8,511 research outputs found
CSP design model and tool support
The CSP paradigm is known as a powerful concept for designing and analysing the architectural and behavioural parts of concurrent software. Although the theory of CSP is useful for mathematicians, the programming language occam has been derived from CSP that is useful for any engineering practice. Nowadays, the concept of occam/CSP can be used for almost every object-oriented programming language. This paper describes a tree-based description model and prototype tool that elevates the use of occam/CSP concepts at the design level and performs code generation to Java, C, C++, and machine-readable CSP for the level of implementation. The tree-based description model can be used to browse through the generated source code. The tool is a kind of browser that is able to assist modern workbenches (like Borland Builder, Microsoft Visual C++ and 20-SIM) with coding concurrency. The tool will guide the user through the design trajectory using support messages and several semantic and syntax rule checks. The machine-readable CSP can be read by FDR, enabling more advanced analysis on the design. Early experiments with the prototype tool show that the browser concept, combined with the tree-based description model, enables a user-friendly way to create a design using the CSP concepts and benefits. The design tool is available from our URL, http://www.rt.el.utwente.nl/javapp
Rigid Origami Vertices: Conditions and Forcing Sets
We develop an intrinsic necessary and sufficient condition for single-vertex
origami crease patterns to be able to fold rigidly. We classify such patterns
in the case where the creases are pre-assigned to be mountains and valleys as
well as in the unassigned case. We also illustrate the utility of this result
by applying it to the new concept of minimal forcing sets for rigid origami
models, which are the smallest collection of creases that, when folded, will
force all the other creases to fold in a prescribed way
The development of biomolecular Raman optical activity spectroscopy
Following its first observation over 40 years ago, Raman optical activity (ROA), which may be measured as a small difference in the intensity of vibrational Raman scattering from chiral molecules in right- and left-circularly polarized incident light or, equivalently, the intensity of a small circularly polarized component in the scattered light using incident light of fixed polarization, has evolved into a powerful chiroptical spectroscopy for studying a large range of biomolecules in aqueous solution. The long and tortuous path leading to the first observations of ROA in biomolecules in 1989, in which the author was closely involved from the very beginning, is documented, followed by a survey of subsequent developments and applications up to the present day. Among other things, ROA provides information about motif and fold, as well as secondary structure, of proteins; solution structure of carbohydrates; polypeptide and carbohydrate structure of intact glycoproteins; new insight into structural elements present in unfolded protein sequences; and protein and nucleic acid structure of intact viruses. Quantum chemical simulations of observed Raman optical activity spectra provide the complete three-dimensional structure, together with information about conformational dynamics, of smaller biomolecules. Biomolecular ROA measurements are now routine thanks to a commercial instrument based on a novel design becoming available in 2004
Introduction to Protein Structure Prediction
This chapter gives a graceful introduction to problem of protein three-
dimensional structure prediction, and focuses on how to make structural sense
out of a single input sequence with unknown structure, the 'query' or 'target'
sequence. We give an overview of the different classes of modelling techniques,
notably template-based and template free. We also discuss the way in which
structural predictions are validated within the global com- munity, and
elaborate on the extent to which predicted structures may be trusted and used
in practice. Finally we discuss whether the concept of a sin- gle fold
pertaining to a protein structure is sustainable given recent insights. In
short, we conclude that the general protein three-dimensional structure
prediction problem remains unsolved, especially if we desire quantitative
predictions. However, if a homologous structural template is available in the
PDB model or reasonable to high accuracy may be generated
Folding and unfolding of a triple-branch DNA molecule with four conformational states
Single-molecule experiments provide new insights into biological processes
hitherto not accessible by measurements performed on bulk systems. We report on
a study of the kinetics of a triple-branch DNA molecule with four
conformational states by pulling experiments with optical tweezers and
theoretical modelling. Three distinct force rips associated with different
transitions between the conformational states are observed in the folding and
unfolding trajectories. By applying transition rate theory to a free energy
model of the molecule, probability distributions for the first rupture forces
of the different transitions are calculated. Good agreement of the theoretical
predictions with the experimental findings is achieved. Furthermore, due to our
specific design of the molecule, we found a useful method to identify
permanently frayed molecules by estimating the number of opened basepairs from
the measured force jump values.Comment: 17 pages, 12 figure
Single-domain protein folding: a multi-faceted problem
We review theoretical approaches, experiments and numerical simulations that
have been recently proposed to investigate the folding problem in single-domain
proteins. From a theoretical point of view, we emphasize the energy landscape
approach. As far as experiments are concerned, we focus on the recent
development of single-molecule techniques. In particular, we compare the
results obtained with two main techniques: single protein force measurements
with optical tweezers and single-molecule fluorescence in studies on the same
protein (RNase H). This allows us to point out some controversial issues such
as the nature of the denatured and intermediate states and possible folding
pathways. After reviewing the various numerical simulation techniques, we show
that on-lattice protein-like models can help to understand many controversial
issues.Comment: 26 pages, AIP Conference Proceeding
The C Terminus of the Ribosomal-Associated Protein LrtA Is an Intrinsically Disordered Oligomer
The 191-residue-long LrtA protein of Synechocystis sp. PCC 6803 is involved in post-stress survival and in stabilizing 70S ribosomal particles. It belongs to the hibernating promoting factor (HPF) family, intervening in protein synthesis. The protein consists of two domains: The N-terminal region (N-LrtA, residues 1-101), which is common to all the members of the HPF, and seems to be well-folded; and the C-terminal region (C-LrtA, residues 102-191), which is hypothesized to be disordered. In this work, we studied the conformational preferences of isolated C-LrtA in solution. The protein was disordered, as shown by computational modelling, 1D-H-1 NMR, steady-state far-UV circular dichroism (CD) and chemical and thermal denaturations followed by fluorescence and far-UV CD. Moreover, at physiological conditions, as indicated by several biochemical and hydrodynamic techniques, isolated C-LrtA intervened in a self-association equilibrium, involving several oligomerization reactions. Thus, C-LrtA was an oligomeric disordered protein.This research was funded by Spanish Ministry of Economy and Competitiveness [CTQ2015-64445-R (to J.L.N.) and MAT2015-63704-P (to A.A.), with Fondo Social Europeo (ESF)], and by the Basque Government [IT-654-13 (to A.A.)
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