EPJ E Highlight - Simulations document self-assembly of proteins and DNA
- Published on 28 March 2018
Colloidal model featuring rigid bodies with two interaction sites explains how biological entities such as protein/DNA combinations can self-assemble
What makes particles self-assemble into complex biological structures? Often, this phenomenon is due to the competition between forces of attraction and repulsion, produced by electric charges in various sections of the particles. In nature, these phenomena often occur in particles that are suspended in a medium - referred to as colloidal particles - such as proteins, DNA and RNA. To facilitate self-assembly, it is possible to "decorate" various sites on the surface of such particles with different charges, called patches. In a new study published in EPJ E, physicists have developed an algorithm to simulate the molecular dynamics of these patchy particles. The findings published by Silvano Ferrari and colleagues from the TU Vienna and the Centre for Computational Materials Science (CMS), Austria, will improve our understanding of what makes self-assembly in biological systems possible.
EPJ E Highlight - The unsuspected synergistic mechanism of the human heart
- Published on 28 February 2018
3D simulations reveals that every part of the human heart works in combination with the others, while all parts influence each other’s dynamics, giving clues to help prevent cardiac conditions
Did you know that the left side of the heart is the most vulnerable to cardiac problems? Particularly the left ventricle, which has to withstand intense pressure differences, is under the greatest strain. As a result, people often suffer from valve failure or impairment of the myocardium. This is why it is important to fully understand how the blood flow within this part of the heart affects its workings. In a new study published in EPJ E, Valentina Meschini from the Gran Sasso Science Institute, L'Aquila, Italy and colleagues introduce a novel model that examines, for the first time with this approach, the mutual interaction of the blood flow with the individual components of the heart. Their work stands out by offering a more holistic and accurate picture of the dynamics of blow flow in the left ventricle. The authors also perform some experimental validations of their model.
EPJ E Highlight - Understanding the wetting of micro-textured surfaces can help give them new functionalities
- Published on 21 February 2018
New theoretical model explains experimental measurement of the friction of liquid droplets sliding on micro-structured surfaces
The wetting and adhesion characteristics of solid surfaces critically depend on their fine structures. However, until now, our understanding of exactly how the sliding behaviour of liquid droplets depends on surface microstructures has been limited. Now, physicists Shasha Qiao, Qunyang Li and Xi-Qiao Feng from Tsinghua University in Beijing, China have conducted experimental and theoretical studies on the friction of liquid droplets on micro-structured surfaces. In a paper published in EPJ E, the authors found that under the same solid fraction, friction on surfaces with a structure made up of micro-holes is much higher than that on surfaces patterned with an array of pillars. Such micro-structured surfaces have helped design new surfaces that mimic surfaces found in nature, such as self-cleaning surfaces, reduced-drag surfaces, surfaces capable of transporting liquids in microfluidic systems, variants with anti-icing or heat transfer properties, and even surfaces that facilitate oil-water separation.
EPJ E Colloquium - A unified description of colloidal thermophoresis
- Published on 23 January 2018
When colloidal particles find themselves in a temperature gradient they move in response to it, in some cases toward the hotter some toward the cooler side, depending on the specific physical chemistry of the colloid and the solvent surrounding it. This process, called thermophoresis, is generally regarded as a phoretic phenomenon: the thermal motion of a colloid is mainly driven by local hydrodynamic stresses in the surrounding liquid. However a complete and unique theoretical description of thermophoresis has been lacking.
EPJ E Highlight - Unexpected undulations in biological membranes
- Published on 09 January 2018
Study of the dynamic properties of biological membranes reveals new anomalous behaviour under specific circumstances
How biological membranes - such as the plasma membrane of animal cells or the inner membrane of bacteria - fluctuate over time is not easy to understand, partly because at the sub-cellular scale, temperature-related agitation makes the membranes fluctuate constantly; and partly because they are in contact with complex media, such as the cells’ structuring element, the cytoskeleton, or the extra-cellular matrix. Previous experimental work described the dynamics of artificial, self-assembled polymer-membrane complexes, embedded in structured fluids. For the first time, Rony Granek from Ben-Gurion University of The Negev, and Haim Diamant from Tel Aviv University, both in Israel, propose a new theory elucidating the dynamics of such membranes when they are embedded in polymer networks. In a new study published in EPJ E, the authors demonstrate that the dynamics of membrane undulations inside such a structured medium are governed by distinctive, anomalous power laws.
EPJ E Highlight - Which sequences make DNA unwrap and breathe?
- Published on 04 December 2017
New study elucidates the DNA sequences that offer the perfect conditions for packaged DNA to unwrap and ‘breathe’, thus allowing genes to be read
Accessing DNA wrapped into basic units of packaging, called nucleosomes, depends on the underlying sequence of DNA building blocks, or base pairs. Like Christmas presents, some nucleosomes are easier to unwrap than others. This is because what makes the double helix stiffer or softer, straight or bent—in other words, what determines its elasticity—is the actual base pair sequence. In a new study published in EPJ E, Jamie Culkin from Leiden University, the Netherlands, and colleagues demonstrate the role of the DNA sequence in making it possible for packaged DNA to open up and let genes be read and expressed.
EPJ E Highlight - Swarm-based simulation strategy proves significantly shorter
- Published on 01 December 2017
New method creates time-efficient way of computing models of complex systems reaching equilibrium
When the maths cannot be done by hand, physicists modelling complex systems, like the dynamics of biological molecules in the body, need to use computer simulations. Such complicated systems require a period of time before being measured, as they settle into a balanced state. The question is: how long do computer simulations need to run to be accurate? Speeding up processing time to elucidate highly complex study systems has been a common challenge. And it cannot be done by running parallel computations. That’s because the results from the previous time lapse matters for computing the next time lapse. Now, Shahrazad Malek from the Memorial University of Newfoundland, Canada, and colleagues have developed a practical partial solution to the problem of saving time when using computer simulations that require bringing a complex system into a steady state of equilibrium and measuring its equilibrium properties. These findings are part of a special issue on “Advances in Computational Methods for Soft Matter Systems,” recently published in EPJ E.
EPJ E Highlight - Resolving tension on the surface of polymer mixes
- Published on 10 October 2017
A new study finds a simple formula to explain what happens on the surface of melted mixes of short- and long-strand polymers
Better than playing with Legos, throwing polymer chains of different lengths into a mix can yield surprising results. In a new study published in EPJ E, physicists focus on how a mixture of chemically identical chains into a melt produces unique effects on their surface. That’s because of the way short and long polymer chains interact with each other. In these kinds of melts, polymer chain ends have, over time, a preference for the surface. Now, Pendar Mahmoudi and Mark Matsen from the University of Waterloo, Ontario, Canada, have studied the effects of enriching long-chain polymer melts with short-chain polymers. They performed numerical simulations to explain the decreased tension on the surface of the melt, due to short chains segregating at the surface over time as disorder grows in the melt. They found an elegant formula to calculate the surface tension of such melts, connected to the relative weight of their components.
EPJ E Highlight - The secret to improving liquid crystal's mechanical performance
- Published on 06 October 2017
Better lubricating properties of lamellar liquid crystals could stem from changing the mobility of their structural dislocations by adding nanoparticles
By deliberately interrupting the order of materials - by introducing different atoms in metal or nanoparticles in liquid crystals - we can induce new qualities. For example, metallic alloys like duralumin, which is composed of 95% of aluminium and 5% copper, are usually harder than the pure metals. This is due to an elastic interaction between the defects of the crystal, called dislocations, and the solute atoms, which form what are referred to as Cottrell clouds around them. In such clouds, the concentration of solute atoms is higher than the mean concentration in the material. In a paper published in EPJ E, Patrick Oswald from the École Normale Supérieure of Lyon, France, and Lubor Lejček from the Czech Academy of Sciences have now theoretically calculated the static and dynamical properties of the Cottrell clouds, which form around edge dislocations in lamellar liquid crystals of the smectic A variety decorated with nanoparticles. This work could be important, for example, in the context of improving the lubricating performance of such liquid crystals.
EPJ E Highlight - Like a game of 'spot the difference' for disease-prone versus healthy people
- Published on 25 July 2017
The change in behaviour of natural nanoparticles, called lipoproteins, under pressure could provide new insights to better understand the genesis of high cholesterol and atherosclerosis
Understanding common diseases sometimes boils down to grasping some of their basic mechanisms. For instance, a specific kind of natural nanoparticles, called low-density lipoproteins (LDL), are fascinating scientists because their modification plays a key role in people affected by high cholesterol. They are also known for their role in the formation of atherosclerosis. Judith Peters from the University Grenoble Alpes and the Institute Laue Langevin, Grenoble, France and colleagues from the Medical University of Graz, Austria, mimicked variations of LDL found in people affected by such diseases. They then compared their responses to temperature variations and increased pressure with those of lipoproteins found in healthy people. Their findings, recently published in EPJ E, show that the LDL from healthy people behaved differently when subjected to high pressure compared to LDL affected by the common diseases studied.