Identification of a discrete intermediate in the assembly disassembly of physalis mottle tymovirus through mutational analysis

Assembly intermediates of icosahedral viruses are usually transient and are difficult to identify. In the present investigation, site-specific and deletion mutants of the coat protein gene of physalis mottle tymovirus (PhMV) were used to delineate the role of specific amino acid residues in the assembly of the virus and to identify intermediates in this process. N-terminal 30, 34, 35 and 39 amino acid deletion and single C-terminal (N188) deletion mutant proteins of PhMV were expressed in Escherichia coli. Site-specific mutants H69A, C75A, W96A, D144N, D144N-T151A, K143E and N188A were also constructed and expressed. The mutant protein lacking 30 amino acid residues from the N terminus self-assembled to T = 3 particles in vivo while deletions of 34, 35 and 39 amino acid residues resulted in the mutant proteins that were insoluble. Interestingly, the coat protein (pR PhCP) expressed using pRSET B vector with an additional 41 amino acid residues at the N terminus also assembled into T = 3 particles that were more compact and had a smaller diameter. These results demonstrate that the amino-terminal segment is flexible and either the deletion or addition of amino acid residues at the N terminus does not affect T = 3 capsid assembly, in contrast, the deletion of even a single residue from the C terminus (PhN188 Delta 1) resulted in capsids that were unstable. These capsids disassembled to a discrete intermediate with a sedimentation coefficent of 19.4 S. However, the replacement of C-terminal asparagine 188 by alanine led to the formation of stable capsids. The C75A and D144N mutant proteins also assembled into capsids that were as stable as the pR PhCP, suggesting that C75A and D144 are not crucial for the T = 3 capsid assembly. pR PhW96A and pR PhD144N-T151A mutant proteins failed to form capsids and were present as heterogeneous aggregates. Interestingly, the pR PhK143E mutant protein behaved in a manner similar to the C-terminal deletion protein in forming unstable capsids. The intermediate with an s value of 19.4 S was the major assembly product of pR PhH69A mutant protein and could correspond to a 30mer. It is possible that the assembly or disassembly is arrested at a similar stage in pR PhN188 Delta 1, pR PhH69A and pR PhK143E mutant proteins.

A global convergence criterion for discrete-time multivariable adaptive systems

The paper deals with the basic problem of adjusting a matrix gain in a discrete-time linear multivariable system. The object is to obtain a global convergence criterion, i.e. conditions under which a specified error signal asymptotically approaches zero and other signals in the system remain bounded for arbitrary initial conditions and for any bounded input to the system. It is shown that for a class of up-dating algorithms for the adjustable gain matrix, global convergence is crucially dependent on a transfer matrix G(z) which has a simple block diagram interpretation. When w(z)G(z) is strictly discrete positive real for a scalar w(z) such that w-1(z) is strictly proper with poles and zeros within the unit circle, an augmented error scheme is suggested and is proved to result in global convergence. The solution avoids feeding back a quadratic term as recommended in other schemes for single-input single-output systems.

New light on the optical equivalence theorem and a new type of discrete diagonal coherent state representation

In many instances we find it advantageous to display a quantum optical density matrix as a generalized statistical ensemble of coherent wave fields. The weight functions involved in these constructions turn out to belong to a family of distributions, not always smooth functions. In this paper we investigate this question anew and show how it is related to the problem of expanding an arbitrary state in terms of an overcomplete subfamily of the overcomplete set of coherent states. This provides a relatively transparent derivation of the optical equivalence theorem. An interesting by-product is the discovery of a new class of discrete diagonal representations.

Scattering theory and the discrete linear optimal control problem

This paper deals with the interpretation of the discrete-time optimal control problem as a scattering process in a discrete medium. We treat the discrete optimal linear regulator, constrained end-point and servo and tracking problems, providing a unified approach to these problems. This approach results in an easy derivation of the desired results as well as several new ones.

Contribution from unresolved discrete sources to the extragalactic gamma-ray background (EGRB)

The origin of the extragalactic gamma-ray background (EGRB) is still an open question, even nearly forty years after its discovery. The emission could originate either from truly diffuse processes or from unresolved point sources. Although the majority of the 271 point sources detected by EGRET (Energetic Gamma Ray Experiment Telescope) are unidentified, of the identified sources, blazars are the dominant candidates. Therefore, unresolved blazars may be considered the main contributor to the EGRB, and many studies have been carried out to understand their distribution, evolution and contribution to the EGRB. Considering that gamma-ray emission comes mostly from jets of blazars and that the jet emission decreases rapidly with increasing jet to line-of-sight angle, it is not surprising that EGRET was not able to detect many large inclination angle active galactic nuclei (AGNs). Though Fermi could only detect a few large inclination angle AGNs during the first three months of its survey, it is expected to detect many such sources in the near future. Since non-blazar AGNs are expected to have higher density as compared to blazars, these could also contribute significantly to the EGRB. In this paper, we discuss contributions from unresolved discrete sources including normal galaxies, starburst galaxies, blazars and off-axis AGNs to the EGRB.

A Joint Source-Channel Coding Scheme for Transmission of Correlated Discrete Sources over a Gaussian Multiple Access Channel

We consider the problem of transmission of correlated discrete alphabet sources over a Gaussian Multiple Access Channel (GMAC). A distributed bit-to-Gaussian mapping is proposed which yields jointly Gaussian codewords. This can guarantee lossless transmission or lossy transmission with given distortions, if possible. The technique can be extended to the system with side information at the encoders and decoder.

A discrete wavelet transform approach to multiresolution complex SAR image generation

We present a signal processing approach using discrete wavelet transform (DWT) for the generation of complex synthetic aperture radar (SAR) images at an arbitrary number of dyadic scales of resolution. The method is computationally efficient and is free from significant system-imposed limitations present in traditional subaperture-based multiresolution image formation. Problems due to aliasing associated with biorthogonal decomposition of the complex signals are addressed. The lifting scheme of DWT is adapted to handle complex signal approximations and employed to further enhance the computational efficiency. Multiresolution SAR images formed by the proposed method are presented.

Block Convolution Using Discrete Trigonometric Transforms and Discrete Fourier Transform

We derive expressions for convolution multiplication properties of discrete cosine transform II (DCT II) starting from equivalent discrete Fourier transform (DFT) representations. Using these expressions, a method for implementing linear filtering through block convolution in the DCT II domain is presented. For the case of nonsymmetric impulse response, additional discrete sine transform II (DST II) is required for implementing the filter in DCT II domain, where as for a symmetric impulse response, the additional transform is not required. Comparison with recently proposed circular convolution technique in DCT II domain shows that the proposed new method is computationally more efficient.

Discrete parameter simulation optimization algorithms with applications to admission control with dependent service times

We propose certain discrete parameter variants of well known simulation optimization algorithms. Two of these algorithms are based on the smoothed functional (SF) technique while two others are based on the simultaneous perturbation stochastic approximation (SPSA) method. They differ from each other in the way perturbations are obtained and also the manner in which projections and parameter updates are performed. All our algorithms use two simulations and two-timescale stochastic approximation. As an application setting, we consider the important problem of admission control of packets in communication networks under dependent service times. We consider a discrete time slotted queueing model of the system and consider two different scenarios - one where the service times have a dependence on the system state and the other where they depend on the number of arrivals in a time slot. Under our settings, the simulated objective function appears ill-behaved with multiple local minima and a unique global minimum characterized by a sharp dip in the objective function in a small region of the parameter space. We compare the performance of our algorithms on these settings and observe that the two SF algorithms show the best results overall. In fact, in many cases studied, SF algorithms converge to the global minimum.

Rendering stiffer walls: a hybrid haptic system using continuous and discrete time feedback

Instability in conventional haptic rendering destroys the perception of rigid objects in virtual environments. Inherent limitations in the conventional haptic loop restrict the maximum stiffness that can be rendered. In this paper we present a method to render virtual walls that are much stiffer than those achieved by conventional techniques. By removing the conventional digital haptic loop and replacing it with a part-continuous and part-discrete time hybrid haptic loop, we were able to render stiffer walls. The control loop is implemented as a combinational logic circuit on an field-programmable gate array. We compared the performance of the conventional haptic loop and our hybrid haptic loop on the same haptic device, and present mathematical analysis to show the limit of stability of our device. Our hybrid method removes the computer-intensive haptic loop from the CPU-this can free a significant amount of resources that can be used for other purposes such as graphical rendering and physics modeling. It is our hope that, in the future, similar designs will lead to a haptics processing unit (HPU).

Optimal threshold policies for admission control in communication networks via discrete parameter stochastic approximation

The problem of admission control of packets in communication networks is studied in the continuous time queueing framework under different classes of service and delayed information feedback. We develop and use a variant of a simulation based two timescale simultaneous perturbation stochastic approximation (SPSA) algorithm for finding an optimal feedback policy within the class of threshold type policies. Even though SPSA has originally been designed for continuous parameter optimization, its variant for the discrete parameter case is seen to work well. We give a proof of the hypothesis needed to show convergence of the algorithm on our setting along with a sketch of the convergence analysis. Extensive numerical experiments with the algorithm are illustrated for different parameter specifications. In particular, we study the effect of feedback delays on the system performance.

Heat transfer in rarefied couette flow on the basis of discrete ordinate method

The method of discrete ordinates, in conjunction with the modified "half-range" quadrature, is applied to the study of heat transfer in rarefied gas flows. Analytic expressions for the reduced distribution function, the macroscopic temperature profile and the heat flux are obtained in the general n-th approximation. The results for temperature profile and heat flux are in sufficiently good accord both with the results of the previous investigators and with the experimental data.

Active vibration suppression of beams with discrete actuators using optimal dynamic inversion

Most of the structural elements like beams, cables etc. are flexible and should be modeled as distributed parameter systems (DPS) to represent the reality better. For large structures, the usual approach of 'modal representation' is not an accurate representation. Moreover, for excessive vibrations (possibly due to strong wind, earthquake etc.), external power source (controller) is needed to suppress it, as the natural damping of these structures is usually small. In this paper, we propose to use a recently developed optinial dynamic inversion technique to design a set of discrete controllers for this purpose. We assume that the control force to the structure is applied through finite number of actuators, which are located at predefined locations in the spatial domain. The method used in this paper determines control forces directly from the partial differential equation (PDE) model of the system. The formulation has better practical significance, both because it leads to a closed form solution of the controller (hence avoids computational issues) as well as because a set of discrete actuators along the spatial domain can be implemented with relative ease (as compared to a continuous actuator).

Protein sequence design on the basis of topology optimization techniques -Using continuous modeling of discrete amino acid types

The notion of optimization is inherent in protein design. A long linear chain of twenty types of amino acid residues are known to fold to a 3-D conformation that minimizes the combined inter-residue energy interactions. There are two distinct protein design problems, viz. predicting the folded structure from a given sequence of amino acid monomers (folding problem) and determining a sequence for a given folded structure (inverse folding problem). These two problems have much similarity to engineering structural analysis and structural optimization problems respectively. In the folding problem, a protein chain with a given sequence folds to a conformation, called a native state, which has a unique global minimum energy value when compared to all other unfolded conformations. This involves a search in the conformation space. This is somewhat akin to the principle of minimum potential energy that determines the deformed static equilibrium configuration of an elastic structure of given topology, shape, and size that is subjected to certain boundary conditions. In the inverse-folding problem, one has to design a sequence with some objectives (having a specific feature of the folded structure, docking with another protein, etc.) and constraints (sequence being fixed in some portion, a particular composition of amino acid types, etc.) while obtaining a sequence that would fold to the desired conformation satisfying the criteria of folding. This requires a search in the sequence space. This is similar to structural optimization in the design-variable space wherein a certain feature of structural response is optimized subject to some constraints while satisfying the governing static or dynamic equilibrium equations. Based on this similarity, in this work we apply the topology optimization methods to protein design, discuss modeling issues and present some initial results.

Geometric quantum computation using fictitious spin-1/2 subspaces of strongly dipolar coupled nuclear spins

Geometric phases have been used in NMR to implement controlled phase shift gates for quantum-information processing, only in weakly coupled systems in which the individual spins can be identified as qubits. In this work, we implement controlled phase shift gates in strongly coupled systems by using nonadiabatic geometric phases, obtained by evolving the magnetization of fictitious spin-1/2 subspaces, over a closed loop on the Bloch sphere. The dynamical phase accumulated during the evolution of the subspaces is refocused by a spin echo pulse sequence and by setting the delay of transition selective pulses such that the evolution under the homonuclear coupling makes a complete 2 pi rotation. A detailed theoretical explanation of nonadiabatic geometric phases in NMR is given by using single transition operators. Controlled phase shift gates, two qubit Deutsch-Jozsa algorithm, and parity algorithm in a qubit-qutrit system have been implemented in various strongly dipolar coupled systems obtained by orienting the molecules in liquid crystal media.