The surfaces of biomolecules are alive with activity, with surface shape and electrostatic interactions leading them to interact with each other. The recent VMD 1.9.1 release includes a new "QuickSurf" graphical representation for molecular surfaces that allows the dynamics of large biomolecules to be animated interactively for the first time. VMD 1.9.1 even enables surface representations for many-million atom complexes. QuickSurf uses fast algorithms, GPU computing techniques, and multi-core CPUs to achieve astonishing performance. The algorithms behind QuickSurf have been recently reported. VMD 1.9.1 adds many other new features including a new Force Field Toolkit (FFTK) plugin that assists researchers in development of CHARMM force field parameters, a new NetworkView plugin for mapping and displaying networks on 3-D molecular structures, an updated ViewChangeRender plugin for making sophisticated demonstrations and movies, and a new VMD remote control tool that allows VMD sessions to be controlled from wireless touch sensitive phones and tablet devices. For more on these and other new features of VMD see the VMD 1.9.1 release page.

The ribosome is the protein assembly line in all living cells. The building material for new proteins is supplied by RNA molecules, called tRNA. They enter and move through the ribosome, each adding a new amino acid to the nascent proteins according to the genetic sequence provided through so-called messenger RNA. During the tRNAs' translation through the ribosome, the ribosome itself is not static either. A ratcheting motion and other large scale motions can be observed. However, the exact tRNA and ribosome motion were not clear. Using images from cryo-electron microscopy, MDFF, a computational method based on NAMD, allows one to see the moving parts within the ribosome in great detail. MDFF (see the June 2008 highlight) already provided crucial and unique insights into different aspects of protein synthesis, such as translational arrest of the ribosome by a nascent chain or translocation of an emergent protein across a membrane. In the work reported recently, MDFF revealed the presence of previously unseen intermediate states of the ribosome and its bound tRNAs during the ratcheting motion. A thorough analysis of these states pictures the ribosome as a molecular machine using Brownian motion for its function. More on our ribosome website.

Many bacteria use sunlight as an energy source. The energy gained from a solar ray absorbed by a molecule, however, lasts only for a very short time (a mere 0.000000001 seconds!) before it dissipates away and is lost. Within this short time, machinery in the bacterial cell must store the light energy in a longer-lasting form so that it can be used later. A series of reviews describes how bacteria exploit quantum physics to bottle the energy of sunlight for a sufficiently long time to fully utilize it. In a first review we introduce the light harvesting systems of bacteria and their key molecular components, in particular the role of chlorophylls. In a second review we describe how thousands of chlorophylls cooperate to transport the short lived energy of absorbed light to the centers where the energy is converted into a more stable form, namely that of a voltage difference across the bacterial cell wall. In a third review we explain how quantum physics enhances this process of energy transport in bacteria (see also our video). In a fourth review we describe how the individual components of this system come together into their overall organization. More information about the machinery and process of photosynthesis can be found here and about the physics of energy transfer in photosynthesis here.

Voltage-gated ion channels, present in the membrane of excitable cells, control the ionic concentrations of the cellular environment by maintaining a potential difference of -100 mV between inside and outside of the cell membrane. Voltage-sensing occurs through distinct protein modules, known as voltage-sensor domains, four of which surround the main conduction pathway in potassium channels. Mutation of a certain amino acid on the voltage sensor domain turns these protein modules into cation channels, known as omega pores, which allow conduction of ions only when the main pathway is closed. Omega pores closely resemble the long-sought voltage-gated proton channels, which were recently identified to follow the same voltage-sensing mechanism as voltage-gated cation channels. In a recent report, researchers have visualized the twisted permeation pathway of the ions through omega pores using the molecular dynamics program NAMD. The simulations revealed a narrow constriction region lined by negatively charged amino acids, acting as a selectivity filter that prefers passage of positively charged ions through the pore. For more detail, see our potassium channel website .

Creatures as varied as mammals, fishes, insects, reptiles, and birds have an intriguing 'sixth' sense that allows them to navigate in the Earth's magnetic field. Despite decades of study, the physical basis of this sense remains elusive. A likely mechanism is furnished by magnetic field sensitive reactions occurring in the retina of animal eyes. A decade ago it was suggested (see our magnetoreception page) that the photoreceptor cryptochrome, arising in the retina, endows birds with magnetoreceptive abilities. The hypothesis gained support during the last years, after it had been shown that the protein exhibits properties required for an animal magnetoreceptor to operate properly. (see prior highlights on A Compass in the Eye, July 2010; on Where's North, Ask Superoxide, July 2009; and on Animal Magnetic Sense Shared by Plant, April 2007). However, the biophysical mechanism of cryptochrome activation and signaling is still poorly understood. A recent study proposed a theoretical analysis method for identifying cryptochrome's signaling reactions involving comparison of measured and calculated reaction kinetics. Application of the method suggest a light-driven reaction cycle which combines electronic excitation with electron and proton transfer reactions in the protein. More details on cryptochrome functioning as a light-driven magnetic compass can be found on our cryptochrome webpage .

Genes encoded in DNA sequence give a complete set of instructions for the development of a new organism. However, an organism, like the human body, develops also over a life time adapting to environment and experience, for example to diet and exercise. Recently, researchers found that such factors act through so-called epigenetic mechanisms that alter an organism's development without altering DNA sequence. One such mechanism involves DNA methylation, a chemical modification of one of the four bases of DNA, cytosine, that replaces a hydrogen atom with a methyl group. There are several ways that DNA methylation exerts its biological function, bringing about a long-time adaptation of an organism to its environment, in some cases even across generations. Our previous experimental and computational studies (see Sep 2011 and Feb 2009 highlights) indicated that methylation changes mechanical properties of DNA which can affect gene expression. DNA methylation can also inhibit gene expression by impeding proteins that control the translation of DNA sequence into protein synthesis. One mechanism involves DNA methylation sites recruiting genetic control proteins that inhibit DNA expression through their local presence. In a recent study, computational biologists performed MD simulations with NAMD along with quantum chemistry calculations to determine recognition of methylated DNA by proteins. The simulations revealed how a certain genetic control protein, called methyl-CpG binding domain protein, acts in tandem with methylated DNA like a key and a lock, methylated DNA and protein perfectly matching each other. More details can be found on our methylated DNA website.