Soft-spring wall based non-periodic boundary conditions for non-equilibrium molecular dynamics of dense fluids

Non-equilibrium molecular dynamics (MD) simulations require imposition of non-periodic boundary conditions (NPBCs) that seamlessly account for the effect of the truncated bulk region on the simulated MD region. Standard implementation of specular boundary conditions in such simulations results in spurious density and force fluctuations near the domain boundary and is therefore inappropriate for coupled atomistic-continuum calculations. In this work, we present a novel NPBC model that relies on boundary atoms attached to a simple cubic lattice with soft springs to account for interactions from particles which would have been present in an untruncated full domain treatment. We show that the proposed model suppresses the unphysical fluctuations in the density to less than 1% of the mean while simultaneously eliminating spurious oscillations in both mean and boundary forces. The model allows for an effective coupling of atomistic and continuum solvers as demonstrated through multiscale simulation of boundary driven singular flow in a cavity. The geometric flexibility of the model enables straightforward extension to nonplanar complex domains without any adverse effects on dynamic properties such as the diffusion coefficient. (c) 2015 AIP Publishing LLC.

GRMHD formulation of highly super-Chandrasekhar magnetized white dwarfs: stable configurations of non-spherical white dwarfs

The topic of magnetized super-Chandrasekhar white dwarfs is in the limelight, particularly in the last few years, since our proposal of their existence. By full-scale general relativistic magnetohydrodynamic (GRMHD) numerical analysis, we confirm in this work the existence of stable, highly magnetized, significantly super-Chandrasekhar white dwarfs with mass more than 3 solar mass. While a poloidal field geometry renders the white dwarfs oblate, a toroidal field makes them prolate retaining an overall quasi-spherical shape, as speculated in our earlier work. These white dwarfs are expected to serve as the progenitors of over-luminous type Ia supernovae.

Non-Abelian gauge redundancy and entropic ambiguities

The von Neumann entropy of a generic quantum state is not unique unless the state can be uniquely decomposed as a sum of extremal or pure states. Therefore one reaches the remarkable possibility that there may be many entropies for a given state. We show that this happens if the GNS representation (of the algebra of observables in some quantum state) is reducible, and some representations in the decomposition occur with non-trivial degeneracy. This ambiguity in entropy, which can occur at zero temperature, can often be traced to a gauge symmetry emergent from the non-trivial topological character of the configuration space of the underlying system. We also establish the analogue of an H-theorem for this entropy by showing that its evolution is Markovian, determined by a stochastic matrix. After demonstrating this entropy ambiguity for the simple example of the algebra of 2 x 2 matrices, we argue that the degeneracies in the GNS representation can be interpreted as an emergent broken gauge symmetry, and play an important role in the analysis of emergent entropy due to non-Abelian anomalies. We work out the simplest situation with such non-Abelian symmetry, that of an ethylene molecule.

Do we see what we should see? Describing non-covalent interactions in protein structures including precision

The power of X-ray crystal structure analysis as a technique is to `see where the atoms are'. The results are extensively used by a wide variety of research communities. However, this `seeing where the atoms are' can give a false sense of security unless the precision of the placement of the atoms has been taken into account. Indeed, the presentation of bond distances and angles to a false precision (i.e. to too many decimal places) is commonplace. This article has three themes. Firstly, a basis for a proper representation of protein crystal structure results is detailed and demonstrated with respect to analyses of Protein Data Bank entries. The basis for establishing the precision of placement of each atom in a protein crystal structure is non-trivial. Secondly, a knowledge base harnessing such a descriptor of precision is presented. It is applied here to the case of salt bridges, i.e. ion pairs, in protein structures; this is the most fundamental place to start with such structure-precision representations since salt bridges are one of the tenets of protein structure stability. Ion pairs also play a central role in protein oligomerization, molecular recognition of ligands and substrates, allosteric regulation, domain motion and alpha-helix capping. A new knowledge base, SBPS (Salt Bridges in Protein Structures), takes these structural precisions into account and is the first of its kind. The third theme of the article is to indicate natural extensions of the need for such a description of precision, such as those involving metalloproteins and the determination of the protonation states of ionizable amino acids. Overall, it is also noted that this work and these examples are also relevant to protein three-dimensional structure molecular graphics software.

Non-invasive pressure monitoring by hoop strain using Fiber Bragg Grating sensor

Non-invasive, real-time dynamic monitoring of pressure inside a column with the aid of Fiber Bragg Grating (FBG) sensor is presented in the present work. A bare FBG sensor is adhered on the circumference of a pressure column normal to its axis, which has the ability to acquire the hoop strain induced by the pressure variation inside the column. Pressure induced hoop strain response obtained using FBG sensor is validated against the pressure measurements obtained from conventional pressure gauge. Further, a protrusion setup on the outer surface of the column has been proposed over which a secondary FBG sensor is bonded normal to its axis, in order to increase the gauge length of this FBG sensor. This is carried out in order to validate the variation in sensitivity of the protrusion bonded FBG sensor compared to the bare FBG sensor bonded over the surface. A comparative study is done between the two FBG sensors and a conventional pressure gauge in order to establish the capacity of FBG sensor obtained hoop strain response for pressure monitoring inside the column.

An enzyme-linked immuno focus assay for rapid detection and enumeration, and a newborn mouse model for human non-polio enteroviruses associated with acute diarrhea

We have recently reported significant association of non-polio enteroviruses (NPEVs) with acute and persistent diarrhea (18-21% of total diarrheal cases), and non-diarrheal Increased Frequency of Bowel Movements (IFoBM-ND) (about 29% of the NPEV infections) in children and that the NPEV-associated diarrhea was as significant as rotavirus diarrhea. However, their diarrhea-causing potential is yet to be demonstrated in an animal model system. Since the determination of virus titers by the traditional plaque assay takes 4-7 days, there is a need for development of a rapid method for virus titer determination to facilitate active clinical research on enterovirus-associated diarrhea. The goal of this study is to develop a cell-based rapid detection and enumeration method and to demonstrate the diarrhea-inducing potential of purified and characterized non-polio enteroviruses, which were isolated from diarrheic children. Here we describe generation of monoclonal and polyclonal antibodies against purified strains belonging to different serotypes, and development of an enzyme-linked immuno focus assay (ELIFA) for detection and enumeration of live NPEV particles in clinical and purified virus samples, and a newborn mouse model for NPEV diarrhea. Plaque-purified NPVEs, belonging to different serotypes, isolated from children with diarrhea, were grown in cell culture and purified by isopycnic CsCl density gradient centrifugation. By ELIFA, NPEVs could be detected and enumerated within 12 h post-infection. Our results demonstrated that Coxsackievirus B1 (CVB1) and CVB5 strains, isolated from diarrheic children, induced severe diarrhea in orally-inoculated 9-12 day-old mouse pups, fulfilling Koch's postulates. The methods described here would facilitate studies on NPEV-associated gastrointestinal disease. (C) 2015 Elsevier B.V. All rights reserved.

Modeling of the non-isothermal liquid droplet impact on a heated solid substrate with heterogeneous wettability

A comprehensive numerical investigation on the impingement and spreading of a non-isothermal liquid droplet on a solid substrate with heterogeneous wettability is presented in this work. The time-dependent incompressible Navier-Stokes equations are used to describe the fluid flow in the liquid droplet, whereas the heat transfer in the moving droplet and in the solid substrate is described by the energy equation. The arbitrary Lagrangian-Eulerian (ALE) formulation with finite elements is used to solve the time-dependent incompressible Navier-Stokes equation and the energy equation in the time-dependent moving domain. Moreover, the Marangoni convection is included in the variational form of the Navier-Stokes equations without calculating the partial derivatives of the temperature on the free surface. The heterogeneous wettability is incorporated into the numerical model by defining a space-dependent contact angle. An array of simulations for droplet impingement on a heated solid substrate with circular patterned heterogeneous wettability are presented. The numerical study includes the influence of wettability contrast, pattern diameter, Reynolds number and Weber number on the confinement of the spreading droplet within the inner region, which is more wettable than the outer region. Also, the influence of these parameters on the total heat transfer from the solid substrate to the liquid droplet is examined. We observe that the equilibrium position depends on the wettability contrast and the diameter of the inner surface. Consequently. the heat transfer is more when the wettability contrast is small and/or the diameter of inner region is large. The influence of the Weber number on the total heat transfer is more compared to the Reynolds number, and the total heat transfer increases when the Weber number increases. (C) 2015 Elsevier Ltd. All rights reserved.

Synthesis, and crystal and electronic structure of sodium metal phosphate for use as a hybrid capacitor in non-aqueous electrolyte

Energy storage devices based on sodium have been considered as an alternative to traditional lithium based systems because of the natural abundance, cost effectiveness and low environmental impact of sodium. Their synthesis, and crystal and electronic properties have been discussed, because of the importance of electronic conductivity in supercapacitors for high rate applications. The density of states of a mixed sodium transition metal phosphate (maricite, NaMn1/3Co1/3Ni1/3PO4) has been determined with the ab initio generalized gradient approximation (GGA)+Hubbard term (U) method. The computed results for the mixed maricite are compared with the band gap of the parent NaFePO4 and the electrochemical experimental results are in good agreement. A mixed sodium transition metal phosphate served as an active electrode material for a hybrid supercapacitor. The hybrid device (maricite versus carbon) in a nonaqueous electrolyte shows redox peaks in the cyclic voltammograms and asymmetric profiles in the charge-discharge curves while exhibiting a specific capacitance of 40 F g(-1) and these processes are found to be quasi-reversible. After long term cycling, the device exhibits excellent capacity retention (95%) and coulombic efficiency (92%). The presence of carbon and the nanocomposite morphology, identified through X-ray photoelectron spectroscopy (XPS) and transmission electron microscopy (TEM) studies, ensures the high rate capability while offering possibilities to develop new cathode materials for sodium hybrid devices.

Transitions and blowoff of unconfined non-premixed swirling flame

The present experimental work reports the first observations of primary and secondary transitions in the time-averaged flame topology in a non-premixed swirling flame as the geometric swirl number S-G (a non dimensional number used to quantify the intensity of imparted swirl) is varied from a magnitude of zero till flame blowout. First observations of two transition types viz. primary and secondary transitions are reported. The primary transition represents a transformation from yellow straight jet flame (at S-G = 0) to lifted flame with blue base and finally to swirling seated (burner attached) yellow flame. Time-averaged streamline plot obtained from 2D PIV in mid-longitudinal plane shows a recirculation zone (RZ) at the immediate vicinity of burner exit. The lifted flame is stabilized along the vortex core of this RZ. Further, when S-G similar to 1.4-3, the first occurrence of vortex breakdown (VB) induced internal recirculation zone (IRZ) is witnessed. The flame now stabilizes at the upstream stagnation point of the VB-IRZ, which is attached to the burner lip. The secondary transition represents a transformation from a swirling seated flame to swirling flame with a conical tailpiece and finally to a highly-swirled near blowout oxidizer-rich flame. This transition is understood to be the result of transition in vortex breakdown modes of the swirling flow field from dual-ring VB bubble to central toroidal recirculation zone (CTRZ). The physics of transition is described on the basis of modified Rossby number (Ro(m)). Finally, when the swirl intensity is very high i.e. SG similar to 10, the flame blows out due to excessive straining and due to entrainment of large amount of oxidizer due to partial premixing. The present investigation involving changes in flame topology is immensely important because any change in global flame structure causes oscillatory heat release that can couple with dynamic pressure and velocity fluctuations leading to unsteady combustion. In this light, understanding mechanisms of flame stabilization is essential to tackle the problem of thermo-acoustic instability. (C) 2015 The Combustion Institute. Published by Elsevier Inc. All rights reserved.

Effect of potassium present in stratum corneum during non-invasive measurement of potassium in human subjects using reverse iontophoresis

Purpose: Reverse iontophoresis (RI) is one of the potential techniques used to monitor the concentration of various analytes in body fluids non -invasively. Transdermal extraction of potassium is investigated using RI. In the present work, the effect of potassium on stratum corneum (SC) during RI, feasibility of RI for continuous monitoring of potassium, and use of potassium as internal standard in RI, are investigated. Methods: Tape stripping experiment is carried out to find potassium concentration in SC. RI is carried out continuously for 180 min without passive diffusion and after passive diffusion for 60 min. Skin impedance measurements are done at 20 Hz and 20 kHz. Results: Potassium is found to be in the range 300-650 nmol/cm(2) on SC by tape stripping experiment. Correlation coefficient between blood potassium and extracted potassium through RI after passive diffusion (R-2 = 0.5870) is more than without passive diffusion (R-2 = 0.5117). The skin impedance measurement shows that RI has more effect on SC than superficial layer of SC during RI. Conclusion: The present investigations conclude that it is possible to monitor potassium continuously through RI and using potassium as internal standard in RI.