- Published on 27 March 2013
Scientists have accurately calculated the sliding mechanism for deciphering the second genetic code written within the DNA base pair sequence
Three-quarters of the DNA in evolved organisms is wrapped around proteins, forming the basic unit of DNA packaging called nucleosomes, like a thread around a spool. The problem lies in understanding how DNA can then be read by such proteins. Now, Arman Fathizadeh, a physicist at Sharif University of Technology in Tehran, Iran, and colleagues have created a model showing how proteins move along DNA, in a paper just published in EPJ E.
- Published on 17 March 2013
EPJE is now accepting submissions for a topical issue on “irreversible dynamics”, dedicated to Paul Manneville. The study of classical physics underwent a revolution in the 1970s-1980s thanks to seminal contributions by Ruelle, Takens, Pomeau and Manneville. The concurrent revival and extension of the theory of dynamical systems encompasses spatiotemporal chaos and coupled oscillator arrays. Applications to fluid dynamics range from pattern formation in convection, to the onset of turbulence in shear flows. The concurrent revival and extension of the theory of dynamical systems encompasses spatiotemporal chaos and coupled oscillator arrays. Applications to fluid dynamics range from pattern formation in convection, to the onset of turbulence in shear flows. Laurette Tuckerman or Patrice Le Gal, Guest Editors of this topical issue, extend a warm invitation to all researchers, with a wide interpretation of the field. The deadline for submission is July 1st 2013. The full call for papers can be found here
- Published on 10 February 2013
A new algorithm could help understand the structure of liquids, and how they flow through porous media
Theoretical physicist Moumita Maiti and colleagues at the Jawaharlal Nehru Centre for Advanced Scientific Research in Bangalore, India, have now implemented an algorithm for analysing void space in sphere packing, where the spheres need not all be the same size. This method, just published in EPJ E, could be applied to analyse the geometry of liquids present between multi-sized spheres that are akin to a model for porous material. This provides a tool for studying the flow of such fluids through porous material. More importantly, it can also be used to study the packing geometry of proteins.
- Published on 04 February 2013
Scientists have unearthed a new dynamic process induced by strong electric fields in thin liquid crystal cells
Liquid crystal displays are ubiquitous. Now, Polish physicists have demonstrated that the application of a very strong alternating electric field to thin liquid crystal cells leads to a new distinct dynamic effect in the response of the cells. The theory of spatio-temporal chaos explains this effect. It was elucidated by Wojciech Jeżewski and colleagues from the Institute of Molecular Physics, Polish Academy of Sciences, in Poznań, Poland, and was just published in EPJ E. This effect has implications for the operation of liquid-crystal devices because their operation is based on the electro-optic switching phenomenon, subject to the newly discovered effect.
- Published on 20 December 2012
A new model could ultimately help robotic fingers, made of a soft surface, manipulate small objects
Imagine a solid ball rolling down a slightly inclined ramp. What could be perceived as child’s play is the focus of serious theoretical research by Manoj Chaudhury and Partho Goohpattader, two physicists from Lehigh University, Bethlehem, Pensylvania, USA. Their study, which has just been published in EPJ E, has one thing in common with childhood behaviour. It introduces a mischievous idea, namely studying the effect of random noise, such as vibrations, on the ball. They found it could lower the energy barrier to set the ball in motion.
- Published on 05 November 2012
A two-order parameter model proposed to describe water-like anomalies, liquid-liquid transition, glass transition, crystal nucleation and quasicrystal formation within the same framework.
The liquid state of matter is far from being a perfectly disordered homogeneous state. In a Colloquium paper published in EPJ E, Hajime Tanaka argues that to achieve a better understanding of liquids, it is crucial to recognize that a liquid has a general tendency to exhibit local structural order, and that this order is intrinsic and universal to any liquid. In other words, there is a need for a new order parameter describing a low local free-energy configuration (this is a bond-orientational order parameter in many cases), in addition to a density order parameter.
- Published on 31 October 2012
The law of hydrodynamics governing the way internally driven systems behave could explain their complex structure
Physicists use hydrodynamics to understand the physical mechanism responsible for changes in the long-range order of groups of particles. Particularly, Aparna Baskaran of Brandeis University, Massachusetts, USA, and Cristina Marchetti of Syracuse University, New York, USA, focused on ordered groups of elongated self-propelled particles. They studied the breakdown of long-range order due to fluctuations that render them unstable and give rise to complex structures, in a study just published in EPJ E within the topical issue on Active Matter.
- Published on 27 October 2012
Models simulate what happens to DNA strands when stretched to the breaking point
Theoretical physicists like to play with very unconventional toys. Manoel Manghi from Toulouse University in France and his colleagues have adopted a seemingly playful approach to examining what happens to a double stranded molecule of DNA when it is stretched to the breaking point, in a study about to be published in EPJ E. Instead of using optical tweezers to stretch DNA as previously done in experimental settings, the authors focused on using a theoretical model to account for the structural deformations of DNA and determine how its mechanical characteristics could explain certain biological processes.
- Published on 23 October 2012
Physicists investigate the cause of striped patterns formed by fine particles deposited on surfaces
Patterns fascinate. Particularly stripes. Found in nature in zebras, they are also found in the most unlikely places, such as powdered drugs’ mixing vessel walls. In an article just published in EPJ E, Nirmal Thyagu and his colleagues from Rutgers University, New Jersey, USA, propose a traffic model to predict the formation of different patterns, ranging from stripes to spots.
- Published on 21 October 2012
Several new simulations performed on polymers outline their scaling-up behaviour at extreme limits where it depends on their density and length.
Scientists use simulations to test the limits of their object of study—in this case thin films of polymers—to extremes of scale. In a study just published in EPJ E, Nava Schulmann, a researcher at Strasbourg University, France, and colleagues use a well-known model capable of providing information on heat and mechanical energy exchange between these polymer chains. They found that polymer blends confined to ultrathin two-dimensional films displayed enhanced compatibility. This was made possible by simulations using a fairly standard model, which is simple enough to allow the efficient computation of dense large-chain systems.