Site-Specific thermodynamics of ising networks: A theorem for linearly connected subsystems

An Ising network consists of a set of N units existing in two possible states, 0 and 1. If two units contact each other in the network, there is a nearest neighbor interaction that depends only on the states of the units. If an Ising network can be split into two independent subsystems by deleting the contact between two units, then these units specify each other's site-specific properties and the state of either unit uniquely specifies the state of the other. This theorem holds regardless of (a) the dimensional embedding of the network as a whole, (b) the precise interaction geometry among the units within either subsystem, and (c) the intrinsic energy for the 0 → 1 switching of any given unit. Either subsystem in the network can be considered as a probe for the state of the unit in the other subsystem to which the probe is connected. Application of the theorem to the analysis of the site-specific properties of the biologically relevant case of a linear network, or heteropolymer, yields a rather counterintuitive result. Knowledge of the state of the end unit in the network, as a function of the change in the thermodynamic driving force for the 0 → 1 transition, is sufficient to completely resolve the energetics of the network. © 1994 John Wiley & Sons, Inc.     

Radiationless energy transfer through a polypeptide chain

Electronic excitation spectra were measured on a donor-acceptor pair which was separated by oligomers of L -proline of gradually increasing lengths. The logarithmic plot of the transfer efficiency versus the donor-acceptor separation, for (pro)_n oligomers with n?5, yielded a slope of 5.8 ± 0.3 in good agreement with the theoretical value of 6, predicted by Forster. The above method is suggested as a tool for the estimation of distances between certain chromophoric groups, covalently bound to macromolecules. The use of any stereoregular polymer for calibrating a certain energy donor-acceptor pair is discussed.     

Derivation and testing of pair potentials for protein folding. When is the quasichemical approximation correct?

Many existing derivations of knowledge-based statistical pair potentials invoke the quasichemical approximation to estimate the expected side-chain contact frequency if there were no amino acid pair-specific interactions. At first glance, the quasichemical approximation that treats the residues in a protein as being disconnected and expresses the side-chain contact probability as being proportional to the product of the mole fractions of the pair of residues would appear to be rather severe. To investigate the validity of this approximation, we introduce two new reference states in which no specific pair interactions between amino acids are allowed, but in which the connectivity of the protein chain is retained. The first estimates the expected number of side-chain contracts by treating the protein as a Gaussian random coil polymer. The second, more realistic reference state includes the effects of chain connectivity, secondary structure, and chain compactness by estimating the expected side-chain contrast probability by placing the sequence of interest in each member of a library of structures of comparable compactness to the native conformation. The side-chain contact maps are not allowed to readjust to the sequence of interest, i.e., the side chains cannot repack. This situation would hold rigorously if all amino acids were the same size. Both reference states effectively permit the factorization of the side-chain contact probability into sequence-dependent and structure-dependent terms. Then, because the sequence distribution of amino acids in proteins is random, the quasichemical approximation to each of these reference states is shown to be excellent. Thus, the range of validity of the quasichemical approximation is determined by the magnitude of the side-chain repacking term, which is, at present, unknown. Finally, the performance of these two sets of pair interaction potentials as well as side-chain contact fraction-based interaction scales is assessed by inverse folding tests both without and with allowing for gaps.     

Cooperation under predation risk: a data-based ESS analysis

Two fish that jointly approach a predator in order to inspect it share the deadly risk of capture depending on the distance between them. Models are developed that seek ESS inspection distances of both single prey and pairs, based on experimental data of the risk that prey (sticklebacks) incur when they approach a predator (pike) to varying distances. Our analysis suggests that an optimal inspection distance can exist for a single fish, and for two equal fish behaving entirely cooperatively so as to maximize the fitness of the pair. Two equal fish inspecting cooperatively should inspect at an equal distance from the predator. The optimal distance is much closer to the predator for cooperative pairs than for single inspectors. However, optimal inspection for two equal fish behaving cooperatively operates across a rather narrow band of conditions relating to the benefits of cooperation. Evolutionarily stable inspection can also exist for two equal fish behaving non-cooperatively such that each acts to make a best reply (in terms of its personal fitness) to its opponent''s strategy. Non-cooperative pairs should also inspect at equal distance from the pike. Unlike the ''single fish'' and ''cooperative'' optima, which are unique inspection distances, there exists a range of ESS inspection distances. If either fish chooses to move to any point in this zone, the best reply of its opponent is to match it (move exactly alongside). Unilateral forward movement in the ''match zone'' may not be possible without some cooperation, but if the pair can ''agree'' to move forward synchronously, maintaining equal distance, inspection will occur at the nearest point in this zone to the predator. This ''near threshold'' is an ESS and is closer to the predator than the single fish optimum: pairs behaving almost selfishly can thus attain greater benefits from inspection by the protection gained from Hamilton''s dilution effect. That pairs should inspect more closely than single fish conforms with empirical findings. Phenotypic asymmetries in costs and benefits between the fish are not yet included in the model.     

A Measure to Evaluate the Closeness of Satterthwaite's Approximation

Satterthwaite's approximation of the distribution of a nonnegative linear combination of independent mean squares is addressed in this article. A measure is developed to quantify the closeness of this approximation by using certain optimization results given by THIBAUDEAU and STYAN (1985). The main advantage of the proposed measure is to provide a theoretical framework for determining conditions under which Satterthwaite's approximation may be inadequate. This is demonstrated in three examples portraying frequently encountered problems in analysis of variance.     

Parallel Double Helices of DNA. Conformational Analysis of Regular Helices with the Second Order Symmetry Axis

Abstract

We have performed a conformational analysis of DNA double helices with parallel directed backbone strands connected with the second order symmetry axis being at the same time the helix axis. The calculations were made for homopolymers poly(dA) · poly(dA), poly(dC) · poly(dC), poly(dG) poly(dG), and poly(dT) · poly(dT). All possible variants of hydrogen bonding of base pairs of the same name were studied for each polymer. The maps of backbone chain geometrical existence were constructed. Conformational and helical parameters corresponding to local minima of conformational energy of “parallel” DNA helices, calculated at atom-atom approximation, were determined. The dependence of conformational energy on the base pair and on the hydrogen bond type was analysed. Two major conformational advantageous for “parallel” DNA's do not depend much on the hydrogen-bonded base pair type were indicated. One of them coincided with the conformational region typical for “antiparallel” DNA in particular for the B-form DNA Conformational energy of “parallel” DNA depends on the base pair type and for the most part is similar to the conformational energy of “antiparallel” B-DNA.     

A Class of Ratio Cum Product-Type Estimator in Double Sampling

A class of ratio cum product-type estimator is proposed in case of double sampling in the present paper. Its bias and variance to the first order of approximation are obtained. For an appropriate weight ‘a’ and a good range of α-values, it is found that the proposed estimator is more efficient than the set of estimator viz., simple mean estimator, usual ratio and product estimators, SRIVASTAVA 's estimator (1967), CHAKARBARTY 's estimator and product-type estimator, which are in fact the particular cases of it. The proposed estimator is as efficient as linear regression estimator in double sampling at optimum value of α.     

A Physical Method for Deriving the Electrostatic Interaction between Rod-Like Polyions at All Mutual Angles

The screened Coulomb interaction between polyelectrolyte cylinders immersed in an ionic bath is examined. The electrostatic force and torque acting between a pair of unlike rods is formulated for all separations in which the electrostatic potential on some dividing surface between rods can be written as a linear superposition of isolated cylinder potentials. (The surface potential on the rods themselves may be much higher than that permitted by a superposition approximation.) The mutual energy in the case of skewed rods is found to be exponential in separation and proportional to 1/sin θ where θ is the twist angle of one rod relative to the other. Rods with similar charge repel each other with a torque acting to make the rods perpendicular while rods of opposite charge attract with the parallel arrangement preferred.     

京津冀地区城市化与生态环境交互耦合关系定量测度

城市化与生态环境之间客观上存在着极其复杂的交互耦合关系,如何实现城市化与生态环境协调发展将是世界经济社会发展的核心议题,也是近年来国内外研究的热点命题。首先构建了城市化和生态环境系统综合评价指标体系,然后借助物理学耦合模型,构建了城市化与生态环境动态耦合协调度模型,定量分析了1980—2011年京津冀地区城市化与生态环境的耦合过程与演进趋势。结果表明:人口城市化和生态压力分别对城市化子系统与生态环境子系统的贡献份额最大,明显高于其他因素;在耦合协调度测算模型中,城市化子系统与生态环境子系统3种不同贡献份额所得出的耦合协调度的变化趋势是一致的,表明耦合协调度模型受城市化与生态环境子系统贡献份额比例的影响很小;1980年以来京津冀地区的城市化与生态环境耦合协调度呈现出S型曲线变化,协调类型从严重不协调-城市化受阻发展到高级协调-生态环境滞后类型;正确认识城市化与生态环境交互胁迫的时空动态耦合规律,采取恰当的区域发展政策和适当的城市发展战略,对进一步加快区域城市化进程,改善生态环境,实现京津冀地区城市化与生态环境的协调和可持续发展具有重要的指导意义。     

The segmental origin of the appendages of the head and anterior body segments of a spiroboloid milliped, Narceus annularis

Study of a series of embryos showed that the spiroboloid leg arrangement (1 pair of legs on each of the first 5 segments) is derived from the typical leg arrangement (no legs on segment 1, 1 pair on segments 2 through 4, and 2 pairs on segment 5) by a shifting forward one segment of the first four pairs of legs. A careful re-examination of the literature, especially papers by Robinson ('07), Silvestri ('03, '49), Pflugfelder ('32), and Manton ('61), combined with observations of Narceus embryos led to the conclusion that (1) the anterior body segments are primatively single (2) the gnathochilarium is composed of only one pair of mouthparts, the diplopod head having but two gnathal segments, and (3) the intercalary segment is present in the Diplopoda.     

Predicting the epidemic sizes of influenza A/H1N1, A/H3N2, and B: a statistical method

Background

The epidemic sizes of influenza A/H3N2, A/H1N1, and B infections vary from year to year in the United States. We use publicly available US Centers for Disease Control (CDC) influenza surveillance data between 1997 and 2009 to study the temporal dynamics of influenza over this period.

Methods and Findings

Regional outpatient surveillance data on influenza-like illness (ILI) and virologic surveillance data were combined to define a weekly proxy for the incidence of each strain in the United States. All strains exhibited a negative association between their cumulative incidence proxy (CIP) for the whole season (from calendar week 40 of each year to calendar week 20 of the next year) and the CIP of the other two strains (the complementary CIP) from the start of the season up to calendar week 2 (or 3, 4, or 5) of the next year. We introduce a method to predict a particular strain''s CIP for the whole season by following the incidence of each strain from the start of the season until either the CIP of the chosen strain or its complementary CIP exceed certain thresholds. The method yielded accurate predictions, which generally occurred within a few weeks of the peak of incidence of the chosen strain, sometimes after that peak. For the largest seasons in the data, which were dominated by A/H3N2, prediction of A/H3N2 incidence always occurred at least several weeks in advance of the peak.

Conclusion

Early circulation of one influenza strain is associated with a reduced total incidence of the other strains, consistent with the presence of interference between subtypes. Routine ILI and virologic surveillance data can be combined using this new method to predict the relative size of each influenza strain''s epidemic by following the change in incidence of a given strain in the context of the incidence of cocirculating strains. Please see later in the article for the Editors'' Summary     

Physical properties of type i collagen in solution: Structure of α-Chains and β- and γ-components and two-component mixtures

The structure of thermally denatured Type I collagen has been studied using laser light scattering. The results indicate that the diffusion coefficients of α-chains and β- and γ-components are 1.550 ± 0.08 × 10^?7, 1.000 ± 0.05 × 10^?7, and 0.835 ± 0.04 × 10^?7 cm²/sec, respectively, at temperatures between 20 and 40°C. It is concluded from diffusion data that these species have hydrodynamic radii of about 13.8 nm (α-chain), 21.5 nm (β-component), and 25.7 nm (γ-component), consistent with previous studies of thermal denaturation by light scattering. It is also concluded, based on volume calculations, that a large volume increase occurs when the triple helix unfolds. Homodyne correlation functions for two component mixtures of α-chains and β-and γ-components appeared to decay exponentially. In all but one case discussed the correlation function could be fitted with a single component having a translational diffusion coefficient which was an intensity weighted average of the diffusion coefficient of each component present.     

Space mediates coexistence of females and hermaphrodites

In gynodioecious populations of flowering plants females and hermaphrodites coexist. Gynodioecy is widespread and occurs in both asexual and sexual species but does not admit a satisfactory explanation from classical sex ratio theory. In sexual populations male fertility restoring genes have evolved to counter non-nuclear male sterility mutations. In pseudogamous asexual populations pollen retention and increased self-fertilization can make male sterility costly. Both of these mechanisms can promote coexistence. However, it remains unclear how either of these mechanisms could evolve if coexistence was not initially possible. In the absence of these adaptations non-spatial models predict that females either fail to invade hermaphrodite populations or else displace them until pollen shortage drives the population to extinction. We develop a pair approximation to a probabilistic cellular automata model in which females and hermaphrodites interact on a regular lattice. The model features independent pollination and colonization processes which take place on different timescales. The timescale separation is exploited to obtain, with perturbation methods, a more manageable aggregated pair approximation. We present both the mean field model which recreates the classical non-spatial predictions and the pair approximation, which strikingly predicts different invasion criteria and coexistence under a wide range of parameters. The pair approximation is shown to correspond well qualitatively with simulation behaviour.     

Female genotype affects male success in sperm competition

The central question addressed by most studies of sperm competition is: ''what determines which male''s sperm are used at fertilization?'' Empirical and theoretical studies that address this question have traditionally focused on adaptations which enhance male fertilization success while treating the female as a receptacle in which sperm competition is played out. Here we provide evidence which suggests that female genotype strongly influences the outcome of sperm competition. When the sperm of two males are in competition the proportion of offspring fathered by the second male to mate (P₂) was found to be highly repeatable only if the male pair were mated to three different, but genetically similar females (full-sisters to each other; unrelated to either of the males). In contrast, if a male pair were mated to three females that were unrelated then P₂ was either non-repeatable or marginally repeatable. We also show that male success in sperm competition is determined, to a large extent, by gamete and/or male–female compatibility. This conclusion is derived from the observation that P₂ was repeatable among full-sisters mated to different, yet genetically similar male pairings, whilst P₂ was non-repeatable among full-sisters mated to different, genetically distinct male pairings.     

Cooperation under predation risk: experiments on costs and benefits

Two fish that cooperatively inspect a predator may have negotiated the share of the risk that each takes. A test of both the costs of predator inspection dependent on the distance from which the predator is approached and the potential benefits of cooperation was carried out strictly experimentally. We made either singletons or pairs of dead sticklebacks, Gasterosteus aculeatus, approach hungry pike, Esox lucius, by remote control according to an algorithm that mimicked natural inspection. The predation risk of both single inspectors and parallel inspecting pairs increased with closer inspection distances. A member of an inspecting pair had only about half the risk of that of a single inspector. In pairs, a companion diluted the lead fish''s risk of being caught, depending on its distance behind the leader. The absolute risk difference between leader and follower was greatest for close inspection distances and decreased further away from the predator. The leader''s relative risk increased with its distance ahead of the laggard. However, for a given distance between leader and laggard, the relative risks of the two fish remained similar with distance from the predator. The cost side of the inequalities that define a ''Prisoner''s Dilemma'' has thus been measured for this system. In a second experiment the ''attack deterrence hypothesis'' of predator inspection (i.e. inspection decreases attack probability) was tested. The pike was offered a choice between two sticklebacks, one of which had carried out a predator inspection visit. There was no indication of attack deterrence through predator inspection.     

Fractionation of proteins with two-sided electro-ultrafiltration

Downstream processing is a major challenge in bioprocess industry due to the high complexity of bio-suspensions itself, the low concentration of the product and the stress sensitivity of the valuable target molecules. A multitude of unit operations have to be joined together to achieve an acceptable purity and concentration of the product. Since each of the unit operations leads to a certain product loss, one important aim in downstream-research is the combination of different separation principles into one unit operation. In the current work a dead-end membrane process is combined with an electrophoresis operation. In the past this concept has proven successfully for the concentration of biopolymers. The present work shows that using different ultrafiltration membranes in a two-sided electro-filter apparatus with flushed electrodes brought significant enhancement of the protein fractionation process. Due to electrophoretic effects, the filtration velocity could be kept on a very high level for a long time, furthermore, the selectivity of a binary separation process carried out exemplarily for bovine serum albumin (BSA) and lysozyme (LZ) could be greatly increased; in the current case up to a value of more than 800. Thus the new two-sided electro-ultrafiltration technique achieves both high product purity and short separation times.