Invasion of cooperators in lattice populations: Linear and non-linear public good games

A generalized version of the N-person volunteer's dilemma (NVD) Game has been suggested recently for illustrating the problem of N-person social dilemmas. Using standard replicator dynamics it can be shown that coexistence of cooperators and defectors is typical in this model. However, the question of how a rare mutant cooperator could invade a population of defectors is still open.     

van der Waals forces influencing adhesion of cells

Adhesion molecules, often thought to be acting by a ‘lock and key’ mechanism, have been thought to control the adhesion of cells. While there is no doubt that a coating of adhesion molecules such as fibronectin on a surface affects cell adhesion, this paper aims to show that such surface contamination is only one factor in the equation. Starting from the baseline idea that van der Waals force is a ubiquitous attraction between all molecules, and thereby must contribute to cell adhesion, it is clear that effects from geometry, elasticity and surface molecules must all add on to the basic cell attractive force. These effects of geometry, elasticity and surface molecules are analysed. The adhesion force measured between macroscopic polymer spheres was found to be strongest when the surfaces were absolutely smooth and clean, with no projecting protruberances. Values of the measured surface energy were then about 35 mJ m⁻², as expected for van der Waals attractions between the non-polar molecules. Surface projections such as abrasion roughness or dust reduced the molecular adhesion substantially. Water cut the measured surface energy to 3.4 mJ m⁻². Surface active molecules lowered the adhesion still further to less than 0.3 mJ m⁻². These observations do not support the lock and key concept.     

Bayesian inference for stochastic kinetic models using a diffusion approximation

This article is concerned with the Bayesian estimation of stochastic rate constants in the context of dynamic models of intracellular processes. The underlying discrete stochastic kinetic model is replaced by a diffusion approximation (or stochastic differential equation approach) where a white noise term models stochastic behavior and the model is identified using equispaced time course data. The estimation framework involves the introduction of m- 1 latent data points between every pair of observations. MCMC methods are then used to sample the posterior distribution of the latent process and the model parameters. The methodology is applied to the estimation of parameters in a prokaryotic autoregulatory gene network.     

Does directed technological change get greener: Empirical evidence from Shanghai's industrial green development transformation

The degree of technological change biased to the environmental factor is crucial to industrial sustainable development. Using the stochastic frontier analysis method based on the translog production function and the panel data of 32 industrial sub-sectors in Shanghai over 1994–2011, this paper combines the evolution dynamic of the frontier technological structure with the evolution dynamic of technological change direction to estimate the output elasticities of production factors and the growth rate of green total factor productivity. Also, we investigate and compare the degrees of technological change biased to four production factors, i.e., capital, labor, energy, and carbon emissions. The results show that the industrial green total factor productivity in Shanghai presents an overall upward trend and mainly depends on the technical efficiency change. The improvements of labor productivity, R&D intensity, and energy efficiency can effectively enhance the green technical efficiency, while capital deepening has a mitigation effect on the green technical efficiency. The technological change of Shanghai's industrial production biases to energy use and capital saving, causing a high energy demand of industrial development. Under the dual impacts of economic development and energy-saving and emission-reduction policies, the degree of technological change biased to the environmental factor (carbon emissions) displays strong and weak alternations, indicating that the green bias of industrial technological change in Shanghai is not stable and that the green transformation of industrial development model needs to be further advanced.     

A numeric study of the noise-induced tremor in a mathematical model of the stretch reflex

A mathematical model of the stretch reflex for the cat soleus muscle is presented. The time-delay differential equations of the model are solved using the fourth-order Runge-Kutta algorithm, introducing a Gaussian-noise term to simulate the environmental noise. The muscle response dynamics are then studied under various levels of average muscle activation. Finally, the feasibility of explaining the so-called physiological tremor from the properties of the stretch reflex mechanisms is discussed by comparing our results with reported experimental evidence.     

Metapopulation theory for fragmented landscapes

We review recent developments in spatially realistic metapopulation theory, which leads to quantitative models of the dynamics of species inhabiting highly fragmented landscapes. Our emphasis is in stochastic patch occupancy models, which describe the presence or absence of the focal species in habitat patches. We discuss a number of ecologically important quantities that can be derived from the full stochastic models and their deterministic approximations, with a particular aim of characterizing the respective roles of the structure of the landscape and the properties of the species. These quantities include the threshold condition for persistence, the contributions that individual habitat patches make to metapopulation dynamics and persistence, the time to metapopulation extinction, and the effective size of a metapopulation living in a heterogeneous patch network.     

Distributed torsion angle grid search in high dimensions: A systematic approach to NMR structure determination

Two complementary approaches for systematic search in torsion angle space are described for the generation of all conformations of polypeptides which satisfy experimental NMR restraints, hard-sphere van der Waals radii, and rigid covalent geometry. The first procedure is based on a recursive, tree search algorithm for the examination of linear chains of torsion angles, and uses a novel treatment to propagate the search results to neighboring regions so that the structural consequences of the restraints are fully realized. The second procedure is based on a binary combination of torsion vector spaces for connected submolecules, and produces intermediate results in Cartesian space for a more robust restraint analysis. Restraints for NMR applications include bounds on torsion angles and internuclear distances, including relational and degenerate restraints involving equivalent and nonstereoassigned protons. To illustrate these methods, conformation search results are given for the tetrapeptide APGA restrained to an idealized -turn conformation, an alanine octapeptide restrained to a right-handed helical conformation, and the structured region of the peptide SYPFDV.     

Two types of modified cardiac Na+ channels after cytosolic interventions at the α-subunit capable of removing Na+ inactivation

Failure of inactivation is the typical response of voltage-gated Na⁺ channels to the cytosolic presence of proteolytic enzymes, protein reagents such as N-bromoacetamide (NBA) or iodate, and antibodies directed against the linker between domains III and IV of the α-subunit. The present patch clamp experiments with cardiac Na⁺ channels aimed to test the hypothesis that these interventions may provoke the occurrence of non-inactivating Na⁺ channels with distinct kinetic properties. A site-directed polyclonal antibody (anti-SLP2, target sequence 1481–1496 of the cardiac Na⁺ channel α-subunit) eliminated fast Na⁺ inactivation to induce burst activity which was accompanied by the occurrence of two open states. A deactivation process terminated channel activity during membrane depolarization proceeding with time constants of close to 40 ms (at –40 mV). NBA-modified and iodate-modified Na⁺ channels were kinetically indistinguishable from the anti-SLP2-modified type since they likewise deactivate and, thus, attain an only moderate P_o of close to 20%. This is fundamentally different from the behaviour of enzymatically-modified Na⁺ channels: after cytosolic proteolysis with α-chymotrypsin, trypsin or pronase, mean P_o during membrane depolarization amounted to approximately 40% because deactivation operated extremely slowly and less efficiently (time constants 100–200 ms at –40 mV, as a minimum) or was virtually non-operating. In-vitro cleavage of the synthetic linker sequence 1481–1496 confirmed that this part of the α-subunit provides a substrate for these peptidases or reactants for NBA but cannot be chemically modified by iodate. This iodate resistance indicates that iodate-modified Na⁺ channels are based on a structural alteration of still another region which is also involved in Na⁺ inactivation, besides the linker between domains III and IV of the α-subunit. Endogenous peptidases such as calpain did not affect Na⁺ inactivation. This stresses the stochastic nature of a kinetic peculiarity of cardiac Na⁺ channels, mode-switching to a non-inactivating mode. Received: 25 May 1996 / Accepted: 12 September 1996     

Structural adaptations of the femur and humerus to arboreal and terrestrial environments in three species of macaque

One reason to measure cross-sectional structural properties of primate long bones is to define mechanically relevant complexes of traits that describe the adaptation of bone to different biomechanical environments. This can be effectively accomplished when congeneric species having different postural and locomotor behaviors are compared. This paper compares the cross-sectional geometry of the femur and humerus in three behaviorally different macaque species as a basis for defining such patterns. Cross-sectional moments of inertia in the standard anatomical planes were calculated at five locations along the diaphyses of the femur and humerus in Macaca fascicularis, M. nemestrina, and M. mulatta. The data suggest that the "barrel-shaped" femur is associated with behaviors for which long limbs and small body size are an asset. This may be associated with, but is not restricted to, leaping behaviors. The data also suggest that structural rigidity of the femur and humerus is greater per unit body weight in primates that spend significant amounts of time in terrestrial environments than in those that are more restricted to climbing in arboreal environments.     

Determination of the NMR solution structure of a specific DNA complex of the Myb DNA-binding domain

Summary The solution structure of a specific DNA complex of the minimum DNA-binding domain of the mouse c-Myb protein was determined by distance geometry calculations using a set of 1732 nuclear Overhauser enhancement (NOE) distance restraints. In order to determine the complex structure independent of the initial guess, we have developed two different procedures for the docking calculation using simulated annealing in four-dimensional space (4D-SA). One is a multiple-step procedure, where the protein and the DNA were first constructed independently by 4D-SA using only the individual intramolecular NOE distance restraints. Here, the initial structure of the protein was a random coil and that of the DNA was a typical B-form duplex. Then, as the starting structure for the next docking procedure, the converged protein and DNA structures were placed in random molecular orientations, separated by 50 Å. The two molecules were docked by 4D-SA utilizing all the restraints, including the additional 66 intermolecular distance restraints. The second procedure comprised a single step, in which a random-coil protein and a typical B-form DNA duplex were first placed 70 Å from each other. Then, using all the intramolecular and intermolecular NOE distance restraints, the complex structure was constructed by 4D-SA. Both procedures yielded the converged complex structures with similar quality and structural divergence, but the multiple-step procedure has much better convergence power than the single-step procedure. A model study of the two procedures was performed to confirm the structural quality, depending upon the number of intermolecular distance restraints, using the X-ray structure of the engrailed homeodomain-DNA complex.Abbreviations rmsd root-mean-square deviation - NOE nuclear Overhauser enhancement - 4D-SA simulated annealing in four-dimensional space - Myb-R2R3 repeats 2 and 3 of the DNA-binding domain of the c-Myb protein - DNA 16 Myb-specific binding DNA duplex with 16 base pairs - IHDD-C residues 3 to 59 of the C-chain of the engrailed homeodomain-DNA complex - DNA11 DNA duplex with base pairs 9 to 19 of the engrailed homeodomain-DNA complex