Analysis of Dynamic Heterogeneity in a Glass Former from the Spatial Correlations of Mobility

The growth of characteristic length scales associated with dynamic heterogeneity in glass-forming liquids is investigated in an extensive computational study of a four-point, time-dependent structure factor defined from spatial correlations of mobility, for a model liquid for system sizes extending up to 351 232 particles, in constant-energy and constant-temperature ensembles. Our estimates for dynamic correlation lengths and susceptibilities are consistent with previous results from finite size scaling. We find scaling exponents that are inconsistent with predictions from inhomogeneous mode coupling theory and a recent simulation confirmation of these predictions.

Genetic Heterogeneity in Wild Isolates of Cellular Slime Mold Social Groups

This study addresses the issues of spatial distribution, dispersal, and genetic heterogeneity in social groups of the cellular slime molds (CSMs). The CSMs are soil amoebae with an unusual life cycle that consists of alternating solitary and social phases. Because the social phase involves division of labor with what appears to be an extreme form of "altruism", the CSMs raise interesting evolutionary questions regarding the origin and maintenance of sociality. Knowledge of the genetic structure of social groups in the wild is necessary for answering these questions. We confirm that CSMs are widespread in undisturbed forest soil from South India. They are dispersed over long distances via the dung of a variety of large mammals. Consistent with this mode of dispersal, most social groups in the two species examined for detailed study, Dictyostelium giganteum and Dictyostelium purpureum, are multi-clonal.

Communication: Evidence of dynamic heterogeneity in glassy polymer monolayers from interface microrheology measurements

We have developed a novel nanoparticle tracking based interface microrheology technique to perform in situ studies on confined complex fluids. To demonstrate the power of this technique, we show, for the first time, how in situ glass formation in polymers confined at air-water interface can be directly probed by monitoring variation of the mean square displacement of embedded nanoparticles as a function of surface density. We have further quantified the appearance of dynamic heterogeneity and hence vitrification in polymethyl methacrylate monolayers above a certain surface density, through the variation of non-Gaussian parameter of the probes. (C) 2010 American Institute of Physics. [doi:10.1063/1.3471584].

Chicken prealbumin: Nature of its heterogeneity and binding of plasma retinol-binding protein and thyroid hormones

The heterogeneity of chicken prealbumin (PA) has been shown to be due to the occurrence of three different plasma proteins (PA1 PA2 and PA3). Equilibrium dialysis studies revealed that the thyroid hormones bind specifically to PA2. These hormones bind at the same site on PA2. Circular dichroism studies failed to reveal conformational changes on interaction of retinol-binding protein and thyroid hormone with PA2. Both retinol-binding protein and thyroid hormone are independently transported by PA2.

Elucidation of the conformational free energy landscape in H.pylori LuxS and its implications to catalysis

Background: One of the major challenges in understanding enzyme catalysis is to identify the different conformations and their populations at detailed molecular level in response to ligand binding/environment. A detail description of the ligand induced conformational changes provides meaningful insights into the mechanism of action of enzymes and thus its function. Results: In this study, we have explored the ligand induced conformational changes in H. pylori LuxS and the associated mechanistic features. LuxS, a dimeric protein, produces the precursor (4,5-dihydroxy-2,3-pentanedione) for autoinducer-2 production which is a signalling molecule for bacterial quorum sensing. We have performed molecular dynamics simulations on H. pylori LuxS in its various ligand bound forms and analyzed the simulation trajectories using various techniques including the structure network analysis, free energy evaluation and water dynamics at the active site. The results bring out the mechanistic details such as co operativity and asymmetry between the two subunits, subtle changes in the conformation as a response to the binding of active and inactive forms of ligands and the population distribution of different conformations in equilibrium. These investigations have enabled us to probe the free energy landscape and identify the corresponding conformations in terms of network parameters. In addition, we have also elucidated the variations in the dynamics of water co-ordination to the Zn2+ ion in LuxS and its relation to the rigidity at the active sites. Conclusions: In this article, we provide details of a novel method for the identification of conformational changes in the different ligand bound states of the protein, evaluation of ligand-induced free energy changes and the biological relevance of our results in the context of LuxS structure-function. The methodology outlined here is highly generalized to illuminate the linkage between structure and function in any protein of known structure.

Blue mussel beds as biodiversity hotspots on the rocky shores of the northern Baltic Sea

ABSTRACT The Baltic Sea is a vulnerable ecosystem currently undergoing a number of changes, both natural and human induced. The changes are likely to affect the species found on these shores, e.g. their distribution and interactions with other species. Blue mussels (Mytilus trossulus x Mytilus edulis) provide one of the main biogenic hard structures on the shallow shores of the Baltic Sea where they aggregate into dense beds and provide a number of resources for over 40 associated macrofaunal species, thus functioning as ecosystem engineers. The blue mussel, being a marine species, is highly likely to be affected by any changes in sea water salinity, circulation and/or water balance. These changes could trickle down also to affect the associated macrofaunal communities. The aims of this thesis were three-fold: first, I examined and described the macrofaunal communities found within blue mussel patches since the fauna associated with mussel patches had never been described in the study area prior to this thesis. Second, I explored how changes in mussel density, size as well as patch size and shape would affect the mussel communities. Finally, I tested how general landscape theories derived from terrestrial studies function in blue mussel systems. Theories included the structural heterogeneity hypothesis, species-area relationships, edge effects and patch isolation effects. The work shows that blue mussels in the northern Baltic Sea have an indisputable function as diversity hotspots and that the faunal assemblages found in mussel patches are extremely rich and unique. Further on, it shows that changes in mussel biomass, size, patch size and amount of edge have the potential to alter the faunal assemblages and diversity within patches. Finally, it shows that although some landscape theories, such as the structural heterogeneity hypothesis, seem to apply also in blue mussel communities, others cannot be directly applied due to the different prevailing conditions in the study system. This is a pioneering work looking at diversity shaping processes on the rocky shores of the Gulf of Finland, making up over 40% of the total water basin. A focus on niche construction, positive facilitation effects and ecosystem engineering could provide new insights and methods for conservation biology, but before this can be done, we need to fully understand the circumstances under which a species becomes an ecosystem engineer and recognize the systems in which it functions.

Indigenous Knowledge for Biodiversity Conservation

Indigenous peoples with a historical continuity of resource-use practices often possess a broad knowledge base of the behavior of complex ecological systems in their own localities. This knowledge has accumulated through a long series of observations transmitted from generation to generation. Such ''diachronic'' observations can be of great value and complement the ''synchronic''observations on which western science is based. Where indigenous peoples have depended, for long periods of time, on local environments for the provision of a variety of resources, they have developed a stake in conserving, and in some cases, enhancing, biodiversity. They are aware that biological diversity is a crucial factor in generating the ecological services and natural resources on which they depend. Some indigenous groups manipulate the local landscape to augment its heterogeneity, and some have been found to be motivated to restore biodiversity in degraded landscapes. Their practices for the conservation of biodiversity were grounded in a series of rules of thumb which are apparently arrived at through a trial and error process over a long historical time period. This implies that their knowledge base is indefinite and their implementation involves an intimate relationship with the belief system. Such knowledge is difficult for western science to understand. It is vital, however, that the value of the knowledge-practice-belief complex of indigenous peoples relating to conservation of biodiversity is fully recognized if ecosystems and biodiversity are to be managed sustainably. Conserving this knowledge would be most appropriately accomplished through promoting the community-based resource-management systems of indigenous peoples.

A landscape approach to conservation of birds

Landscape ecology as a discipline in science is rather young. However its principles appear promising in outlining conservation strategies including a wide range of organisms, particularly birds. Birds due to their mobility use a variety of environmental resources, especially habitats. However, currently these habitats are only available in patches over most of the tropical world. Further whatever is left is under constant human pressure. This paper, therefore, addresses this problem and suggests means of dealing with it using the landscape approach as outlined by landscape ecology. The landscape approach starts with the realization that patches of habitats are open and interact with one another. Corridors of trees along roads, hedgerows and canals in a landscape can aid in the movement of species. Hence the landscape approach considers patches of habitats as interacting elements in the large matrix of the landscape. The landscape approach also integrates concepts. It puts together often debated issues such as whether to preserve maximum species diversity, to maximize representativeness, or to preserve only the valuable species. Based on a case study of the Uttara Kannada district in Karnataka, these oft-opposing views and complications can be dealt with practically and synthesized into a conservation strategy far the diverse avifauna of the Western Chats.

Assortative mating and the adaptive landscape

The ability of a population to shift from one adaptive peak to another was examined for a two-locus model with different degrees of assortative mating, selection, and linkage. As expected, if the proportion of the population that mates assortatively increases, so does its ability to shift to a new peak. Assortative mating affects this process by allowing the mean fitness of a population to increase monotonically as it passes through intermediate gene frequencies on the way to a new, higher, homozygotic peak. Similarly, if the height of the new peak increases or selection against intermediates becomes less severe, the population becomes more likely to shift to a new peak. Close linkage also helps the shift to a new adaptive peak and acts similarly to assortative mating, but it is not necessary for such a shift as was previously thought. When a population shifts to a new peak, the number of generations required is significantly less than that needed to return to the original peak when that happens. The short period of time required may be an explanation for rapid changes in the geological record. Under extremely high degrees of assortative mating, the shift takes longer, presumably because of the difficulty of breaking up less favored allelic combinations.

Synthon polymorphism and pseudopolymorphism in co-crystals. The 4,4 `-bipyridine-4-hydroxybenzoic acid structural landscape

Co-crystals of 4,4'-bipyridine and 4-hydroxybenzoic acid (1 : 2) show synthon polymorphism with the former being more stable. A 2 : 1 co-crystal is pseudopolymorphic within the same structural landscape with the structural roles of the two bipyridine N-atoms being distinct, as evidenced by mimicry by 4-phenylpyridine.

Polymorphs, Pseudopolymorphs, and Co-Crystals of Orcinol: Exploring the Structural Landscape with High Throughput Crystallography

An extensive search of the structural landscape of orcinol, 5-methyl-1,3-dihydroxybenzene, has been carried out with high throughput techniques. Polymorphs, pseudopolymorphs (solvates), and co-crystals are described. Several packing modes driven by O-H center dot center dot center dot N hydrogen bonds were identified for the orcinol N-base co-crystals and their hydrates. In these several structural variations, the OH group conformations in the orcinol molecule were found to depend on the choice of co-formers and the crystallization conditions employed. The structural landscape of a molecule is properly described by a sufficiently large number of related crystal structures, and high throughput crystallization followed by rapid structure determinations enables one to access these structures efficiently. Any understanding of this landscape would enable the crystal engineer to reasonably anticipate crystal structures of benzene-1,3-diol co-crystals with N-bases.

Levitation effect and its relationship with the underlying potential energy landscape

Positions of potential energy minima for spherical monatomic sorbates in zeolite NaY have been identified for different sizes of the sorbate. It is found that for small sorbates (sigma less than or equal to 4.96 Angstrom) there are only six adsorption sites per alpha-cage, which are located close to the inner surface of the alpha-cage. For larger sorbates, additional sites of comparable energies appear close to the 12-ring window which forms the bottleneck for intercage diffusion. Minimum energy paths between these sites have been computed. These suggest that the barriers for both intracage and intercage site-to-site migrations are comparable and decrease with increase in sorbate size. Earlier simulation studies on the diffusion of monatomic sorbates in zeolites indicated that there is a dramatic change in the nature of dependence of D on sorbate size around 4.96 Angstrom, for zeolite NaY. Therefore, the present results suggest that the dependence of D on sorbate size and the changes in the potential energy landscape are correlated. The sorbate-zeolite system is characterized by a flatter potential energy landscape when the sorbate size is large. (C) 1999 American Institute of Physics. [S0021-9606(99)51110-0].

Understanding glassy dynamics from the free-energy landscape

Many interesting features of the dynamics of simple liquids near the glass transition may be understood in terms of properties of the free-energy landscape obtained from numerical studies of a model free-energy functional. Main results obtained from this approach are summarized and a list of references to relevant publications is provided. (C) 2002 Elsevier Science B.V. All rights reserved.