Nuclear Sciences & Technologies

EPJ E Highlight - Remote control of transport through nanopores

Dynamics of dextran sulfate transport through aerolysin nanopore.

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.

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EPJE Highlight - Tumorcode, a software to simulate vascularized tumors

Rendering of a bulk tissue tumor simulation.

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 [1]. 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.

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EPJ E Highlight - Simulations document self-assembly of proteins and DNA

Representation of a charged patchy particle with two different patches.

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.

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EPJ E Highlight - The unsuspected synergistic mechanism of the human heart

3D simulations of the heart mechanisms.

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.

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EPJ E Highlight - Understanding the wetting of micro-textured surfaces can help give them new functionalities

Snapshots of contact line configurations when water droplets slide on surfaces with micro-pillars.

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.

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EPJ E Colloquium - A unified description of colloidal thermophoresis

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.

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EPJ E Highlight - Unexpected undulations in biological membranes

Schematic illustration of the fluctuating membrane in a structured fluid.

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.

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EPJ E Highlight - Which sequences make DNA unwrap and breathe?

Nucleosome model with the fully wrapped complex (left) and a partially unwrapped complex.

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.

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EPJ E Highlight - Swarm-based simulation strategy proves significantly shorter

Water droplets we used as a test case in this paper © the authors.

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.

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EPJ E Highlight - Resolving tension on the surface of polymer mixes

Polymers © iker-urteaga via Unsplash.

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.

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Editors-in-Chief
G. Moutiers and A. Nicolas
ISSN: 2491-9292 (Electronic Edition)

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