Symmetry of one-dimensional dynamical systems in terms of transfer matrix parameters

The concept of symmetry for passive, one-dimensional dynamical systems is well understood in terms of the impedance matrix, or alternatively, the mobility matrix. In the past two decades, however, it has been established that the transfer matrix method is ideally suited for the analysis and synthesis of such systems. In this paper an investigatiob is described of what symmetry means in terms of the transfer matrix parameters of an passive element or a set of elements. One-dimensional flexural systems with 4 × 4 transfer matrices as well as acoustical and mechanical systems characterized by 2 × 2 transfer matrices are considered. It is shown that the transfer matrix of a symmetrical system, defined with respect to symmetrically oriented state variables, is involutory, and that a physically symmetrical system may not necessarily be functionally or dynamically symmetrical.

Transfer matrix modeling of hyperbolic and parabolic ducts with incompressible mean flow

A general differential equation for the propagation of sound in a variable area duct or nozzle carrying incompressible mean flow (of low Mach number) is derived and solved for hyperbolic and parabolic shapes. Expressions for the state variables of acoustic pressure and acoustic mass velocity of the shapes are derived. Self‐consistent expressions for the four‐pole parameters are developed. The conical, exponential, catenoidal, sine, and cosine ducts are shown to be special cases of hyperbolic ducts. Finally, it is shown that if the mean flow in computing the transmission loss of the mufflers involving hyperbolic and parabolic shapes was not neglected, little practical benefit would be derived.

Optimised form of acceleration correction algorithm within SPH-based simulations of impact mechanics

In the context of SPH-based simulations of impact dynamics, an optimised and automated form of the acceleration correction algorithm (Shaw and Reid, 2009a) is developed so as to remove spurious high frequency oscillations in computed responses whilst retaining the stabilizing characteristics of the artificial viscosity in the presence of shocks and layers with sharp gradients. A rational framework for an insightful characterisation of the erstwhile acceleration correction method is first set up. This is followed by the proposal of an optimised version of the method, wherein the strength of the correction term in the momentum balance and energy equations is optimised. For the first time, this leads to an automated procedure to arrive at the artificial viscosity term. In particular, this is achieved by taking a spatially varying response-dependent support size for the kernel function through which the correction term is computed. The optimum value of the support size is deduced by minimising the (spatially localised) total variation of the high oscillation in the acceleration term with respect to its (local) mean. The derivation of the method, its advantages over the heuristic method and issues related to its numerical implementation are discussed in detail. (C) 2011 Elsevier Ltd. All rights reserved.

Preliminary X-ray crystallographic studies on acetate kinase (AckA) from Salmonella typhimurium in two crystal forms

Acetate kinase (AckA) catalyzes the reversible transfer of a phosphate group from acetyl phosphate to ADP, generating acetate and ATP, and plays a central role in carbon metabolism. In the present work, the gene corresponding to AckA from Salmonella typhimurium (StAckA) was cloned in the IPTG-inducible pRSET C vector, resulting in the attachment of a hexahistidine tag to the N-terminus of the expressed enzyme. The recombinant protein was overexpressed, purified and crystallized in two different crystal forms using the microbatch-under-oil method. Form I crystals diffracted to 2.70 angstrom resolution when examined using X-rays from a rotating-anode X-ray generator and belonged to the monoclinic space group C2, with unit-cell parameters a = 283.16, b = 62.17, c = 91.69 angstrom, beta = 93.57 degrees. Form II crystals, which diffracted to a higher resolution of 2.35 angstrom on the rotating-anode X-ray generator and to 1.90 angstrom on beamline BM14 of the ESRF, Grenoble, also belonged to space group C2 but with smaller unit-cell parameters (a = 151.01, b = 78.50, c = 97.48 angstrom, beta = 116.37 degrees). Calculation of Matthews coefficients for the two crystal forms suggested the presence of four and two protomers of StAckA in the asymmetric units of forms I and II, respectively. Initial phases for the form I diffraction data were obtained by molecular replacement using the coordinates of Thermotoga maritima AckA (TmAckA) as the search model. The form II structure was phased using a monomer of form I as the phasing model. Inspection of the initial electron-density maps suggests dramatic conformational differences between residues 230 and 300 of the two crystal forms and warrants further investigation.

Implications of unitarity and analyticity for the D pi form factors

We consider the vector and scalar form factors of the charm-changing current responsible for the semileptonic decay D -> pi/nu. Using as input dispersion relations and unitarity for the moments of suitable heavy-light correlators evaluated with Operator Product Expansions, including O(alpha(2)(s)) terms in perturbative QCD, we constrain the shape parameters of the form factors and find exclusion regions for zeros on the real axis and in the complex plane. For the scalar form factor, a low-energy theorem and phase information on the unitarity cut are also implemented to further constrain the shape parameters. We finally propose new analytic expressions for the D pi form factors, derive constraints on the relevant coefficients from unitarity and analyticity, and briefly discuss the usefulness of the new parametrizations for describing semileptonic data.

Automatic extraction of free-form surface features (FFSFs)

This paper presents a new algorithm for extracting Free-Form Surface Features (FFSFs) from a surface model. The extraction algorithm is based on a modified taxonomy of FFSFs from that proposed in the literature. A new classification scheme has been proposed for FFSFs to enable their representation and extraction. The paper proposes a separating curve as a signature of FFSFs in a surface model. FFSFs are classified based on the characteristics of the separating curve (number and type) and the influence region (the region enclosed by the separating curve). A method to extract these entities is presented. The algorithm has been implemented and tested for various free-form surface features on different types of free-form surfaces (base surfaces) and is found to correctly identify and represent the features irrespective of the type of underlying surface. The representation and extraction algorithm are both based on topology and geometry. The algorithm is data-driven and does not use any pre-defined templates. The definition presented for a feature is unambiguous and application independent. The proposed classification of FFSFs can be used to develop an ontology to determine semantic equivalences for the feature to be exchanged, mapped and used across PLM applications. (C) 2011 Elsevier Ltd. All rights reserved.

Charge transfer complex states in diketopyrrolopyrrole polymers and fullerene blends: Implications for organic solar cell efficiency

The spectral photocurrent characteristics of two donor-acceptor diketopyrrolopyrrole (DPP)-based copolymers (PDPP-BBT and TDPP-BBT) blended with a fullerene derivative [6,6]-phenyl C-61-butyric acid methyl ester (PCBM) were studied using Fourier-transform photocurrent spectroscopy (FTPS) and monochromatic photocurrent (PC) method. PDPP-BBT: PCBM shows the onset of the lowest charge transfer complex (CTC) state at 1.42 eV, whereas TDPP-BBT: PCBM shows no evidence of the formation of a midgap CTC state. The FTPS and PC spectra of P3HT:PCBM are also compared. The larger singlet state energy difference of TDPP-BBT and PCBM compared to PDPP-BBT/P3HT and PCBM obliterates the formation of a midgap CTC state resulting in an enhanced photovoltaic efficiency over PDPP-BBT: PCBM. (C) 2011 American Institute of Physics. [doi:10.1063/1.3670043]

Effect of gas injection on drag and surface heat transfer rates for a 30 degrees semi-apex angle blunt body flying at Mach 5.75

Effect of coolant gas injection in the stagnation region on the surface heat transfer rates and aerodynamic drag for a large angle blunt body flying at hypersonic Mach number is reported for two stagnation enthalpies. A 60° apex-angle blunt cone model is employed for this purpose with air injection at the nose through a hole of 2mm diameter. The convective surface heating rates and aerodynamic drag are measured simultaneously using surface mounted platinum thin film sensors and internally mounted accelerometer balance system, respectively. About 35–40% reduction in surface heating rates is observed in the vicinity of stagnation region whereas 15–25% reduction in surface heating rates is felt beyond the stagnation region at stagnation enthalpy of 1.6MJ/kg. The aerodynamic drag expressed in terms of drag coefficient is found to increase by 20% due to the air injection.

Surface pressure and heat transfer measurements in the unsteady separated hypersonic flow field over double cones

Reliable bench mark experimental database in the separated hypersonic flow regime is necessary to validate high resolution CFD codes. In this paper we report the surface pressure and heat transfer measurements carried out on double cones (first cone semi-apex angle = 15, 25 deg.; second cone semi-apex angle= 35, 68 deg.) at hypersonic speeds that will be useful for CFD code validation studies. The surface pressure measurements are carried out at nominal Mach number of 8.35 in the IISc hypersonic wind tunnel. On the other hand the surface heat transfer measurements are carried out at a nominal Mach number of 5.75 in the IISc hypersonic shock tunnel. The flow separation point on the first cone, flow reattachment on the second cone and the wild fluctuation of the transmitted shock on the second cone surface (25/68 deg. double cone) in the presence of severe adverse pressure gradient are some of the flow features captured in the measurements. The results from the CFD studies indicate good agreement with experiments in the attached flow regime while considerable differences are noticeable in the separated flow regime.

Structure-function relationship in serine hydroxymethyltransferase

Serine hydroxymethyltransferase (SHMT), a pyridoxal-5V-phosphate (PLP)-dependent enzyme catalyzes thetetrahydrofolate (H4-folate)- dependent retro-aldol cleavage of serine to form 5,10-methylene H4-folate and glycine. The structure–function relationship of SHMT wasstudied in our laboratory initially by mutation of residues that are conserved in all SHMTs and later by structure-based mutagenesis of residues located in the active site. The analysis of mutants showed that K71, Y72, R80, D89, W110, S202, C203, H304, H306 and H356 residues are involved in maintenance of the oligomeric structure. The mutation of D227, a residue involved in charge relay system, led to the formation of inactive dimers, indicating that this residue has a role in maintaining the tetrameric structure and catalysis. E74, a residue appropriately positioned in the structure of the enzyme to carry out proton abstraction, was shown by characterization of E74Q and E74K mutants to be involved in conversion of the enzyme from an ‘open’ to ‘closed’ conformation rather than proton abstraction from the hydroxylgroup of serine. K256, the residue involved in the formation of Schiffs base with PLP, also plays a crucial role in the maintenance of the tetrameric structure. Mutation of R262 residue established the importance of distal interactions in facilitating catalysis and Y82 is not involved in the formaldehyde transfer via the postulated hemiacetal intermediate but plays a role in stabilizing the quinonoid intermediate.The mutational analysis of scSHMT along with the structure of recombinant Bacillus stearothermophilus SHMT and its substrate(s)complexes was used to provide evidence for a direct transfer mechanism rather than retro-aldol cleavage for the reaction catalyzed by SHMT.

Study on the structure and vibrational spectra of efavirenz conformers using DFT: Comparison to experimental data

Efavirenz, (S)-6-chloro-4-(cyclopropylethynyl)-1,4-dihydro-4-(trifluoromethyl)-2H-3 ,1-benzoxazin-2-one, is an anti HIV agent belonging to the class of the non-nucleoside inhibitors of the HIV-1 virus reverse transcriptase. A systematic quantum chemical study of the possible conformations, their relative stabilities and vibrational spectra of efavirenz has been reported. Structural and spectral characteristics of efavirenz have been studied by vibrational spectroscopy and quantum chemical methods. Density functional theory (DFT) calculations for potential energy curve, optimized geometries and vibrational spectra have been carried out using 6-311++G(d,p) basis sets and B3LYP functionals. Based on these results, we have discussed the correlation between the vibrational modes and the crystalline structure of the most stable form of efavirenz. A complete analysis of the experimental infrared and Raman spectra has been reported on the basis of wavenumber of the vibrational bands and potential energy distribution. The infrared and the Raman spectra of the molecule based on OFT calculations show reasonable agreement with the experimental results. The calculated HOMO and LUMO energies shows that charge transfer occur within the molecule. (C) 2011 Elsevier B.V. All rights reserved.

Distributed Storage Codes With Repair-by-Transfer and Nonachievability of Interior Points on the Storage-Bandwidth Tradeoff

Regenerating codes are a class of recently developed codes for distributed storage that, like Reed-Solomon codes, permit data recovery from any subset of k nodes within the n-node network. However, regenerating codes possess in addition, the ability to repair a failed node by connecting to an arbitrary subset of d nodes. It has been shown that for the case of functional repair, there is a tradeoff between the amount of data stored per node and the bandwidth required to repair a failed node. A special case of functional repair is exact repair where the replacement node is required to store data identical to that in the failed node. Exact repair is of interest as it greatly simplifies system implementation. The first result of this paper is an explicit, exact-repair code for the point on the storage-bandwidth tradeoff corresponding to the minimum possible repair bandwidth, for the case when d = n-1. This code has a particularly simple graphical description, and most interestingly has the ability to carry out exact repair without any need to perform arithmetic operations. We term this ability of the code to perform repair through mere transfer of data as repair by transfer. The second result of this paper shows that the interior points on the storage-bandwidth tradeoff cannot be achieved under exact repair, thus pointing to the existence of a separate tradeoff under exact repair. Specifically, we identify a set of scenarios which we term as ``helper node pooling,'' and show that it is the necessity to satisfy such scenarios that overconstrains the system.