- Published on 30 May 2018
Patchy particles is the name given to a large class of systems of mesoscopic particles characterized by a repulsive core and a discrete number of short-range and highly directional interaction sites. Numerical simulations have contributed significantly to our understanding of the behaviour of patchy particles, but, although simple in principle, advanced simulation techniques are often required to sample the low temperatures and long time-scales associated with their self-assembly behaviour.
In this EPJ E colloquium paper, Rovigatti et al. review the most popular simulation techniques that have been used to study patchy particles, with a special focus on Monte Carlo methods.
- Published on 23 May 2018
A new study shows how to couple highly accurate and simplified models of the same system to extract thermodynamics information using simulations
Computer simulations are used to understand the properties of soft matter - such as liquids, polymers and biomolecules like DNA - which are too complicated to be described by equations. They are often too expensive to simulate in full, given the intensive computational power required. Instead, a helpful strategy is to couple an accurate model - applied in the areas of the system that require greater attention - with a simpler, idealised model. In a recent paper published in EPJ E, Maziar Heidari, from the Max Planck Institute for Polymer Research, Mainz, Germany and colleagues make the accurate model in high-resolution coincide seamlessly with an exactly solvable representation at lower resolution.
- Published on 14 May 2018
New study outlines key factors affecting the transfer of molecules through biological channels
In our bodies, the transfer of genetic information, viral infections and protein trafficking, as well as the synthesis and the degradation of biomolecules, are all phenomena that require the transport of molecules through channels. Improving our control of these channels and the capacity of molecules to get across could have many potential applications in the fields of energy, biotechnology and medicine. These include ultra-fast DNA sequencing, detection of biological markers used in disease diagnostics, protein folding, high-resolution determination of the size of biological molecules or even the control of ion or biomolecule transport through the protein sensor. In a new study published in EPJ E, Manuela Pastoriza-Gallego from the University Paris-Seine, France, and colleagues have shown how to alter external factors, such as external voltage, to control the transport of a dextran sulfate molecule - a polyelectrolyte - through the nanopores of the aerolysin protein channel.
- Published on 27 April 2018
An open source software that is able to construct synthetic blood vessel networks in 3D, matching the properties observed in real tumor samples.
The tumor vasculature is a major target of anticancer therapies. Rieger, Fredrich and Welter at Saarland University, Germany have been pursuing a quantitative analysis of the physical determinants of vascularized tumors for several years . With the help of computer simulations they have been able to recapitulate the knowledge accrued from in vitro research of tumor spheroids, animal models and clinical studies and have re-created a vascularized tumor system in silico.
- 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.
- 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.
- 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.
- 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.
- 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.