Shyamal Somaroo

Are protein–protein interfaces more conserved in sequence than the rest of the protein surface?

Protein interfaces are thought to be distinguishable from the rest of the protein surface by their greater degree of residue conservation. We test the validity of this approach on an expanded set of 64 protein–protein interfaces using conservation scores derived from two multiple sequence alignment types, one of close homologs/orthologs and one of diverse homologs/paralogs. Overall, we find that the interface is slightly more conserved than the rest of the protein surface when using either alignment type, with alignments of diverse homologs showing marginally better discrimination. However, using a novel surface‐patch definition, we find that the interface is rarely significantly more conserved than other surface patches when using either alignment type. When an interface is among the most conserved surface patches, it tends to be part of an enzyme active site. The most conserved surface patch overlaps with 39% (± 28%) and 36% (± 28%) of the actual interface for diverse and close homologs, respectively. Contrary to results obtained from smaller data sets, this work indicates that residue conservation is rarely sufficient for complete and accurate prediction of protein interfaces. Finally, we find that obligate interfaces differ from transient interfaces in that the former have significantly fewer alignment gaps at the interface than the rest of the protein surface, as well as having buried interface residues that are more conserved than partially buried interface residues.

EXPERIMENTAL QUANTUM ERROR CORRECTION

Quantum error correction is required to compensate for the fragility of the state of a quantum computer. We report the first experimental implementations of quantum error correction and confirm the expected state stabilization. A precise analysis of the decay behavior is performed in alanine and a full implementation of the error correction procedure is realized in trichloroethylene. In NMR computing, however, a net improvement in the signal to noise would require very high polarization. The experiment implemented the three-bit code for phase errors using liquid state NMR.

QUANTUM SIMULATIONS ON A QUANTUM COMPUTER

We present a general scheme for performing a simulation of the dynamics of one quantum system using another. This scheme is used to experimentally simulate the dynamics of truncated quantum harmonic and anharmonic oscillators using nuclear magnetic resonance. We believe this to be the first explicit physical realization of such a simulation. {copyright} {ital 1999} {ital The American Physical Society }

Spacetime Algebra and Electron Physics

Publisher Summary This chapter presents a survey on the application of “geometric algebra” to the physics of electrons. Geometric algebra is the simplest and most coherent language available for mathematical physics and provides a single unified approach to a vast range of mathematical physics, and formulating and solving a problem in geometric algebra invariably leads to new physical insights. The chapter discusses aspects encompassing a wider range of topics relevant to electron physics. The idea that Clifford algebra provides the framework for a unified language for physics has been advocated most strongly by Hestenes, who is largely responsible for shaping the modern form of the subject. A list of some of the algebraic systems and techniques employed in modern theoretical physics (and especially particle physics) is presented in the chapter. The chapter focuses on the geometric algebra of spacetime—the spacetime algebra. The chapter explains that spacetime algebra, simiplifies the study of the Dirac theory, and discusses that the Dirac theory once formulated in the spacetime algebra is a powerful and flexible tool for the analysis of all aspects of electron physics—not just relativistic theory. The chapter begins with an introduction to the spacetime algebra (STA); concentrating on how the algebra of the STA is used to encode geometric ideas, such as lines, planes, and rotations.

PFAAT version 2.0: A tool for editing, annotating, and analyzing multiple sequence alignments

BackgroundBy virtue of their shared ancestry, homologous sequences are similar in their structure and function. Consequently, multiple sequence alignments are routinely used to identify trends that relate to function. This type of analysis is particularly productive when it is combined with structural and phylogenetic analysis.ResultsHere we describe the release of PFAAT version 2.0, a tool for editing, analyzing, and annotating multiple sequence alignments. Support for multiple annotations is a key component of this release as it provides a framework for most of the new functionalities. The sequence annotations are accessible from the alignment and tree, where they are typically used to label sequences or hyperlink them to related databases. Sequence annotations can be created manually or extracted automatically from UniProt entries. Once a multiple sequence alignment is populated with sequence annotations, sequences can be easily selected and sorted through a sophisticated search dialog. The selected sequences can be further analyzed using statistical methods that explicitly model relationships between the sequence annotations and residue properties. Residue annotations are accessible from the alignment viewer and are typically used to designate binding sites or properties for a particular residue.Residue annotations are also searchable, and allow one to quickly select alignment columns for further sequence analysis, e.g. computing percent identities. Other features include: novel algorithms to compute sequence conservation, mapping conservation scores to a 3D structure in Jmol, displaying secondary structure elements, and sorting sequences by residue composition.ConclusionPFAAT provides a framework whereby end-users can specify knowledge for a protein family in the form of annotation. The annotations can be combined with sophisticated analysis to test hypothesis that relate to sequence, structure and function.

Expressing the operations of quantum computing in multiparticle geometric algebra

We show how the basic operations of quantum computing can be expressed and manipulated in a clear and concise fashion using a multiparticle version of geometric (aka Clifford) algebra. This algebra encompasses the product operator formalism of NMR spectroscopy, and hence its notation leads directly to implementations of these operations via NMR pulse sequences.

Protein family annotation in a multiple alignment viewer

SUMMARY The Pfaat protein family alignment annotation tool is a Java-based multiple sequence alignment editor and viewer designed for protein family analysis. The application merges display features such as dendrograms, secondary and tertiary protein structure with SRS retrieval, subgroup comparison, and extensive user-annotation capabilities. AVAILABILITY The program and source code are freely available from the authors under the GNU General Public License at http://www.pfizerdtc.com

Geometric algebra and the causal approach to multiparticle quantum mechanics

It is argued that geometric algebra, in the form of the multiparticle spacetime algebra, is well suited to the study of multiparticle quantum theory, with advantages over conventional techniques both in ease of calculation and in providing an intuitive geometric understanding of the results. This is illustrated by comparing the geometric algebra approach for a system of two spin-1/2 particles with the nonrelativistic approach of Holland [Phys. Rep. 169, 294 (1988)].

Principles and Demonstrations of Quantum Information Processing by NMR Spectroscopy

Abstract. This paper surveys our recent research on quantum information processing by nuclear magnetic resonance (NMR) spectroscopy. We begin with a geometric introduction to the NMR of an ensemble of indistinguishable spins, and then show how this geometric interpretation is contained within an algebra of multispin product operators. This algebra is used throughout the rest of the paper to demonstrate that it provides a facile framework within which to study quantum information processing more generally. The implementation of quantum algorithms by NMR depends upon the availability of special kinds of mixed states, called pseudo-pure states, and we consider a number of different methods for preparing these states, along with analyses of how they scale with the number of spins. The quantum-mechanical nature of processes involving such macroscopic pseudo-pure states also is a matter of debate, and in order to discuss this issue in concrete terms we present the results of NMR experiments which constitute a macroscopic analogue Hardys paradox. Finally, a detailed product operator description is given of recent NMR experiments which demonstrate a three-bit quantum error correcting code, using field gradients to implement a precisely-known decoherence model.

Tunnelling times of electrons

Abstract We consider a fully relativistic method for the calculation of tunnelling times based on the streamlines of the conserved probability flux. This method is similar to that proposed by Leavens but is not based on the Bohmian interpretation. The method is applied to single- and two-particle tunnelling in Dirac theory.