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Self-assembly of proteins is a biological phenomenon which gives rise to spontaneous formation of amyloid fibrils or polymers. The starting point of this phase, called nucleation exhibits an important variability among replicated…

Biomolecules · Quantitative Biology 2016-03-22 Marie Doumic , Sarah Eugene , Philippe Robert

We derive and introduce anisotropic effective pair potentials to coarse-grain solutions of semiflexible rings polymers of various lengths. The system has been recently investigated by means of full monomer-resolved computer simulations,…

Soft Condensed Matter · Physics 2015-07-21 Peter Poier , Christos N. Likos , Angel J. Moreno , Ronald Blaak

The influence of different boundary conditions on the density of random packings of disks is studied. Packings are generated using the random sequential adsorption algorithm with three different types of boundary conditions: periodic, open,…

Statistical Mechanics · Physics 2018-04-26 Michał Cieśla , Robert M. Ziff

We study a single flexible chain molecule grafted to a membrane which has pores of size slightly larger than the monomer size. On both sides of the membrane there is the same solvent. When this solvent is good, i.e. when the polymer is…

Soft Condensed Matter · Physics 2015-06-25 Hsiao-Ping Hsu , Peter Grassberger

We investigate the adsorption of a flexible polymer at a hexagonally patterned monolayer. All conformational polymer phases are identified, which enables the construction of a hyperphase diagram, parameterized by temperature and monolayer…

Soft Condensed Matter · Physics 2019-12-03 Benjamin Liewehr , Michael Bachmann

The slip phenomena in thin polymer films confined by either flat or periodically corrugated surfaces are investigated by molecular dynamics and continuum simulations. For atomically flat surfaces and weak wall-fluid interactions, the shear…

Soft Condensed Matter · Physics 2008-10-15 Anoosheh Niavarani , Nikolai V. Priezjev

The asymmetric simple exclusion process (ASEP) is an important model from statistical physics describing particles that hop randomly from one site to the next along an ordered lattice of sites, but only if the next site is empty. ASEP has…

Quantitative Methods · Quantitative Biology 2015-08-18 Alon Raveh , Yoram Zarai , Michael Margaliot , Tamir Tuller

We develop a model to describe the properties of random assemblies of polydisperse hard spheres. We show that the key features to describe the system are (i) the dependence between the free volume of a sphere and the various coordination…

Disordered Systems and Neural Networks · Physics 2015-05-19 Maximilien Danisch , Yuliang Jin , Hernan A. Makse

The adsorption of polymer and surfactant molecules onto colloidal particles or droplets in solution can be characterized non-destructively by scattering techniques. In a first part, the general framework of Dynamic Light Scattering, Small…

Soft Condensed Matter · Physics 2007-05-24 Julian Oberdisse

In this paper we consider in detail the connection between the problem of a polymer in a random medium and that of a quantum particle in a random potential. We are interested in a system of finite volume where the polymer is known to be…

Disordered Systems and Neural Networks · Physics 2009-10-31 Yohannes Shiferaw , Yadin Y. Goldschmidt

Two-dimensional semiflexible polymer rings are studied both by imaging circular DNA adsorbed on a mica surface and by Monte Carlo simulations of phantom polymers as well as of polymers with finite thickness. Comparison of size and shape of…

Biomolecules · Quantitative Biology 2010-04-15 Fabian Drube , Karen Alim , Guillaume Witz , Giovanni Dietler , Erwin Frey

The random walk of a bonded monomer in a polymer melt is anisotropic due to local order and bond connectivity. We investigate both effects by molecular-dynamics simulations on melts of fully-flexible linear chains ranging from dimers…

Soft Condensed Matter · Physics 2016-05-06 S. Bernini , D. Leporini

Building structures with hierarchical order through the self-assembly of smaller blocks is not only a prerogative of nature, but also a strategy to design artificial materials with tailored functions. We explore in simulation the…

Soft Condensed Matter · Physics 2020-02-17 Santi Prestipino , Domenico Gazzillo , Gianmarco Munaò , Dino Costa

A self-interacting polymer with one end attached to a sticky surface has been studied by means of a flat-histogram stochastic growth algorithm known as FlatPERM. We examined the four-dimensional parameter space of the number of monomers up…

Statistical Mechanics · Physics 2009-11-10 J. Krawczyk , A. L. Owczarek , T. Prellberg , A. Rechnitzer

We study the conformational properties of heteropolymers containing two types of monomers A and B, modeled as self-avoiding random walks on a regular lattice. Such a model can describe in particular the sequences of hydrophobic and…

Disordered Systems and Neural Networks · Physics 2014-09-01 Viktoria Blavatska , Wolfhard Janke

We study ground states of a hybrid system consisting of a polymer and an attractive nanowire by means of computer simulations. Depending on structural and energetic properties of the substrate, we find different adsorbed polymer…

Soft Condensed Matter · Physics 2011-03-10 Thomas Vogel , Michael Bachmann

The aim of this paper is to investigate the distribution of a continuous homopolymer in the presence of an attractive finitely supported potential. The most intricate behavior can be observed if we simultaneously vary two parameters: the…

Probability · Mathematics 2013-01-23 Leonid Koralov , Zsolt Pajor-Gyulai

We introduce a sequential model for the deposition and aggregation of particles in the submonolayer regime. Once a particle has been randomly deposited on the substrate, it sticks to the closest atom or island within a distance \ell,…

Statistical Mechanics · Physics 2007-05-23 Paolo Politi , Yukio Saito

The adsorption of a single polymer to a flat surface in shear is investigated using Brownian hydrodynamics simulations and scaling arguments. Competing effects are disentangled: in the absence of hydrodynamic interactions, shear drag…

Soft Condensed Matter · Physics 2015-05-20 Andreas Serr , Christian Sendner , Florian Mueller , Thomas R. Einert , Roland R. Netz

We address the response of a random heteropolymer to preferential solvation of certain monomer types at the globule-solvent interface. For each set of monomers that can comprise the molecule's surface, we represent the ensemble of allowed…

Soft Condensed Matter · Physics 2009-11-10 Philip Geissler , Eugene Shakhnovich , Alexander Grosberg