The evolution of cooperation in asymmetric systems

Explaining "Tragedy of the Commons" of evolution of cooperation remains one of the greatest problems for both biology and social science. Asymmetrical interaction, which is one of the most important characteristics of cooperative system, has not been sufficiently considered in the existing models of the evolution of cooperation. Considering the inequality in the number and payoff between the cooperative actors and recipients in cooperation systems, discriminative density-dependent interference competition will occur in limited dispersal systems. Our model and simulation show that the local but not the global stability of a cooperative interaction can be maintained if the utilization of common resource remains unsaturated, which can be achieved by density-dependent restraint or competition among the cooperative actors. More intense density dependent interference competition among the cooperative actors and the ready availability of the common resource, with a higher intrinsic contribution ratio of a cooperative actor to the recipient, will increase the probability of cooperation. The cooperation between the recipient and the cooperative actors can be transformed into conflict and, it oscillates chaotically with variations of the affecting factors under different environmental or ecological conditions. The higher initial relatedness (i.e. similar to kin or reciprocity relatedness), which is equivalent to intrinsic contribution ratio of a cooperative actor to the recipient, can be selected for by penalizing less cooperative or cheating actors but rewarding cooperative individuals in asymmetric systems. The initial relatedness is a pivot but not the aim of evolution of cooperation. This explains well the direct conflict observed in almost all cooperative systems.

Three-dimensional image reconstruction of dephosphorylated smooth muscle heavy meromyosin reveals asymmetry in the interaction between myosin heads and placement of subfragment 2

Regulation of the actin-activated ATPase of smooth muscle myosin II is known to involve an interaction between the two heads that is controlled by phosphorylation of the regulatory light chain. However, the three-dimensional structure of this inactivated form has been unknown. We have used a lipid monolayer to obtain two-dimensional crystalline arrays of the unphosphorylated inactive form of smooth muscle heavy meromyosin suitable for structural studies by electron cryomicroscopy of unstained, frozen-hydrated specimens. The three-dimensional structure reveals an asymmetric interaction between the two myosin heads. The ATPase activity of one head is sterically “blocked” because part of its actin-binding interface is positioned onto the converter domain of the second head. ATPase activity of the second head, which can bind actin, appears to be inhibited through stabilization of converter domain movements needed to release phosphate and achieve strong actin binding. When the subfragment 2 domain of heavy meromyosin is oriented as it would be in an actomyosin filament lattice, the position of the heads is very different from that needed to bind actin, suggesting an additional contribution to ATPase inhibition in situ.

Crystal structures and hydrogen bonding in the anhydrous tryptaminium salts of the isomeric (2,4-dichlorophenoxy)acetic and (3,5-dichlorophenoxy)acetic acids

The anhydrous salts of 1H-indole-3-ethanamine (tryptamine) with isomeric (2,4-dichlorophenoxy)acetic acid (2,4-D) and (3,5-dichlorophenoxy)acetic (3,5-D), C10H13N2+ (C8H5Cl2O3)-, [(I) and (II), respectively] have been determined and their one-dimensional hydrogen-bonded polymeric structures are described. In the crystal of (I),the aminium H-atoms are involved in three separate inter-species N-H...O hydrogen-bonding interactions, two with carboxyl O-atom acceptors and the third in an asymmetric three-centre bidentate carboxyl O,O' chelate [graph set R2/1(4)]. The indole H-atom forms an N-H...O~carboxyl~ hydrogen bond, extending the chain structure along the b axial direction. In (II), two of the three aminium H-atoms are also involved in N-H...O(carboxyl) hydrogen bonds similar to (I) but with the third, a three-centre asymmetric interaction with carboxyl and phenoxy O-atoms is found [graph set R2/1(5)]. The chain polymeric extension is also along b. There are no pi--pi ring interactions in either of the structures. The aminium side chain conformations differ significantly between the two structures, reflecting the conformational ambivalence of the tryptaminium cation, as found also in the benzoate salts.

Interaction of ecoP15I DNA methyltransferase with oligonucleotides containing the asymmetric sequence 5?-CAGCAG-3

EcoP15I DNA methyltransferase (Mtase) recognizes the asymmeteric sequence CAGCAG and catalyzes the transfer of a methyl group from S-adenosyl-L-methionine to the second adenine residue. We have investigated the DNA binding properties of EcoP15I DNA Mtase using gel mobility shift assays. EcoP15I DNA Mtase binds approximately threefold more tightly to DNA containing its recognition sequence, CAGCAG, than to non-specific sequences in the absence or presence of cofactors. Interestingly, in the presence of ATP the discrimination between specific and non-specific sequences increases significantly. These results suggest for the first time a role for ATP in DNA recognition by type III restriction-modification enzymes. In addition, we have shown that bromodeoxyuridine-containing oligonucleotides form complexes with EcoP15I DNA Mtase that are crosslinked upon irradiation. More importantly, we have shown that the crosslink site is at the site of DNA binding, since it can be suppressed by an excess of unmodified oligonucleotide. EcoP15I DNA Mtase exhibited Michaelis-Menten kinetics with both unmodified and bromodeoxyuridine-substituted DNA, with a higher specificity constant for the latter. Furthermore, gel mobility shift assays showed that proteolyzed EcoP15I DNA Mtase formed a specific complex with DNA, which had similar mobility as the native protein-DNA complex. Taken together these results form the basis fora detailed structure-function analysis of EcoP15I DNA Mtase.

Co-constructed interaction in a paired speaking test : the rater's perspective

The definition and operationalisation of interactional competence in speaking tests that entail co-construction of discourse is an area of language testing requiring further research. This article explores the reactions of four trained raters to paired candidates who oriented to asymmetric patterns of interaction in a discussion task. Through an analysis of candidate discourse combined with rater notes, stimulated verbal recalls, rater discussions and scores awarded for interactional effectiveness, the article examines the extent to which raters compensate or penalise candidates for their role in co-constructing asymmetric interactional patterns. The article argues that key features of the interaction are perceived by the raters as mutual achievements, and it further suggests that the awarding of shared scores for interactional competence is one way of acknowledging the inherently co-constructed nature of interaction in a paired speaking test.

Theoretical investigation of mechanisms of formation and interaction of nanoparticles

In this thesis an investigation into theoretical models for formation and interaction of nanoparticles is presented. The work presented includes a literature review of current models followed by a series of five chapters of original research. This thesis has been submitted in partial fulfilment of the requirements for the degree of doctor of philosophy by publication and therefore each of the five chapters consist of a peer-reviewed journal article. The thesis is then concluded with a discussion of what has been achieved during the PhD candidature, the potential applications for this research and ways in which the research could be extended in the future. In this thesis we explore stochastic models pertaining to the interaction and evolution mechanisms of nanoparticles. In particular, we explore in depth the stochastic evaporation of molecules due to thermal activation and its ultimate effect on nanoparticles sizes and concentrations. Secondly, we analyse the thermal vibrations of nanoparticles suspended in a fluid and subject to standing oscillating drag forces (as would occur in a standing sound wave) and finally on lattice surfaces in the presence of high heat gradients. We have described in this thesis a number of new models for the description of multicompartment networks joined by a multiple, stochastically evaporating, links. The primary motivation for this work is in the description of thermal fragmentation in which multiple molecules holding parts of a carbonaceous nanoparticle may evaporate. Ultimately, these models predict the rate at which the network or aggregate fragments into smaller networks/aggregates and with what aggregate size distribution. The models are highly analytic and describe the fragmentation of a link holding multiple bonds using Markov processes that best describe different physical situations and these processes have been analysed using a number of mathematical methods. The fragmentation of the network/aggregate is then predicted using combinatorial arguments. Whilst there is some scepticism in the scientific community pertaining to the proposed mechanism of thermal fragmentation,we have presented compelling evidence in this thesis supporting the currently proposed mechanism and shown that our models can accurately match experimental results. This was achieved using a realistic simulation of the fragmentation of the fractal carbonaceous aggregate structure using our models. Furthermore, in this thesis a method of manipulation using acoustic standing waves is investigated. In our investigation we analysed the effect of frequency and particle size on the ability for the particle to be manipulated by means of a standing acoustic wave. In our results, we report the existence of a critical frequency for a particular particle size. This frequency is inversely proportional to the Stokes time of the particle in the fluid. We also find that for large frequencies the subtle Brownian motion of even larger particles plays a significant role in the efficacy of the manipulation. This is due to the decreasing size of the boundary layer between acoustic nodes. Our model utilises a multiple time scale approach to calculating the long term effects of the standing acoustic field on the particles that are interacting with the sound. These effects are then combined with the effects of Brownian motion in order to obtain a complete mathematical description of the particle dynamics in such acoustic fields. Finally, in this thesis, we develop a numerical routine for the description of "thermal tweezers". Currently, the technique of thermal tweezers is predominantly theoretical however there has been a handful of successful experiments which demonstrate the effect it practise. Thermal tweezers is the name given to the way in which particles can be easily manipulated on a lattice surface by careful selection of a heat distribution over the surface. Typically, the theoretical simulations of the effect can be rather time consuming with supercomputer facilities processing data over days or even weeks. Our alternative numerical method for the simulation of particle distributions pertaining to the thermal tweezers effect use the Fokker-Planck equation to derive a quick numerical method for the calculation of the effective diffusion constant as a result of the lattice and the temperature. We then use this diffusion constant and solve the diffusion equation numerically using the finite volume method. This saves the algorithm from calculating many individual particle trajectories since it is describes the flow of the probability distribution of particles in a continuous manner. The alternative method that is outlined in this thesis can produce a larger quantity of accurate results on a household PC in a matter of hours which is much better than was previously achieveable.

Interaction between the Z-type DNA duplex and 1,3-propanediamine:crystal structure of d(CACGTG)(2) at 1.2 angstrom resolution

The crystal structure of a hexamer duplex d(CACGTG)(2) has been determined and refined to an R-factor of 18.3% using X-ray data up to 1.2 angstrom resolution. The sequence crystallizes as a left-handed Z-form double helix with Watson-Crick base pairing. There is one hexamer duplex, a spermine molecule, 71 water molecules, and an unexpected diamine (Z-5, 1,3-propanediamine, C3H10N2)) in the asymmetric unit. This is the high-resolution non-disordered structure of a Z-DNA hexamer containing two AT base pairs in the interior of a duplex with no modifications such as bromination or methylation on cytosine bases. This structure does not possess multivalent cations such as cobalt hexaammine that are known to stabilize Z-DNA. The overall duplex structure and its crystal interactions are similar to those of the pure-spermine form of the d(CGCGCG)(2) structure. The spine of hydration in the minor groove is intact except in the vicinity of the T5A8 base pair. The binding of the Z-5 molecule in the minor grove of the d(CACGTG)(2) duplex appears to have a profound effect in conferring stability to a Z-DNA conformation via electrostatic complementarity and hydrogen bonding interactions. The successive base stacking geometry in d(CACGTG)(2) is similar to the corresponding steps in d(CG)(3). These results suggest that specific polyamines such as Z-5 could serve as powerful inducers of Z-type conformation in unmodified DNA sequences with AT base pairs. This structure provides a molecular basis for stabilizing AT base pairs incorporated into an alternating d(CG) sequence.

Molecular dynamics simulation of interaction of a dislocation array from a crack tip with grain boundaries

The interaction of a dislocation array emitted from a crack tip under mode II loading with asymmetric tilt grain boundaries (GBs) is analysed by the molecular dynamics method. The GBs can generally be described by planar and linear matching zones and unmatching zones. All GBs are observed to emit dislocations. The GBs migrated easily due to their planar and linear matching structure and asymmetrical type. The diffusion induced by stress concentration is found to promote the GB migration. The transmissions of dislocations are either along the matched plane or along another plane depending on tilt angle theta. Alternate processes of stress concentration and stress relaxation take place ahead of the pileup. The stress concentration can be released either by transmission of dislocations, by atom diffusion along GBs, or by migration of GBs by formation of twinning bands. The simulated results also unequivocally demonstrate two processes, i.e. asymmetrical GBs evolving into symmetrical ones and unmatching zones evolving into matching ones during the loading process.

Generation of periodic ultrashort electron bunches and strongly asymmetric ion Coulomb explosion in nanometer foils interacting with ultra-intense laser pulse

The interaction of a linearly polarized intense laser pulse with an ultrathin nanometer plasma layer is investigated to understand the physics of the ion acceleration. It is shown by the computer simulation that the plasma response to the laser pulse comprises two steps. First, due to the vxB effect, electrons in the plasma layer are extracted and periodic ultrashort relativistic electron bunches are generated every half of a laser period. Second, strongly asymmetric Coulomb explosion of ions in the foil occurs due to the strong electrostatic charge separation, once the foil is burnt through. Followed by the laser accelerated electron bunch, the ion expansion in the forward direction occurs along the laser beam that is much stronger as compared to the backward direction. (c) 2008 American Institute of Physics.

Anomalous Rashba spin-orbit interaction in InAs/GaSb quantum wells

We theoretically investigate the Rashba spin-orbit interaction in InAs/GaSb quantum wells (QWs). We find that the Rashba spin-splitting (RSS) sensitively depends on the thickness of the InAs layer. The RSS exhibits nonlinear behavior for narrow InAs/GaSb QWs and the oscillating feature for wide InAs/GaSb QWs. The nonlinear and oscillating behaviors arise from the weakened and enhanced interband coupling. The RSS also show asymmetric features respect to the direction of the external electric field. (C) 2008 American Institute of Physics.

Asymmetric stark shifts of exciton in InAs/GaAs pyramidal quantum dots

Within the framework of the single-band effective-mass envelope-function theory, the effect of electric field on the electronic structures of pyramidal quantum dot is investigated. Taking the Coulomb interaction between the heavy holes and electron into account, the quantum confined Stark shift of the exciton as functions of the strength and direction of applied electric field and the size of the quantum dot are obtained. An interesting asymmetry of Stark shifts around the zero field is found. (C) 1997 Elsevier Science Ltd.

Differential isospin-fractionation in dilute asymmetric nuclear matter

The differential isospin-fractionation (IsoF) during the liquid-gas phase transition in dilute asymmetric nuclear matter is studied as a function of nucleon momentum. Within a self-consistent thermal model it is shown that the neutron/proton ratio of the gas phase becomes smaller than that of the liquid phase for energetic nucleons, although the gas phase is overall more neutron-rich. Clear indications of the differential IsoF consistent with the thermal model predictions are demonstrated within a transport model for heavy-ion reactions. Future comparisons with experimental data will allow us to extract critical information about the momentum dependence of the isovector strong interaction.