Soft Matter Blog

In the tightly packed molecular world of the cell DNA is protected and wrapped up into small packages called chromatins. The complex plays a crucial role in living organisms because its dynamic organization is a key factor for controlling the regulation of gene expression.

To investigate the unwrapping process Qianqian Cao and coworkers at Jilin University, China, used coarse-grained molecular dynamics simulations to study the unwinding of a DNA-nanosphere complex when a force exerted on the DNA chain.

The team found that the wrapping degree and the folding state of DNA around the sphere is significantly dependent on the surface charge density and the salt concentration. When an external force is applied to two ends of DNA chain, different stages are observed in the stretching process as the complex is unwrapped. The team say that this behaviour also has been observed in experiments and other simulations on the stretching of chromatin.

Read Cao’s full article for free in Soft Matter here:  Qianqian Cao, Chuncheng Zuo, Yanhong Ma, Lujuan Li and Zhou Zhang, Soft Matter, 2011, DOI:10.1039/C0SM00512F

Have you ever wondered what’s going on in a foam when it flows? In her latest Soft Matter paper, Isabelle Cantat at the Université Rennes, France, simulates the dissipation of bubbles in foam. Cantat used 2D numerical simulations involving 500 bubbles under simple shear, in a non-quasi static regime to study the dissipation of bubbles.

Cantat shows that small tension dynamical inhomogeneities induce foam structure modifications responsible for the largest part of the stress increase. The stress increase with increasing shear rate is mainly due to increasing bubble elongation that can be interpreted as an increase of the plastic threshold.

Interested to know more? Read Cantat’s Soft Matter paper here:

UK Scientists have created a hybrid system that uses non-biological energy to drive biological processes. Harnessing non-biological energy to power biological processes offers a convenient method to rapidly turn on and off biochemical reactions and the technology could be useful in many bioengineering applications.

Led by Lars Jeuken researchers at University of Leeds, UK, used a gold electrode to drive the removal of protons from lipid vesicles adsorbed onto the electrode’s surface. The system uses the electrode to reduce ubiquinone in the vesicles. Protons are then pumped across the lipid bilayer and out of the vesicle by an enzyme (ubiquinol oxidase) which re-oxidises the ubiquinone. Actively pumping protons out of the vesicle creates a proton gradient between the vesicle’s interior and the surroundings which the team detected using a fluorescent probe.

The team says that this technology could open a way to use the pH gradient to drive other reactions such as active transport of organic substrates across the membrane or ATP synthesis.

Read the full article for free here:

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A simple method for simultaneously patterning different biomolecules on a surface can create complex patterns in a single step. These patterns can direct the adhesion, polarization, and guide neurites in neurons. The technique called vacuum soft lithography was developed by a team led by Sarah Heilshorn, University of California, Berkeley, USA, and could be used in to prepared surfaces for use in tissue engineering or translational medicine the team say.

To create the complex patterns, biomolecules are physically adsorbed onto glass slides using a removable polydimethylsiloxane microfluidic template. The method uses the gas permeability of PDMS to fill circuitous and dead-end microfluidic channels. Upon removal from vacuum, degassed PDMS templates store a negative pressure relative to atmosphere which can be used to pull solutions through closed microfluidic channels. The technique is capable of preparing designs with better than 2 µm resolution.

Interested to know more? Read the full article here: J. Tanner Nevill, Alexander Mo, Branden J. Cord, Theo D. Palmer, Mu-ming Poo, Luke P. Lee and Sarah C. Heilshorn, Soft Matter, 2011, DOI:10.1039/C0SM00869A

Inspired by floating flowers, a passive pipetting mechanism allows for water to be grabbed with a flexible solid.

The technique was developed by a team led by Pedro Reis at Massachusetts Institute of Technology, USA, and co-workers in USA and France. The passive pipetting mechanism relies purely on the coupling of the elasticity of thin plates and the hydrodynamic forces at the liquid interface. By developing a theoretical model the team were able to design petal-shaped objects with maximum grabbing capacity.

Interested to know more? Read the full paper here: Pedro M. Reis, Jérémy Hure, Sungwan Jung, John W. M. Bush and Christophe Clanet, Soft Matter, 2010, DOI:10.1039/C0SM00895H

Eran Sharon and Efi Efrati from The Hebrew University of Jerusalem, Israel, discuss the mechanics of non-Euclidean plates in a Tutorial Review. Non-Euclidean plates are “stacks” of identical surfaces whose two-dimensional intrinsic geometry cannot be realized in a flat configuration. They can be generated via different mechanisms, such as plastic deformation, natural growth or differential swelling.

The review covers theoretical and experimental works that focus on shape selection in non-Euclidean plates and provides an overview of the governing principles of this field.

Read the Tutorial Review here:

Understanding gelator–gelator, fibre–fibre and fibre–solvent interactions is important for developing effective models for the dynamic self-assembly of gel-phase materials. A team lead by David Smith at the University of York, UK, have used Kamlet–Taft parameters to shed light on how the choice of solvent can mediate these interactions interactions. Fancy reading more? Download the full article here:

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