Thermodynamic competition between membrane protein oligomeric states

Self-assembly of protein monomers into distinct membrane protein oligomers provides a general mechanism for diversity in the molecular architectures, and resulting biological functions, of membrane proteins. We develop a general physical framework describing the thermodynamic competition between different oligomeric states of membrane proteins. Using the mechanosensitive channel of large conductance as a model system, we show how the dominant oligomeric states of membrane proteins emerge from the interplay of protein concentration in the cell membrane, protein-induced lipid bilayer deformations, and direct monomer-monomer interactions. Our results suggest general physical mechanisms and principles underlying regulation of protein function via control of membrane protein oligomeric state.Comment: 7 pages, 5 figure

An approach to rollback recovery of collaborating mobile agents

Fault-tolerance is one of the main problems that must be resolved to improve the adoption of the agents' computing paradigm. In this paper, we analyse the execution model of agent platforms and the significance of the faults affecting their constituent components on the reliable execution of agent-based applications, in order to develop a pragmatic framework for agent systems fault-tolerance. The developed framework deploys a communication-pairs independent check pointing strategy to offer a low-cost, application-transparent model for reliable agent- based computing that covers all possible faults that might invalidate reliable agent execution, migration and communication and maintains the exactly-one execution property

Controlling the shape of membrane protein polyhedra

Membrane proteins and lipids can self-assemble into membrane protein polyhedral nanoparticles (MPPNs). MPPNs have a closed spherical surface and a polyhedral protein arrangement, and may offer a new route for structure determination of membrane proteins and targeted drug delivery. We develop here a general analytic model of how MPPN self-assembly depends on bilayer-protein interactions and lipid bilayer mechanical properties. We find that the bilayer-protein hydrophobic thickness mismatch is a key molecular control parameter for MPPN shape that can be used to bias MPPN self-assembly towards highly symmetric and uniform MPPN shapes. Our results suggest strategies for optimizing MPPN shape for structural studies of membrane proteins and targeted drug delivery

Cosine Similarity Measure According to a Convex Cost Function

In this paper, we describe a new vector similarity measure associated with a convex cost function. Given two vectors, we determine the surface normals of the convex function at the vectors. The angle between the two surface normals is the similarity measure. Convex cost function can be the negative entropy function, total variation (TV) function and filtered variation function. The convex cost function need not be differentiable everywhere. In general, we need to compute the gradient of the cost function to compute the surface normals. If the gradient does not exist at a given vector, it is possible to use the subgradients and the normal producing the smallest angle between the two vectors is used to compute the similarity measure

Hydrologic homogeneous regions using monthly Streamflow in Turkey

Cluster analysis of gauged streamflow records into homogeneous and robust regions is an important tool for the characterization of hydrologic systems. In this paper we applied the hierarchical cluster analysis to the task of objectively classifying streamflow data into regions encompassing similar streamflow patterns over Turkey. The performance of three standardization techniques was also tested, and standardizing by range was found better than standardizing with zero mean and unit variance. Clustering was carried out using Ward’s minimum variance method which became prominent in managing water resources with squared Euclidean dissimilarity measures on 80 streamflow stations. The stations have natural flow regimes where no intensive river regulation had occurred. A general conclusion drawn is that the zones having similar streamflow pattern were not be overlapped well with the conventional climate zones of Turkey; however, they are coherent with the climate zones of Turkey recently redefined by the cluster analysis to total precipitation data as well as homogenous streamflow zones of Turkey determined by the rotated principal component analysis. The regional streamflow information in this study can significantly improve the accuracy of flow predictions in ungauged watersheds

Multi-nucleon transfer in 58Ni+60Ni{}^{58}\text{Ni}+{}^{60}\text{Ni} and 60Ni+60Ni{}^{60} \text{Ni}+{}^{60}\text{Ni} in stochastic mean-field approach

The multi-nucleon exchange mechanism in ${}^{58} \text{Ni}+{}^{60} \text{Ni}$ and ${}^{60} \text{Ni}+{}^{60}\text{Ni}$ collisions is analyzed in the framework of the stochastic mean-field approach. The results of calculations are compared with the TDRPA calculations and the recent data of ${}^{58} \text{Ni}+{}^{60} \text{Ni}$. A good description of the data and a relatively good agreement with the TDRPA calculations are found.Comment: 6 pages, 6 figure