Study of DNA Origami Dimerization and Dimer Dissociation Dynamics and of the Factors that Limit Dimerization

Organizing DNA origami building blocks into higher order structures is essential for fabrication of large structurally and functionally diverse devices and molecular machines. Unfortunately, the yields of origami building block attachment reactions are typically not sufficient to allow programed assembly of DNA devices made from more than a few origami building blocks. To investigate possible reasons for these low yields, a detailed single‐molecule fluorescence study of the dynamics of rectangular origami dimerization and origami dimer dissociation reactions is conducted. Reactions kinetics and yields are investigated at different origami and ion concentrations, for different ion types, for different lengths of bridging strands, and for the “sticky end” and “weaving welding” attachment techniques. Dimerization yields are never higher than 86%, which is typical for such systems. Analysis of the dynamic data shows that the low yield cannot be explained by thermodynamic instability or structural imperfections of the origami constructs. Atomic force microscopy and gel electrophoresis evidence reveal self‐dimerization of the origami monomers, likely via blunt‐end interactions made possible by the presence of bridging strands. It is suggested that this mechanism is the major factor that inhibits correct dimerization and means to overcome it are discussed.     

Accelerating scientific computations with mixed precision algorithms

On modern architectures, the performance of 32-bit operations is often at least twice as fast as the performance of 64-bit operations. By using a combination of 32-bit and 64-bit floating point arithmetic, the performance of many dense and sparse linear algebra algorithms can be significantly enhanced while maintaining the 64-bit accuracy of the resulting solution. The approach presented here can apply not only to conventional processors but also to other technologies such as Field Programmable Gate Arrays (FPGA), Graphical Processing Units (GPU), and the STI Cell BE processor. Results on modern processor architectures and the STI Cell BE are presented.

Program summary

Program title: ITER-REFCatalogue identifier: AECO_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AECO_v1_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 7211No. of bytes in distributed program, including test data, etc.: 41 862Distribution format: tar.gzProgramming language: FORTRAN 77Computer: desktop, serverOperating system: Unix/LinuxRAM: 512 MbytesClassification: 4.8External routines: BLAS (optional)Nature of problem: On modern architectures, the performance of 32-bit operations is often at least twice as fast as the performance of 64-bit operations. By using a combination of 32-bit and 64-bit floating point arithmetic, the performance of many dense and sparse linear algebra algorithms can be significantly enhanced while maintaining the 64-bit accuracy of the resulting solution.Solution method: Mixed precision algorithms stem from the observation that, in many cases, a single precision solution of a problem can be refined to the point where double precision accuracy is achieved. A common approach to the solution of linear systems, either dense or sparse, is to perform the LU factorization of the coefficient matrix using Gaussian elimination. First, the coefficient matrix A is factored into the product of a lower triangular matrix L and an upper triangular matrix U. Partial row pivoting is in general used to improve numerical stability resulting in a factorization PA=LU, where P is a permutation matrix. The solution for the system is achieved by first solving Ly=Pb (forward substitution) and then solving Ux=y (backward substitution). Due to round-off errors, the computed solution, x, carries a numerical error magnified by the condition number of the coefficient matrix A. In order to improve the computed solution, an iterative process can be applied, which produces a correction to the computed solution at each iteration, which then yields the method that is commonly known as the iterative refinement algorithm. Provided that the system is not too ill-conditioned, the algorithm produces a solution correct to the working precision.Running time: seconds/minutes     

Pulsed laser deposition of Mn-Zn ferrite thin films

Mn-Zn ferrite thin films were deposited on sapphire substrates by pulsed laser deposition from sintered Mn_{1 – x}Zn _x Fe₂O₄ ceramic targets. A full stoichiometric transfer from targets to substrates was achieved. Magnetic inplane measurements in two perpendicular directions were carried out and the macromagnetic properties of films were determined. The hysteresis loops obtained are rectangular and the values of the coercive force, the saturation, and the remanent magnetization are comparable to the same parameters of the bulk Mn-Zn ferrite. The films were characterized using a vibrating sample magnetometer (VSM), a scanning electron microscope (SEM) and by X-ray photoelectron spectroscopy (XPS).     

Liulin-type spectrometry-dosimetry instruments

The main purpose of Liulin-type spectrometry-dosimetry instruments (LSDIs) is cosmic radiation monitoring at the workplaces. An LSDI functionally is a low mass, low power consumption or battery-operated dosemeter. LSDIs were calibrated in a wide range of radiation fields, including radiation sources, proton and heavy-ion accelerators and CERN-EC high-energy reference field. Since 2000, LSDIs have been used in the scientific programmes of four manned space flights on the American Laboratory and ESA Columbus modules and on the Russian segment of the International Space Station, one Moon spacecraft and three spacecraft around the Earth, one rocket, two balloons and many aircraft flights. In addition to relative low price, LSDIs have proved their ability to qualify the radiation field on the ground and on the above-mentioned carriers.     

Comparison of the phase transfer oxidation of benzyl alcohol in a pump cell and stirred-tank reactor

The oxidation of benzyl alcohol by electrogenerated hypobromite in a two-phase emulsion has been studied using a quaternary ammonium salt as a phase transfer agent. The performances of a stirred-tank batch reactor and a bipolar electrochemical pump cell have been compared and the differences found are discussed in terms of the different mixing/transport/reaction regimes of the two cells. Benzaldehyde can be produced at a rate of 0.2 mol h^–1 dm^–2 of electrode area for 4.20 kWh kg^–1.     

Modification of the properties of HTSC YBCO thin films on silicon by superfast laser annealing in oxygen with a CW CO2 Laser

The use of superfast CW CO₂ laser annealing in O₂ for modifying the properties of laser deposited Y₁Ba₂Cu₃O_{7 –x} thin films is described. The film resistivity could be controlled reversibly by laser irradiation at 40 W cm^–2. The resistivity was measuredin situ during the annealing process.     

Direct ceramic inkjet printing of yttria-stabilized zirconia electrolyte layers for anode-supported solid oxide fuel cells

Electromagnetic drop-on-demand direct ceramic inkjet printing (EM/DCIJP) was employed to fabricate dense yttria-stabilized zirconia (YSZ) electrolyte layers on a porous NiO-YSZ anode support from ceramic suspensions. Printing parameters including pressure, nozzle opening time and droplet overlapping were studied in order to optimize the surface quality of the YSZ coating. It was found that moderate overlapping and multiple coatings produce the desired membrane quality. A single fuel cell with a NiO-YSZ/YSZ (∼6 μm)/LSM + YSZ/LSM architecture was successfully prepared. The cell was tested using humidified hydrogen as the fuel and ambient air as the oxidant. The cell provided a power density of 170 mW cm⁻² at 800 °C. Scanning electron microscopy (SEM) revealed a highly coherent dense YSZ electrolyte layer with no open porosity. These results suggest that the EM/DCIJP inkjet printing technique can be successfully implemented to fabricate electrolyte coatings for SOFC thinner than 10 μm and comparable in quality to those fabricated by more conventional ceramic processing methods.     

Tridiagonalization of a dense symmetric matrix on multiple GPUs and its application to symmetric eigenvalue problems

For software to fully exploit the computing power of emerging heterogeneous computers, not only must the required computational kernels be optimized for the specific hardware architectures but also an effective scheduling scheme is needed to utilize the available heterogeneous computational units and to hide the communication between them. As a case study, we develop a static scheduling scheme for the tridiagonalization of a symmetric dense matrix on multicore CPUs with multiple graphics processing units (GPUs) on a single compute node. We then parallelize and optimize the Basic Linear Algebra Subroutines (BLAS)‐2 symmetric matrix‐vector multiplication, and the BLAS‐3 low rank symmetric matrix updates on the GPUs. We demonstrate the good scalability of these multi‐GPU BLAS kernels and the effectiveness of our scheduling scheme on twelve Intel Xeon processors and three NVIDIA GPUs. We then integrate our hybrid CPU‐GPU kernel into computational kernels at higher‐levels of software stacks, that is, a shared‐memory dense eigensolver and a distributed‐memory sparse eigensolver. Our experimental results show that our kernels greatly improve the performance of these higher‐level kernels, not only reducing the solution time but also enabling the solution of larger‐scale problems. Because such symmetric eigenvalue problems arise in many scientific and engineering simulations, our kernels could potentially lead to new scientific discoveries. Furthermore, these dense linear algebra algorithms present algorithmic characteristics that can be found in other algorithms. Hence, they are not only important computational kernels on their own but also useful testbeds to study the performance of the emerging computers and the effects of the various optimization techniques. Copyright © 2013 John Wiley & Sons, Ltd.     

Stimulated Brillouin scattering of KrF laser radiation in dichlorodifluoromethane

Experimental measurements have been made of the stimulated Brillouin backscatter from CCl2F2gas in the range of pressures from 1 to 5.75 atm. Using narrow-linewidth KrF laser radiation as the pump backscatter efficiencies of up to 35 percent have been achieved, while at low backscatter efficiencies pulses as short as 1.5 ns in width were obtained.     

Actively mode-locked and Q-controlled Nd:glass laser

A Q-controlled Nd:glass ring laser system has been developed which is actively mode-locked by means of either KD *P or LiNbO(3) electro-optic modulators and is capable of producing 1.5 mJ, 100 ps, 1.06 mum pulses synchronized to better than 400 ps to an external event. By using prelase methods or saturable absorbers shorter pulses from 37 to 15 ps duration can be generated with poorer synchronization.