Recognition of Interaction Interface Residues in Low-Resolution Structures of Protein Assemblies Solely from the Positions of C alpha Atoms

Background: The number of available structures of large multi-protein assemblies is quite small. Such structures provide phenomenal insights on the organization, mechanism of formation and functional properties of the assembly. Hence detailed analysis of such structures is highly rewarding. However, the common problem in such analyses is the low resolution of these structures. In the recent times a number of attempts that combine low resolution cryo-EM data with higher resolution structures determined using X-ray analysis or NMR or generated using comparative modeling have been reported. Even in such attempts the best result one arrives at is the very course idea about the assembly structure in terms of trace of the C alpha atoms which are modeled with modest accuracy. Methodology/Principal Findings: In this paper first we present an objective approach to identify potentially solvent exposed and buried residues solely from the position of C alpha atoms and amino acid sequence using residue type-dependent thresholds for accessible surface areas of C alpha. We extend the method further to recognize potential protein-protein interface residues. Conclusion/Significance: Our approach to identify buried and exposed residues solely from the positions of C alpha atoms resulted in an accuracy of 84%, sensitivity of 83-89% and specificity of 67-94% while recognition of interfacial residues corresponded to an accuracy of 94%, sensitivity of 70-96% and specificity of 58-94%. Interestingly, detailed analysis of cases of mismatch between recognition of interface residues from C alpha positions and all-atom models suggested that, recognition of interfacial residues using C alpha atoms only correspond better with intuitive notion of what is an interfacial residue. Our method should be useful in the objective analysis of structures of protein assemblies when positions of only C alpha positions are available as, for example, in the cases of integration of cryo-EM data and high resolution structures of the components of the assembly.

Geometric Representation of Graphs in Low Dimension Using Axis Parallel Boxes

An axis-parallel k-dimensional box is a Cartesian product R-1 x R-2 x...x R-k where R-i (for 1 <= i <= k) is a closed interval of the form [a(i), b(i)] on the real line. For a graph G, its boxicity box(G) is the minimum dimension k, such that G is representable as the intersection graph of (axis-parallel) boxes in k-dimensional space. The concept of boxicity finds applications in various areas such as ecology, operations research etc. A number of NP-hard problems are either polynomial time solvable or have much better approximation ratio on low boxicity graphs. For example, the max-clique problem is polynomial time solvable on bounded boxicity graphs and the maximum independent set problem for boxicity d graphs, given a box representation, has a left perpendicular1 + 1/c log n right perpendicular(d-1) approximation ratio for any constant c >= 1 when d >= 2. In most cases, the first step usually is computing a low dimensional box representation of the given graph. Deciding whether the boxicity of a graph is at most 2 itself is NP-hard. We give an efficient randomized algorithm to construct a box representation of any graph G on n vertices in left perpendicular(Delta + 2) ln nright perpendicular dimensions, where Delta is the maximum degree of G. This algorithm implies that box(G) <= left perpendicular(Delta + 2) ln nright perpendicular for any graph G. Our bound is tight up to a factor of ln n. We also show that our randomized algorithm can be derandomized to get a polynomial time deterministic algorithm. Though our general upper bound is in terms of maximum degree Delta, we show that for almost all graphs on n vertices, their boxicity is O(d(av) ln n) where d(av) is the average degree.

Low ML-Decoding Complexity, Large Coding Gain, Full-Rate, Full-Diversity STBCs for 2 x 2 and 4 x 2 MIMO Systems

This paper deals with low maximum-likelihood (ML)-decoding complexity, full-rate and full-diversity space-time block codes (STBCs), which also offer large coding gain, for the 2 transmit antenna, 2 receive antenna (2 x 2) and the 4 transmit antenna, 2 receive antenna (4 x 2) MIMO systems. Presently, the best known STBC for the 2 2 system is the Golden code and that for the 4 x 2 system is the DjABBA code. Following the approach by Biglieri, Hong, and Viterbo, a new STBC is presented in this paper for the 2 x 2 system. This code matches the Golden code in performance and ML-decoding complexity for square QAM constellations while it has lower ML-decoding complexity with the same performance for non-rectangular QAM constellations. This code is also shown to be information-lossless and diversity-multiplexing gain (DMG) tradeoff optimal. This design procedure is then extended to the 4 x 2 system and a code, which outperforms the DjABBA code for QAM constellations with lower ML-decoding complexity, is presented. So far, the Golden code has been reported to have an ML-decoding complexity of the order of for square QAM of size. In this paper, a scheme that reduces its ML-decoding complexity to M-2 root M is presented.

High-Rate Space-Time Coded Large-MIMO Systems: Low-Complexity Detection and Channel Estimation

In this paper, we present a low-complexity algorithm for detection in high-rate, non-orthogonal space-time block coded (STBC) large-multiple-input multiple-output (MIMO) systems that achieve high spectral efficiencies of the order of tens of bps/Hz. We also present a training-based iterative detection/channel estimation scheme for such large STBC MIMO systems. Our simulation results show that excellent bit error rate and nearness-to-capacity performance are achieved by the proposed multistage likelihood ascent search (M-LAS) detector in conjunction with the proposed iterative detection/channel estimation scheme at low complexities. The fact that we could show such good results for large STBCs like 16 X 16 and 32 X 32 STBCs from Cyclic Division Algebras (CDA) operating at spectral efficiencies in excess of 20 bps/Hz (even after accounting for the overheads meant for pilot based training for channel estimation and turbo coding) establishes the effectiveness of the proposed detector and channel estimator. We decode perfect codes of large dimensions using the proposed detector. With the feasibility of such a low-complexity detection/channel estimation scheme, large-MIMO systems with tens of antennas operating at several tens of bps/Hz spectral efficiencies can become practical, enabling interesting high data rate wireless applications.

Two-temperature accretion around rotating black holes: a description of the general advective flow paradigm in the presence of various cooling processes to explain low to high luminous sources

We investigate viscous two-temperature accretion disc flows around rotating black holes. We describe the global solution of accretion flows with a sub-Keplerian angular momentum profile, by solving the underlying conservation equations including explicit cooling processes self-consistently. Bremsstrahlung, synchrotron and inverse Comptonization of soft photons are considered as possible cooling mechanisms. We focus on the set of solutions for sub-Eddington, Eddington and super-Eddington mass accretion rates around Schwarzschild and Kerr black holes with a Kerr parameter of 0.998. It is found that the flow, during its infall from the Keplerian to sub-Kepleria transition region to the black hole event horizon, passes through various phases of advection: the general advective paradigm to the radiatively inefficient phase, and vice versa. Hence, the flow governs a much lower electron temperature similar to 10(8)-10(9.5) K, in the range of accretion rate in Eddington units 0.01 less than or similar to (M) over dot less than or similar to 100, compared to the hot protons of temperature similar to 10(10.2)-10(11.8) K. Therefore, the solution may potentially explain the hard X-rays and gamma-rays emitted from active galactic nuclei (AGNs) and X-ray binaries. We then compare the solutions for two different regimes of viscosity. We conclude that a weakly viscous flow is expected to be cooling dominated, particularly at the inner region of the disc, compared to its highly viscous counterpart, which is radiatively inefficient. With all the solutions in hand, we finally reproduce the observed luminosities of the underfed AGNs and quasars (e. g. Sgr A*) to ultraluminous X-ray sources (e. g. SS433), at different combinations of input parameters, such as the mass accretion rate and the ratio of specific heats. The set of solutions also predicts appropriately the luminosity observed in highly luminous AGNs and ultraluminous quasars (e. g. PKS 0743-67).

Ce0.67Cr0.33O2.11: A New Low-Temperature O-2 Evolution Material and H-2 Generation Catalyst by Thermochemical Splitting of Water

Ce0.67Cr0.33O2.11 was synthesized by hydrothermal method using diethylenetriamine as complexing agent (Chem. Mater. 2008, 20, 7268). Ce0.67Cr0.33O2.11 being the only compound likes UO2+delta to have excess oxygen, it releases a large proportion of its lattice oxygen (0.167 M [O]/mole of compound) at relatively low temperature (465 degrees C) directly and it has been utilized for generation of H-2 by thermo-splitting of water. An almost stoichiometric amount of H-2 (0.152 M/Mole of compound) is generated at much lower temperature (65 degrees C). There is an almost comparable amount of oxygen release and hydrogen generation over this material at very low temperature comparedto other CeO2-MOx (Mn, Fe, Cu, and Ni) mixed-oxide solid solutions (O-2 evolution >= 1300 degrees C and H-2 generation at 1000 degrees C). The reversible nature of oxygen release and intake of this material is attributed to its fluorite Structure and coupling between the Ce4+/Ce3+ and Cr4+/6+/Cr3+ redox couples. Compound shows reversible oxygen release and intake by H2O absorption and subsequent hydrogen release to gain parent structure and hence this material can be utilized for generation of H-2 at very low temperature by thermo-chemical splitting of water.

Low-lying states of transverse substituted trans-polyacetylene and trans-polyacetylene: A comparative DMRG study

The density-matrix renormalization group (DMRG) method is used for a comparative study of low-lying excitations in trans-polyacetylene (t-PA) and transversely substituted t-PA (TS-t-PA). We have employed the Pariser-Parr-Pople model Hamiltonian which incorporates long-range electronic correlations to model these systems. We find some fundamental differences in the excited states of the t-PA and TS-t-PA. We find that the lowest two-photon allowed excited state in TS-t-PA is not made up of two triplet excitons and the gap to this state is nonzero even for undimerized chains in the thermodynamic limit. Contrary to earlier results for the Hubbard model, we find that the lowest two-photon state is always below the first optically allowed state in all the systems studied here making TS-t-PA systems only weakly fluorescent materials. Nonresonant tumbling averaged linear and third harmonic generation optic coefficients of TS-t-PA systems are also much smaller than that of t-PA.

A Low-Complexity Near-ML Performance Achieving Algorithm for Large MIMO Detection

In this paper, we present a low-complexity, near maximum-likelihood (ML) performance achieving detector for large MIMO systems having tens of transmit and receive antennas. Such large MIMO systems are of interest because of the high spectral efficiencies possible in such systems. The proposed detection algorithm, termed as multistage likelihood-ascent search (M-LAS) algorithm, is rooted in Hopfield neural networks, and is shown to possess excellent performance as well as complexity attributes. In terms of performance, in a 64 x 64 V-BLAST system with 4-QAM, the proposed algorithm achieves an uncoded BER of 10(-3) at an SNR of just about 1 dB away from AWGN-only SISO performance given by Q(root SNR). In terms of coded BER, with a rate-3/4 turbo code at a spectral efficiency of 96 bps/Hz the algorithm performs close to within about 4.5 dB from theoretical capacity, which is remarkable in terms of both high spectral efficiency as well as nearness to theoretical capacity. Our simulation results show that the above performance is achieved with a complexity of just O(NtNt) per symbol, where N-t and N-tau denote the number of transmit and receive antennas.

Algebraic distributed space-time codes with low ML decoding complexity

"Extended Clifford algebras" are introduced as a means to obtain low ML decoding complexity space-time block codes. Using left regular matrix representations of two specific classes of extended Clifford algebras, two systematic algebraic constructions of full diversity Distributed Space-Time Codes (DSTCs) are provided for any power of two number of relays. The left regular matrix representation has been shown to naturally result in space-time codes meeting the additional constraints required for DSTCs. The DSTCs so constructed have the salient feature of reduced Maximum Likelihood (ML) decoding complexity. In particular, the ML decoding of these codes can be performed by applying the lattice decoder algorithm on a lattice of four times lesser dimension than what is required in general. Moreover these codes have a uniform distribution of power among the relays and in time, thus leading to a low Peak to Average Power Ratio at the relays.

A non-orthogonal cooperative multiple access (NCMA) protocol and low ML decoding complexity codes

A half-duplex constrained non-orthogonal cooperative multiple access (NCMA) protocol suitable for transmission of information from N users to a single destination in a wireless fading channel is proposed. Transmission in this protocol comprises of a broadcast phase and a cooperation phase. In the broadcast phase, each user takes turn broadcasting its data to all other users and the destination in an orthogonal fashion in time. In the cooperation phase, each user transmits a linear function of what it received from all other users as well as its own data. In contrast to the orthogonal extension of cooperative relay protocols to the cooperative multiple access channels wherein at any point of time, only one user is considered as a source and all the other users behave as relays and do not transmit their own data, the NCMA protocol relaxes the orthogonality built into the protocols and hence allows for a more spectrally efficient usage of resources. Code design criteria for achieving full diversity of N in the NCMA protocol is derived using pair wise error probability (PEP) analysis and it is shown that this can be achieved with a minimum total time duration of 2N - 1 channel uses. Explicit construction of full diversity codes is then provided for arbitrary number of users. Since the Maximum Likelihood decoding complexity grows exponentially with the number of users, the notion of g-group decodable codes is introduced for our setup and a set of necesary and sufficient conditions is also obtained.

Low power pipelined TCAM employing mismatch dependent power allocation technique

This paper presents design of a Low power 256x72 bit TCAM in 0.13um CMOS technology. In contrast to conventional Match line (ML) sensing scheme in which equal power is consumed irrespective of match or mismatch, the ML scheme employed in this design allocates less power to match decisions involving a large number of mismatched bits. Typically, the probability of mismatch is high so this scheme results in significant CAM power reduction. We propose to use this technique along with pipelining of search operation in which the MLs are broken into several segments. Since most words fail to match in first segment, the search operation for subsequent segments is discontinued, resulting in further reduction in power consumption. The above architecture provides 70% power reduction while performing search in 3ns.

Low PAPR STBCs from Complex Partial-Orthogonal Designs (CPODs)

Space-time codes from complex orthogonal designs (CODs) with no zero entries offer low Peak to Average power ratio (PAPR) and avoid the problem of turning off antennas. But CODs for 2(a) antennas with a + 1 complex variables, with no zero entries are not known in the literature for a >= 4. In this paper, a method of obtaining no zero entry (NZE) codes, called Complex Partial-Orthogonal Designs (CPODs), for 2(a+1) antennas whenever a certain type of NZE code exists for 2(a) antennas is presented. This is achieved with slight increase in the ML decoding complexity for regular QAM constellations and no increase for other complex constellations. Since NZE CODs have been constructed recently for 8 antennas our method leads to NZE CPODs for 16 antennas. Moreover, starting from certain NZE CPODs for n antennas, a construction procedure is given to obtain NZE CPODs for 2n antennas. The class of CPODs do not offer full-diversity for all complex constellations. For the NZE CPODs presented in the paper, conditions on the signal sets which will guarantee full-diversity are identified. Simulations results show that bit error performance of our codes under average power constraint is same as that of the CODs and superior to CODs under peak power constraint.

Low correlation sequences over AM-PSK and QAM alphabets

A construction for a family of sequences over the 8-ary AM-PSK constellation that has maximum nontrivial correlation magnitude bounded as theta(max) less than or similar to root N is presented here. The famfly is asymptotically optimal with respect to the Welch bound on maximum magnitude of correlation. The 8-ary AM-PSK constellation is a subset of the 16-QAM constellation. We also construct two families of sequences over 16-QAM with theta(max) less than or similar to root 2 root N. These families are constructed by interleaving sets of sequences. A construction for a famBy of low-correlation sequences over QAM alphabet of size 2(2m) is presented with maximum nontrivial normalized correlation parameter bounded above by less than or similar to a root N, where N is the period of the sequences in the family and where a ranges from 1.61 in the case of 16-QAM modulation to 2.76 for large m. When used in a CDMA setting, the family will permit each user to modulate the code sequence with 2m bits of data. Interestingly, the construction permits users on the reverse link of the CDMA channel to communicate using varying data rates by switching between sequence famflies; associated to different values of the parameter m. Other features of the sequence families are improved Euclidean distance between different data symbols in comparison with PSK signaling and compatibility of the QAM sequence families with sequences belonging to the large quaternary sequence families {S(p)}.

Low-temperature Er3+ emission in Ge-S-Ga glasses excited by host absorption

The photoluminescence (PL) of a series of (GeS2)(80)(Ga2S3)(20) glasses doped with different amounts of Er (0.17, 0.35, 0.52, 1.05 and 1.39 at.%) at 77 and 4.2 K has been studied. The influence of the temperature on the emission cross-section of the PL bands at -> 1540, 980 and 820 nm under host excitation has been defined. A quenching effect of the host photoluminescence has been established from the compositional dependence of the PL intensity. It has been found that the present Er3+-doped Ge-S-Ga glasses posses PL lifetime values about 3.25 ms. (C) 2007 Elsevier B.V. All rights reserved.

Highly biocompatible and water-dispersible, amine functionalized magnetite nanoparticles, prepared by a low temperature, air-assisted polyol process: a new platform for bio-separation and diagnostics

A low temperature polyol process, based on glycolaldehyde mediated partial reduction of FeCl3 center dot 6H(2)O at 120 degrees C in the presence of sodium acetate as an alkali source and 2,2'-(ethylenedioxy)-bis-(ethylamine) as an electrostatic stabilizer has been used for the gram-scale preparation of biocompatible, water-dispersible, amine functionalized magnetite nanoparticles (MNPs) with an average diameter of 6 +/- 0.75 nm. With a reasonably high magnetization (37.8 e.m.u.) and amine groups on the outer surface of the nanoparticles, we demonstrated the magnetic separation and concentration implications of these ultrasmall particles in immunoassay. MRI studies indicated that these nanoparticles had the desired relaxivity for T-2 contrast enhancement in vivo. In vitro biocompatibility, cell uptake and MR imaging studies established that these nanoparticles were safe in clinical dosages and by virtue of their ultrasmall sizes and positively charged surfaces could be easily internalized by cancer cells. All these positive attributes make these functional nanoparticles a promising platform for further in vitro and in vivo evaluations.