A new perspective on the analysis of helix-helix packing preferences in globular proteins

For many years it had been believed that steric compatibility of helix interfaces could be the source of the observed preference for particular angles between neighbouring helices as emerging from statistical analysis of protein databanks. Several elegant models describing how side chains on helices can interdigitate without steric clashes were able to account quite reasonably for the observed distributions. However, it was later recognized (Bowie, 1997 and Walther, 1998) that the ``bare'' measured angle distribution should be corrected to avoid statistical bias. Disappointingly, the rescaled distributions dramatically lost their similarity with theoretical predictions casting many doubts on the validity of the geometrical assumptions and models. In this report we elucidate a few points concerning the proper choice of the random reference distribution. In particular we show the existence of crucial corrections due to the correct implementation of the approach used to discriminate whether two helices are in contact or not and to measure their relative orientations. By using this new rescaling, the ``true'' packing angle preferences are well described, even more than with the original ``bare'' distribution, by regular packing models.Comment: 23 pages, 5 figure

Simple solvation potential for coarse-grained models of proteins

We formulate a simple solvation potential based on a coarsed-grain representation of amino acids with two spheres modeling the $C_\alpha$ atom and an effective side-chain centroid. The potential relies on a new method for estimating the buried area of residues, based on counting the effective number of burying neighbours in a suitable way. This latter quantity shows a good correlation with the buried area of residues computed from all atom crystallographic structures. We check the discriminatory power of the solvation potential alone to identify the native fold of a protein from a set of decoys and show the potential to be considerably selective.Comment: 18 pages, 8 tables, 3 figure

A model for the analysis of security policies in service function chains

Two emerging architectural paradigms, i.e., Software Defined Networking (SDN) and Network Function Virtualization (NFV), enable the deployment and management of Service Function Chains (SFCs). A SFC is an ordered sequence of abstract Service Functions (SFs), e.g., firewalls, VPN-gateways,traffic monitors, that packets have to traverse in the route from source to destination. While this appealing solution offers significant advantages in terms of flexibility, it also introduces new challenges such as the correct configuration and ordering of SFs in the chain to satisfy overall security requirements. This paper presents a formal model conceived to enable the verification of correct policy enforcements in SFCs. Software tools based on the model can then be designed to cope with unwanted network behaviors (e.g., security flaws) deriving from incorrect interactions of SFs in the same SFC

Elucidation of the disulfide folding pathway of hirudin by a topology-based approach

A theoretical model for the folding of proteins containing disulfide bonds is introduced. The model exploits the knowledge of the native state to favour the progressive establishment of native interactions. At variance with traditional approaches based on native topology, not all native bonds are treated in the same way; in particular, a suitable energy term is introduced to account for the special strength of disulfide bonds (irrespective of whether they are native or not) as well as their ability to undergo intra-molecular reshuffling. The model thus possesses the minimal ingredients necessary to investigated the much debated issue of whether the re-folding process occurs through partially structured intermediates with native or non-native disulfide bonds. This strategy is applied to a context of particular interest, the re-folding process of Hirudin, a thrombin-specific protease inhibitor, for which conflicting folding pathways have been proposed. We show that the only two parameters in the model (temperature and disulfide strength) can be tuned to reproduce well a set of experimental transitions between species with different number of formed disulfide. This model is then used to provide a characterisation of the folding process and a detailed description of the species involved in the rate-limiting step of Hirudin refolding.Comment: 14 pages, 9 figure

Brownian yet non-Gaussian diffusion: from superstatistics to subordination of diffusing diffusivities

A growing number of biological, soft, and active matter systems are observed to exhibit normal diffusive dynamics with a linear growth of the mean squared displacement, yet with a non-Gaussian distribution of increments. Based on the Chubinsky-Slater idea of a diffusing diffusivity we here establish and analyze a minimal model framework of diffusion processes with fluctuating diffusivity. In particular, we demonstrate the equivalence of the diffusing diffusivity process with a superstatistical approach with a distribution of diffusivities, at times shorter than the diffusivity correlation time. At longer times a crossover to a Gaussian distribution with an effective diffusivity emerges. Specifically, we establish a subordination picture of Brownian but non-Gaussian diffusion processes, that can be used for a wide class of diffusivity fluctuation statistics. Our results are shown to be in excellent agreement with simulations and numerical evaluations.Comment: 19 pages, 6 figures, RevTeX. Physical Review X, at pres

Kinship composition and the evolution of sociality

Group living and cooperation are deeply entwined and we are yet to explain their diversity and distribution across the animal kingdom. Relatedness facilitates the evolution of group living and cooperation as kin provide direct and indirect fitness benefits whereas non-kin only provide direct benefits. Yet, available data from societies that feature multiple individuals of the same sex suggest that living with same-sex non-kin is not rare, even though individuals would get larger fitness from living and cooperating with same-sex kin. In this thesis, I provide foundational knowledge about which species of mammals live with non-kin, why they do that and what consequences that has for the social structure of societies. First, I assembled a dataset of mammalian kinship composition, which is a group-level attribute of the extent to which groups are constituted by kin, non-kin or both. Approximately half of the 18 species in the dataset lived with kin and non-kin, while the other half lived only with kin. Then, I used agent-based models to formally assess how group-augmentation via non-kin immigration constitutes a possible route for the evolution of societies that feature same-sex non-kin. The models illustrated situations in which the benefits of living in optimal group size via non-kin immigration outweigh the costs of living with non-kin. Using an analytical model, I also showed that living with non-kin is beneficial when the mean relatedness between kin is low and when non-kin provide substantially more direct fitness benefits than kin. Finally, using empirical behavioural and pedigree data from a population of macaques, I found no evidence that kinship composition influences social structure. However, agent-based models showed that such a relationship is expected to exist but may only be detectable with larger sample size and variance in kinship composition. Overall, my work shows that it is not rare for mammals to live with non-kin, illustrates how living with non-kin might evolve, and showed how kinship composition might influence social structure, further corroborating the idea that direct benefits work together with indirect benefits to explain the diversity of group-life and cooperative behaviour observed across mammalian societies.European Commissio

Assessment System to Determine the Major in Smk 3 Tangerang Using Visual Basic 6.0

Scientific writing contains a description of the assessment system to determine the direction for students of SMK N 3 which sits in semester 1 class with 2 by using Microsoft Visual Basic 6.0. As for who should fill the first time on this program is to form students and the value. In this program penjurusan Parent Student Number (NIS) is the next key that will lead to students penjurusan process. Calculation process in determining this direction is by dividing the total value of some of the relevant subjects with the number of subjects so that the results obtained Index Options Program (IPP). From the IPP is to be processed and eventually will determine the direction for students