Self-Organization of n-Alkane Chains in Water: Length Dependent Crossover from Helix and Toroid to Molten Globule

We demonstrate a chain length dependent crossover in the structural properties of linear hydrocarbon (n-alkane) chains using detailed atomistic simulations in explicit water. We identify a number of exotic structures of the polymer chain through energy minimization of representative snapshots collected from molecular dynamics trajectory. While the collapsed state is ring-like (circular) for small chains (CnH2n+2; n <= 20) and spherical for very long ones (n = 100), we find the emergence of ordered helical structures at intermediate lengths (n similar to 40). We find different types of disordered helices and toroid-like structures at n = 60. We also report a sharp transition in the stability of the collapsed state as a function of the chain length through relevant free energy calculations. While the collapsed state is only marginally metastable for C20H42, a clear bistable free energy surface emerges only when the chain is about 30 monomers long. For n = 30, the polymer exhibits an intermittent oscillation between the collapsed and the coil structures, characteristic of two stable states separated by a small barrier.

1-D hydrogen-bonded organization of hexanuclear {3d-4f-5d} complexes: evidence for slow relaxation of the magnetization for [{LMe2Ni(H2O)Ln(H2O)4.5}2{W(CN)8}2] with Ln = Tb and Dy

Heterometallic {3d-4f-5d} aggregates with formula [{LMe2Ni(H2O)Ln(H2O)4.5}2{W(CN)8}2]·15H2O, (LMe2 stands for N,N-2,2-dimethylpropylenedi(3-methoxysalicylideneiminato) Schiff-base ligand) with Ln = Gd, Tb, Dy, have been obtained by reacting bimetallic [LMe2Ni(H2O)2Ln(NO3)3] and Cs3{W(CN)8} in H2O. The hexanuclear complexes are organized in 1-D arrays by means of hydrogen bonds established between the solvent molecules coordinated to Ln and the CN ligands of an octacyanometallate moiety. The X-ray structure was solved for the Tb derivative. Magnetic behavior indicates ferromagnetic {W–Ni} and {Ni–Ln} interactions (JNiW = 18.5 cm-1, JNiGd = 1.85 cm-1) as well as ferromagnetic intermolecular interactions mediated by the H-bonds. Dynamic magnetic susceptibility studies reveal slow magnetic relaxation processes for the Tb and Dy derivatives, suggesting SMM type behavior for these compounds.

Organization of the Board of Trustees

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Correspondence with Mr. Joseph regarding organization of board

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Spatiotemporal Organization of AT- and GC-rich DNA and Their Association With Transition Proteins TP1 and TP2 in Rat Condensing Spermatids

Transition protein 1 (TP1) and TP2 replace histones during midspermiogenesis (stages 12-15) and are finally replaced by protamines. TPs play a predominant role in DNA condensation and chromatin remodeling during mammalian spermiogenesis. TP2 is a zinc metalloprotein with two novel zinc finger modules that condenses DNA in vitro in a GC-preference manner. TP2 also localizes to the nucleolus in transfected HeLa and Cos-7 cells, suggesting a GC-rich preference, even in vivo. We have now studied the localization pattern of TP2 in the rat spermatid nucleus. Colocalization studies using GC-selective DNA-binding dyes chromomycin A3 and 7-amino actinomycin D and an AT-selective dye, 4',6-diamidino-2-phenylindole, indicate that TP2 is preferentially localized to GC-rich sequences. Interestingly, as spermatids mature, TP2 and GC-rich DNA moves toward the nuclear periphery, and in the late stages of spermatid maturation, TP2 is predominantly localized at the nuclear periphery. Another interesting observation is the mutually exclusive localization of GC- and AT-rich DNA in the elongating and elongated spermatids. A combined immunofluorescence experiment with anti-TP2 and anti-TP1 antibodies revealed several foci of overlapping localization, indicating that TP1 and TP2 may have concerted functional roles during chromatin remodeling in mammalian spermiogenesis.

Social organization of household finance: Understanding artful financial systems in the home

In this paper we discuss results of a field study focused on understanding the ways money and financial issues are handled within family settings. Families develop ‘systems’ or methods through which they coordinate and manage their everyday financial activities. Through an analysis of our fieldwork data collected from fifteen families, we provide several examples of such systems, highlighting their qualities and illustrating how such systems come to support the handling of financial activities in the home. Our results show that these systems are developed with a careful consideration of familial values, relationships and routines; and incorporate the use of physical and digital tools. Consequently, we suggest that design should consider the use and non-use of technology when supporting household financial management, taking into account the richness of families’ existing organically formed practices surrounding financial systems. Finally, our findings point to the fact that financial management in the domestic setting is socially organized and is closely connected to supporting everyday household activities.

Three-dimensional organization of fenestrae labyrinths in liver sinusoidal endothelial cells

- Background/Aims Liver sinusoidal endothelial cell (LSEC) fenestrae are membrane-bound pores that are grouped in sieve plates and act as a bidirectional guardian in regulating transendothelial liver transport. The high permeability of the endothelial lining is explained by the presence of fenestrae and by various membrane-bound transport vesicles. The question as to whether fenestrae relate to other transport compartments remains unclear and has been debated since their discovery almost 40 years ago. - Methods In this study, novel insights concerning the three-dimensional (3D) organization of the fenestrated cytoplasm were built on transmission electron tomographical observations on isolated and cultured whole-mount LSECs. Classical transmission electron microscopy and atomic force microscopy imaging was performed to accumulate cross-correlative structural evidence. - Results and Conclusions The data presented here indicate that different arrangements of fenestrae have to be considered: i.e. open fenestrae that lack any structural obstruction mainly located in the thin peripheral cytoplasm and complexes of multifolded fenestrae organized as labyrinth-like structures that are found in the proximity of the perinuclear area. Fenestrae in labyrinths constitute about one-third of the total LSEC porosity. The 3D reconstructions also revealed that coated pits and small membrane-bound vesicles are exclusively interspersed in the non-fenestrated cytoplasmic arms.

A unified construction of space-time codes with optimal rate-diversity tradeoff

The problem of constructing space-time (ST) block codes over a fixed, desired signal constellation is considered. In this situation, there is a tradeoff between the transmission rate as measured in constellation symbols per channel use and the transmit diversity gain achieved by the code. The transmit diversity is a measure of the rate of polynomial decay of pairwise error probability of the code with increase in the signal-to-noise ratio (SNR). In the setting of a quasi-static channel model, let n(t) denote the number of transmit antennas and T the block interval. For any n(t) <= T, a unified construction of (n(t) x T) ST codes is provided here, for a class of signal constellations that includes the familiar pulse-amplitude (PAM), quadrature-amplitude (QAM), and 2(K)-ary phase-shift-keying (PSK) modulations as special cases. The construction is optimal as measured by the rate-diversity tradeoff and can achieve any given integer point on the rate-diversity tradeoff curve. An estimate of the coding gain realized is given. Other results presented here include i) an extension of the optimal unified construction to the multiple fading block case, ii) a version of the optimal unified construction in which the underlying binary block codes are replaced by trellis codes, iii) the providing of a linear dispersion form for the underlying binary block codes, iv) a Gray-mapped version of the unified construction, and v) a generalization of construction of the S-ary case corresponding to constellations of size S-K. Items ii) and iii) are aimed at simplifying the decoding of this class of ST codes.

BER analysis of space-time block codes from generalized complex orthogonal designs for M-PSK

In this paper, we present an analysis for the bit error rate (BER) performance of space-time block codes (STBC) from generalized complex orthogonal designs for M-PSK modulation. In STBCs from complex orthogonal designs (COD), the norms of the column vectors are the same (e.g., Alamouti code). However, in generalized COD (GCOD), the norms of the column vectors may not necessarily be the same (e.g., the rate-3/5 and rate-7/11 codes by Su and Xia in [1]). STBCs from GCOD are of interest because of the high rates that they can achieve (in [2], it has been shown that the maximum achievable rate for STBCs from GCOD is bounded by 4/5). While the BER performance of STBCs: from COD (e.g., Alamouti code) can be simply obtained from existing analytical expressions for receive diversity with the same diversity order by appropriately scaling the SNR, this can not be done for STBCs from GCOD (because of the unequal norms of the column vectors). Our contribution in this paper is that we derive analytical expressions for the BER performance of any STBC from GCOD. Our BER analysis for the GCOD captures the performance of STBCs from COD as special cases. We validate our results with two STBCs from GCOD reported by Su and Xia in [1], for 5 and 6 transmit antennas (G(5) and G(6) in [1]) with rates 7/11 and 3/5, respectively.

BER analysis of space-time block codes from generalized complex orthogonal designs for M-PSK

In this paper, we present an analysis for the bit error rate (BER) performance of space-time block codes (STBC) from generalized complex orthogonal designs for M-PSK modulation. In STBCs from complex orthogonal designs (COD), the norms of the column vectors are the same (e.g., Alamouti code). However, in generalized COD (GCOD), the norms of the column vectors may not necessarily be the same (e.g., the rate-3/5 and rate-7/11 codes by Su and Xia in [1]). STBCs from GCOD are of interest because of the high rates that they can achieve (in [2], it has been shown that the maximum achievable rate for STBCs from GCOD is bounded by 4/5). While the BER performance of STBCs: from COD (e.g., Alamouti code) can be simply obtained from existing analytical expressions for receive diversity with the same diversity order by appropriately scaling the SNR, this can not be done for STBCs from GCOD (because of the unequal norms of the column vectors). Our contribution in this paper is that we derive analytical expressions for the BER performance of any STBC from GCOD. Our BER analysis for the GCOD captures the performance of STBCs from COD as special cases. We validate our results with two STBCs from GCOD reported by Su and Xia in [1], for 5 and 6 transmit antennas (G(5) and G(6) in [1]) with rates 7/11 and 3/5, respectively.

BER analysis of space-time block codes from generalized complex orthogonal designs for M-PSK

In this paper, we present an analysis for the bit error rate (BER) performance of space-time block codes (STBC) from generalized complex orthogonal designs for M-PSK modulation. In STBCs from complex orthogonal designs (COD), the norms of the column vectors are the same (e.g., Alamouti code). However, in generalized COD (GCOD), the norms of the column vectors may not necessarily be the same (e.g., the rate-3/5 and rate-7/11 codes by Su and Xia in [1]). STBCs from GCOD are of interest because of the high rates that they can achieve (in [2], it has been shown that the maximum achievable rate for STBCs from GCOD is bounded by 4/5). While the BER performance of STBCs: from COD (e.g., Alamouti code) can be simply obtained from existing analytical expressions for receive diversity with the same diversity order by appropriately scaling the SNR, this can not be done for STBCs from GCOD (because of the unequal norms of the column vectors). Our contribution in this paper is that we derive analytical expressions for the BER performance of any STBC from GCOD. Our BER analysis for the GCOD captures the performance of STBCs from COD as special cases. We validate our results with two STBCs from GCOD reported by Su and Xia in [1], for 5 and 6 transmit antennas (G(5) and G(6) in [1]) with rates 7/11 and 3/5, respectively.

Unveiling the Role of Dps in the Organization of Mycobacterial Nucleoid

In order to preserve genetic information in stress conditions, bacterial DNA is organized into higher order nucleoid structure. In this paper, with the help of Atomic Force Microscopy, we show the different structural changes in mycobacterial nucleoid at different points of growth in the presence of different concentrations of glucose in the medium. We also observe that in Mycobacterium smegmatis, two different Dps proteins (Dps1 and Dps2) promote two types of nucleoid organizations. At the late stationary phase, under low glucose availability, Dps1 binds to DNA to form a very stable toroid structure. On the other hand, under the same condition, Dps2-DNA complex forms an incompletely condensed toroid and finally forms a further stable coral reef structure in the presence of RNA. This coral reef structure is stable in high concentration of bivalent ion like Mg2+.

Diversity in Functional Organization of Class I and Class II Biotin Protein Ligase

The cell envelope of Mycobacterium tuberculosis (M. tuberculosis) is composed of a variety of lipids including mycolic acids, sulpholipids, lipoarabinomannans, etc., which impart rigidity crucial for its survival and pathogenesis. Acyl CoA carboxylase (ACC) provides malonyl-CoA and methylmalonyl-CoA, committed precursors for fatty acid and essential for mycolic acid synthesis respectively. Biotin Protein Ligase (BPL/BirA) activates apo-biotin carboxyl carrier protein (BCCP) by biotinylating it to an active holo-BCCP. A minimal peptide (Schatz), an efficient substrate for Escherichia coli BirA, failed to serve as substrate for M. tuberculosis Biotin Protein Ligase (MtBPL). MtBPL specifically biotinylates homologous BCCP domain, MtBCCP87, but not EcBCCP87. This is a unique feature of MtBPL as EcBirA lacks such a stringent substrate specificity. This feature is also reflected in the lack of self/promiscuous biotinylation by MtBPL. The N-terminus/HTH domain of EcBirA has the selfbiotinable lysine residue that is inhibited in the presence of Schatz peptide, a peptide designed to act as a universal acceptor for EcBirA. This suggests that when biotin is limiting, EcBirA preferentially catalyzes, biotinylation of BCCP over selfbiotinylation. R118G mutant of EcBirA showed enhanced self and promiscuous biotinylation but its homologue, R69A MtBPL did not exhibit these properties. The catalytic domain of MtBPL was characterized further by limited proteolysis. Holo-MtBPL is protected from proteolysis by biotinyl-59 AMP, an intermediate of MtBPL catalyzed reaction. In contrast, apo-MtBPL is completely digested by trypsin within 20 min of co-incubation. Substrate selectivity and inability to promote self biotinylation are exquisite features of MtBPL and are a consequence of the unique molecular mechanism of an enzyme adapted for the high turnover of fatty acid biosynthesis.

Evidence for supramolecular organization of alkane and surfactant molecules in the process of forming mesoporous silica

Investigations of the pore expansion in mesoporous silica in the presence of n-alkanes suggest a cooperative organization of the surfactant and alkane molecules, involving additivity of chain lengths.