Generation of high-energy, sub-20-fs pulses in the deep ultraviolet by using spectral broadening during filamentation in argon

Generation of sub-20-fs UV pulses with more than 300 μJ energy at 268 nm is reported. First, the UV pulses are produced by successive second-harmonic and third-harmonic (TH) generation of 805 nm pulses of a 1 kHz Ti:sapphire laser amplifier. The spectral broadening of TH pulses is realized in a filament, generated in argon. The produced pulses are compressed in a simple double-pass prism-pair compressor. Starting from 100 fs pulses, we achieve a fivefold pulse shortening.     

Striking patterns in natural magic squares’ associated electrostatic potentials: Matrices of the 4th and 5th order

A magic square is a square matrix whereby the sum of any row, column, or any one of the two principal diagonals is equal. A surrogate of this abstract mathematical construct, introduced in 2012 by Fahimi and Jaleh, is the “electrostatic potential (ESP)” that results from treating the matrix elements of the magic square as electric charges. The overarching idea is to characterize patterns associated with these matrices that can possibly be used, in the future, in reverse to generate these squares. This study focuses on squares of order 4 and 5 with 880 and 275,305,224 distinct (irreducible/unique) realizations, respectively. It is shown that characteristic patterns emerge from plots of the ESPs of the matrices representing the studied squares. The electrostatic potentials for natural magic squares exhibit a striking pattern of maxima and minima in all distinct 880 of the 4th order and all distinct 275,305,224 of the 5th order matrices. The minimum values of ESP of Dudeney groups are discussed. Equipotential points and certain constants are found among the ESP sums along horizontal and vertical lines on the square lattice. These findings may help to open a new perspective regarding magic squares unsolved problems. While mathematics often leads discovery in physics, the latter (physics) is used here to detect otherwise invisible patterns in a mathematical object such as magic squares.     

MP-NeRF: A massively parallel method for accelerating protein structure reconstruction from internal coordinates

The conversion of proteins between internal and cartesian coordinates is a limiting step in many pipelines, such as molecular dynamics simulations and machine learning models. This conversion is typically carried out by sequential or parallel applications of the Natural extension of Reference Frame (NeRF) algorithm. This work proposes a massively parallel NeRF implementation which, depending on the polymer length, achieves speedups between 400 and 1200× over the previous state-of-the-art. It accomplishes this by dividing the conversion into three main phases: parallel composition of the monomer backbone, assembly of backbone subunits, and parallel elongation of sidechains; and by batching these computations into a minimal number of efficient matrix operations. Special emphasis is placed on reusability and ease of use. We open source the code (available at https://github.com/EleutherAI/mp_nerf ) and provide a corresponding python package.     

Improving protein secondary structure prediction: the evolutionary optimized classification algorithms

Structural Chemistry - Determining protein structures plays an important role in the field of drug design. Currently, the machine learning methods including artificial neural network (ANN) and...     

Near-Infrared Study of the Hydrogen Bonding in Acetone-Methanol and Acetone-Ethanol Mixtures: Roles of Mechanical and Electrical Anharmonicities of Hydroxyl Oscillator

Near-infrared spectra of methanol-acetone and ethanol-acetone mixtures in the entire mole fraction range in increments of 0.1 were recorded in the region of 7500–6000 cm^?1. The first overtone bands of the hydroxyl (OH) groups were assigned to the polymeric and oligomeric OH associations. In both solutions, the frequency of the polymeric OH band decreased with the increase in the mole fraction of alcohol, which indicated the increase in the hydrogen bonding strength. The integrated area of the polymeric OH band followed the opposite trend to the frequency with the mole fraction. The nonlinearity of the plot of the integrated band area of the polymeric OH band of methanol versus the mole fraction of acetone revealed the nonideal character of the methanol-acetone mixtures, whereas the opposite was observed for the ethanol-acetone mixtures. These observations have been explained in terms of mechanical and electrical anharmonicities of the OH oscillator.     

The effect of polymers onto the size of zinc layered hydroxide salt and its calcined product

Zinc hydroxide nitrate, a brucite-like layered material was synthesized using pH control method. Poly(vinyl alcohol) and poly(ethylene glycol) were used at various percentages as size decreasing agents during the synthesis of zinc hydroxide nitrate. SEM and PXRD showed the decrease of size and thickness of the resultant zinc hydroxide nitrates. TG and surface area data confirmed the decrease of the particle sizes, too. When zinc hydroxide nitrates were heat treated at 500 °C, the physical properties of nano zinc oxides obtained depended on the parent material, zinc hydroxide nitrate.     

Thermal decomposition pathway of undoped and doped zinc layered gallate nanohybrid with Fe3+, Co2+ and Ni2+ to produce mesoporous and high pore volume carbon material

A series of brucite-like materials, undoped and doped zinc layered hydroxide nitrate with 2% (molar) Fe³⁺, Co²⁺ and Ni²⁺ were synthesized. Organic–inorganic nanohybrid material with gallate anion as a guest, and zinc hydroxide nitrate, as an inorganic layered host was prepared by the ion-exchange method. The nanohybrid materials were heat-treated at various temperatures, 400–700 °C. X-ray diffraction, thermal analysis and also Fourier transform infrared results showed that incorporation of the doping agents within the zinc layered hydroxide salt layers has enhanced the heat-resistivity of the nanohybrid materials in the thermal decomposition pathway. Porous carbon materials can be obtained from the heat-treating the nanohybrids at 600 and 700 °C. Calcination of the nanohybrids at 700 °C under nitrogen atmosphere produces mesoporous and high pore volume carbon materials.     

Gallate-Zn-Al-layered double hydroxide as an intercalated compound with new controlled release formulation of anticarcinogenic agent

A new organic-clay material, in which the organic moiety is intercalated into the inorganic interlayer, was prepared using gallate anion (GA) as a guest, and Zn-Al-layered double hydroxide, as clay host. The ion-exchange technique was found to be effective for the intercalation process in the formation of the compound. Although the basal spacings of the LDH and its intercalated product were fairly similar, FTIR, CHNS and TGA/DTG results indicated that the GA was actually intercalated into the interlayer of the host in parallel orientation. The resulting nanostructure material possessed a well ordered layered structure with 42.2% GA loading (w/w). The release of the anion from the interlayer of the intercalated compound was found to be of controlled manner, governed by the first order kinetic and it was also concentration dependent. The material has potential as a nano-storage of anticarcenogenic agent with controlled delivery capability.     

A method for direct simulation of flexible fiber suspensions using lattice Boltzmann equation with external boundary force

The computational method presented here can be used to study the effect of volume fraction and particle deformation on the rheology and microstructure of deformable fibers suspended in Newtonian fluid. In this method, the flow is computed on a fixed regular ‘lattice’ using the lattice Boltzmann method, where each solid particle is mapped onto a Lagrangian frame moving continuously through the domain. Instead of the standard bounce-back method, an external boundary force is used to impose the no-slip boundary condition at the fluid–solid interface for stationary or moving boundaries. The motion and orientation of the fiber are obtained from Newtonian dynamics equations. Although the external boundary force method is general, in this application it is used in conjunction with a flexible fiber model, which calculates the flexible fiber deformation by the real material properties. The methodology is validated by comparing with experimental and theoretical results.     

Liquid crystal assemblies in biologically inspired systems

In this paper, which is part of a collection in honour of Noel Clark’s remarkable career on liquid crystal (LC) and soft matter research, we present examples of biologically inspired systems, which form LC phases with their LC nature impacting biological function in cells or being important in biomedical applications. One area focuses on understanding network and bundle formation of cytoskeletal polyampholytes (filamentous actin, microtubules and neurofilaments (NFs)). Here, we describe studies on NFs, the intermediate filaments of neurons, which form open network nematic LC hydrogels in axons. Synchrotron small-angle-X-ray scattering studies of NF protein dilution experiments and NF hydrogels subjected to osmotic stress show that NF networks are stabilised by competing long-range repulsion and attractions mediated by the NF’s polyampholytic sidearms. The attractions are present both at very large inter-filament spacings, in the weak sidearm-interpenetrating regime, and at smaller inter-filament spacings, in the strong sidearm-interpenetrating regime. A second series of experiments will describe the structure and properties of cationic liposomes (CLs) complexed with nucleic acids (NAs). CL-NA complexes form liquid crystalline phases, which interact in a structure-dependent manner with cellular membranes enabling the design of complexes for efficient delivery of NA (DNA and RNA) in therapeutic applications.