Heat loss in Dumbo: a theoretical approach

A flat plate model was used to calculate heat loss from the pinnae of the animated elephant Dumbo. In conditions of high wind velocity and large gradients, Dumbo could potentially dissipate more heat than he produces. This suggests that he may need the large ears to help lose the excess heat produced while flying.     

Extra-pair copulations,intra-specific brood parasitism,and quasi-parasitism in birds: a theoretical approach

Although 90 % of all bird species are monogamous, many species practice alternative reproductive strategies as extra-pair copulations, intra-specific brood parasitism, and quasi-parasitism. In territorial monogamous species, both partners hold and defend the territory from intruders. Often, the intruders are males and usually the local male banishes the intruders. Indeed, many studies focused on the response of the local male toward intruder males. However, the benefits and costs associated with the responses of the local male toward intruder females have been largely overlooked. Focusing mainly on alternative reproductive strategies, we developed a model to predict the aggression a monogamous male may demonstrate toward an intruder female during the pre-egg laying stage of his local female partner. This model demonstrates that the intensity of aggression that the local male shows toward an intruder female depends on the extra-pair copulations that his local female partner may perform. Further, the aggression also depends upon intra-specific brood parasitism and quasi-parasitism that might be carried out by the intruder female. Our approach suggests that when considering mating strategies, there is a need to assess how these three alternative reproductive strategies may affect the local male's aggression toward intruder females.     

A theoretical approach to zonation in a bioartificial liver

Bioartificial livers have yet to gain clinical acceptance. In a previous study, a theoretical model was utilized to create operating region charts that graphically illustrated viable bioartificial liver configurations. On this basis a rationale for the choice of operating and design parameters for the device was created. The concept is extended here to include aspects of liver zonation for further design optimization. In vivo, liver cells display heterogeneity with respect to metabolic activity according to their position in the liver lobule. It is thought that oxygen tension is a primary modulator of this heterogeneity and on this assumption a theoretical model to describe the metabolic zonation within an in vitro bioartificial liver device has been adopted. The distribution of the metabolic zones under varying design and operating parameters is examined. In addition, plasma flow rates are calculated that give rise to an equal distribution of the metabolic zones. The results show that when a clinically relevant number of cells are contained in the BAL (10 billion), it is possible to constrain each of the three metabolic zones to approximately one-third of the cell volume. This is the case for a number of different bioreactor designs. These considerations allow bioartificial liver design to be optimized.     

Growth of large polymer-actin complexes

Polymer-actin complexes as large as 10-50 microm with filamentous, branched, stranded, and ring shapes are obtained when fluorescent phalloidin-labeled F-actin is mixed with some synthetic polymers carrying positive charges such as poly-L-lysine, x,y-ionene bromide polymers. All growth of these complexes occurs cooperatively at some certain critical polymer concentrations, regardless of the chemical structure of the polymer, while the morphology of the complexes is substantially influenced by the chemical structure of the polymer. Poly-Lys-actin complex grows preferentially along the filament axis even above the critical concentration. 3,3-ionene-actin complexes show completely homogeneous filaments below the critical concentration but forms bundles at a higher concentration. Occasionally, ring shape complexes can be observed in the 6,6-ionene-actin complex.     

Heme ferrous-hydroperoxo complexes: some theoretical considerations

We report density functional calculations on complexes of ferrous hemes with hydroperoxide, where the axial ligand trans to OOH(-) is imidazole, thiolate, or phenoxide. The geometrical parameters and charge distributions within the Fe-O-O-H moiety are identical between the ferrous complexes reported here and their ferric counterparts previously described, even though the latter contain one unpaired electron on iron as opposed to the former, which are diamagnetic. The extra negative charge upon going from a formally ferric state to formally ferrous appears to be distributed essentially on the porphyrin. These findings support recent experimental data showing that the ferrous state of certain hemoproteins can interact with peroxides in a catalytically competent fashion, cleaving the O-O bond heterolytically in a manner reminiscent of the "canonical" ferric-peroxo complexes, and contrary to any expectations based on the Fenton concept commonly invoked in non-heme chemistry.     

Intercalation of a flavonoid,silibinin into DNA base pairs: Experimental and theoretical approach

Polyphenols are secondary plant metabolites, which have received much attention because of their potential health benefits. Silibinin (SIL) is a well‐known naturally occurring flavonolignan, which is extensively used in treating a wide variety of diseases as a dietary supplement as well as a prescribed drug. The mechanism of binding of SIL to calf thymus DNA (ctDNA) was investigated by employing multispectroscopic techniques, viz., absorption, fluorescence, and circular dichroism besides viscosity measurements and docking studies. Analysis of fluorescence results indicated that SIL has interacted with ctDNA and quenched its intensity through static quenching mechanism. The binding constant at room temperature was found to be 2.48×10⁴ mol^?1, suggesting moderate binding affinity between SIL and ctDNA. The hypochromicity observed in the absorption spectra of ctDNA in the presence of SIL revealed the intercalation of SIL into ctDNA base pairs. Further, the intercalative mode of binding between SIL and ctDNA was confirmed by viscosity measurements and molecular docking studies. The outcome of present study helps to decipher the interaction mechanism between SIL and DNA at physiological pH, which further assists in the design of a new analogue for better therapeutic effects.     

Information theoretical quantification of cooperativity in signalling complexes

Background  

Intra-cellular information exchange, propelled by cascades of interacting signalling proteins, is essential for the proper functioning and survival of cells. Now that the interactome of several organisms is being mapped and several structural mechanisms of cooperativity at the molecular level in proteins have been elucidated, the formalization of this fundamental quantity, i.e. information, in these very diverse biological contexts becomes feasible.     

Trapping electrophoresis and ratchets: a theoretical study for DNA-protein complexes.

Recently, Griess and Serwer (1998. Biophys. J. 74:A71) showed that it was possible to use trapping electrophoresis and unbiased but asymmetrical electric field pulses to build a correlation ratchet that would allow the efficient separation of naked DNAs from identical DNAs that form a complex with a bulky object such as a protein. Here we present a theoretical investigation of this novel macromolecular separation process. We start by looking at the general features of this electrophoretic ratchet mechanism in the zero-frequency limit. We then examine the effects of finite frequencies on velocity and diffusion. Finally, we use the biased reptation model and computer simulations to understand the band-broadening processes. Our study establishes the main experimental regimes that can provide good resolution for specific applications.     

A multidomain flexible docking approach to deal with large conformational changes in the modeling of biomolecular complexes

Binding-induced backbone and large-scale conformational changes represent one of the major challenges in the modeling of biomolecular complexes by docking. To address this challenge, we have developed a flexible multidomain docking protocol that follows a divide-and-conquer approach to model both large-scale domain motions and small- to medium-scale interfacial rearrangements: the flexible binding partner is treated as an assembly of subparts/domains that are docked simultaneously making use of HADDOCK's multidomain docking ability. For this, the flexible molecules are cut at hinge regions predicted using an elastic network model. The performance of this approach is demonstrated on a benchmark covering an unprecedented range of conformational changes of 1.5 to 19.5 ?. We show from a statistical survey of known complexes that the cumulative sum of eigenvalues obtained from the elastic network has some predictive power to indicate the extent of the conformational change to be expected.     

Catalysis of decarboxylation by an adjacent negative charge: a theoretical approach

We have calculated the rate acceleration in decarboxylation reactions that can be accomplished by charge-charge repulsion between the substrate carboxylate and an adjacent negative charge in media of various dielectric constants. It has been shown that a full negative charge or surrounding partial negative charges will have the same effect. It is concluded that the rate of decarboxylation could be greatly accelerated by the presence of a negative charge nearby. For example, in media with dielectric constants from 5.62 to 20.7, a 10(8)-fold rate acceleration could be achieved by a negative charge placed 3.77 A away from the substrate carboxylate group. However, pK(a) perturbation on two carboxylate groups at close proximity may limit the extent of catalysis. It should also be noted that the extent of catalysis does not change much when the dielectric constant varies from 5.62 to 20.7.     

Controlling tick-borne diseases through domestic animal management: a theoretical approach

Vector-borne diseases are of global importance to human and animal health. Empirical trials of effective methods to control vectors and their pathogens can be difficult for practical, financial and ethical reasons. Here, therefore, we use a mathematical model to predict the effectiveness of a vector-borne disease control method. As a case study, we use the tick-louping ill virus system, where sheep are treated with acaricide in an attempt to control ticks and disease in red grouse , an economically important game bird. We ran the model under different scenarios of sheep flock sizes, alternative host (deer) densities, acaricide efficacies and tick burdens. The model predicted that, with very low deer densities, using sheep as tick mops can reduce the tick population and virus prevalence. However, treatment is ineffective above a certain threshold deer density, dependent on the comparative tick burden on sheep and deer. The model also predicted that high efficacy levels of acaricide must be maintained for effective tick control. This study suggests that benignly managing one host species to protect another host species from a vector and pathogen can be effective under certain conditions. It also highlights the importance of understanding the ecological complexity of a system, in order to target control methods only under certain circumstances for maximum effectiveness.     

Mating strategies in primates: a game theoretical approach to infanticide

Infanticide by newly immigrated or newly dominant males is reported among a variety of taxa, such as birds, rodents, carnivores and primates. Here we present a game theoretical model to explain the presence and prevalence of infanticide in primate groups. We have formulated a three-player game involving two males and one female and show that the strategies of infanticide on the males' part and polyandrous mating on the females' part emerge as Nash equilibria that are stable under certain conditions. Moreover, we have identified all the Nash equilibria of the game and arranged them in a novel hierarchical scheme. Only in the subspace spanned by the males are the Nash equilibria found to be strict, and hence evolutionarily stable. We have therefore proposed a selection mechanism informed by adaptive dynamics to permit the females to transition to, and remain in, optimal equilibria after successive generations. Our model concludes that polyandrous mating by females is an optimal strategy for the females that minimizes infanticide and that infanticide confers advantage to the males only in certain regions of parameter space. We have shown that infanticide occurs during turbulent changes accompanying male immigration into the group. For changes in the dominance hierarchy within the group, we have shown that infanticide occurs only in primate groups where the chance for the killer to sire the next infant is high. These conclusions are confirmed by observations in the wild. This model thus has enabled us to pinpoint the fundamental processes behind the reproductive decisions of the players involved, which was not possible using earlier theoretical studies.     

DNA conformation and energy in nucleosome core: a theoretical approach

DNA conformation in complex with proteins is far from its canonical B-form. The affinity of complex formation and structure of DNA depend on its attachment configuration and sequence. In this article, we develop a mechanical model to address the problem of DNA structure and energy under deformation. DNA in nucleosome core particle is described as an example. The structure and energy of nucleosomal DNA is calculated based on its sequence and positioning state. The inferred structure has remarkable similarity with X-ray data. Although there is no sequence-specific interaction of bases and the histone core, we found considerable sequence dependency for the nucleosomal DNA positioning. The affinity of nucleosome formation for several sequences is examined and the differences are compatible with observations. We argue that structural energy determines the natural state of nucleosomal DNA and is the main reason for affinity differences in vitro. This theory can be utilized for the DNA structure and energy determination in protein–DNA complexes in general.

An animated Interactive 3D Complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:JBSD:17     

Maximum running speed limitations on terrestrial mammals: a theoretical approach

Here we study maximum running speed (MRS) limitations on a previously proposed model of energetic and muscle-tendon unit functions on running mammals. In the present work the MRS and some anatomical or physiological limitations are estimated for mammals with body mass between 1.5 and 300 kg. The MRS variations with body mass are discussed and compared with results of previous experimental and observational studies. The tendon strength seems to be the most relevant limitation, but leg extensor muscle mass and metabolic costs could be relevant also. The physiological maximum muscle speed seems to be less important in the body mass range studied here.