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The microtubule assembly process has been extensively studied, but the underlying molecular mechanism remains poorly understood. The structure of an artificially generated sheet polymer that alternates two types of lateral contacts and that…

Biomolecules · Quantitative Biology 2009-11-10 Zhanghan Wu , Hong-Wei Wang , Weihua Mu , Zhongcan Ouyang , Eva Nogales , Jianhua Xing

This paper examines the mechanisms of destruction and synthesis for macromolecules, which may be propelled by external acoustic fields in the flows of polymeric liquids containing a large number of gas bubbles. The dynamics of these bubbles…

We report molecular dynamics simulations of a system of repulsive, polymer-tethered colloidal particles. We use an explicit polymer model to explore how the length and the behavior of the polymer (ideal or self-avoiding) affect the ability…

Soft Condensed Matter · Physics 2015-05-14 Behnaz Bozorgui , Maya Sen , William L. Miller , Josep C. Pamies , Angelo Cacciuto

Thermoreversible sol-gel transitions in solutions of rod-like associating polymers are analyzed by computer simulations and by mean field models. The sol-gel transition is determined by the divergence of the cluster weight average. The…

Condensed Matter · Physics 2015-06-24 Min Sun Yeom , Alexander V. Ermoshkin , Monica Olvera de la Cruz

We study at- and out-of-equilibrium dynamics of a single homopolymer chain at low temperature using molecular dynamics simulations. The main quantities of interest are the average root mean square displacement of the monomers below the…

Soft Condensed Matter · Physics 2009-11-07 Nikolay V. Dokholyan , Estelle Pitard , Sergey V. Buldyrev , H. Eugene Stanley

We investigated the formation of cocontinuous structures in polymer blends. These polymeric bijels (bicontinuous interfacially jammed emulsion gels) were composed of polystyrene oligomer, polybutene and fluorescent hydrophobic silica…

Soft Condensed Matter · Physics 2015-02-03 Lian Bai , John Fruehwirth , Xiang Cheng , Christopher W. Macosko

The competition of depletion attractions and longer-ranged repulsions between colloidal particles in colloid-polymer mixtures leads to the formation of heterogeneous gel-like structures. For instance, gel networks, i.e., states where the…

Soft Condensed Matter · Physics 2021-06-24 Matthias Gimperlein , Michael Schmiedeberg

The isothermal, isobaric spontaneous crystallization of a supercooled polymer melt is investigated by MD simulation of an ensemble of fully-flexible linear chains. Frustration is introduced via two incommensurate length scales set by the…

Soft Condensed Matter · Physics 2018-11-19 Andrea Giuntoli , Sebastiano Bernini , Dino Leporini

We define a lattice model for the interaction of a polymer with water. We solve the model in a suitable approximation. In the case of a non-polar homopolymer, for reasonable values of the parameters, the polymer is found in a non-compact…

Statistical Mechanics · Physics 2009-10-31 Pierpaolo Bruscolini , Lapo Casetti

We have studied the competition between helix formation and aggregation for a simple polymer model. We present simulation results for a system of two such polymers, examining the potential of mean force, the balance between inter and…

Soft Condensed Matter · Physics 2007-05-23 James E. Magee , Zhankai Song , Robin A. Curtis , Leo Lue

In this work we presented a novel computational model of precipitation polymerization allowing one to obtain core-shell microgels via a realistic cross-linking process based on the experimental procedure. We showed that the…

Soft Condensed Matter · Physics 2020-04-24 Alexey A. Gavrilov , Vladimir Yu. Rudyak , Alexander V. Chertovich

A nonequilibrium molecular dynamics computer simulation on microsegregated solutions of symmetrical diblock copolymers is reported. As the polymer concentration increases, the system undergoes phase transitions in the following order: body…

Soft Condensed Matter · Physics 2007-05-23 Igor Rychkov , Kenichi Yoshikawa

We study colloidal gels formed by competing electrostatic repulsion and short-range attraction by means of extensive numerical simulations under external shear. We show that, upon varying the repulsion strength, the gel structure and its…

Soft Condensed Matter · Physics 2020-04-23 José Ruiz-Franco , Fabrizio Camerin , Nicoletta Gnan , Emanuela Zaccarelli

We model the behaviour of a single colloid embedded in a cross-linked polymer gel, immersed in a viscous background fluid. External fields actuate the particle into a periodic motion, which deforms the embedding matrix and creates a local…

Soft Condensed Matter · Physics 2022-11-09 Guido L. A. Kusters , Cornelis Storm , Paul van der Schoot

We enumerate all minimal energy packings (MEPs) for small single linear and ring polymers composed of spherical monomers with contact attractions and hard-core repulsions, and compare them to corresponding results for monomer packings. We…

Soft Condensed Matter · Physics 2015-05-18 Robert S. Hoy , Corey S. O'Hern

Transitions in structural heterogeneity of colloidal depletion gels formed through short-range attractive interactions are correlated with their dynamical arrest. The system is a density and refractive index matched suspension of 0.20…

Soft Condensed Matter · Physics 2009-11-11 C. J. Dibble , M. Kogan , M. J. Solomon

In systems of highly charged linear polyelectrolytes and oppositely charged colloidal particles, long-lived clusters of polyelectrolyte-decorated particles form in an interval of concentrations around the isoelectric point, where reentrant…

Soft Condensed Matter · Physics 2008-07-24 S. Sennato , D. Truzzolillo , F. Bordi , C. Cametti

When a swollen, thermoresponsive polymer gel is heated in a solvent bath, it expels solvent and deswells. When this heating is slow, deswelling proceeds homogeneously, as observed in a toroid-shaped gel that changes volume whilst…

Star cluster formation in giant molecular clouds involves the local collapse of the cloud into small gas-rich subclusters, which can then subsequently collide and merge to build up the final star cluster(s). In this paper, we simulate…

Astrophysics of Galaxies · Physics 2022-05-25 Jeremy Karam , Alison Sills

We use machine learning algorithms to detect the crystalline phase in undercooled melts in molecular dynamics simulations. Our classification method is based on local conformation and environmental fingerprints of individual monomers. In…

Soft Condensed Matter · Physics 2023-11-02 Atmika Bhardwaj , Jens-Uwe Sommer , Marco Werner
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