137 research outputs found
Concentration Dependent IonâProtein Interaction Patterns Underlying Protein Oligomerization Behaviours
Most proteins do not exist as monomers. Instead, proteins assemble into oligomeric structures, which range from small dimers to intermediately sized clusters to large polymers. Oligomerization is driven by proteinâprotein interactions between charged residues, (induced) dipoles, aromatic residues and hydrophobic patches. Ionic proteinâprotein interactions, and thus the oligomeric state of a protein, can be influenced by metal ions. There are several theories that strive to explain interactions between metal ions and charged proteins. Continuum electrostatic theories assume a decaying electrostatic potential from a charged protein surface which attracts oppositely charged ions to the point of charge neutralization, while the water solvent is treated as passive medium characterized only by its permittivity. More recent concepts, however, recognize the importance of water coordination. The hydration enthalpy of metal ions and ionic protein groups is envisaged as the driving force for ion pairing. Research and theory have so far focussed on single protein species in simple aqueous solutions. This work comparatively analyses Ca2+-induced oligomerization of the negatively charged SNAP25 protein in solution and in the crowded multi-component environment of the plasma membrane. It proves ion-induced protein oligomerization to be a fundamental chemico-physical principle that is conserved in both environments. The restricted protein movement and the manifold interactions with other proteins and lipids in the membrane appear to mainly influence the number of monomers comprised in an oligomer, but not the phenomenon of oligomerization itself. Comparison of Ca2+ to other positively charged metal ions indicates that ions need to convey a certain charge density and to possess a certain water affinity to induce membrane protein clustering. The results suggest a direct interaction between calcium ions and negatively charged protein residues. It appears that the stoichiometry of calciumâcarboxylate group interactions determines the degree of oligomerization. At low calcium concentrations which induce protein clustering, the ions function as bridges between the carboxylate groups, and attenuate the negative protein charge and thus repulsive proteinâprotein interactions. At high calcium concentrations, binding of one or more calcium ions to a single negatively charged residue is frequently encountered. The calcium ions thus no longer function as bridges between several carboxylate groups. In addition, the local overcharging entails repulsive forces between proteins which again favour protein dispersion. The study provides a conceptual framework for the influence of ions on electrostatically driven proteinâprotein interactions and protein aggregation with implications for biological and industrial settings
Data perspective in process choreographies : modeling and execution
Process choreographies - communication between different organizations to exchange information - is part of daily business. While the correct ordering of exchanged messages can be modeled and enacted with current choreography techniques, no approach exists to describe the data perspective for a successful process choreography. In this paper, we describe an entirely model-driven approach for BPMN, the industry standard, to include the data perspective while maintaining control flow aspects by utilizing a recent concept to enact data dependencies in internal processes. This work provides a modeling guideline with the require artifacts and their operational semantics to allow automatic choreography enactment covering data retrieval, transformation, and correlation. We show applicability of our approach by an implementation for the Camunda BPM platform, a java-based process engine, and validate it with the service interaction patterns. Keywords: Process Modeling, Data Modeling, Process Choreographies, Process Enactment, BPMN, SQ
On the Relationships between Decision Management and Performance Measurement
Decision management is of utmost importance for the achievement of strategic and operational goals in any organisational context. Therefore, decisions should be considered as first-class citizens that need to be modelled, analysed, monitored to track their performance, and redesigned if necessary. Up to now, existing literature that studies decisions in the context of business processes has focused on the analysis of the definition of decisions themselves, in terms of accuracy, certainty, consistency, covering and correctness. However, to the best of our knowledge, no prior work exists that analyses the relationship between decisions and performance measurement. This paper identifies and analyses this relationship from three different perspectives, namely: the impact of decisions on process performance, the performance measurement of decisions, and the use of performance indicators in the definition of decisions. Furthermore, we also introduce solutions for the representation of these relationships based, amongst others, on the DMN standard.Ministerio de EconomĂa y Competitividad BELI (TIN2015-70560-R)Junta de AndalucĂa P12-TIC-1867Junta de AndalucĂa P10-TIC-590
Phase Transitions of Single Semi-stiff Polymer Chains
We study numerically a lattice model of semiflexible homopolymers with
nearest neighbor attraction and energetic preference for straight joints
between bonded monomers. For this we use a new algorithm, the "Pruned-Enriched
Rosenbluth Method" (PERM). It is very efficient both for relatively open
configurations at high temperatures and for compact and frozen-in low-T states.
This allows us to study in detail the phase diagram as a function of
nn-attraction epsilon and stiffness x. It shows a theta-collapse line with a
transition from open coils to molten compact globules (large epsilon) and a
freezing transition toward a state with orientational global order (large
stiffness x). Qualitatively this is similar to a recently studied mean field
theory (Doniach et al. (1996), J. Chem. Phys. 105, 1601), but there are
important differences. In contrast to the mean field theory, the
theta-temperature increases with stiffness x. The freezing temperature
increases even faster, and reaches the theta-line at a finite value of x. For
even stiffer chains, the freezing transition takes place directly without the
formation of an intermediate globule state. Although being in contrast with
mean filed theory, the latter has been conjectured already by Doniach et al. on
the basis of low statistics Monte Carlo simulations. Finally, we discuss the
relevance of the present model as a very crude model for protein folding.Comment: 11 pages, Latex, 8 figure
A new bond fluctuation method for a polymer undergoing gel electrophoresis
We present a new computational methodology for the investigation of gel
electrophoresis of polyelectrolytes. We have developed the method initially to
incorporate sliding motion of tight parts of a polymer pulled by an electric
field into the bond fluctuation method (BFM). Such motion due to tensile force
over distances much larger than the persistent length is realized by non-local
movement of a slack monomer at an either end of the tight part. The latter
movement is introduced stochastically. This new BFM overcomes the well-known
difficulty in the conventional BFM that polymers are trapped by gel fibers in
relatively large fields. At the same time it also reproduces properly
equilibrium properties of a polymer in a vanishing filed limit. The new BFM
thus turns out an efficient computational method to study gel electrophoresis
in a wide range of the electric field strength.Comment: 15 pages, 11 figure
Polydisperse star polymer solutions
We analyze the effect of polydispersity in the arm number on the effective
interactions, structural correlations and the phase behavior of star polymers
in a good solvent. The effective interaction potential between two star
polymers with different arm numbers is derived using scaling theory. The
resulting expression is tested against monomer-resolved molecular dynamics
simulations. We find that the theoretical pair potential is in agreement with
the simulation data in a much wider polydispersity range than other proposed
potentials. We then use this pair potential as an input in a many-body theory
to investigate polydispersity effects on the structural correlations and the
phase diagram of dense star polymer solutions. In particular we find that a
polydispersity of 10%, which is typical in experimental samples, does not
significantly alter previous findings for the phase diagram of monodisperse
solutions.Comment: 14 pages, 7 figure
A New Monte Carlo Algorithm for Protein Folding
We demonstrate that the recently proposed pruned-enriched Rosenbluth method
(P. Grassberger, Phys. Rev. E 56 (1997) 3682) leads to extremely efficient
algorithms for the folding of simple model proteins. We test them on several
models for lattice heteropolymers, and compare to published Monte Carlo
studies. In all cases our algorithms are faster than all previous ones, and in
several cases we find new minimal energy states. In addition to ground states,
our algorithms give estimates for the partition sum at finite temperatures.Comment: 4 pages, Latex incl. 3 eps-figs., submitted to Phys. Rev. Lett.,
revised version with changes in the tex
Scaling of Star Polymers with one to 80 Arms
We present large statistics simulations of 3-dimensional star polymers with
up to arms, and with up to 4000 monomers per arm for small values of
. They were done for the Domb-Joyce model on the simple cubic lattice. This
is a model with soft core exclusion which allows multiple occupancy of sites
but punishes each same-site pair of monomers with a Boltzmann factor . We
use this to allow all arms to be attached at the central site, and we use the
`magic' value to minimize corrections to scaling. The simulations are
made with a very efficient chain growth algorithm with resampling, PERM,
modified to allow simultaneous growth of all arms. This allows us to measure
not only the swelling (as observed from the center-to-end distances), but also
the partition sum. The latter gives very precise estimates of the critical
exponents . For completeness we made also extensive simulations of
linear (unbranched) polymers which give the best estimates for the exponent
.Comment: 7 pages, 7 figure
A review of Monte Carlo simulations of polymers with PERM
In this review, we describe applications of the pruned-enriched Rosenbluth
method (PERM), a sequential Monte Carlo algorithm with resampling, to various
problems in polymer physics. PERM produces samples according to any given
prescribed weight distribution, by growing configurations step by step with
controlled bias, and correcting "bad" configurations by "population control".
The latter is implemented, in contrast to other population based algorithms
like e.g. genetic algorithms, by depth-first recursion which avoids storing all
members of the population at the same time in computer memory. The problems we
discuss all concern single polymers (with one exception), but under various
conditions: Homopolymers in good solvents and at the point, semi-stiff
polymers, polymers in confining geometries, stretched polymers undergoing a
forced globule-linear transition, star polymers, bottle brushes, lattice
animals as a model for randomly branched polymers, DNA melting, and finally --
as the only system at low temperatures, lattice heteropolymers as simple models
for protein folding. PERM is for some of these problems the method of choice,
but it can also fail. We discuss how to recognize when a result is reliable,
and we discuss also some types of bias that can be crucial in guiding the
growth into the right directions.Comment: 29 pages, 26 figures, to be published in J. Stat. Phys. (2011
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