Ab initio molecular dynamics using density based energy functionals: application to ground state geometries of some small clusters

The ground state geometries of some small clusters have been obtained via ab initio molecular dynamical simulations by employing density based energy functionals. The approximate kinetic energy functionals that have been employed are the standard Thomas-Fermi $(T_{TF})$ along with the Weizsacker correction $T_W$ and a combination $F(N_e)T_{TF} + T_W$. It is shown that the functional involving $F(N_e)$ gives superior charge densities and bondlengths over the standard functional. Apart from dimers and trimers of Na, Mg, Al, Li, Si, equilibrium geometries for $Li_nAl, n=1,8$ and $Al_{13}$ clusters have also been reported. For all the clusters investigated, the method yields the ground state geometries with the correct symmetries with bondlengths within 5\% when compared with the corresponding results obtained via full orbital based Kohn-Sham method. The method is fast and a promising one to study the ground state geometries of large clusters.Comment: 15 pages, 3 PS figure

The scaling attractor and ultimate dynamics for Smoluchowski's coagulation equations

We describe a basic framework for studying dynamic scaling that has roots in dynamical systems and probability theory. Within this framework, we study Smoluchowski's coagulation equation for the three simplest rate kernels $K(x,y)=2$, $x+y$ and $xy$. In another work, we classified all self-similar solutions and all universality classes (domains of attraction) for scaling limits under weak convergence (Comm. Pure Appl. Math 57 (2004)1197-1232). Here we add to this a complete description of the set of all limit points of solutions modulo scaling (the scaling attractor) and the dynamics on this limit set (the ultimate dynamics). The main tool is Bertoin's L\'{e}vy-Khintchine representation formula for eternal solutions of Smoluchowski's equation (Adv. Appl. Prob. 12 (2002) 547--64). This representation linearizes the dynamics on the scaling attractor, revealing these dynamics to be conjugate to a continuous dilation, and chaotic in a classical sense. Furthermore, our study of scaling limits explains how Smoluchowski dynamics ``compactifies'' in a natural way that accounts for clusters of zero and infinite size (dust and gel)

Two-soliton solution for the derivative nonlinear Schr\"odinger equation with nonvanishing boundary conditions

An explicit two-soliton solution for the derivative nonlinear Schr\"odinger equation with nonvanishing boundary conditions is derived, demonstrating details of interactions between two bright solitons, two dark solitons, as well as one bright soliton and one dark soliton. Shifts of soliton positions due to collisions are analytically obtained, which are irrespective of the bright or dark characters of the participating solitons.Comment: 11 pages, 4 figures. Phys. Lett. A 2006 (in press

Effect of tcdR Mutation on Sporulation in the Epidemic Clostridium difficile Strain R20291

Citation: Girinathan, B. P., Monot, M., Boyle, D., McAllister, K. N., Sorg, J. A., Dupuy, B., & Govind, R. (2017). Effect of tcdR Mutation on Sporulation in the Epidemic Clostridium difficile Strain R20291. Msphere, 2(1), 14. doi:10.1128/mSphere.00383-16Clostridium difficile is an important nosocomial pathogen and the leading cause of hospital-acquired diarrhea. Antibiotic use is the primary risk factor for the development of C. difficile-associated disease because it disrupts normally protective gut flora and enables C. difficile to colonize the colon. C. difficile damages host tissue by secreting toxins and disseminates by forming spores. The toxin-encoding genes, tcdA and tcdB, are part of a pathogenicity locus, which also includes the tcdR gene that codes for TcdR, an alternate sigma factor that initiates transcription of tcdA and tcdB genes. We created a tcdR mutant in epidemic-type C. difficile strain R20291 in an attempt to identify the global role of tcdR. A site-directed mutation in tcdR affected both toxin production and sporulation in C. difficile R20291. Spores of the tcdR mutant were more heat sensitive than the wild type (WT). Nearly 3-fold more taurocholate was needed to germinate spores from the tcdR mutant than to germinate the spores prepared from the WT strain. Transmission electron microscopic analysis of the spores also revealed a weakly assembled exosporium on the tcdR mutant spores. Accordingly, comparative transcriptome analysis showed many differentially expressed sporulation genes in the tcdR mutant compared to the WT strain. These data suggest that regulatory networks of toxin production and sporulation in C. difficile strain R20291 are linked with each other. IMPORTANCE C. difficile infects thousands of hospitalized patients every year, causing significant morbidity and mortality. C. difficile spores play a pivotal role in the transmission of the pathogen in the hospital environment. During infection, the spores germinate, and the vegetative bacterial cells produce toxins that damage host tissue. Thus, sporulation and toxin production are two important traits of C. difficile. In this study, we showed that a mutation in tcdR, the toxin gene regulator, affects both toxin production and sporulation in epidemic-type C. difficile strain R20291

Selective and regulated trapping of nicotinic receptor weak base ligands and relevance to smoking cessation

© The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in eLife 6 (2017): e25651, doi:10.7554/eLife.25651.To better understand smoking cessation, we examined the actions of varenicline (Chantix) during long-term nicotine exposure. Varenicline reduced nicotine upregulation of α4β2-type nicotinic receptors (α4β2Rs) in live cells and neurons, but not for membrane preparations. Effects on upregulation depended on intracellular pH homeostasis and were not observed if acidic pH in intracellular compartments was neutralized. Varenicline was trapped as a weak base in acidic compartments and slowly released, blocking 125I-epibatidine binding and desensitizing α4β2Rs. Epibatidine itself was trapped; 125I-epibatidine slow release from acidic vesicles was directly measured and required the presence of α4β2Rs. Nicotine exposure increased epibatidine trapping by increasing the numbers of acidic vesicles containing α4β2Rs. We conclude that varenicline as a smoking cessation agent differs from nicotine through trapping in α4β2R-containing acidic vesicles that is selective and nicotine-regulated. Our results provide a new paradigm for how smoking cessation occurs and suggest how more effective smoking cessation reagents can be designed.This work was supported by National Institutes of Health RO1DA 035430 and a Pilot Project from the University of Chicago Can- cer Center

PROPORTIONAL FEEDBACK CONTROL OF DUTY CYCLE FOR DC HYBRID ACTIVE POWER FILTER

This thesis deals with the design and implementation of a feedback control scheme for a DC Hybrid Active Power Filter used to filter harmonics from a Switched Reluctance Motor (SRM) Drive load. Power electronic systems are non-linear & dynamic [1,3,5]. Power electronic systems employ switching circuits to maximize their efficiency at the penalty that switching circuits generate electrical noise called ripple current and voltage or conducted electromagnetic interference (EMI). The ripple current drawn by the power electronic systems needs to be attenuated to an acceptable level. Filters attenuate this to an acceptable level. Traditionally filters with passive inductors and capacitors are used. Active filters contain switching elements in addition to passive inductors and capacitors which reduce overall size of passive components used. Two control approaches, full-state state space, and plain proportional feedback, are evaluated for this filter. Circuit models are simulated in SPICE and mathematical models are simulated in Matlab/Simulink for evaluating these control approaches. Proportional feedback control was chosen for implementation and the reason for this is provided in the thesis. The active filter was tested with chosen feedback control and experimental results were compared with simulation results. Inferences and scope for further work are finally presented

An orbital-free molecular dynamics study of melting in K_20, K_55, K_92, K_142, Rb_55 and Cs_55 clusters

The melting-like transition in potasium clusters K_N, with N=20, 55, 92 and 142, is studied by using an orbital-free density-functional constant-energy molecular dynamics simulation method, and compared to previous theoretical results on the melting-like transition in sodium clusters of the same sizes. Melting in potasium and sodium clusters proceeds in a similar way: a surface melting stage develops upon heating before the homogeneous melting temperature is reached. Premelting effects are nevertheless more important and more easily established in potasium clusters, and the transition regions spread over temperature intervals which are wider than in the case of sodium. For all the sizes considered, the percentage melting temperature reduction when passing from Na to K clusters is substantially larger than in the bulk. Once those two materials have been compared for a number of different cluster sizes, we study the melting-like transition in Rb_55 and Cs_55 clusters and make a comparison with the melting behavior of Na_55 and K_55. As the atomic number increases, the height of the specific heat peaks decreases, their width increases, and the melting temperature decreases as in bulk melting, but in a more pronounced way.Comment: LaTeX file. 6 pages with 17 pictures. Final version with minor change

The Cone Phase of Liquid Crystals: Triangular Lattice of Double-Tilt Cylinders

We predict the existence of a new defect-lattice phase near the nematic - smectic-C (NC) transition. This tilt- analogue of the blue phase is a lattice of double-tilt cylinders. We discuss the structure and stability of the cone phase. We suggest that many `nematics' exhibiting short range layering and tilt order may in fact be in the molten cone phase, which is a line liquid.Comment: 4 Pages, 3 Figure