Role of Water in the Enzymatic Catalysis: Study of ATP plus AMP -> 2ADP Conversion by Adenylate Kinase

The catalytic conversion ATP + AMP -> 2ADP by the enzyme adenylate kinase (ADK) involves the binding of one ATP. molecule to the LID domain and one AMP molecule to the NMP domain. The latter is followed by a. phosphate transfer and then the release of two ADP molecules. We have computed a novel two-dimensional configurational free energy surface (2DCFES), with one reaction coordinate each for the LID and the NMP domain motions, while considering explicit water interactions. Our computed 2DCFES clearly reveals the existence of a stable half-open half-closed (HOHC) intermediate stale of the enzyme. Cycling of the enzyme through the HOHC state reduces the conformational free energy barrier for. the reaction by about 20 kJ/mol. We find that the stability of the HOHC state (missed in all earlier studies with implicit solvent model) is largely because of the increase of specific interactions of the polar amino acid side chains with water, particularly with the arginine and the histidine residues. Free energy surface of the LID domain is rather rugged, which can conveniently slow down LID's conformational motion, thus facilitating a new substrate capture after the product release in the catalytic cycle.

Transport coefficients for the shear dynamo problem at small Reynolds numbers

We build on the formulation developed in S. Sridhar and N. K. Singh J. Fluid Mech. 664, 265 (2010)] and present a theory of the shear dynamo problem for small magnetic and fluid Reynolds numbers, but for arbitrary values of the shear parameter. Specializing to the case of a mean magnetic field that is slowly varying in time, explicit expressions for the transport coefficients alpha(il) and eta(iml) are derived. We prove that when the velocity field is nonhelical, the transport coefficient alpha(il) vanishes. We then consider forced, stochastic dynamics for the incompressible velocity field at low Reynolds number. An exact, explicit solution for the velocity field is derived, and the velocity spectrum tensor is calculated in terms of the Galilean-invariant forcing statistics. We consider forcing statistics that are nonhelical, isotropic, and delta correlated in time, and specialize to the case when the mean field is a function only of the spatial coordinate X-3 and time tau; this reduction is necessary for comparison with the numerical experiments of A. Brandenburg, K. H. Radler, M. Rheinhardt, and P. J. Kapyla Astrophys. J. 676, 740 (2008)]. Explicit expressions are derived for all four components of the magnetic diffusivity tensor eta(ij) (tau). These are used to prove that the shear-current effect cannot be responsible for dynamo action at small Re and Rm, but for all values of the shear parameter.

Study of Layering Procedures in Finite-Element Analysis of RC Flexural and Torsional Elements

A new postcracking formulation for concrete, along with both implicit and explicit layering procedures, is used in the analysis of reinforced-concrete (RC) flexural and torsional elements. The postcracking formulation accounts for tension stiffening in concrete along the rebar directions, compression softening in cracked concrete based on either stresses or strains, and aggregate interlock based on crack-confining normal stresses. Transverse shear stresses computed using the layering procedures are included in material model considerations that permit the development of inclined cracks through the RC cross section. Examples of a beam analyzed by both the layering techniques, a torsional element, and a column-slab connection region analyzed by the implicit layering procedure are presented here. The study highlights the primary advantages and disadvantages of each layering approach, identifying the class of problems where the application of either procedure is more suitable.

Critical buckling temperature of single-walled carbon nanotubes embedded in a one-parameter elastic medium based on nonlocal continuum mechanics

In this paper, the critical budding temperature of single-walled carbon nanotubes (SWCNTs), which are embedded in one-parameter elastic medium (Winkler foundation) is estimated under the umbrella of continuum mechanics theory. Nonlocal continuum theory is incorporated into Timoshenko beam model and the governing differential equations of motion are derived. An explicit expression for the non-dimensional critical buckling temperature is also derived in this work. The effect of the nonlocal small scale coefficient, the Winkler foundation parameter and the ratio of the length to the diameter on the critical buckling temperature is investigated in detail. It can be observed that the effects of nonlocal small scale parameter and the Winkler foundation parameter are significant and should be considered for thermal analysis of SWCNTs. The results presented in this paper can provide useful guidance for the study and design of the next generation of nanodevices that make use of the thermal buckling properties of embedded single-walled carbon nanotubes. (C) 2011 Elsevier B.V. All rights reserved.

Exact complex-wave reconstruction in digital holography

We address the problem of exact complex-wave reconstruction in digital holography. We show that, by confining the object-wave modulation to one quadrant of the frequency domain, and by maintaining a reference-wave intensity higher than that of the object, one can achieve exact complex-wave reconstruction in the absence of noise. A feature of the proposed technique is that the zero-order artifact, which is commonly encountered in hologram reconstruction, can be completely suppressed in the absence of noise. The technique is noniterative and nonlinear. We also establish a connection between the reconstruction technique and homomorphic signal processing, which enables an interpretation of the technique from the perspective of deconvolution. Another key contribution of this paper is a direct link between the reconstruction technique and the two-dimensional Hilbert transform formalism proposed by Hahn. We show that this connection leads to explicit Hilbert transform relations between the magnitude and phase of the complex wave encoded in the hologram. We also provide results on simulated as well as experimental data to validate the accuracy of the reconstruction technique. (C) 2011 Optical Society of America

Suboptimal Midcourse Guidance of Interceptors for High-Speed Targets with Alignment Angle Constraint

Using the recently developed computationally efficient model predictive static programming and a closely related model predictive spread control concept, two nonlinear suboptimal midcourse guidance laws are presented in this paper for interceptors engaging against incoming high-speed ballistic missiles. The guidance laws are primarily based on nonlinear optimal control theory, and hence imbed effective trajectory optimization concepts into the guidance laws. Apart from being energy efficient by minimizing the control usage throughout the trajectory (minimum control usage leads to minimum turning, and hence leads to minimum induced drag), both of these laws enforce desired alignment constraints in both elevation and azimuth in a hard-constraint sense. This good alignment during midcourse is expected to enhance the effectiveness of the terminal guidance substantially. Both point mass as well as six-degree-of-freedom simulation results (with a realistic inner-loop autopilot based on dynamic inversion) are presented in this paper, which clearly shows the effectiveness of the proposed guidance laws. It has also been observed that, even with different perturbations of missile parameters, the performance of guidance is satisfactory. A comparison study, with the vector explicit guidance scheme proposed earlier in the literature, also shows that the newly proposed model-predictive-static-programming-based and model-predictive-spread-control-based guidance schemes lead to lesser lateral acceleration demand and lesser velocity loss during engagement.

A Dual Scale Model for Macrosegregation in Alloy Solidification

A numerical approach for coupling the temperature and concentration fields using a micro/macro dual scale model for a solidification problem is presented. The dual scale modeling framework is implemented on a hybrid explicit-implicit solidification scheme. The advantage of this model lies in more accurate consideration of microsegregation occurring at micro-scale using a subgrid model. The model is applied to the case of solidification of a Pb-40% Sn alloy in a rectangular cavity. The present simulation results are compared with the corresponding experimental results reported in the literature, showing improvement in macrosegregation predictions. Subsequently, a comparison of macrosegregation prediction between the results of the present method with those of a parameter model is performed, showing similar trends.

Minimal set of generators for the derivation module of certain monomial curves

Let K be a field of characteristic zero and let m(0),..., m(e-1) be a sequence of positive integers. Let C be an algebroid monomial curve in the affine e-space A(K)(e) defined parametrically by X-0 = T-m0,..., Xe-1 = Tme-1 and let A be the coordinate ring of C. In this paper, we assume that some e - 1 terms of m(0),..., m(e-1) form an arithmetic sequence and construct a minimal set of generators for the derivation module Der(K)(A) of A and write an explicit formula for mu (Der(K)(A)).

Theory of coexisting charge and spin-density waves in (TMTTF)(2)Br, (TMTSF)(2)PF6, and alpha-(BEDT-TTF)(2)MHg(SCN)(4)

Recent experiments indicate that the spin-density waves (SDWs) in (TMTTF)(2)Br, (TMTSF)(2)PF6, and alpha-(BEDT-TTF)(2)MHg(SCN)(4) are highly unconventional and coexist with charge-density waves (CDWs). We present a microscopic theory of this unusual CDW-SDW coexistence. A complete understanding requires the explicit inclusion of strong Coulomb interactions, lattice discreteness, the anisotropic two-dimensional nature of the lattice, and the correct hand filling within the starting Hamiltonian. [S0031-9007(99)08498-7].

A game theoretical multiple resource interaction approach to resource allocation in an air campaign

In this paper we propose a multiple resource interaction model in a game-theoretical framework to solve resource allocation problems in theater level military campaigns. An air raid campaign using SEAD aircraft and bombers against an enemy target defended by air defense units is considered as the basic platform. Conditions for the existence of saddle point in pure strategies is proved and explicit feedback strategies are obtained for a simplified model with linear attrition function limited by resource availability. An illustrative example demonstrates the key features.

Relay Load Balancing in Queued Cooperative Wireless Networks with Rateless Codes

Relay selection combined with buffering of packets of relays can substantially increase the throughput of a cooperative network that uses rateless codes. However, buffering also increases the end-to-end delays due to the additional queuing delays at the relay nodes. In this paper we propose a novel method that exploits a unique property of rateless codes that enables a receiver to decode a packet from non-contiguous and unordered portions of the received signal. In it, each relay, depending on its queue length, ignores its received coded bits with a given probability. We show that this substantially reduces the end-to-end delays while retaining almost all of the throughput gain achieved by buffering. In effect, the method increases the odds that the packet is first decoded by a relay with a smaller queue. Thus, the queuing load is balanced across the relays and traded off with transmission times. We derive explicit necessary and sufficient conditions for the stability of this system when the various channels undergo fading. Despite encountering analytically intractable G/GI/1 queues in our system, we also gain insights about the method by analyzing a similar system with a simpler model for the relay-to-destination transmission times.

On approximately universal schemes for two-hop networks

Full-duplex and half-duplex two-hop networks are considered. Explicit coding schemes which are approximately universal over a class of fading distributions are identified, for the case when the network has either one or two relays.

DMT of multi-hop cooperative networks

Some basic results that help in determining the Diversity-Multiplexing Tradeoff (DMT) of cooperative multihop networks are first identified. As examples, the maximum achievable diversity gain is shown to equal the min-cut between source and sink, whereas the maximal multiplexing gain is shown to equal the minimum rank of the matrix characterizing the MIMO channel appearing across a cut in the network. Two multi-hop generalizations of the two-hop network are then considered, namely layered networks as well as a class of networks introduced here and termed as K-parallel-path (KPP) networks. The DMT of KPP networks is characterized for K > 3. It is shown that a linear DMT between the maximum diversity dmax and the maximum multiplexing gain of 1 is achievable for fully-connected, layered networks. Explicit coding schemes achieving the DMT that make use of cyclic-division-algebra-based distributed space-time codes underlie the above results. Two key implications of the results in the paper are that the half-duplex constraint does not entail any rate loss for a large class of cooperative networks and that simple, amplify-and-forward protocols are often sufficient to attain the optimal DMT.

Machine-tool selection and operation allocation in FMS: solving a fuzzy goal-programming model using a genetic algorithm

The decision-making process for machine-tool selection and operation allocation in a flexible manufacturing system (FMS) usually involves multiple conflicting objectives. Thus, a fuzzy goal-programming model can be effectively applied to this decision problem. The paper addresses application of a fuzzy goal-programming concept to model the problem of machine-tool selection and operation allocation with explicit considerations given to objectives of minimizing the total cost of machining operation, material handling and set-up. The constraints pertaining to the capacity of machines, tool magazine and tool life are included in the model. A genetic algorithm (GA)-based approach is adopted to optimize this fuzzy goal-programming model. An illustrative example is provided and some results of computational experiments are reported.

Multiple scales without center manifold reductions for delay differential equations near Hopf bifurcations

We study small perturbations of three linear Delay Differential Equations (DDEs) close to Hopf bifurcation points. In analytical treatments of such equations, many authors recommend a center manifold reduction as a first step. We demonstrate that the method of multiple scales, on simply discarding the infinitely many exponentially decaying components of the complementary solutions obtained at each stage of the approximation, can bypass the explicit center manifold calculation. Analytical approximations obtained for the DDEs studied closely match numerical solutions.