In the field of biology, MD simulations are continuously used to investigate biological studies. A Molecular Dynamics (MD) system is defined by the position and momentum of particles and their interactions. The dynamics of a system can be evaluated by an N-body problem and the simulation is continued until the energy reaches equilibrium. Thus, solving the dynamics numerically and evaluating the interaction is computationally expensive even for a small number of particles in the system. We are focusing on long-ranged interactions, since the calculation time is O(N^2) for an N particle system. In this dissertation, we are proposing two research directions for the MD simulation. First, we design a new variation of Multigrid (MG) algorithm called Multi-level charge assignment (MCA) that requires O(N) time for accurate and efficient calculation of the electrostatic forces. We apply MCA and back interpolation based on the structure of molecules to enhance the accuracy of the simulation. Our second research utilizes reconfigurable models to achieve fast calculation time. We have been working on exploiting two reconfigurable models. We design FPGA-based MD simulator implementing MCA method for Xilinx Virtex-IV. It performs about 10 to 100 times faster than software implementation depending on the simulation accuracy desired. We also design fast and scalable Reconfigurable mesh (R-Mesh) algorithms for MD simulations. This work demonstrates that the large scale biological studies can be simulated in close to real time. The R-Mesh algorithms we design highlight the feasibility of these models to evaluate potentials with faster calculation times. Specifically, we develop R-Mesh algorithms for both Direct method and Multigrid method. The Direct method evaluates exact potentials and forces, but requires O(N^2) calculation time for evaluating electrostatic forces on a general purpose processor. The MG method adopts an interpolation technique to reduce calculation time to O(N) for a given accuracy. However, our R-Mesh algorithms require only O(N) or O(logN) time complexity for the Direct method on N linear R-Mesh and N¡¿N R-Mesh, respectively and O(r)+O(logM) time complexity for the Multigrid method on an X¡¿Y¡¿Z R-Mesh. r is N/M and M = X¡¿Y¡¿Z is the number of finest grid points.

The clock is the important synchronizing element in all synchronous digital systems. The difference in the clock arrival time between sink points is called the clock skew. This uncertainty in arrival times will limit operating frequency and might cause functional errors. Various clock routing techniques can be broadly categorized into 'balanced tree' and 'fixed mesh' methods. The skew and delay using the balanced tree method is higher compared to the fixed mesh method. Although fixed mesh inherently uses more wire length, the redundancy created by loops in a mesh structure reduces undesired delay variations. The fixed mesh method uses a single mesh over the entire chip but it is hard to introduce clock gating in a single clock mesh. This thesis deals with the introduction of 'reconfigurability' by using control structures like transmission gates between sub-clock meshes, thus enabling clock gating in clock mesh. By using the optimum value of size for PMOS and NMOS of transmission gate (SZF) and optimum number of transmission gates between sub-clock meshes (NTG) for 4x4 reconfigurable mesh, the average of the maximum skew for all benchmarks is reduced by 18.12 percent compared to clock mesh structure when no transmission gates are used between the sub-clock meshes (reconfigurable mesh with NTG =0). Further, the research deals with a ‘modified zero skew method' to connect synchronous flip-flops or sink points in the circuit to the clock grids of clock mesh. The wire length reduction algorithms can be applied to reduce the wire length used for a local clock distribution network. The modified version of ‘zero skew method’ of local clock routing which is based on Elmore delay balancing aims at minimizing wire length for the given bounded skew of CDN using clock mesh and H-tree. The results of ‘modified zero skew method' (HC_MZSK) show average local wire length reduction of 17.75 percent for all ISPD benchmarks compared to direct connection method. The maximum skew is small for HC_MZSK in most of the test cases compared to other methods of connections like direct connections and modified AHHK. Thus, HC_MZSK for local routing reduces the wire length and maximum skew.