Thermodynamics of Neutral Protein Evolution

Naturally evolving proteins gradually accumulate mutations while continuing to fold to thermodynamically stable native structures. This process of neutral protein evolution is an important mode of genetic change, and forms the basis for the molecular clock. Here we present a mathematical theory that predicts the number of accumulated mutations, the index of dispersion, and the distribution of stabilities in an evolving protein population from knowledge of the stability effects (ddG values) for single mutations. Our theory quantitatively describes how neutral evolution leads to marginally stable proteins, and provides formulae for calculating how fluctuations in stability cause an overdispersion of the molecular clock. It also shows that the structural influences on the rate of sequence evolution that have been observed in earlier simulations can be calculated using only the single-mutation ddG values. We consider both the case when the product of the population size and mutation rate is small and the case when this product is large, and show that in the latter case proteins evolve excess mutational robustness that is manifested by extra stability and increases the rate of sequence evolution. Our basic method is to treat protein evolution as a Markov process constrained by a minimal requirement for stable folding, enabling an evolutionary description of the proteins solely in terms of the experimentally measureable ddG values. All of our theoretical predictions are confirmed by simulations with model lattice proteins. Our work provides a mathematical foundation for understanding how protein biophysics helps shape the process of evolution

CORBYS cognitive control architecture for robotic follower

In this paper the novel generic cognitive robot control architecture CORBYS is presented. The objective of the CORBYS architecture is the integration of high-level cognitive modules to support robot functioning in dynamic environments including interacting with humans. This paper presents the preliminary integration of the CORBYS architecture to support a robotic follower. Experimental results on high-level empowerment-based trajectory planning have demonstrated the effectiveness of ROS-based communication between distributed modules developed in a multi-site research environment as typical for distributed collaborative projects such as CORBYS

A Non - Singular Cosmological Model with Shear and Rotation

We have investigated a non-static and rotating model of the universe with an imperfect fluid distribution. It is found that the model is free from singularity and represents an ever expanding universe with shear and rotation vanishing for large value of time.Comment: 10 pages, late

Research and development work carried out on edible oysters in Gujarat

Oyster resources survey was conducted by the transect method from Jakhau in the Gulf of Kutch to Umargaon in south Gujarat. Crassostrea gryphoides was dominant followed by Saccostrea cucullata and C. rividari

Thermal Particle Creation in Cosmological Spacetimes: A Stochastic Approach

The stochastic method based on the influence functional formalism introduced in an earlier paper to treat particle creation in near-uniformly accelerated detectors and collapsing masses is applied here to treat thermal and near-thermal radiance in certain types of cosmological expansions. It is indicated how the appearance of thermal radiance in different cosmological spacetimes and in the two apparently distinct classes of black hole and cosmological spacetimes can be understood under a unifying conceptual and methodological framework.Comment: 17 pages, revtex (aps, eqsecnum), submitted to PRD, April 199

Crystal structure of a mixed solvated form of amoxapine acetate

The mixed solvated salt 4-(2-chloro­dibenzo[b,f][1,4]oxazepin-11-yl)piperazin-1-ium acetate-acetic acid-cyclo­hexane (2/2/1), C17H17ClN3O+·C2H3O2-·C2H4O2·0.5C6H12, crystallizes with one mol­ecule of protonated amoxapine (AXPN), an acetate anion and a mol­ecule of acetic acid together with half a mol­ecule of cyclo­hexane. In the centrosymmetric crystal, both enanti­omers of the protonated AXPN mol­ecule stack alternatively along [001]. Acetate anions connect the AXPN cations through N-H...O hydrogen bonding in the [010] direction, creating a sheet lying parallel to (100). The acetic acid mol­ecules are linked to the acetate anions via O-H...O hydrogen bonds within the sheets. Within the sheets there are also a number of C-H...O hydrogen bonds present. The cyclo­hexane solvent mol­ecules occupy the space between the sheets

Molecular Clock on a Neutral Network

The number of fixed mutations accumulated in an evolving population often displays a variance that is significantly larger than the mean (the overdispersed molecular clock). By examining a generic evolutionary process on a neutral network of high-fitness genotypes, we establish a formalism for computing all cumulants of the full probability distribution of accumulated mutations in terms of graph properties of the neutral network, and use the formalism to prove overdispersion of the molecular clock. We further show that significant overdispersion arises naturally in evolution when the neutral network is highly sparse, exhibits large global fluctuations in neutrality, and small local fluctuations in neutrality. The results are also relevant for elucidating the topological structure of a neutral network from empirical measurements of the substitution process.Comment: 10 page