Soumyendu Raha

Parallel implementation of AutoDock

Computational docking of ligands to protein structures is a key step in structure-based drug design. Currently, the time required for each docking run is high and thus limits the use of docking in a high-throughput manner, warranting parallelization of docking algorithms. AutoDock, a widely used tool, has been chosen for parallelization. Near-linear increases in speed were observed with 96 processors, reducing the time required for docking ligands to HIV-protease from 81 min, as an example, on a single IBM Power-5 processor ( 1.65 GHz), to about 1 min on an IBM cluster, with 96 such processors. This implementation would make it feasible to perform virtual ligand screening using AutoDock.

Composite Guidance for Impact Angle Control Against Higher Speed Targets

In the literature, the impact angle control problem has been addressed mostly against lower speed or stationary targets. However, in the current defense scenario, targets of much higher speeds than interceptors are a reality. Moreover, approaching a higher speed target from a specified angle is important for effective seeker acquisition and enhanced warhead effectiveness. This paper proposes a composite proportional navigation guidance law using a combination of the standard proportional navigation and the recently proposed retroproportional navigation guidance laws for intercepting higher speed nonmaneuvering targets at specified impact angles in three-dimensional engagements. An analysis of the set of achievable impact angles by the composite proportional navigation guidance law is presented. It is shown that there exists an impulse bias that, when added to the composite proportional navigation guidance command, expands this set further by reversing the direction of the line-of-sight angular rotation vector. A bound on the magnitude of the bias is also derived. Finally, an implementation of this impulse bias, in the form of a series of pulses, is proposed and analyzed. Simulation results are also presented to support the analysis.

Capturability of Augmented Pure Proportional Navigation Guidance Against Time-Varying Target Maneuvers

This paper proposes a variation of the pure proportional navigation guidance law, called augmented pure proportional navigation, to account for target maneuvers, in a realistic nonlinear engagement geometry, and presents its capturability analysis. These results are in contrast to most work in the literature on augmented proportional navigation laws that consider a linearized geometry imposed upon the true proportional navigation guidance law. Because pure proportional navigation guidance law is closer to a realistic implementation of proportional navigation than true proportional navigation law, and any engagement process is predominantly nonlinear, the results obtained in this paper are more realistic than any available in the literature. Sufficient conditions on speed ratio, navigation gain, and augmentation parameter for capturability, and boundedness of lateral acceleration, against targets executing piecewise continuous maneuvers with time, are obtained. Further, based on a priori knowledge of the maximum maneuver capability of the target, a significant simplification of the guidance law is proposed in this paper. The proposed guidance law is also shown to require a shorter time of interception than standard pure proportional navigation and augmented proportional navigation. To remove chattering in the interceptor maneuver at the end phase of the engagement, a hybrid guidance law using augmented pure proportional navigation and pure proportional navigation is also proposed. Finally, the guaranteed capture zones of standard and augmented pure proportional navigation guidance laws against maneuvering targets are analyzed and compared in the normalized relative velocity space. It is shown that the guaranteed capture zone expands significantly when augmented pure proportional navigation is used instead of pure proportional navigation. Simulation results are given to support the theoretical findings.

Rollover-Preventive Force Synthesis at Active Suspensions in a Vehicle Performing a Severe Maneuver With Wheels Lifted Off

Among the intelligent safety technologies for road vehicles, active suspensions controlled by embedded computing elements for preventing rollover have received a lot of attention. The existing models for synthesizing and allocating forces in such suspensions are conservatively based on the constraints that are valid until no wheels lift off the ground. However, the fault tolerance of the rollover-preventive systems can be enhanced if the smart/active suspensions can intervene in the more severe situation in which the wheels have just lifted off the ground. The difficulty in computing control in the last situation is that the vehicle dynamics then passes into the regime that yields a model involving disjunctive constraints on the dynamics. Simulation of dynamics with disjunctive constraints in this context becomes necessary to estimate, synthesize, and allocate the intended hardware realizable forces in an active suspension. In this paper, we give an algorithm for the previously mentioned problem by solving it as a disjunctive dynamic optimization problem. Based on this, we synthesize and allocate the roll-stabilizing time-dependent active suspension forces in terms of sensor output data. We show that the forces obtained from disjunctive dynamics are comparable with existing force allocations and, hence, are possibly realizable in the existing hardware framework toward enhancing the safety and fault tolerance.

Unified Time-to-Go Algorithms for Proportional Navigation Class of Guidance

This paper presents unified time-to-go algorithms that achieve generalizations in several aspects. In particular, they are applicable to the general class of proportional navigation guidance laws in which the navigation gain ranges from negative to positive values. They are also applicable to a general class of targets: stationary targets, targets with speeds lower than the interceptor, and targets with speeds that are several times higher than the interceptor. Finally, they are applicable to general three-dimensional engagements that subsume the traditional planar engagements addressed in the literature. First, a time-to-go algorithm is derived as a closed-form approximation function of range, navigation gain, and heading error. This is followed by an algorithm that is based on simple recursive numerical computations. In terms of accuracy over the engagement period, the first is found to be comparable, and sometimes better, with respect to existing algorithms, while the latter is found to perform the best in almost all cases.

Micro-architectural Enhancements in Distributed Memory CGRAs for LU and QR Factorizations

LU and QR factorizations are the computationally dear part of many applications ranging from large scale simulations (e.g. Computational fluid dynamics) to augmented reality. These factorizations exhibit time complexity of O (n3) and are difficult to accelerate due to presence of bandwidth bound kernels, BLAS-1 or BLAS-2 (level-1 or level-2 Basic Linear Algebra Subprograms) along with compute bound kernels (BLAS-3, level-3 BLAS). On the other hand, Coarse Grained Reconfigurable Architectures (CGRAs) have gained tremendous popularity as accelerators in embedded systems due to their flexibility and ease of use. Provisioning these accelerators in High Performance Computing (HPC) platforms is the research challenge wrestled by the computer scientists. We consider a CGRA environment in which several Compute Elements (CEs) enhanced with Custom Functional Units (CFUs) are interconnected over a Network-on-Chip (NoC). In this paper, we carry out extensive micro-architectural exploration for accelerating core kernels like Matrix Multiplication (MM) (BLAS-3) for LU and QR factorizations. Our 5 different design enhancements lead to the reduction in the latency of BLAS-3 kernels. On a stand-alone CFU, we achieve up to 8x speed-up for MM. A commensurate improvement is observed for MM in a CGRA environment. We achieve better GF LOP S/mm2 compared to recent implementations.

Capturability Analysis of a 3-D Retro-PN Guidance Law for Higher Speed Nonmaneuvering Targets

This brief presents the capturability analysis of a 3-D Retro-proportional navigation (Retro-PN) guidance law, which uses a negative navigation constant (as against the usual positive one), for intercepting targets having higher speeds than interceptors. This modification makes it possible to achieve collision conditions that were inaccessible to the standard PN law. A modified polar coordinate system, that makes the model more compact, is used in this brief for capturability analysis. In addition to the ratio of the target to interceptor speeds, the directional cosines of the interceptor, and target velocity vectors play a crucial role in the capturability. The existence of nontrivial capture zone of the Retro-PN guidance law and necessary and sufficient conditions, for capturing the target in finite time, are presented. A sufficient condition on the navigation constant is derived to ensure finiteness of the line-of-sight turn rate. The results are more extensive than those available for 2-D engagements, which can be obtained as special cases of this brief. Simulation results are given to support the analytical results.

Performance metrics in a hybrid MPI-OpenMP based molecular dynamics simulation with short-range interactions

We discuss the computational bottlenecks in molecular dynamics (MD) and describe the challenges in parallelizing the computation-intensive tasks. We present a hybrid algorithm using MPI (Message Passing Interface) with OpenMP threads for parallelizing a generalized MD computation scheme for systems with short range interatomic interactions. The algorithm is discussed in the context of nano-indentation of Chromium films with carbon indenters using the Embedded Atom Method potential for Cr-Cr interaction and the Morse potential for Cr-C interactions. We study the performance of our algorithm for a range of MPI-thread combinations and find the performance to depend strongly on the computational task and load sharing in the multi-core processor. The algorithm scaled poorly with MPI and our hybrid schemes were observed to outperform the pure message passing scheme, despite utilizing the same number of processors or cores in the cluster. Speed-up achieved by our algorithm compared favorably with that achieved by standard MD packages.

Physically consistent simulation of mesoscale chemical kinetics: The non-negative FIS-α method

Biochemical pathways involving chemical kinetics in medium concentrations (i.e., at mesoscale) of the reacting molecules can be approximated as chemical Langevin equations (CLE) systems. We address the physically consistent non-negative simulation of the CLE sample paths as well as the issue of non-Lipschitz diffusion coefficients when a species approaches depletion and any stiffness due to faster reactions. The non-negative Fully Implicit Stochastic @a (FIS @a) method in which stopped reaction channels due to depleted reactants are deleted until a reactant concentration rises again, for non-negativity preservation and in which a positive definite Jacobian is maintained to deal with possible stiffness, is proposed and analysed. The method is illustrated with the computation of active Protein Kinase C response in the Protein Kinase C pathway.

Three dimensional retro-PN based impact time control for higher speed nonmaneuvering targets

In the implementation of modern guidance laws, especially in impact time constrained engagement scenario or multiple agent salvo attack scenario, a good estimate of time-to-go is extremely crucial. The most widely used time-to-go estimate range over closing speed has several limitations. Very few work is there in existing literature which actually try to estimate the time-to-go. Most of them are meant for the engagement of lower speed target with a higher speed interceptor. However, in the current defence scenario, targets of higher speed than the interceptor is a reality. This paper first discusses a recursive time-to-go estimation method for three dimensional engagement of a Retro-PN guided interceptor with higher speed non-maneuvering target and then presents a navigation gain scheduling algorithm to achieve the interception at a pre-specified time. The effectiveness of the time-to-go estimation method and the gain scheduling algorithm is justified with simulation results.