A Field Programmable Gate Array Architecture for Two-Dimensional Partial Reconfiguration

Reconfigurable machines can accelerate many applications by adapting to their needs through hardware reconfiguration. Partial reconfiguration allows the reconfiguration of a portion of a chip while the rest of the chip is busy working on tasks. Operating system models have been proposed for partially reconfigurable machines to handle the scheduling and placement of tasks. They are called OS4RC in this dissertation. The main goal of this research is to address some problems that come from the gap between OS4RC and existing chip architectures and the gap between OS4RC models and practical applications. Some existing OS4RC models are based on an impractical assumption that there is no data exchange channel between IP (Intellectual Property) circuits residing on a Field Programmable Gate Array (FPGA) chip and between an IP circuit and FPGA I/O pins. For models that do not have such an assumption, their inter-IP communication channels have severe drawbacks. Those channels do not work well with 2-D partial reconfiguration. They are not suitable for intensive data stream processing. And frequently they are very complicated to design and very expensive. To address these problems, a new chip architecture that can better support inter-IP and IP-I/O communication is proposed and a corresponding OS4RC kernel is then specified. The proposed FPGA architecture is based on an array of clusters of configurable logic blocks, with each cluster serving as a partial reconfiguration unit, and a mesh of segmented buses that provides inter-IP and IP-I/O communication channels. The proposed OS4RC kernel takes care of the scheduling, placement, and routing of circuits under the constraints of the proposed architecture. Features of the new architecture in turns reduce the kernel execution times and enable the runtime scheduling, placement and routing. The area cost and the configuration memory size of the new chip architecture are calculated and analyzed. And the efficiency of the OS4RC kernel is evaluated via simulation using three different task models

Deliverable JRA1.1: Evaluation of current network control and management planes for multi-domain network infrastructure

This deliverable includes a compilation and evaluation of available control and management architectures and protocols applicable to a multilayer infrastructure in a multi-domain Virtual Network environment.The scope of this deliverable is mainly focused on the virtualisation of the resources within a network and at processing nodes. The virtualization of the FEDERICA infrastructure allows the provisioning of its available resources to users by means of FEDERICA slices. A slice is seen by the user as a real physical network under his/her domain, however it maps to a logical partition (a virtual instance) of the physical FEDERICA resources. A slice is built to exhibit to the highest degree all the principles applicable to a physical network (isolation, reproducibility, manageability, ...). Currently, there are no standard definitions available for network virtualization or its associated architectures. Therefore, this deliverable proposes the Virtual Network layer architecture and evaluates a set of Management- and Control Planes that can be used for the partitioning and virtualization of the FEDERICA network resources. This evaluation has been performed taking into account an initial set of FEDERICA requirements; a possible extension of the selected tools will be evaluated in future deliverables. The studies described in this deliverable define the virtual architecture of the FEDERICA infrastructure. During this activity, the need has been recognised to establish a new set of basic definitions (taxonomy) for the building blocks that compose the so-called slice, i.e. the virtual network instantiation (which is virtual with regard to the abstracted view made of the building blocks of the FEDERICA infrastructure) and its architectural plane representation. These definitions will be established as a common nomenclature for the FEDERICA project. Other important aspects when defining a new architecture are the user requirements. It is crucial that the resulting architecture fits the demands that users may have. Since this deliverable has been produced at the same time as the contact process with users, made by the project activities related to the Use Case definitions, JRA1 has proposed a set of basic Use Cases to be considered as starting point for its internal studies. When researchers want to experiment with their developments, they need not only network resources on their slices, but also a slice of the processing resources. These processing slice resources are understood as virtual machine instances that users can use to make them behave as software routers or end nodes, on which to download the software protocols or applications they have produced and want to assess in a realistic environment. Hence, this deliverable also studies the APIs of several virtual machine management software products in order to identify which best suits FEDERICA’s needs.Postprint (published version

Proceedings of the First International Workshop on Sustainable Ultrascale Computing Systems (NESUS 2014): Porto, Portugal

Proceedings of: First International Workshop on Sustainable Ultrascale Computing Systems (NESUS 2014). Porto (Portugal), August 27-28, 2014

Inclusion of Enclosed Hydration Effects in the Binding Free Energy Estimation of Dopamine D3 Receptor Complexes

Confined hydration and conformational flexibility are some of the challenges encountered for the rational design of selective antagonists of G-protein coupled receptors. We present a set of C3-substituted (-)-stepholidine derivatives as potent binders of the dopamine D3 receptor. The compounds are characterized biochemically, as well as by computer modeling using a novel molecular dynamics-based alchemical binding free energy approach which incorporates the effect of the displacement of enclosed water molecules from the binding site. The free energy of displacement of specific hydration sites is obtained using the Hydration Site Analysis method with explicit solvation. This work underscores the critical role of confined hydration and conformational reorganization in the molecular recognition mechanism of dopamine receptors and illustrates the potential of binding free energy models to represent these key phenomena.Comment: This is the first report of using enclosed hydration in estimating binding free energies of protein-ligand complexes using implicit solvatio

Establishment of Kerala Agricultural University Campus Wide Information System and Network: Feasibility Report

A Feasibility Report prepared by Centre for Agricultural Informatics in 1995 on establishing a Campus Network for Kerala Agricultural University’s (KAU) main campus (at Vellanikkara, Thrissur) and a state-of-the art Electronic Data Complex in its University Library premises. For the dissemination of topical awareness and global information to those in agricultural sector of the State, KAU needs to build a Campus LAN and state-of-the art Agricultural Digital Library and Data Complex within its central library. This can become a show case of the electronic age in agriculture and allied disciplines and will promote, propagate and catalogue the agricultural economy that India is so dependent on. The data complex will be a cached repository of agricultural information available worldwide, besides acting as a data silo for research forums, concurrent research, electronic publishing and global bulletin boards. The scattered campuses of KAU and allied institutions also need to be linked through electronic bridges that enable spontaneous exchange of information between the agricultural Diaspora of students, faculties, researchers, extension workers and administrators. The report covers mandate of the proposed system, detailed discussion on computer and communication stack that KAU Campus Wide Information System and Network needs, the architecture prescription, network design, MultiStack and DEChub 900 options available, host environment, financial terms, implementation methodology, installation support continuum, network synthesis and integration, systems engineering support, time frames and the administrative arrangements required. Open Network, with Protocol Switching and Networked Systems Management based on Digital's enVISN Networking Architecture and Enterprise Management Solutions is recommended. Detailed Technical literature and specifications of each and every item of computer and communication stack and solution recommended is appended to the report. Even though the report was prepared in 1995 it can be of interest for critical studies on history of ICT development in India especially in agricultural sector and for comparison of quality of systems and recommendations of a specific time in the past

From FPGA to ASIC: A RISC-V processor experience

This work document a correct design flow using these tools in the Lagarto RISC- V Processor and the RTL design considerations that must be taken into account, to move from a design for FPGA to design for ASIC

Dynamics of protein-drug interactions inferred from structural ensembles and physics-based models

The conformational flexibility of target proteins is a major challenge in understanding and modeling protein-drug interactions. A fundamental issue, yet to be clarified, is whether the observed conformational changes are controlled by the protein, or induced by the inhibitor. While the concept of induced fit has been widely adopted for describing the structural changes that accompany ligand binding, there is growing evidence in support of the dominance of proteins' intrinsic dynamics, which has been evolutionarily optimized to accommodate its functional interactions. The wealth of structural data for target proteins in the presence of different ligands now permits us to make a critical assessment of the balance between these two effects in selecting the bound forms. We focused on three widely studied drug targets, HIV-1 reverse transcriptase, p38 MAP kinase, and cyclin-dependent kinase 2. A total of 292 structures determined for these enzymes in the presence of different inhibitors as well as unbound form permitted us to perform an extensive comparative analysis of the conformational space accessed upon ligand binding, and its relation to the intrinsic dynamics prior to ligand binding as predicted by elastic network model analysis. Further, we analyzed NMR ensembles of ubiquitin and calmodulin representing their microseconds range solution dynamics. Our results show that the ligand selects the conformer that best matches its structural and dynamic properties amongst the conformers intrinsically accessible to the protein in the unliganded form. The results suggest that simple but robust rules encoded in the protein structure play a dominant role in pre-defining the mechanisms of ligand binding, which may be advantageously exploited in designing inhibitors. We apply these lessons to the study of MAP kinase phosphatases (MKPs), which are therapeutically relevant but challenging signaling enzymes. Our study provides insights into the interactions and selectivity of MKP inhibitors and shows how an allosteric inhibition mechanism holds for a recently discovered inhibitor of MKP-3. We also provide evidence for the functional significance of the structure-encoded dynamics of rhodopsin and nicotinic acetylcholine receptor, members of two membrane proteins classes serving as targets for more than 40% of all current FDA approved drugs