Many-body effects in electrochemisorption : Part III. Beyond mean field and hartree-fock

Several channels provided by many-body couplings — both fermion-fermion and fermion-boson — for the evolution of the chemisorption system are discussed. This provides an opportunity of a systematic study of the effects of correlations reflected through the intricate pole structure of the absorbate Green functions. The results of Newns, Anda and others in the context of chemisorption are generalized.

Many-body effects in electrochemisorption : Part IV. Multi-boson formalism

Several boson subsystems may be involved in electrosorption phenomena. To accommodate this possibility, the one-boson formalism described in Parts I–III is extended to this case. The hierarchy in the superoperator scheme, the evaluation of operator averages for closure and several special cases are indicated. As an illustration, some calculations are presented to indicate the trends of many-body corrections in chemisorption.

Can a single resource support many consumer species

The conclusion that the number of species co-existing within a biological community cannot exceed the number of limiting factors is not valid if we assume that (i) the relative efficiency of two competing species in utilizing a resource is not independent of the resource density, but one species may be more efficient at a lower density and less efficient at a higher density and (ii) there is a spatial or temporal heterogeneity in the density of the resource. This spatial or temporal heterogeneity does not have to be furnished by factors external to the biological community, but may be generated within the biological community itself as in the case of a vertical gradient of light in a plant community. This possibility of a stable co-existence of more than one species in a community limited by a single resource, even when the resource is being supplied uniformly in space and time, is formally demonstrated.

Landau-Zener problem with waiting at the minimum gap and related quench dynamics of a many-body system

We discuss a technique for solving the Landau-Zener (LZ) problem of finding the probability of excitation in a two-level system. The idea of time reversal for the Schrodinger equation is employed to obtain the state reached at the final time and hence the excitation probability. Using this method, which can reproduce the well-known expression for the LZ transition probability, we solve a variant of the LZ problem, which involves waiting at the minimum gap for a time t(w); we find an exact expression for the excitation probability as a function of t(w). We provide numerical results to support our analytical expressions. We then discuss the problem of waiting at the quantum critical point of a many-body system and calculate the residual energy generated by the time-dependent Hamiltonian. Finally, we discuss possible experimental realizations of this work.

One protein�many functions

The concept of one enzyme-one activity had influenced biochemistry for over half a century. Over 1000 enzymes are now described. Many of them are highly 'specific'. Some of them are crystallized and their three-dimensional structures determined. They range from 12 to 1000 kDa in molecular weight and possess 124 to several hundreds of amino acids. They occur as single polypeptides or multiple-subunit proteins. The active sites are assembled on these by appropriate tertiary folding of the polypeptide chain, or by interaction of the constituent subunits. The substrate is held by the side-chains of a few amino acids at the active site on the surface, occupying a tiny fraction of the total area. What is the bulk of the protein behind the active site doing? Do all proteins have only one function each? Why not a protein have more than one active site on its large surface? Will we discover more than one activity for some proteins? These newer possibilities are emerging and are finding experimental support. Some proteins purified to homogeneity using assay methods for different activities are now recognized to have the same molecular weight and a high degree of homology of amino acid sequence. Obviously they are identical. They represent the phenomenon of one protein-many functions.

Imaging cellular signalling: many `moving tales' in MAP kinase odyssey

Cellular signalling events are at the core of every adaptive response. Signalling events link environmental changes to physiological responses, consequently allowing cellular and organismal sustenance and survival. Classical approaches to study cellular signalling have relied on a variety of cell disruptive techniques which yield limited kinetic information, while the underlying events are much more complex. In this article, we discuss how modern live cell imaging microscopy has found increasing utilization in revealing spatio temporal dynamics of various signalling pathways. Utilizing the well studied mitogen-activated protein kinase (MAPK) signalling cascade as a template, the design, construction and utilization of `mobile' (translocation proficient) biosensors, suitable for studying MAPK signalling in living cells are described in detail. Experimental setup and results obtained from these biosensors, based on different proteins involved in the MAPK signalling cascade, have been described along with the setup of a microscope optimal for live cell imaging applications. Utilizing the ability to activate or deactivate signalling pathways using defined activators and specific pharmacological inhibitors, we also show how these sensors can yield unique spatial and temporal kinetic information of signalling in living cells.

How Many Initiator tRNA Genes Does Escherichia coli Need?

Multiple copies of a gene require enhanced investment on the part of the cell and, as such, call for an explanation. The observation that Escherichia coli has four copies of initiator tRNA (tRNA(i)) genes, encoding a special tRNA (tRNA(fMet)) required to start protein synthesis, is puzzling particularly because the cell appears to be unaffected by the removal of one copy. However, the fitness of an organism has both absolute and relative connotations. Thus, we carried out growth competition experiments between E. coli strains that differ in the number of tRNA(i) genes they contain. This has enabled us to uncover an unexpected link between the number of tRNA(i) genes and protein synthesis, nutritional status, and fitness. Wild-type strains with the canonical four tRNA(i) genes are favored in nutrient-rich environments, and those carrying fewer are favored in nutrient-poor environments. Auxotrophs behave as if they have a nutritionally poor internal environment. A heuristic model that links tRNA(i) gene copy number, genetic stress, and growth rate accounts for the findings. Our observations provide strong evidence that natural selection can work through seemingly minor quantitative variations in gene copy number and thereby impact organismal fitness.

Belief propagation for minimum weight many-to-one matchings in the random complete graph

In a complete bipartite graph with vertex sets of cardinalities n and n', assign random weights from exponential distribution with mean 1, independently to each edge. We show that, as n -> infinity, with n' = n/alpha] for any fixed alpha > 1, the minimum weight of many-to-one matchings converges to a constant (depending on alpha). Many-to-one matching arises as an optimization step in an algorithm for genome sequencing and as a measure of distance between finite sets. We prove that a belief propagation (BP) algorithm converges asymptotically to the optimal solution. We use the objective method of Aldous to prove our results. We build on previous works on minimum weight matching and minimum weight edge cover problems to extend the objective method and to further the applicability of belief propagation to random combinatorial optimization problems.

A coat of many scents: Cuticular hydrocarbons in multitrophic interactions of fig wasps with ants

The fig fig wasp system of Ficus racemosa constitutes an assemblage of galler and parasitoid wasps in which tritrophic interactions occur. Since predatory ants (Oecophylla smaragdina and Technomyrmex albipes) or mostly trophobiont-tending ants (Myrmicaria brunnea) were previously shown to differentially use volatile organic compounds (VOCs) from figs as proximal cues for predation on fig wasps, we examined the response of these ants to the cuticular hydrocarbons (CHCs) of the wasps. CHC signatures of gallers were distinguished from those of parasitoids by the methyl-branched alkanes 5-methylpentacosane and 13-methylnonacosane which characterised trophic group membership. CHC profiles of wasp predator and wasp prey were congruent suggesting that parasitoids acquire CHCs from their prey; the CHC composition of the parasitoid Apocrypta sp 2 clustered with that of its galler host Apocryptophagus fusca, while the CHC profile of the parasitoid Apocryptophagus agraensis clustered with its galler prey, the fig pollinator Ceratosolen fusciceps. In behavioural assays with ants, parasitoid CHC extracts evoked greater response in all ant species compared to galler extracts, suggesting that parasitoid CHC extracts contain more elicitors of ant behaviour than those of plant feeders. CHCs of some wasp species did not elicit significant responses even in predatory ants, suggesting chemical camouflage. Contrary to earlier studies which demonstrated that predatory ants learned to associate wasp prey with specific fig VOCs, prior exposure to fig wasp CHCs did not affect the reaction of any ant species to these CHCs. (C) 2015 Elsevier Masson SAS. All rights reserved.

Imaging cellular signalling: many `moving tales' in MAP kinase odyssey

Cellular signalling events are at the core of every adaptive response. Signalling events link environmental changes to physiological responses, consequently allowing cellular and organismal sustenance and survival. Classical approaches to study cellular signalling have relied on a variety of cell disruptive techniques which yield limited kinetic information, while the underlying events are much more complex. In this article, we discuss how modern live cell imaging microscopy has found increasing utilization in revealing spatio temporal dynamics of various signalling pathways. Utilizing the well studied mitogen-activated protein kinase (MAPK) signalling cascade as a template, the design, construction and utilization of `mobile' (translocation proficient) biosensors, suitable for studying MAPK signalling in living cells are described in detail. Experimental setup and results obtained from these biosensors, based on different proteins involved in the MAPK signalling cascade, have been described along with the setup of a microscope optimal for live cell imaging applications. Utilizing the ability to activate or deactivate signalling pathways using defined activators and specific pharmacological inhibitors, we also show how these sensors can yield unique spatial and temporal kinetic information of signalling in living cells.

Ultra-sensitive pressure dependence of bandgap of rutile-GeO2 revealed by many body perturbation theory

The reported values of bandgap of rutile GeO2 calculated by the standard density functional theory within local-density approximation (LDA)/generalized gradient approximation (GGA) show a wide variation (similar to 2 eV), whose origin remains unresolved. Here, we investigate the reasons for this variation by studying the electronic structure of rutile-GeO2 using many-body perturbation theory within the GW framework. The bandgap as well as valence bandwidth at Gamma-point of rutile phase shows a strong dependence on volume change, which is independent of bandgap underestimation problem of LDA/GGA. This strong dependence originates from a change in hybridization among O-p and Ge-(s and p) orbitals. Furthermore, the parabolic nature of first conduction band along X-Gamma-M direction changes towards a linear dispersion with volume expansion. (C) 2015 AIP Publishing LLC.

Many-Body Localization in the Presence of a Single-Particle Mobility Edge

In one dimension, noninteracting particles can undergo a localization-delocalization transition in a quasiperiodic potential. Recent studies have suggested that this transition transforms into a many-body localization (MBL) transition upon the introduction of interactions. It has also been shown that mobility edges can appear in the single particle spectrum for certain types of quasiperiodic potentials. Here, we investigate the effect of interactions in two models with such mobility edges. Employing the technique of exact diagonalization for finite-sized systems, we calculate the level spacing distribution, time evolution of entanglement entropy, optical conductivity, and return probability to detect MBL. We find that MBL does indeed occur in one of the two models we study, but the entanglement appears to grow faster than logarithmically with time unlike in other MBL systems.

On the Gaussian Many-to-One X Channel

In this paper, the Gaussian many-to-one X channel (XC), which is a special case of general multiuser XC, is studied. In the Gaussian many-to-one XC, communication links exist between all transmitters and one of the receivers, along with a communication link between each transmitter and its corresponding receiver. As per the XC assumption, transmission of messages is allowed on all the links of the channel. This communication model is different from the corresponding manyto- one interference channel (IC). Transmission strategies, which involve using Gaussian codebooks and treating interference from a subset of transmitters as noise, are formulated for the above channel. Sum-rate is used as the criterion of optimality for evaluating the strategies. Initially, a 3 x 3 many-to-one XC is considered and three transmission strategies are analyzed. The first two strategies are shown to achieve sum-rate capacity under certain channel conditions. For the third strategy, a sum-rate outer bound is derived and the gap between the outer bound and the achieved rate is characterized. These results are later extended to the K x K case. Next, a region in which the many-to-one XC can be operated as a many-to-one IC without the loss of sum-rate is identified. Furthermore, in the above region, it is shown that using Gaussian codebooks and treating interference as noise achieve a rate point that is within K/2 -1 bits from the sum-rate capacity. Subsequently, some implications of the above results to the Gaussian many-to-one IC are discussed. Transmission strategies for the many-to-one IC are formulated, and channel conditions under which the strategies achieve sum-rate capacity are obtained. A region where the sum-rate capacity can be characterized to within K/2 -1 bits is also identified. Finally, the regions where the derived channel conditions are satisfied for each strategy are illustrated for a 3 x 3 many-to-one XC and the corresponding many-to-one IC.