- Published on 20 August 2018
Natural switching of DNA and RNA polarisation opens possibilities to develop novel biosensors and high-capacity data storage
DNA and RNA are naturally polarised molecules containing electric dipole moments due to the presence of a significant number of charged atoms at neutral pH. Scientists believe that these molecules have an in-built polarity that can be reoriented or reversed fully or in part under an electric field—a property referred to as bioferroelectricity. However, the mechanism of these properties remains unclear. In a new study published in EPJ E, See-Chuan Yam from the University of Malaya, Kuala Lumpur, Malaysia, and colleagues show that all the DNA and RNA building blocks, or nucleobases, exhibit a non-zero polarisation in the presence of polar atoms or molecules such as amidogen and carbonyl. They have two stable states, indicating that DNA and RNA basically have memory properties, just like a ferroelectric or ferromagnetic material. This is relevant for finding better ways of storing data in DNA and RNA because they have a high capacity for storage and offer a stable storage medium. Such physical properties may play an important role in biological processes and functions. Specifically, these properties could also be extremely useful for possible applications as a biosensor to detect DNA damage and mutation.
- Published on 26 June 2018
New study of how positive and negative electrical charge disorder at the ends of polymers acts like a green or red light for proteins to pass through biological membranes
Nature’s way of allowing proteins across its gates, through porous biological membranes, depends, among others, on their electrical charge. For a protein to cross this type of membrane, it needs to be stimulated by an electrical field. A new study focuses on a particular kind of proteins that have multiple functions - dubbed Intrinsically Disordered Proteins - because the electric charge disorder on their surface makes it possible for them to take multiple shapes. In the work, recently published in EPJ E, Albert Johner from the Charles Sadron Institute (part of the CNRS) in Strasbourg, France and Jean-Francois Joanny from Paris reveal how the mixed electrical charge at the ends of the proteins influences biological membrane crossing. This has potential implications for our understanding of how proteins travel across the body, and of disease mechanisms.
- 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.