Volume conservation issues in incompressible smoothed particle hydrodynamics

A divergence-free velocity field is usually sought in numerical simulations of incompressible fluids. We show that the particle methods that compute a divergence-free velocity field to achieve incompressibility suffer from a volume conservation issue when a finite time-step position update scheme is used. Further, we propose a deformation gradient based approach to arrive at a velocity field that reduces the volume conservation issues in free surface flows and maintains density uniformity in internal flows while retaining the simplicity of first order time updates. (C) 2015 Elsevier Inc. All rights reserved.

Role of the Molar Volume on Estimated Diffusion Coefficients

The role of the molar volume on the estimated diffusion parameters has been speculated for decades. The Matano-Boltzmann method was the first to be developed for the estimation of the variation of the interdiffusion coefficients with composition. However, this could be used only when the molar volume varies ideally or remains constant. Although there are no such systems, this method is still being used to consider the ideal variation. More efficient methods were developed by Sauer-Freise, Den Broeder, and Wagner to tackle this problem. However, there is a lack of research indicating the most efficient method. We have shown that Wagner's method is the most suitable one when the molar volume deviates from the ideal value. Similarly, there are two methods for the estimation of the ratio of intrinsic diffusion coefficients at the Kirkendall marker plane proposed by Heumann and van Loo. The Heumann method, like the Matano-Boltzmann method, is suitable to use only when the molar volume varies more or less ideally or remains constant. In most of the real systems, where molar volume deviates from the ideality, it is safe to use the van Loo method. We have shown that the Heumann method introduces large errors even for a very small deviation of the molar volume from the ideal value. On the other hand, the van Loo method is relatively less sensitive to it. Overall, the estimation of the intrinsic diffusion coefficient is more sensitive than the interdiffusion coefficient.

Systematic Analysis of Mycobacterial Acylation Reveals First Example of Acylation-mediated Regulation of Enzyme Activity of a Bacterial Phosphatase

Protein lysine acetylation is known to regulate multiple aspects of bacterial metabolism. However, its presence in mycobacterial signal transduction and virulence-associated proteins has not been studied. In this study, analysis of mycobacterial proteins from different cellular fractions indicated dynamic and widespread occurrence of lysine acetylation. Mycobacterium tuberculosis proteins regulating diverse physiological processes were then selected and expressed in the surrogate host Mycobacterium smegmatis. The purified proteins were analyzed for the presence of lysine acetylation, leading to the identification of 24 acetylated proteins. In addition, novel lysine succinylation and propionylation events were found to co-occur with acetylation on several proteins. Protein-tyrosine phosphatase B (PtpB), a secretory phosphatase that regulates phosphorylation of host proteins and plays a critical role in Mycobacterium infection, is modified by acetylation and succinylation at Lys-224. This residue is situated in a lid region that covers the enzyme's active site. Consequently, acetylation and succinylation negatively regulate the activity of PtpB.

Mechanism of improvement in the strength and volume change behavior of lime stabilized soil

An attempt has been made to bring out the influence on strength and volume change behavior of fabric changes and new cementitious compound formation in a soil upon addition of various lime contents and with curing periods. The effects of changes in fabric of treatment with various lime contents (0, 2,4 and 6%) and with curing periods (0, 7, 14 and 28 days) have been evaluated by one-dimensional consolidation tests, in terms of void ratio changes and compressibility. The strength of soil treated with different lime contents with curing periods up to 28 days, and with the optimum lime content of 6% up to one year has been determined by unconfined compression tests. Comparison of effects of lime on the strength and volume change behavior of the soil brings out that the formation of flocculated fabric and cation exchange significantly reduces the compressibility of soil but marginally increases the strength. Cementation of soil particles and filling with cementitious compounds of the voids of flocculated fabric in the soil marginally reduces the compressibility but significantly increases the strength. Thus, the mechanism of volume change behavior of soil treated with lower lime content at short curing periods is distinctly different from that of the soil treated with optimum lime content at longer curing periods. This is consistent with the increase in the permeability caused by the addition from 2 to 4% lime and the decrease following the addition of 6% lime. Changes consistent with mechanical behavior have been determined by scanning electron microscope, X-ray diffraction and thermal analyses, energy dispersive X-ray spectrometer and pH value in microstructure, mineralogy, chemical composition and alkalinity, respectively. (C) 2015 Published by Elsevier B.V.

Volume change behavior of lime treated gypseous soil - influence of mineralogy and microstructure

Series of oedometer tests and micro-analytical studies (XRD, SEM and EDAX) have been carried out to investigate the influence of varying gypsum content on swell, compressibility and permeability of lime treated montmorillonitic soil after curing for different period. Immediate swell is observed on inundation of compacted samples with water and continuously increased with gypsum content. However, changes in swell are found to be marginal with curing. This is attributed to the formation and growth of ettringite crystals by ionic reactions of aluminum calcium-sulfate in the presence of water which is confirmed through detailed micro-analysis. The higher swell in uncured specimens and gradual reduction in swell with increase in curing periods are due to relative dominance of formation and growth of ettringite and cementitious compounds, respectively. Also, the ionic reaction products are found to bear a significant influence on the compressibility and permeability behavior. (C) 2015 Elsevier B.V. All rights reserved.

Limited-view light sheet fluorescence microscopy for three dimensional volume imaging

We propose and demonstrate a limited-view light sheet microscopy (LV-LSM) for three dimensional (3D) volume imaging. Realizing that longer and frequent image acquisition results in significant photo-bleaching, we have taken limited angular views (18 views) of the macroscopic specimen and integrated with maximum likelihood (ML) technique for reconstructing high quality 3D volume images. Existing variants of light-sheet microscopy require both rotation and translation with a total of approximately 10-fold more views to render a 3D volume image. Comparatively, LV-LSM technique reduces data acquisition time and consequently minimizes light-exposure by many-folds. Since ML is a post-processing technique and highly parallelizable, this does not cost precious imaging time. Results show noise-free and high contrast volume images when compared to the state-of-the-art selective plane illumination microscopy. (C) 2015 AIP Publishing LLC.

Regulation of Acetate Metabolism and Acetyl Co-a Synthetase 1 (ACS1) Expression by Methanol Expression Regulator 1 (Mxr1p) in the Methylotrophic Yeast Pichia pastoris

Methanol expression regulator 1 (Mxr1p) is a zinc finger protein that regulates the expression of genes encoding enzymes of the methanol utilization pathway in the methylotrophic yeast Pichia pastoris by binding to Mxr1p response elements (MXREs) present in their promoters. Here we demonstrate that Mxr1p is a key regulator of acetate metabolism as well. Mxr1p is cytosolic in cells cultured in minimal medium containing a yeast nitrogen base, ammonium sulfate, and acetate (YNBA) but localizes to the nucleus of cells cultured in YNBA supplemented with glutamate or casamino acids as well as nutrient-rich medium containing yeast extract, peptone, and acetate (YPA). Deletion of Mxr1 retards the growth of P. pastoris cultured in YNBA supplemented with casamino acids as well as YPA. Mxr1p is a key regulator of ACS1 encoding acetyl-CoA synthetase in cells cultured in YPA. A truncated Mxr1p comprising 400 N-terminal amino acids activates ACS1 expression and enhances growth, indicating a crucial role for the N-terminal activation domain during acetate metabolism. The serine 215 residue, which is known to regulate the expression of Mxr1p-activated genes in a carbon source-dependent manner, has no role in the Mxr1p-mediated activation of ACS1 expression. The ACS1 promoter contains an Mxr1p response unit (MxRU) comprising two MXREs separated by a 30-bp spacer. Mutations that abrogate MxRU function in vivo abolish Mxr1p binding to MxRU in vitro. Mxr1p-dependent activation of ACS1 expression is most efficient in cells cultured in YPA. The fact that MXREs are conserved in genes outside of the methanol utilization pathway suggests that Mxr1p may be a key regulator of multiple metabolic pathways in P. pastoris.

Perturbation of nucleo-cytoplasmic transport affects size of nucleus and nucleolus in human cells

Size regulation of human cell nucleus and nucleolus are poorly understood subjects. 3D reconstruction of live image shows that the karyoplasmic ratio (KR) increases by 30-80% in transformed cell lines compared to their immortalized counterpart. The attenuation of nucleo-cytoplasmic transport causes the KR value to increase by 30-50% in immortalized cell lines. Nucleolus volumes are significantly increased in transformed cell lines and the attenuation of nucleo-cytoplasmic transport causes a significant increase in the nucleolus volume of immortalized cell lines. A cytosol and nuclear fraction swapping experiment emphasizes the potential role of unknown cytosolic factors in nuclear and nucleolar size regulation.

Regulation of Growth, Cell Shape, Cell Division, and Gene Expression by Second Messengers (p)ppGpp and Cyclic Di-GMP in Mycobacterium smegmatis

The alarmone (p)ppGpp regulates transcription, translation, replication, virulence, lipid synthesis, antibiotic sensitivity, biofilm formation, and other functions in bacteria. Signaling nucleotide cyclic di-GMP (c-di-GMP) regulates biofilm formation, motility, virulence, the cell cycle, and other functions. In Mycobacterium smegmatis, both (p) ppGpp and c-di-GMP are synthesized and degraded by bifunctional proteins Rel(Msm) and DcpA, encoded by rel(Msm) and dcpA genes, respectively. We have previously shown that the Delta rel(Msm) and Delta dcpA knockout strains are antibiotic resistant and defective in biofilm formation, show altered cell surface properties, and have reduced levels of glycopeptidolipids and polar lipids in their cell wall (K. R. Gupta, S. Kasetty, and D. Chatterji, Appl Environ Microbiol 81:2571-2578, 2015, http://dx.doi.org/10.1128/AEM.03999-14). In this work, we have explored the phenotypes that are affected by both (p) ppGpp and c-di-GMP in mycobacteria. We have shown that both (p) ppGpp and c-di-GMP are needed to maintain the proper growth rate under stress conditions such as carbon deprivation and cold shock. Scanning electron microscopy showed that low levels of these second messengers result in elongated cells, while high levels reduce the cell length and embed the cells in a biofilm-like matrix. Fluorescence microscopy revealed that the elongated Delta rel(Msm) and Delta dcpA cells are multinucleate, while transmission electron microscopy showed that the elongated cells are multiseptate. Gene expression analysis also showed that genes belonging to functional categories such as virulence, detoxification, lipid metabolism, and cell-wall-related processes were differentially expressed. Our results suggests that both (p) ppGpp and c-di-GMP affect some common phenotypes in M. smegmatis, thus raising a possibility of cross talk between these two second messengers in mycobacteria. IMPORTANCE Our work has expanded the horizon of (p) ppGpp and c-di-GMP signaling in Gram-positive bacteria. We have come across a novel observation that M. smegmatis needs (p) ppGpp and c-di-GMP for cold tolerance. We had previously shown that the Delta rel(Msm) and Delta dcpA strains are defective in biofilm formation. In this work, the overproduction of (p) ppGpp and c-di-GMP encased M. smegmatis in a biofilm-like matrix, which shows that both (p) ppGpp and c-di-GMP are needed for biofilm formation. The regulation of cell length and cell division by (p) ppGpp was known in mycobacteria, but our work shows that c-di-GMP also affects the cell size and cell division in mycobacteria. This is perhaps the first report of c-di-GMP regulating cell division in mycobacteria.

Perturbational Finite Volume Method For The Solution of 2-D Navier-Stokes Equations on Unstructured and Structured Colocated Meshes

Based on the first-order upwind and second-order central type of finite volume( UFV and CFV) scheme, upwind and central type of perturbation finite volume ( UPFV and CPFV) schemes of the Navier-Stokes equations were developed. In PFV method, the mass fluxes of across the cell faces of the control volume (CV) were expanded into power series of the grid spacing and the coefficients of the power series were determined by means of the conservation equation itself. The UPFV and CPFV scheme respectively uses the same nodes and expressions as those of the normal first-order upwind and second-order central scheme, which is apt to programming. The results of numerical experiments about the flow in a lid-driven cavity and the problem of transport of a scalar quantity in a known velocity field show that compared to the first-order UFV and second-order CFV schemes, upwind PFV scheme is higher accuracy and resolution, especially better robustness. The numerical computation to flow in a lid-driven cavity shows that the under-relaxation factor can be arbitrarily selected ranging from 0.3 to 0. 8 and convergence perform excellent with Reynolds number variation from 102 to 104.

Simulation of Free-Surface Flow in a Tank Using the Navier-Stokes Model and Unstructured Finite Volume Method

Modelling free-surface flow has very important applications in many engineering areas such as oil transportation and offshore structures. Current research focuses on the modelling of free surface flow in a tank by solving the Navier-Stokes equation. An unstructured finite volume method is used to discretize the governing equations. The free surface is tracked by dynamically adapting the mesh and making it always surface conforming. A mesh-smoothing scheme based on the spring analogy is also implemented to ensure mesh quality throughout the computaiton. Studies are performed on the sloshing response of a liquid in an elastic container subjected to various excitation frequencies. Further investigations are also carried out on the critical frequency that leads to large deformation of the tank walls. Another numerical simulation involves the free-surface flow past as submerged obstacle placed in the tank to show the flow separation and vortices. All these cases demonstrate the capability of this numerical method in modelling complicated practical problems.

Effect of liquid bridge volume on the instability in small-Prandtl-number half zones

A perturbation method is used to examine the linear instability of thermocapillary convection in a liquid bridge of floating half-zone filled with a small Prandtl number fluid. The influence of liquid bridge volume on critical Marangoni number and flow features is analyzed. The neutral modes show that the instability is mainly caused by the bulk flow that is driven by the nonuniform thermocapillary forces acting on the free surface. The hydrodynamic instability is dominant in the case of small Prandtl number fluid and the first instability mode is a stationary bifurcation. The azimuthal wave number for the most dangerous mode depends on the liquid bridge volume, and is not always two as in the case of a cylindrical liquid bridge with aspect ratio near 0.6. Its value may be equal to unity when the liquid bridge is relatively slender.