Wrinkled and slack membranes: nonlinear 3D elasticity solutions via smooth DMS-FEM and experiment

The smooth DMS-FEM, recently proposed by the authors, is extended and applied to the geometrically nonlinear and ill-posed problem of a deformed and wrinkled/slack membrane. A key feature of this work is that three-dimensional nonlinear elasticity equations corresponding to linear momentum balance, without any dimensional reduction and the associated approximations, directly serve as the membrane governing equations. Domain discretization is performed with triangular prism elements and the higher order (C1 or more) interelement continuity of the shape functions ensures that the errors arising from possible jumps in the first derivatives of the conventional C0 shape functions do not propagate because the ill-conditioned tangent stiffness matrices are iteratively inverted. The present scheme employs no regularization and exhibits little sensitivity to h-refinement. Although the numerically computed deformed membrane profiles do show some sensitivity to initial imperfections (nonplanarity) in the membrane profile needed to initiate transverse deformations, the overall patterns of the wrinkles and the deformed shapes appear to be less so. Finally, the deformed profiles, computed through the DMS FEM-based weak formulation, are compared with those obtained through an experiment on an ultrathin Kapton membrane, wherein wrinkles form because of the applied boundary displacement conditions. Comparisons with a reported experiment on a rectangular membrane are also provided. These exercises lend credence to the feasibility of the DMS FEM-based numerical route to computing post-wrinkled membrane shapes. Copyright (c) 2012 John Wiley & Sons, Ltd.

Inter-domain interactions influence the stability and catalytic activity of the bi-domain protein tyrosine phosphatase PTP99A

The two protein tyrosine phosphatase (PTP) domains in bi-domain PTPs share high sequence and structural similarity. However, only one of the two PIP domains is catalytically active. Here we describe biochemical studies on the two tandem PTP domains of the bi-domain PTP, PTP99A. Phosphatase activity, monitored using small molecule as well as peptide substrates, revealed that the inactive (D2) domain activates the catalytic (D1) domain. Thermodynamic measurements suggest that the inactive D2 domain stabilizes the bi-domain (D1-D2) protein. The mechanism by which the D2 domain activates and stabilizes the bi-domain protein is governed by few interactions at the inter-domain interface. In particular, mutating Lys990 at the interface attenuates inter-domain communication. This residue is located at a structurally equivalent location to the so-called allosteric site of the canonical single domain PIP, PTP1B. These observations suggest functional optimization in bi-domain PTPs whereby the inactive PTP domain modulates the catalytic activity of the bi-domain enzyme. (C) 2012 Elsevier B.V. All rights reserved.

Self-Assembly and Catalytic Activity of Metal Nanoparticles Immobilized in Polymer Membrane Prepared via Layer-by-Layer Approach

Densely packed nanoparticles distributed in a stable and robust thin film is a highly preferred system for utilizing the various applications of nanoparticles. Here, we report covalent bond mediated layer-by-layer (LbL) self-assembled thin films of nanoparticles embedded in polymer membrane. Polymer with complementary functional group is utilized for fabrication of thin film via covalent bonding. UV-visible spectroscopy, atomic force microscopy (AFM) and scanning electron microscopy (SEM) were used to monitor the growth of LbL thin film. Subsequently, the composite thin film is used for catalysis of an organic electron transfer reaction of p-nitrophenol to p-aminophenol by sodium borohydride. The catalytic activity of these composite films is assayed multiple times, proving its applicability as a catalyst. The kinetic data obtained by monitoring reduction of p-nitrophenol suggest that the reaction rates are directly related to the sizes of the nanoparticle and porosity of the membrane.

Zero-crossing approach to high-resolution reconstruction in frequency-domain optical-coherence tomography

We address the problem of high-resolution reconstruction in frequency-domain optical-coherence tomography (FDOCT). The traditional method employed uses the inverse discrete Fourier transform, which is limited in resolution due to the Heisenberg uncertainty principle. We propose a reconstruction technique based on zero-crossing (ZC) interval analysis. The motivation for our approach lies in the observation that, for a multilayered specimen, the backscattered signal may be expressed as a sum of sinusoids, and each sinusoid manifests as a peak in the FDOCT reconstruction. The successive ZC intervals of a sinusoid exhibit high consistency, with the intervals being inversely related to the frequency of the sinusoid. The statistics of the ZC intervals are used for detecting the frequencies present in the input signal. The noise robustness of the proposed technique is improved by using a cosine-modulated filter bank for separating the input into different frequency bands, and the ZC analysis is carried out on each band separately. The design of the filter bank requires the design of a prototype, which we accomplish using a Kaiser window approach. We show that the proposed method gives good results on synthesized and experimental data. The resolution is enhanced, and noise robustness is higher compared with the standard Fourier reconstruction. (c) 2012 Optical Society of America

Frequency domain turbo equalization for MIMO-CPSC systems with large delay spreads

In this paper, we consider low-complexity turbo equalization for multiple-input multiple-output (MIMO) cyclic prefixed single carrier (CPSC) systems in MIMO inter-symbol interference (ISI) channels characterized by large delay spreads. A low-complexity graph based equalization is carried out in the frequency domain. Because of the reduction in correlation among the noise samples that happens for large frame sizes and delay spreads in frequency domain processing, improved performance compared to time domain processing is shown to be achieved. This improved performance is attractive for equalization in severely delay spread ISI channels like ultrawideband channels and underwater acoustic channels.

Optimal sparsifying bases for frequency-domain optical-coherence tomography

We address the reconstruction problem in frequency-domain optical-coherence tomography (FDOCT) from under-sampled measurements within the framework of compressed sensing (CS). Specifically, we propose optimal sparsifying bases for accurate reconstruction by analyzing the backscattered signal model. Although one might expect Fourier bases to be optimal for the FDOCT reconstruction problem, it turns out that the optimal sparsifying bases are windowed cosine functions where the window is the magnitude spectrum of the laser source. Further, the windowed cosine bases can be phase locked, which allows one to obtain higher accuracy in reconstruction. We present experimental validations on real data. The findings reported in this Letter are useful for optimal dictionary design within the framework of CS-FDOCT. (C) 2012 Optical Society of America

Antibodies against the extracellular domain of human Notch1 receptor reveal the critical role of epidermal-growth-factor-like repeats 25-26 in ligand binding and receptor activation

The Notch signalling pathway is implicated in a wide variety of cellular processes throughout metazoan development. Although the downstream mechanism of Notch signalling has been extensively studied, the details of its ligand-mediated receptor activation are not clearly understood. Although the role of Notch ELRs EGF (epidermal growth factor)-like-repeats] 11-12 in ligand binding is known, recent studies have suggested interactions within different ELRs of the Notch receptor whose significance remains to be understood. Here, we report critical inter-domain interactions between human Notch1 ELRs 21-30 and the ELRs 11-15 that are modulated by calcium. Surface plasmon resonance analysis revealed that the interaction between ELRs 21-30 and ELRs 11-15 is similar to 10-fold stronger than that between ELRs 11-15 and the ligands. Although there was no interaction between Notch 1 ELRs 21-30 and the ligands in vitro, addition of pre-clustered Jagged1Fc resulted in the dissociation of the preformed complex between ELRs 21-30 and 11-15, suggesting that inter-domain interactions compete for ligand binding. Furthermore, the antibodies against ELRs 21-30 inhibited ligand binding to the full-length Notch1 and subsequent receptor activation, with the antibodies against ELRs 25-26 being the most effective. These results suggest that the ELRs 25-26 represent a cryptic ligand-binding site which becomes exposed only upon the presence of the ligand. Thus, using specific antibodies against various domains of the Notch1 receptor, we demonstrate that, although ELRs 11-12 are the principal ligand-binding site, the ELRs 25-26 serve as a secondary binding site and play an important role in receptor activation.

AN ITERATIVE ALGORITHM FOR PHASE RETRIEVAL WITH SPARSITY CONSTRAINTS: APPLICATION TO FREQUENCY DOMAIN OPTICAL COHERENCE TOMOGRAPHY

We address the problem of phase retrieval, which is frequently encountered in optical imaging. The measured quantity is the magnitude of the Fourier spectrum of a function (in optics, the function is also referred to as an object). The goal is to recover the object based on the magnitude measurements. In doing so, the standard assumptions are that the object is compactly supported and positive. In this paper, we consider objects that admit a sparse representation in some orthonormal basis. We develop a variant of the Fienup algorithm to incorporate the condition of sparsity and to successively estimate and refine the phase starting from the magnitude measurements. We show that the proposed iterative algorithm possesses Cauchy convergence properties. As far as the modality is concerned, we work with measurements obtained using a frequency-domain optical-coherence tomography experimental setup. The experimental results on real measured data show that the proposed technique exhibits good reconstruction performance even with fewer coefficients taken into account for reconstruction. It also suppresses the autocorrelation artifacts to a significant extent since it estimates the phase accurately.

Optimal control problem for the time-dependent Kirchhoff-Love plate in a domain with rough boundary

In this paper, we study the asymptotic behavior of an optimal control problem for the time-dependent Kirchhoff-Love plate whose middle surface has a very rough boundary. We identify the limit problem which is an optimal control problem for the limit equation with a different cost functional.

Mapping the apoptosis inducing domain of an immunomodulatory protein: glycodelin A

Glycodelin A (GdA) is a dimeric glycoprotein synthesized by the human endometrium under progesterone regulation. Based on the high sequence similarity with beta-lactoglobulin, it is placed under the lipocalin superfamily. The protein is one of the local immunomodulators present at the feto-maternal interface which affects both the innate as well as the acquired arms of the immune system, thereby bringing about successful establishment and progression of pregnancy. Our previous studies revealed that the domain responsible for the immunosuppressive activity of glycodelin lies on its protein backbone and the glycans modulate the same. This study attempts to further delineate the apoptosis inducing region of GdA. Our results demonstrate that the stretch of amino acid sequence between Met24 to Leu105 is necessary and sufficient to inhibit proliferation of T cells and induce apoptosis in them. Further, within this region the key residues involved in harboring the activity were shown to be present between Asp52 and Ser65.

Regulation of lipid biosynthesis, sliding motility, and biofilm formation by a membrane-anchored nucleoid-associated protein of mycobacterium tuberculosis

Bacteria use a number of small basic proteins for organization and compaction of their genomes. By their interaction with DNA, these nucleoid-associated proteins (NAPs) also influence gene expression. Rv3852, a NAP of Mycobacterium tuberculosis, is conserved among the pathogenic and slow-growing species of mycobacteria. Here, we show that the protein predominantly localizes in the cell membrane and that the carboxy-terminal region with the propensity to form a transmembrane helix is necessary for its membrane localization. The protein is involved in genome organization, and its ectopic expression in Mycobacterium smegmatis resulted in altered nucleoid morphology, defects in biofilm formation, sliding motility, and change in apolar lipid profile. We demonstrate its crucial role in regulating the expression of KasA, KasB, and GroEL1 proteins, which are in turn involved in controlling the surface phenotypes in mycobacteria.

Tethering preferences of domain families co-occurring in multi-domain proteins

Genomic data of several organisms have revealed the presence of a vast repertoire of multi-domain proteins. The role played by individual domains in a multi-domain protein has a profound influence on the overall function of the protein. In the present analysis an attempt has been made to better understand the tethering preferences of domain families that occur in multi-domain proteins. The analysis has been carried out on an exhaustive dataset of 2 961 898 sequences of proteins from 930 organisms, where 741 274 proteins are comprised of at least two domain families. For every domain family, the number of other domain families with which it co-occurs within a protein in this dataset has been enumerated and is referred to as the tethering number of the domain family. It was found that, in the general dataset, the AAA ATPase family and the family of Ser/Thr kinases have the highest tethering numbers of 450 and 444 respectively. Further analysis reveals significant correlation between the number of members in a family and its tethering number. Positive correlation was also observed for the extent of a sequence and functional diversity within a family and the tethering numbers of domain families. Domain families that are present ubiquitously in diverse organisms tend to have large tethering numbers, while organism/kingdom-specific families have low tethering numbers. Thus, the analysis uncovers how domain families recombine and evolve to give rise to multi-domain proteins.

Exact internal controllability for a hyperbolic problem in a domain with highly oscillating boundary

In this paper, by using the Hilbert Uniqueness Method (HUM), we study the exact controllability problem described by the wave equation in a three-dimensional horizontal domain bounded at the bottom by a smooth wall and at the top by a rough wall. The latter is assumed to consist in a plane wall covered with periodically distributed asperities whose size depends on a small parameter epsilon > 0, and with a fixed height. Our aim is to obtain the exact controllability for the homogenized equation. In the process, we study the asymptotic analysis of wave equation in two setups, namely solution by standard weak formulation and solution by transposition method.

Joint Antenna Selection and Frequency-Domain Scheduling in OFDMA Systems with Imperfect Estimates from Dual Pilot Training Scheme

Transmit antenna selection (AS) has been adopted in contemporary wideband wireless standards such as Long Term Evolution (LTE). We analyze a comprehensive new model for AS that captures several key features about its operation in wideband orthogonal frequency division multiple access (OFDMA) systems. These include the use of channel-aware frequency-domain scheduling (FDS) in conjunction with AS, the hardware constraint that a user must transmit using the same antenna over all its assigned subcarriers, and the scheduling constraint that the subcarriers assigned to a user must be contiguous. The model also captures the novel dual pilot training scheme that is used in LTE, in which a coarse system bandwidth-wide sounding reference signal is used to acquire relatively noisy channel state information (CSI) for AS and FDS, and a dense narrow-band demodulation reference signal is used to acquire accurate CSI for data demodulation. We analyze the symbol error probability when AS is done in conjunction with the channel-unaware, but fair, round-robin scheduling and with channel-aware greedy FDS. Our results quantify how effective joint AS-FDS is in dispersive environments, the interactions between the above features, and the ability of the user to lower SRS power with minimal performance degradation.

N-Terminal disordered domain of saccharomyces cerevisiae Hop1 protein Is dispensable for DNA binding, bridging, and synapsis of double-stranded DNA molecules but is ecessary for spore formation

The cytological architecture of the synaptonemal complex (SC), a meiosis-specific proteinaceous structure, is evolutionarily conserved among eukaryotes. However, little is known about the biochemical properties of SC components or the mechanisms underlying their roles in meiotic chromosome synapsis and recombination. Functional analysis of Saccharomyces cerevisiae Hop1, a key structural component of SC, has begun to reveal important insights into its function in interhomolog recombination. Previously, we showed that Hop1 is a structure-specific DNA-binding protein, exhibits higher binding affinity for the Holliday junction, and induces structural distortion at the core of the junction. Furthermore, Hop1 promotes DNA condensation and intra- and intermolecular synapsis between duplex DNA molecules. Here, we show that Hop1 possesses a modular domain organization, consisting of an intrinsically disordered N-terminal domain and a protease-resistant C-terminal domain (Hop1CTD). Furthermore, we found that Hop1CTD exhibits strong homotypic as well as heterotypic protein protein interactions, and its biochemical activities were similar to those of the full-length Hop1 protein. However, Hop1CTD failed to complement the meiotic recombination defects of the Delta hop1 strain, indicating that both N- and C-terminal domains of Hop1 are essential for meiosis and spore formation. Altogether, our findings reveal novel insights into the structure-function relationships of Hop1 and help to further our understanding of its role in meiotic chromosome synapsis and recombination.