Distribution of transverse chain fluctuations in harmonically confined semiflexible polymers

Two different experimental studies of polymer dynamics based on single-molecule fluorescence imaging have recently found evidence of heterogeneities in the widths of the putative tubes that surround filaments of F-actin during their motion in concentrated solution. In one J. Glaser, D. Chakraborty, K. Kroy, I. Lauter, M. Degawa, N. Kirchesner, B. Hoffmann, R. Merkel, and M. Giesen, Phys. Rev. Lett. 105, 037801 (2010)], the observations were explained in terms of the statistics of a worm-like chain confined to a potential determined self-consistently by a binary collision approximation, and in the other B. Wang, J. Guan, S. M. Anthony, S. C. Bae, K. S. Schweizer, and S. Granick, Phys. Rev. Lett. 104, 118301 (2010)], they were explained in terms of the scaling properties of a random fluid of thin rods. In this paper, we show, using an exact path integral calculation, that the distribution of the length-averaged transverse fluctuations of a harmonically confined weakly bendable rod (one possible realization of a semiflexible chain in a tube), is in good qualitative agreement with the experimental data, although it is qualitatively different in analytic structure from the earlier theoretical predictions. We also show that similar path integral techniques can be used to obtain an exact expression for the time correlation function of fluctuations in the tube cross section. (C) 2012 American Institute of Physics. http://dx.doi.org/10.1063/1.4712306]

Confinement and viscoelastic effects on chain closure dynamics

Chemical reactions inside cells are typically subject to the effects both of the cell's confining surfaces and of the viscoelastic behavior of its contents. In this paper, we show how the outcome of one particular reaction of relevance to cellular biochemistry - the diffusion-limited cyclization of long chain polymers - is influenced by such confinement and crowding effects. More specifically, starting from the Rouse model of polymer dynamics, and invoking the Wilemski-Fixman approximation, we determine the scaling relationship between the mean closure time t(c) of a flexible chain (no excluded volume or hydrodynamic interactions) and the length N of its contour under the following separate conditions: (a) confinement of the chain to a sphere of radius d and (b) modulation of its dynamics by colored Gaussian noise. Among other results, we find that in case (a) when d is much smaller than the size of the chain, t(c) similar to Nd-2, and that in case (b), t(c) similar to N-2/(2 (2H)), H being a number between 1/2 and 1 that characterizes the decay of the noise correlations. H is not known a priori, but values of about 0.7 have been used in the successful characterization of protein conformational dynamics. At this value of H (selected for purposes of illustration), t(c) similar to N-3.4, the high scaling exponent reflecting the slow relaxation of the chain in a viscoelastic medium. (C) 2012 American Institute of Physics. http://dx.doi.org/10.1063/1.4729041]

A Rare Phenoxido/Acetato/Azido Bridged Trinuclear and an Unprecedented Phenoxido/Azido Bridged One-Dimensional Polynuclear Nickel(II) Complexes: Synthesis, Crystal Structure, and Magnetic Properties with Theoretical Investigations on the Exchange Mechanism

The reaction of a tridentate Schiff base ligand HL (2-(3-dimethylaminopropylimino)-methyl]-phenol) with Ni(II) acetate or perchlorate salts in the presence of azide as coligand has led to two new Ni(II) complexes of formulas Ni3L2(OAc)(2)(mu(1,1)-N-3)(2)(H2O)(2)]center dot 2H(2)O (1) and Ni2L2(mu(1,1)-N-3) (mu(1,3)-N-3)](n)(2). Single crystal X-ray structures show that complex 1 is a linear trinuclear Ni(II) compound containing a mu(2)-phenwddo, an end-on (EO) azido and a syn-syn acetato bridge between the terminal and the central Ni(II) ions. Complex 2 can be viewed as a one-dimensional (1D) chain in which the triply bridged (di-mu(2)-phenoxido and EO azido) dimeric Ni-2 units are linked to each other in a zigzag pattern by a single end-to-end (EE) azido bridge. Variable-temperature magnetic susceptibility studies indicate the presence of moderate ferromagnetic exchange coupling in complex 1 with J value of 16.51(6) cm(-1). The magnetic behavior of 2 can be fitted in an alternating ferro- and antiferromagnetic model J(FM) = +34.2(2.8) cm(-1) and J(AF) = -21.6(1.1) cm(-1)] corresponding to the triple bridged dinuclear core and EE azido bridge respectively. Density functional theory (DFT) calculations were performed to corroborate the magnetic results of 1 and 2. The contributions of the different bridges toward magnetic interactions in both compounds have also been calculated.

Retrobiosynthetic Approach Delineates the Biosynthetic Pathway and the Structure of the Acyl Chain of Mycobacterial Glycopeptidolipids

Glycopeptidolipids (GPLs) are dominant cell surface molecules present in several non-tuberculous and opportunistic mycobacterial species. GPLs from Mycobacterium smegmatis are composed of a lipopeptide core unit consisting of a modified C-26-C-34 fatty acyl chain that is linked to a tetrapeptide (Phe-Thr-Ala-alaninol). The hydroxyl groups of threonine and terminal alaninol are further modified by glycosylations. Although chemical structures have been reported for 16 GPLs from diverse mycobacteria, there is still ambiguity in identifying the exact position of the hydroxyl group on the fatty acyl chain. Moreover, the enzymes involved in the biosynthesis of the fatty acyl component are unknown. In this study we show that a bimodular polyketide synthase in conjunction with a fatty acyl-AMP ligase dictates the synthesis of fatty acyl chain of GPL. Based on genetic, biochemical, and structural investigations, we determine that the hydroxyl group is present at the C-5 position of the fatty acyl component. Our retrobiosynthetic approach has provided a means to understand the biosynthesis of GPLs and also resolve the long-standing debate on the accurate structure of mycobacterial GPLs.

On the Role of Higher-Order Evanescent Modes in End-Offset Inlet and End-Centered Outlet Elliptical Flow-Reversal Chamber Mufflers

This paper deals with the role of the higher-order evanescent modes generated at the area discontinuities in the acoustic attenuation characteristics of an elliptical end-chamber muffler with an end-offset inlet and end-centered outlet. It has been observed that with an increase in length, the muffler undergoes a transition from being acoustically short to acoustically long. Short end chambers and long end chambers are characterized by transverse plane waves and axial plane waves, respectively, in the low-frequency range. The nondimensional frequency limit k(0)(D-1/2) or k(0)R(0) as well as the chamber length to inlet/outlet pipe diameter ratio, i.e., L/d(0), up to which the muffler behaves like a short chamber and the corresponding limit beyond which the muffler is acoustically long are determined. The limits between which neither the transverse plane-wave model nor the conventional axial plane-wave model gives a satisfactory prediction have also been determined, the region being called the intermediate range. The end-correction expression for this muffler configuration in the acoustically long limit has been obtained using 3-D FEA carried on commercial software, covering most of the dimension range used in the design exercise. Development of a method of combining the transverse plane wave model with the axial plane wave model using the impedance Z] matrix is another noteworthy contribution of this work.

Markov chain modeling of evolution of strains in reinforced concrete flexural beams

From the analysis of experimentally observed variations in surface strains with loading in reinforced concrete beams, it is noted that there is a need to consider the evolution of strains (with loading) as a stochastic process. Use of Markov Chains for modeling stochastic evolution of strains with loading in reinforced concrete flexural beams is studied in this paper. A simple, yet practically useful, bi-level homogeneous Gaussian Markov Chain (BLHGMC) model is proposed for determining the state of strain in reinforced concrete beams. The BLHGMC model will be useful for predicting behavior/response of reinforced concrete beams leading to more rational design.

A Compliant End-Effector to Passively Limit the Force in Tele-Operated Tissue-Cutting

This paper presents a compliant end-effector that cuts soft tissues and senses the cutting forces. The end-effector is designed to have an upper threshold on cutting forces to facilitate safe handling of tissue during automated cutting. This is demonstrated with nonlinear finite element analysis and experimental results obtained by cutting inhomogeneous phantom tissue. The cutting forces are estimated using a vision-based technique that uses amplified elastic deformation of the compliant end-effector. We also demonstrate an immersive tele-operated tissue-cutting system together with a haptic device that gives real-time force feedback to the user. DOI: 10.1115/1.4007638]

An Inhibitor of Nonhomologous End-Joining Abrogates Double-Strand Break Repair and Impedes Cancer Progression

DNA Ligase IV is responsible for sealing of double-strand breaks (DSBs) during nonhomologous end-joining (NHEJ). Inhibiting Ligase IV could result in amassing of DSBs, thereby serving as a strategy toward treatment of cancer. Here, we identify a molecule, SCR7 that inhibits joining of DSBs in cell-free repair system. SCR7 blocks Ligase IV-mediated joining by interfering with its DNA binding but not that of T4 DNA Ligase or Ligase I. SCR7 inhibits NHEJ in a Ligase IV-dependent manner within cells, and activates the intrinsic apoptotic pathway. More importantly, SCR7 impedes tumor progression in mouse models and when coadministered with DSB-inducing therapeutic modalities enhances their sensitivity significantly. This inhibitor to target NHEJ offers a strategy toward the treatment of cancer and improvement of existing regimens.

Influence of Side-Chain on Structural Order and Photophysical Properties in Thiophene Based Diketopyrrolopyrroles: A Systematic Study

In this work, we have synthesized a series of TDPP derivatives with different alkyl groups such as n-hexyl (-C6H13) 3a, 2-ethylhexyl (-(2-C2H5)C6H12) 3b, triethylene glycol mono methyl ether (-(CH2CH2O)(3c)H-3, TEG) 3c, and octadodecyl (-(8-C8H17)C12H22) 3d. N,N dialkylation of Othiophene-diketopyrrolopyrrole (TDPP, 1) strongly influences its solubility, solid state packing, and structural order. These materials allow us to explicitly study the influence of alkyl chain on solid state packing and photophysical properties. TDPP moiety containing two different alkyl groups 3e (TEG and 2-ethylhexyl) and 3f (TEG and n-hexyl) were synthesized for the first time. The absorption spectra of all derivatives exhibited a red shift in solid state when compared to their solution spectra. The type of alkyl chains leads to change in the optical band gaps in solid state. The fluorescence study reveals that TDPP derivatives have strong pi-pi interaction in the solid state and the extent of bathochromic shift is due to combination of intramolecular interaction and formation of aggregates in solid state. This behavior strongly depends on the nature of alkyl chain. The presence of strong C-H center dot center dot center dot O inter chain interactions and CH-pi interactions in solid state exhibits strong influence on the photophysical properties of TDPP chromophore.

Methodology for Pavement Design Reliability and Back Analysis Using Markov Chain Monte Carlo Simulation

Given the increasing cost of designing and building new highway pavements, reliability analysis has become vital to ensure that a given pavement performs as expected in the field. Recognizing the importance of failure analysis to safety, reliability, performance, and economy, back analysis has been employed in various engineering applications to evaluate the inherent uncertainties of the design and analysis. The probabilistic back analysis method formulated on Bayes' theorem and solved using the Markov chain Monte Carlo simulation method with a Metropolis-Hastings algorithm has proved to be highly efficient to address this issue. It is also quite flexible and is applicable to any type of prior information. In this paper, this method has been used to back-analyze the parameters that influence the pavement life and to consider the uncertainty of the mechanistic-empirical pavement design model. The load-induced pavement structural responses (e.g., stresses, strains, and deflections) used to predict the pavement life are estimated using the response surface methodology model developed based on the results of linear elastic analysis. The failure criteria adopted for the analysis were based on the factor of safety (FOS), and the study was carried out for different sample sizes and jumping distributions to estimate the most robust posterior statistics. From the posterior statistics of the case considered, it was observed that after approximately 150 million standard axle load repetitions, the mean values of the pavement properties decrease as expected, with a significant decrease in the values of the elastic moduli of the expected layers. An analysis of the posterior statistics indicated that the parameters that contribute significantly to the pavement failure were the moduli of the base and surface layer, which is consistent with the findings from other studies. After the back analysis, the base modulus parameters show a significant decrease of 15.8% and the surface layer modulus a decrease of 3.12% in the mean value. The usefulness of the back analysis methodology is further highlighted by estimating the design parameters for specified values of the factor of safety. The analysis revealed that for the pavement section considered, a reliability of 89% and 94% can be achieved by adopting FOS values of 1.5 and 2, respectively. The methodology proposed can therefore be effectively used to identify the parameters that are critical to pavement failure in the design of pavements for specified levels of reliability. DOI: 10.1061/(ASCE)TE.1943-5436.0000455. (C) 2013 American Society of Civil Engineers.

Structure, molecular dynamics, and stress in a linear polymer

We present a study correlating uniaxial stress in a polymer with its underlying structure when it is strained. The uniaxial stress is significantly influenced by the mean-square bond length and mean bond angle. In contrast, the size and shape of the polymer, typically represented by the end-to-end length, mass ratio, and radius of gyration, contribute negligibly. Among externally set control variables, density and polymer chain length play a critical role in influencing the anisotropic uniaxial stress. Short chain polymers more or less behave like rigid molecules. Temperature and rate of loading, in the range considered, have a very mild effect on the uniaxial stress.

A nine-level inverter topology for medium-voltage induction motor drive with open-end stator winding

A new scheme for nine-level voltage space-vector generation for medium-voltage induction motor (IM) drives with open-end stator winding is presented in this paper. The proposed nine-level power converter topology consists of two conventional three-phase two-level voltage source inverters powered by isolated dc sources and six floating-capacitor-connected H-bridges. The H-bridge capacitor voltages are effectively maintained at the required asymmetrical levels by employing a space vector modulation (SVPWM) based control strategy. An interesting feature of this topology is its ability to function in five-or three-level mode, in the entire modulation range, at full-power rating, in the event of any failure in the H-bridges. This feature significantly improves the reliability of the proposed drive system. Each leg of the three-phase two-level inverters used in this topology switches only for a half cycle of the reference voltage waveform. Hence, the effective switching frequency is reduced by half, resulting in switching loss reduction in high-voltage devices. The transient as well as the steady-state performance of the proposed nine-level inverter-fed IM drive system is experimentally verified in the entire modulation range including the overmodulation region.

Elasticity of DNA and the effect of dendrimer binding

Negatively charged DNA can be compacted by positively charged dendrimers and the degree of compaction is a delicate balance between the strength of the electrostatic interaction and the elasticity of DNA. We report various elastic properties of short double-stranded DNA (dsDNA) and the effect of dendrimer binding using fully atomistic molecular dynamics and numerical simulations. In equilibrium at room temperature, the contour length distribution P(L) and the end-to-end distance distribution P(R) are nearly Gaussian, the former gives an estimate of the stretch modulus gamma(1) of dsDNA in quantitative agreement with the literature value. The bend angle distribution P(.) of the dsDNA also has a Gaussian form and allows to extract a persistence length, L-p of 43 nm. When the dsDNA is compacted by positively charged dendrimer, the stretch modulus stays invariant but the effective bending rigidity estimated from the end-to-end distance distribution decreases dramatically due to backbone charge neutralization of dsDNA by dendrimer. We support our observations with numerical solutions of the worm-like-chain (WLC) model as well as using non-equilibrium dsDNA stretching simulations. These results are helpful in understanding the dsDNA elasticity at short length scales as well as how the elasticity is modulated when dsDNA binds to a charged object such as a dendrimer or protein.

chain complex and quadrilaterals for normal surfaces

We interpret a normal surface in a (singular) three-manifold in terms of the homology of a chain complex. This allows us to study the relation between normal surfaces and their quadrilateral coordinates. Specifically, we give a proof of an (unpublished) observation independently given by Casson and Rubinstein saying that quadrilaterals determine a normal surface up to vertex linking spheres. We also characterize the quadrilateral coordinates that correspond to a normal surface in a (possibly ideal) triangulation.

The sequence and structure of snake gourd (Trichosanthes anguina) seed lectin, a three-chain nontoxic homologue of type II RIPs

The sequence and structure of snake gourd seed lectin (SGSL), a nontoxic homologue of type II ribosome-inactivating proteins (RIPs), have been determined by mass spectrometry and X-ray crystallography, respectively. As in type II RIPs, the molecule consists of a lectin chain made up of two beta-trefoil domains. The catalytic chain, which is connected through a disulfide bridge to the lectin chain in type II RIPs, is cleaved into two in SGSL. However, the integrity of the three-dimensional structure of the catalytic component of the molecule is preserved. This is the first time that a three-chain RIP or RIP homologue has been observed. A thorough examination of the sequence and structure of the protein and of its interactions with the bound methyl-alpha-galactose indicate that the nontoxicity of SGSL results from a combination of changes in the catalytic and the carbohydrate-binding sites. Detailed analyses of the sequences of type II RIPs of known structure and their homologues with unknown structure provide valuable insights into the evolution of this class of proteins. They also indicate some variability in carbohydrate-binding sites, which appears to contribute to the different levels of toxicity exhibited by lectins from various sources.