Comparison of Prediction Based LSF Quantization Methods using Split VQ

Further improvement in performance, to achieve near transparent quality LSF quantization, is shown to be possible by using a higher order two dimensional (2-D) prediction in the coefficient domain. The prediction is performed in a closed-loop manner so that the LSF reconstruction error is the same as the quantization error of the prediction residual. We show that an optimum 2-D predictor, exploiting both inter-frame and intra-frame correlations, performs better than existing predictive methods. Computationally efficient split vector quantization technique is used to implement the proposed 2-D prediction based method. We show further improvement in performance by using weighted Euclidean distance.

Solution NMR studies of acetohydroxy acid synthase I: Identification of the sites of inter-subunit interactions using multidimensional NMR methods

The novel multidomain organization in the multimeric Escherichia coli AHAS I (ilvBN) enzyme has been dissected to generate polypeptide fragments. These fragments when cloned, expressed and purified reassemble in the presence of cofactors to yield a catalytically competent enzyme. Structural characterization of AHAS has been impeded due to the fact that the holoenzyme is prone to dissociation leading to heterogeneity in samples. Our approach has enabled the structural characterization using high-resolution nuclear magnetic resonance methods. Near complete sequence specific NMR assignments for backbone H-N, N-15, C-13 alpha and C-13(beta) atoms of the FAD binding domain of ilvB have been obtained on samples isotopically enriched in H-2, C-13 and N-15. The secondary structure determined on the basis of observed C-13(alpha) secondary chemical shifts and sequential NOEs indicates that the secondary structure of the FAD binding domain of E. coli AHAS large Subunit (ilvB) is similar to the structure of this domain in the catalytic subunit of yeast AHAS. Protein-protein interactions involving the regulatory subunit (ilvN) and the domains of the catalytic subunit (ilvB) were studied using circular dichroic and isotope edited solution nuclear magnetic resonance spectroscopic methods. Observed changes in circular dichroic spectra indicate that the regulatory subunit (ilvN) interacts with ilvB alpha and ilvB beta domains of the catalytic subunit and not with the ilvB gamma domain. NMR chemical shift mapping methods show that ilvN binds close to the FAD binding site in ilvB beta and proximal to the intrasubunit ilvB alpha/ilvB beta domain interface. The implication of this interaction on the role of the regulatory subunit oil the activity of the holoenzyme is discussed. NMR studies of the regulatory domains show that these domains are structured in solution. Preliminary evidence for the interaction of ilvN with the metabolic end product of the pathway, viz., valine is also presented.

Spatial correlation in grain misorientation distribution

Grain misorientation was studied in relation to the nearest neighbor's mutual distance using electron back-scattered diffraction measurements. The misorientation correlation function was defined as the probability density for the occurrence of a certain misorientation between pairs of grains separated by a certain distance. Scale-invariant spatial correlation between neighbor grains was manifested by a power law dependence of the preferred misorientation vs. inter-granular distance in various materials after diverse strain paths. The obtained negative scaling exponents were in the range of -2 +/- 0.3 for high-angle grain boundaries. The exponent decreased in the presence of low-angle grain boundaries or dynamic recrystallization, indicating faster decay of correlations. The correlations vanished in annealed materials. The results were interpreted in terms of lattice incompatibility and continuity conditions at the interface between neighboring grains. Grain-size effects on texture development, as well as the implications of such spatial correlations on texture modeling, were discussed.

Ligand dependent intra and inter subunit communication in human tryptophanyl tRNA synthetase as deduced from the dynamics of structure networks

Homodimeric protein tryptophanyl tRNA synthetase (TrpRS) has a Rossmann fold domain and belongs to the 1c subclass of aminoacyl tRNA synthetases. This enzyme performs the function of acylating the cognate tRNA. This process involves a number of molecules (2 protein subunits, 2 tRNAs and 2 activated Trps) and thus it is difficult to follow the complex steps in this process. Structures of human TrpRS complexed with certain ligands are available. Based on structural and biochemical data, mechanism of activation of Trp has been speculated. However, no structure has yet been solved in the presence of both the tRNA(Trp) and the activated Trp (TrpAMP). In this study, we have modeled the structure of human TrpRS bound to the activated ligand and the cognate tRNA. In addition, we have performed molecular dynamics (MD) simulations on these models as well as other complexes to capture the dynamical process of ligand induced conformational changes. We have analyzed both the local and global changes in the protein conformation from the protein structure network (PSN) of MD snapshots, by a method which was recently developed in our laboratory in the context of the functionally monomeric protein, methionyl tRNA synthetase. From these investigations, we obtain important information such as the ligand induced correlation between different residues of this protein, asymmetric binding of the ligands to the two subunits of the protein as seen in the crystal structure analysis, and the path of communication between the anticodon region and the aminoacylation site. Here we are able to elucidate the role of dimer interface at a level of detail, which has not been captured so far.

Inter-helical Interactions in Membrane Proteins: Analysis Based on the Local Backbone Geometry and the Side Chain Interactions

The availability of a significant number of the Structures of helical membrane proteins has prompted us to investigate the mode of helix-helix packing. In the present study, we have considered a dataset of alpha-helical membrane proteins representing Structures solved from all the known superfamilies. We have described the geometry of all the helical residues in terms of local coordinate axis at the backbone level. Significant inter-helical interactions have been considered as contacts by weighing the number of atom-atom contacts, including all the side-chain atoms. Such a definition of local axis and the contact criterion has allowed us to investigate the inter-helical interaction in a systematic and quantitative manner. We show that a single parameter (designated as alpha), which is derived from the parameters representing the Mutual orientation of local axes, is able to accurately Capture the details of helix-helix interaction. The analysis has been carried Out by dividing the dataset into parallel, anti-parallel, and perpendicular orientation of helices. The study indicates that a specific range of alpha value is preferred for interactions among the anti-parallel helices. Such a preference is also seen among interacting residues of parallel helices, however to a lesser extent. No such preference is seen in the case of perpendicular helices, the contacts that arise mainly due to the interaction Of Surface helices with the end of the trans-membrane helices. The Study Supports the prevailing view that the anti-parallel helices are well packed. However, the interactions between helices of parallel orientation are non-trivial. The packing in alpha-helical membrane proteins, which is systematically and rigorously investigated in this study, may prove to be useful in modeling of helical membrane proteins.

Investigation of inter-ion interactions in N,N,N',N'-tetramethylethylenediammonium dithiocyanate via experimental and theoretical charge density studies

The crystal structure of the N,N,N',N'-tetramethylethylenediammonium dithiocyanate salt has been examined by experimental charge density studies from high-resolution X-ray diffraction data. The corresponding results are compared with multipole refinements, using theoretical structure factors obtained from a periodic density functional theory calculation at the B3LYP level with a 6-31G** basis set. The salt crystallizes in space group P (1) over bar and contains only a single ion pair with an inversion center in the cation. The salt has thus one unique classical N+-H center dot center dot center dot(NCS)(-) hydrogen bond but also has six other weaker interactions: four C-H center dot center dot center dot S, one C-H center dot center dot center dot N, and one C-H center dot center dot center dot C-pi. The nature of all these interactions has been examined topologically using Bader's quantum theory of "atoms in molecules" and all eight of the Koch-Popelier criteria. The experimental and theoretical approaches agree well and both show that the inter-ion interactions, even in this simplest of systems, play an integrated and complex role in the packing of the ions in the crystal. Electrostatic potential maps are derived from experimental charge densities. This is the first time such a system has been examined in detail by these methods.

Vibrational phase relaxation of O–H stretch in bulk water: Role of large amplitude angular jumps and negative cross-correlations among the forces on the O–H bond

The ultrafast vibrational phase relaxation of O–H stretch in bulk water is investigated in molecular dynamics simulations. The dephasing time (T2) of the O–H stretch in bulk water calculated from the frequency fluctuation time correlation function (Cω(t)) is in the range of 70–80 femtosecond (fs), which is comparable to the characteristic timescale obtained from the vibrational echo peak shift measurements using infrared photon echo [W.P. de Boeij, M.S. Pshenichnikov, D.A. Wiersma, Ann. Rev. Phys. Chem. 49 (1998) 99]. The ultrafast decay of Cω(t) is found to be responsible for the ultrashort T2 in bulk water. Careful analysis reveals the following two interesting reasons for the ultrafast decay of Cω(t). (A) The large amplitude angular jumps of water molecules (within 30–40 fs time duration) provide a large scale contribution to the mean square vibrational frequency fluctuation and gives rise to the rapid spectral diffusion on 100 fs time scale. (B) The projected force, due to all the atoms of the solvent molecules on the oxygen (FO(t)) and hydrogen (FH(t)) atom of the O–H bond exhibit a large negative cross-correlation (NCC). We further find that this NCC is partly responsible for a weak, non-Arrhenius temperature dependence of the dephasing rate.

Safeguarding against new privacy threats in inter-enterprise collaboration environments

Inter-enterprise collaboration has become essential for the success of enterprises. As competition increasingly takes place between supply chains and networks of enterprises, there is a strategic business need to participate in multiple collaborations simultaneously. Collaborations based on an open market of autonomous actors set special requirements for computing facilities supporting the setup and management of these business networks of enterprises. Currently, the safeguards against privacy threats in collaborations crossing organizational borders are both insufficient and incompatible to the open market. A broader understanding is needed of the architecture of defense structures, and privacy threats must be detected not only on the level of a private person or enterprise, but on the community and ecosystem levels as well. Control measures must be automated wherever possible in order to keep the cost and effort of collaboration management reasonable. This article contributes to the understanding of the modern inter-enterprise collaboration environment and privacy threats in it, and presents the automated control measures required to ensure that actors in inter-enterprise collaborations behave correctly to preserve privacy.

A Model for Creating Strategic Alliances. A Study of Inter-firm Cooperation in the North European ICT Sector

In this study, it is argued that the view on alliance creation presented in the current academic literature is limited, and that using a learning approach helps to explain the dynamic nature of alliance creation. The cases in this study suggest that a wealth of inefficiency elements can be found in alliance creation. These elements can further be divided into categories, which help explain the dynamics of alliance creation. The categories –combined with two models brought forward by the study– suggest that inefficiency can be avoided through learning during the creation process. Some elements are especially central to this argumentation. First, the elements related to the clarity and acceptance of the strategy of the company, the potential lack of an alliance strategy and the elements related to changes in the strategic context. Second, the elements related to the length of the alliance creation processes and the problems a long process entails. It is further suggested that the different inefficiency elements may create a situation, where the alliance creation process is –sequentially and successfully– followed to the end, but where the different inefficiencies create a situation where the results are not aligned with the strategic intent. The proposed solution is to monitor and assess the risk for inefficiency elements during the alliance creation process. The learning, which occurs during the alliance creation process as a result of the monitoring, can then lead to realignments in the process. This study proposes a model to mitigate the risk related to the inefficiencies. The model emphasizes creating an understanding of the other alliance partner’s business, creating a shared vision, using pilot cooperation and building trust within the process. An analytical approach to assessing the benefits of trust is also central in this view. The alliance creation approach suggested by this study, which emphasizes trust and pilot cooperation, is further critically reviewed against contracting as a way to create alliances.

Managing Project Business Development: an Inter-Organizational and Intra-Organizational Perspective (summary section only)

The driving force behind this study is the gap between the reality of the firms engaged in project business and the available studies covering project management and business process development. Previous studies show that project-based organizations were ‘immature’ in terms of the project-management ‘maturity model’, as few firms were found to be optimizing processes. Even within those, very little attention was paid to combine inter-organizational and intra-organizational perspectives. In this study an effort is made to elaborate some thoughts and views on project management, which interrelate firms’ external and internal activities. In line with the integration, the dissertation uses an approach to the management of project-business interdependencies in the networks of actors, activities and resources. Firstly, the study develops an understanding for inter-organizational perspectives by exploring the complementarities of process activities in the basic development of project business. It presents a framework that is elaborated on the basis of the reciprocal interactions of activities within and outside the organization—thus providing a coherent basis for continuous business-process improvement. In addition, the study presents new tools that can be used to develop project-business processes in each of its functional areas. The research demonstrates how project-business activities can be optimized using the right resources at the right time with the right actors and the right actions. The selected five articles included in this dissertation explain the basic framework for the development of project business. Each paper covers various aspects of inter-organizational and intra-organizational perspectives for project management. The study develops a valuable and procedural model for business-process improvement using the Delphi method that can be used not only in academia but also as a guide for practitioners that takes them through a series of well-defined steps when making informed, consistent and efficient changes to their business processes.

Analysis of Dynamic Heterogeneity in a Glass Former from the Spatial Correlations of Mobility

The growth of characteristic length scales associated with dynamic heterogeneity in glass-forming liquids is investigated in an extensive computational study of a four-point, time-dependent structure factor defined from spatial correlations of mobility, for a model liquid for system sizes extending up to 351 232 particles, in constant-energy and constant-temperature ensembles. Our estimates for dynamic correlation lengths and susceptibilities are consistent with previous results from finite size scaling. We find scaling exponents that are inconsistent with predictions from inhomogeneous mode coupling theory and a recent simulation confirmation of these predictions.

Coupled ocean-atmosphere inter-decadal modes in the tropics

Homogencous upper air data for 50 years (1949-1998) from the National Centers for Environmental Prediction/National Center for Atmospheric Research (NCEP/NCAR) reanalysis project, sea surface temperatures and sea level pressure are used to bring out the three dimensional structure of two dominant decadal/multi-decadal variations in the tropics. The global three dimensional modes represent generalized forms of inter-decadal modes studied earlier only with surface data. In the vertical, both modes show approximate first baroclinic structures over the tropics. The Walker circulation associated with the multidecadal mode has a wavenumber two structure in the zonal direction. It is shown that the magnitude of major ascending and descending motions associated with the multi-decadal Hadley and Walker circulations, are comparable to those associated with the dominant inter-annual mode. Implications of these large scale global circulations associated with the low frequency oscillations in modulating regional climate on a inter-annual time scale are discussed.

Effects of electron correlations in conjugated organic molecules and solids

The discrepancies between the non-interacting models and experimental results for conjugated systems is highlighted in this brief review. The interacting model hamiltonians correctly give the forbidden singlet state below the optical gap in polyenes and also explain both the nonvanishing optical gap in polyacetylenes and the vanishing optical gap in symmetric cyanine dyes. The negative spin densities in polyene radicals is also understood in terms of a correlated picture. The role of electron-electron interactions in other strongly correlated systems, such as polydiacetylene and mixed and segregated stack charge transfer solids, are also briefly discussed.