RNA has an important role not only as the messenger of genetic information but also as a regulator of gene expression. Given its central role in cell biology, there is significant interest in ...studying the structural and dynamic behavior of RNA in relation to other biomolecules. Coarse-grain molecular dynamics simulations are a key tool to that end. Here, we have extended the coarse-grain Martini force field to include RNA after our recent extension to DNA. In the same way DNA was modeled, the tertiary structure of RNA is constrained using an elastic network. This model, therefore, is not designed for applications involving RNA folding but rather offers a stable RNA structure for studying RNA interactions with other (bio)molecules. The RNA model is compatible with all other Martini models and opens the way to large-scale explicit-solvent molecular dynamics simulations of complex systems involving RNA.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
We systematically parameterized a coarse-grained (CG) model for DNA that is compatible with the Martini force field. The model maps each nucleotide into six to seven CG beads and is parameterized ...following the Martini philosophy. The CG nonbonded interactions are based on partitioning of the nucleobases between polar and nonpolar solvents as well as base–base potential of mean force calculations. The bonded interactions are fit to single-stranded DNA (ssDNA) atomistic simulations and an elastic network is used to retain double-stranded DNA (dsDNA) and other specific DNA conformations. We present the implementation of the Martini DNA model and demonstrate the properties of individual bases, ssDNA as well as dsDNA, and DNA–protein complexes. The model opens up large-scale simulations of DNA interacting with a wide range of other (bio)molecules that are available within the Martini framework.
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The power of coarse graining in biomolecular simulations Ingólfsson, Helgi I.; Lopez, Cesar A.; Uusitalo, Jaakko J. ...
Wiley interdisciplinary reviews. Computational molecular science,
May/June 2014, Volume:
4, Issue:
3
Journal Article
Peer reviewed
Open access
Computational modeling of biological systems is challenging because of the multitude of spatial and temporal scales involved. Replacing atomistic detail with lower resolution, coarse grained (CG), ...beads has opened the way to simulate large‐scale biomolecular processes on time scales inaccessible to all‐atom models. We provide an overview of some of the more popular CG models used in biomolecular applications to date, focusing on models that retain chemical specificity. A few state‐of‐the‐art examples of protein folding, membrane protein gating and self‐assembly, DNA hybridization, and modeling of carbohydrate fibers are used to illustrate the power and diversity of current CG modeling.
This article is categorized under:
Molecular and Statistical Mechanics > Molecular Dynamics and Monte-Carlo Methods
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Recently, a rapid increase in radiocarbon (
C) was observed in Japanese tree rings at AD 774/775. Various explanations for the anomaly have been offered, such as a supernova, a γ-ray burst, a ...cometary impact, or an exceptionally large Solar Particle Event (SPE). However, evidence of the origin and exact timing of the event remains incomplete. In particular, a key issue of latitudinal dependence of the
C intensity has not been addressed yet. Here, we show that the event was most likely caused by the Sun and occurred during the spring of AD 774. Particularly, the event intensities from various locations show a strong correlation with the latitude, demonstrating a particle-induced
C poleward increase, in accord with the solar origin of the event. Furthermore, both annual
C data and carbon cycle modelling, and separate earlywood and latewood
C measurements, confine the photosynthetic carbon fixation to around the midsummer.
Recently developed DNA-based analogues of membrane proteins have advanced synthetic biology. A fundamental question is how hydrophilic nanostructures reside in the hydrophobic environment of the ...membrane. Here, we use multiscale molecular dynamics (MD) simulations to explore the structure, stability and dynamics of an archetypical DNA nanotube inserted via a ring of membrane anchors into a phospholipid bilayer. Coarse-grained MD reveals that the lipids reorganize locally to interact closely with the membrane-spanning section of the DNA tube. Steered simulations along the bilayer normal establish the metastable nature of the inserted pore, yielding a force profile with barriers for membrane exit due to the membrane anchors. Atomistic, equilibrium simulations at two salt concentrations confirm the close packing of lipid around of the stably inserted DNA pore and its cation selectivity, while revealing localized structural fluctuations. The wide-ranging and detailed insight informs the design of next-generation DNA pores for synthetic biology or biomedicine.
The absolute transmission values of the RITU gas-filled recoil separator have been measured for several fusion evaporation products. Three different beams and several targets were used to create ...fusion evaporation residues in mass region
A=170–190 mainly in neutron evaporation channels. Measured absolute transmission values from around 7% up to round about 90% have been observed for very asymmetric and symmetric reactions, respectively. For the reactions studied it was observed that the angular spread of products after the target and the angular acceptance of RITU determine the transmission probability relatively accurately. Magnetic rigidities and equilibrium charges of the product ions were seen to systemically decrease and increase, respectively, with increasing gas pressure. The comparison of observed equilibrium charges to various formulae is carried out. Clear minima of image width were found in case of asymmetric reactions as a function of gas pressure. Effects of the position of an additional movable beam stopper and the field strength of the first quadrupole magnet on transmission have been studied and are reported.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
Excited states in the Tz=0,−1 nuclei 62Ga and 62Ge were populated in direct reactions of relativistic radioactive ion beams at the RIBF. Coincident γ rays were measured with the DALI2+ array and ...uniquely assigned to the A=62 isobars. In addition, 62Ge was also studied independently at JYFL-ACCLAB using the 24Mg(40Ca,2n)62Ge fusion-evaporation reaction. The first excited T=1,Jπ=2+ states in 62Ga and 62Ge were identified at 979(1) and 965(1) keV, respectively, resolving discrepant interpretations in the literature. States beyond the first 2+ state in 62Ge were also identified for the first time in the present work. The results are compared with shell-model calculations in the fp model space. Mirror and triplet energy differences are analyzed in terms of individual charge-symmetry and charge-independence breaking contributions. The MED results confirm the shrinkage of the p-orbits' radii when they are occupied by at least one nucleon on average.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
► Ethanol prod via alkaline pretreatment enables a coproduction of valuable lignin. ► Lignin content of 2.5% on pulp was found optimum for aspen and 5% on pulp for pine. ► Aspen required lower alkali ...charge and lower temperature compared to pine. ► Yield gain of fermentable sugars is 1–2% charging AQ(0.1% on wood) in pretreatment. ► Ethanol yield between 81.6% and 87.8% on theoretical max was obtained.
Ethanol production from lignocellulosic raw materials will generate multiple streams, since only a certain fraction of the material can be converted into sugars and then fermented to ethanol. This requires a ‘poly-generation’ approach, where by-products also must have high value (e.g. lignin, sugars from hemicellulose). To reach the large scale required for profitability, it is proposed that the best way is to integrate the new processes with existing industries, preferably those that already operate biomass-to-materials or biomass-to-fuels plants. One of the largest industry branches in this respect is the pulp and paper industry. Production of second generation ethanol (or other products) via sugars from lignocellulosic materials includes a relatively costly pre-treatment of the raw material in order to separate the lignin from the cellulose. This separation of the wood components already takes place in the chemical pulp mill, and the long proven technology in pulp production known as soda cooking (pre-treatment under alkaline conditions) is further evaluated in this study. It can be directly integrated into the recovery of chemicals and energy in the pulp mill. The pre-treatment of the lignocellulosic material studied in this work is alkaline and sulphur-free, and results in a technically pure cellulose to be fed to the hydrolysis stage, which makes it different compared to most of the other processes that aim to produce ethanol from lignocelluloses. The process chain from enzymatic hydrolysis to ethanol is very similar to that being used today for grain ethanol.
The aim of this study was to define the conditions in alkaline pre-treatment stage for the separation of wood to a carbohydrate fraction for hydrolysis and ethanol production, and to a lignin fraction for the production of lignin products. Aspen (Populus tremula) and pine (Pinus sylvestris) wood from Nordic mills were studied. The reference case was alkaline pre-treatment according to the well-known soda pulping technique. The pulps of alkaline pre-treated aspen could be enzymatically hydrolysed very efficiently and fermented to ethanol with high yields (82–88% ethanol yield from theoretical maximum). It should be possible to use raw material of lower quality and cost than wood from the pulp industry. However, it can then be important to be able to take out non-process elements (NPEs) that otherwise accumulate in the process. This can be done by introducing an acidic prehydolysis stage prior to the alkaline fractionation. The content of Mg and Mn ions in the wood was possible to reduce by 85–90% and Ba and Ca ions by 75–80%. Potassium was virtually completely removed during the acidic pre-treatment stage.
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The superheavy element with atomic number Z=117 was produced as an evaporation residue in the (48)Ca+(249)Bk fusion reaction at the gas-filled recoil separator TASCA at GSI Darmstadt, Germany. The ...radioactive decay of evaporation residues and their α-decay products was studied using a detection setup that allowed measuring decays of single atomic nuclei with half-lives between sub-μs and a few days. Two decay chains comprising seven α decays and a spontaneous fission each were identified and are assigned to the isotope (294)117 and its decay products. A hitherto unknown α-decay branch in (270)Db (Z = 105) was observed, which populated the new isotope (266)Lr (Z = 103). The identification of the long-lived (T(1/2) = 1.0(-0.4)(+1.9) h) α-emitter (270)Db marks an important step towards the observation of even more long-lived nuclei of superheavy elements located on an "island of stability."
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