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The specificity and thermal reversibility of DNA interactions have enabled the self-assembly of crystal structures, self-replicating materials and colloidal molecules. Grafting DNA onto liquid interfaces of emulsions leads to exciting new…

Soft Condensed Matter · Physics 2013-10-31 Lang Feng , Lea-Laetitia Pontani , Remi Dreyfus , Paul Chaikin , Jasna Brujic

We report on the formation of colloidal complexes resulting from the electrostatic self-assembly of polyelectrolyte-neutral block copolymers and oppositely charged surfactants. The copolymers investigated are asymmetric and characterized by…

Soft Condensed Matter · Physics 2007-05-23 Jean-Francois Berret , Pascal Herve , Isabelle Grillo

Spin coating is an out-of-equilibrium technique for producing polymer films and colloidal crystals quickly and reproducibly. In this review, we present an overview of theoretical and experimental studies of the spin coating of colloidal…

Soft Condensed Matter · Physics 2013-02-26 Moorthi Pichumani , Payam Bagheri , Kristin M. Poduska , Wenceslao Gonzalez-Vinas , Anand Yethiraj

We study the melting of a double stranded DNA in the presence of stretching forces, via 3D Monte-Carlo simulations, exactly solvable models and heuristic arguments. The resulting force-temperature phase diagram is dramatically different for…

Soft Condensed Matter · Physics 2008-07-22 D. Marenduzzo , A. Maritan , E. Orlandini , F. Seno , A. Trovato

With the help of one-dimensional random Potts-like model we study the origins of fine structure observed on differential melting profiles of double-stranded DNA. We assess the effects of sequence arrangement on DNA melting curves through…

Soft Condensed Matter · Physics 2024-04-11 Arevik V. Asatryan , Albert S. Benight , Artem V. Badasyan

We study the motion of long polymers (eg DNA) in a gel under the influence of an external force acting locally on small segments of the polymer. In particular, we examine the dependence of the drift velocity on the position where the force…

Statistical Mechanics · Physics 2015-06-25 M. J. E. Richardson , G. M. Schütz

To simulate long time and length scale processes involving DNA it is necessary to use a coarse-grained description. Here we provide an overview of different approaches to such coarse graining, focussing on those at the nucleotide level that…

We report on a molecular simulation method which captures the self-assembly of cationic lipid-DNA (CL-DNA) gene delivery complexes. Computational efficiency required for large length- and time-scale simulations is achieved through a…

Soft Condensed Matter · Physics 2007-05-23 Oded Farago , Niels Grønbech-Jensen , Philip Pincus

We present micro-rheological measurments of the drag force on colloids pulled through a solution of lambda-DNA (used here as a monodisperse model polymer) with an optical tweezer. The experiments show a violation of the Stokes-Einstein…

Soft Condensed Matter · Physics 2009-11-13 Christof Gutsche , Friedrich Kremer , Matthias Krüger , Markus Rauscher , Rudolf Weeber , Jens Harting

The mechanism responsible for the compaction of the genomic DNA of bacteria inside a structure called the nucleoid is a longstanding but still lively debated question. Most puzzling is the fact that the nucleoid occupies only a small…

Biological Physics · Physics 2018-09-20 Marc Joyeux

In living cells, proteins self-assemble into large functional structures based on specific interactions between molecularly complex patches. Due to this complexity, protein self-assembly results from a competition between a large number of…

Soft Condensed Matter · Physics 2024-12-10 Lara Koehler , Pierre Ronceray , Martin Lenz

Strongly correlated electrostatics of DNA systems has drawn the interest of many groups, especially the condensation and overcharging of DNA by multivalent counterions. By adding counterions of different valencies and shapes, one can…

Biomolecules · Quantitative Biology 2017-05-25 Nguyen Viet Duc , Toan T. Nguyen , Paolo Carloni

We systematically explore the self-assembly of semi-flexible polymers in deformable spherical confinement across a wide regime of chain stiffness, contour lengths and packing fractions by means of coarse-grained molecular dynamics…

Soft Condensed Matter · Physics 2021-07-12 Maxime M. C. Tortora , Daniel Jost

The interaction of amphiphilic polymers with small colloids, capable to reversibly stick onto the chains, is studied. Adhesive small colloids in solution are able to dynamically bind two polymer segments. This association leads to…

Soft Condensed Matter · Physics 2010-11-10 Vladimir A. Baulin , Albert Johner , Josep Bonet Avalos

Molecular combing is a powerful and simple method for aligning DNA molecules onto a surface. Using this technique combined with fluorescence microscopy, we observed that the length of lambda-DNA molecules was extended to about 1.6 times…

Biomolecules · Quantitative Biology 2009-11-10 Yu-Ying Liu , Peng-Ye Wang , Shuo-Xing Dou , Wei-Chi Wang , Ping Xie , Hua-Wei Yin , Xing-Dong Zhang

The field of complex self-assembly is moving toward the design of multi-particle structures consisting of thousands of distinct building blocks. To exploit the potential benefits of structures with such `addressable complexity,' we need to…

Soft Condensed Matter · Physics 2015-06-02 William M. Jacobs , Aleks Reinhardt , Daan Frenkel

While the statistical mechanical description of DNA has a long tradition, renewed interest in DNA melting from a physics perspective is nourished by measurements of the fluctuation dynamics of local denaturation bubbles by single molecule…

Biomolecules · Quantitative Biology 2009-11-13 Tobias Ambjornsson , Suman K. Banik , Oleg Krichevsky , Ralf Metzler

We propose a mathematical model of DNA self-assembly using 2D tiles to form 3D nanostructures. This is the first work to combine studies in self-assembly and nanotechnology in 3D, just as Rothemund and Winfree did in the 2D case. Our model…

Computational Complexity · Computer Science 2007-05-23 Ming-Yang Kao , Vijay Ramachandran

We report a study of the structure of droplets of colloidal gels containing dissolved sodium chloride. The components segregate and form intricate patterns. The salt crystalizes in fractal and multi-fractal dendritic forms which are…

Soft Condensed Matter · Physics 2012-08-03 Moutushi Dutta Choudhury , Sayanee Jana , Sruti Dutta , Sujata Tarafdar

Block copolymer are ideal matrices to control the localisation of colloids. Furthermore, anisotropic nanoparticles such as Janus nanoparticles possess an additional orientational degree of freedom that can play a crucial role in the…

Soft Condensed Matter · Physics 2019-08-13 Javier Diaz , Marco Pinna , Andrei Zvelindovsky , Ignacio Pagonabarraga