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"Akbal-Delibas, Bahar"
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Introduction to Compiler Construction in a Java World
Immersing students in Java and the JVM, this text enables a deep understanding of the Java programming language and its implementation. It focuses on design, organization, and testing, helping students learn good software engineering skills and become better programmers.
eBook
A conservation and biophysics guided stochastic approach to refining docked multimeric proteins
Background
We introduce a protein docking refinement method that accepts complexes consisting of any number of monomeric units. The method uses a scoring function based on a tight coupling between evolutionary conservation, geometry and physico-chemical interactions. Understanding the role of protein complexes in the basic biology of organisms heavily relies on the detection of protein complexes and their structures. Different computational docking methods are developed for this purpose, however, these methods are often not accurate and their results need to be further refined to improve the geometry and the energy of the resulting complexes. Also, despite the fact that complexes in nature often have more than two monomers, most docking methods focus on dimers since the computational complexity increases exponentially due to the addition of monomeric units.
Results
Our results show that the refinement scheme can efficiently handle complexes with more than two monomers by biasing the results towards complexes with native interactions, filtering out false positive results. Our refined complexes have better IRMSDs with respect to the known complexes and lower energies than those initial docked structures.
Conclusions
Evolutionary conservation information allows us to bias our results towards possible functional interfaces, and the probabilistic selection scheme helps us to escape local energy minima. We aim to incorporate our refinement method in a larger framework which also enables docking of multimeric complexes given only monomeric structures.
Journal Article
A conservation and rigidity based method for detecting critical protein residues
Background
Certain amino acids in proteins play a critical role in determining their structural stability and function. Examples include flexible regions such as hinges which allow domain motion, and highly conserved residues on functional interfaces which allow interactions with other proteins. Detecting these regions can aid in the analysis and simulation of protein rigidity and conformational changes, and helps characterizing protein binding and docking. We present an analysis of critical residues in proteins using a combination of two complementary techniques. One method performs in-silico mutations and analyzes the protein's rigidity to infer the role of a point substitution to Glycine or Alanine. The other method uses evolutionary conservation to find functional interfaces in proteins.
Results
We applied the two methods to a dataset of proteins, including biomolecules with experimentally known critical residues as determined by the free energy of unfolding. Our results show that the combination of the two methods can detect the vast majority of critical residues in tested proteins.
Conclusions
Our results show that the combination of the two methods has the potential to detect more information than each method separately. Future work will provide a confidence level for the criticalness of a residue to improve the accuracy of our method and eliminate false positives. Once the combined methods are integrated into one scoring function, it can be applied to other domains such as estimating functional interfaces.
Journal Article
Celebrity Compilers
Here we survey some of the popular Java (or Java-like) compilers. For each of these, we
discuss issues or features that are peculiar to the compiler in question. The compilers we
discuss are the following:• Oracle’s Java HotSpotTM compiler
• IBM’s Eclipse compiler for Java
• The GNU Java compiler
• Microsoft’s C# compilerThis chapter will only give a taste of these compilers. The reader may wish to consult
some of the recommended readings in the Further Readings section (Section 8.6) at the end
of this chapter for a deeper understanding of them.
Book Chapter
Type Checking
Type checking, or more formally semantic analysis, is the final step in the analysis phase. It
is the compiler’s last chance to collect information necessary to begin the synthesis phase.
Semantic analysis includes the following:• Determining the types of all names and expressions.
• Type checking: insuring that all expressions are properly typed, for example, that theoperands of an operator have the proper types.
Book Chapter
Parsing
Once we have identified the tokens in our program, we then want to determine its syntactic
structure. That is, we want to put the tokens together to make the larger syntactic entities:
expressions, statements, methods, and class definitions. This process of determining the
syntactic structure of a program is called parsing.
Book Chapter
Compilation
A compiler is a program that translates a source program written in a high-level programming language such as Java, C#, or C, into an equivalent target program in a lower, level
language such as machine code, which can be executed directly by a computer. This translation is illustrated in Figure 1.1.
Book Chapter
Register Allocation
Register allocation is the process of assigning as many local variables and temporaries to
physical registers as possible. The more values that we can keep in registers instead of in
memory, the faster our programs will run. This makes register allocation the most effective
optimization technique that we have.
Book Chapter
Lexical Analysis
The first step in compiling a program is to break it into tokens. For example, given the j--
programwe want to produce the sequence of tokens package, pass, ;, import, java, ., lang, .,
System, ;, public, class, Factorial, {, public, static, int, factorial, (, int, n,), {,
if, (, n, <=, 0, ), }, return, 1, ;, else, return, n, *, factorial, (, n, -, 1, ), }, ;, },
public, static, void, main, (, String, [, ], args, ), }, {, int, x, =, n, ;, System, ., out,
., println, (, x, +, \"!=\", +, factorial, (, x, ), ), }, ;, }, static, int, n, =, 5, ;, and }.
Book Chapter