Overview of E-Learning Environment for Web-Based Study of Testing and Diagnostics of Digital Systems

In this paper, we present an overview of latest developments taking place at Tallinn Technical University (TTU) in the area of e-learning supported by Europea

Evolution-guided Engineering of Alpha/Beta Hydrolases

University of Minnesota Ph.D. dissertation. June 2017. Major: Biochemistry, Molecular Bio, and Biophysics. Advisor: Romas Kazlauskas. 1 computer file (PDF); xx, 321 pages.This work applies principles from evolution to engineering enzyme properties. Specifically, by examining the phylogeny and evolved sequence diversity in a group of α/β-hydrolase fold enzymes from plants, we are able to engineer proteins with broader chemoselectivity, altered enantioselectivity, and increased stability. A number of ancestral α/β-hydrolases fold proteins were reconstructed in one set of experiments. These were more likely than related modern proteins to have relaxed chemoselectivities and, in one case, was more useful for synthesizing medicinally important molecules. Relative to modern enzymes, ancestral enzymes near functional branch points could catalyze more esterase and hydroxynitrile lyase reactions, as well as a number of other types of reactions: decarboxylation, Michael addition, γ-lactam hydrolysis, and 1,5-diketone hydrolysis. This finding helps to demonstrate the important role that enzyme promiscuity plays in the evolution of new enzymes. Additional experiments and structural analysis on one of these reconstructed ancestral enzymes, the early hydroxynitrile lyase HNL1 found that it is both more thermostable and more promiscuous than its modern relatives, HbHNL and MeHNL. X-ray crystallographic studies revealed, counterintuitively, that larger amino acids in the active site of the ancestor actually increased the size of the substrate binding pocket relative to modern relatives. To take advantage of the promiscuity observed in HNL1, it was used in the asymmetric synthesis of a precursor for the important pharmaceutical propranolol. Another set of experiments altered enantioselectivity by making phylogenetically informed mutations. The active sites from two related hydroxynitrile lyases, HbHNL and AtHNL, were modified to resemble their last common ancestor. This resulted in altered enantioselectivity, and in the case of AtHNL, reversed enantioselectivity. Surprisingly modeling suggested that some of these mutants use a previously undescribed mechanism. This may have been the extinct ancestral mechanism that served as an evolutionary stepping stone that allowed descendant lineages to diverge to either the S-HNL mechanism used by HbHNL, or the R-HNL mechanism used by AtHNL. A final set of experiments used a variety of methods to identify stabilizing mutations in another plant α/β-hydrolase, SABP2. All of the methods were able to identify stabilizing mutations. The most stabilizing mutations were identified by methods that used no structural information. Random mutagenesis identified highly stabilizing mutations, but required screening thousands of mutants. The most efficient approaches were found to be those that used sequence information from either one stable homolog, or the consensus of many homologs, to identify potential stabilizing mutations. Residues that evolution has conserved are often important for stabilizing a protein. We created a software application, Consensus Finder, to automate the process of identifying stabilizing mutations by consensus

On Efficient Logic-Level Simulation of Digital Circuits Represented by the SSBDD Model

Logic-level simulation is still one of the most often used operations on digital designs during both design and test stages. This makes it a critical issue affecting the overall cost of a project. In this paper we investigate and show the origins of common advantages of four recently proposed efficient simulation methods of different classes: logic simulation, multi-valued simulation, timing simulation, and fault simulation. Described advantages became possible due to use of a highly efficient model called Structurally Synthesized Binary Decision Diagrams (SSBDD). This very compact model preserves the structural information about the modeled circuit and utilizes circuit partitioning into a set of macros represented each by its own SSBDD. All this makes the SSBDD model a good choice as a logic-level digital design representation. The analysis is made on the basis of experimental data acquired using ISCAS'85 benchmark circuits

SSBDDs: Advantageous Model and Efficient Algorithms for Digital Circuits . . .

In this paper we sum up the research that was done during the last decade on the topic of Structurally Synthesized Binary Decision Diagrams (SSBDDs). We describe general properties of SSBDDs, which make this model very efficient for circuit structure dependent methods and algorithms. In addition, we describe a deterministic test generation algorithm based on SSBDDs and four efficient simulation methods of different classes: logic simulation, multi-valued simulation, timing simulation, and fault simulation. We investigate and show the origins of their common advantages and draw conclusions, which hold for all the described algorithms. The analysis is made on the basis of experimental data acquired when applying these algorithms to ISCAS'85 benchmark circuits. The experiments unveil some new properties of these benchmarks, which we also present in our paper

Structurally Synthesized Binary Decision Diagrams

Current paper presents a special case of BDDs called Structurally Synthesized BDDs

Fast Static Compaction of Test Sequences Using Implications and Greedy Search

Current paper presents a new technique for static compaction of sequential circuit tests that are divided into independent test sequences. The technique implements effective representation of fault matrices by weighted bipartite graphs. The approach contains a preprocessing step for determining the set of essential vectors. Subsequently, implications and a greedy search algorithm is applied. The proposed method offers significantly faster performance in terms of run times than earlier, genetic algorithm based methods. Moreover, the average compaction provided by current method is better

On In-System Programming of Non-volatile Memories

With the continuous growth of capacity of non-volatile memories (NVM) in-system programming (ISP) has become the most time-consuming step in post-assembly phase of board manufacturing. This paper presents a method to assess ISP solutions for on-chip and on-board NVMs. The major contribution of the approach is the formal basis for comparison of state-of-the-art ISP solutions. The effective comparison pin-points the time losses, that can be eliminated by the use of multiple page buffers. The technique has proven to achieve exceptionally short programming time, which is close to the operational speed limit of modern NVMs. The method is based on the ubiquitous JTAG access bus which makes it applicable for the most board manufacturing strategies despite a slow nature of JTAG bus