterns ◽  
Periodic Continuation

Computer simulations of electron diffraction patterns and images are an essential step in the process of structure and/or defect elucidation. So far most programs are designed to deal specifically with crystals, requiring frequently the space group as imput parameter. In such programs the deviations from perfect periodicity are dealt with by means of “periodic continuation”.However, for many applications involving amorphous materials, quasiperiodic materials or simply crystals with defects (including finite shape effects) it is convenient to have an algorithm capable of handling non-periodicity. Our program “HeGo” is an implementation of the well known multislice equations in which no periodicity assumption is made whatsoever. The salient features of our implementation are: 1) We made Gaussian fits to the atomic scattering factors for electrons covering the whole periodic table and the ranges [0-2]Å−1 and [2-6]Å−1.

Computer simulations for the TEM bend contour technique

1996 ◽  
Vol 54 ◽  
pp. 134-135
Author(s):  
Vladimir Yu. Kolosov ◽  
Anders R. Thölén
Keyword(s):  
Computer Simulations ◽  
Real Space ◽  
Advantages And Disadvantages ◽  
Short Overview ◽  
Diffraction Contrast ◽  
Beam Method ◽  
Convergent Beam ◽  
Contour Technique

In this paper we give a short overview of two TEM applications utilizing the extinction bend contour technique (BC) giving the advantages and disadvantages; especially we consider two areas in which the BC technique remains unique. Special attention is given to an approach including computer simulations of TEM micrographs.BC patterns are often observed in TEM studies but are rarely exploited in a serious way. However, this type of diffraction contrast was one of the first to be used for analysis of imperfections in crystalline foils, but since then only some groups have utilized the BC technique. The most extensive studies were performed by Steeds, Eades and colleagues. They were the first to demonstrate the unique possibilities of the BC method and named it real space crystallography, which developed later into the somewhat similar but more powerful convergent beam method. Maybe, due to the difficulties in analysis, BCs have seldom been used in TEM, and then mainly to visualize different imperfections and transformations.

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