Influence of the solvent on the self-assembly of a modified amyloid beta peptide fragment. II. NMR and computer simulation investigation

The conformation of a model peptide AAKLVFF based on a fragment of the amyloid beta peptide A beta 16-20, KLVFF, is investigated in methanol and water via solution NMR experiments and Molecular dynamics computer simulations. In previous work, we have shown that AAKLVFF forms peptide nanotubes in methanol and twisted fibrils in water. Chemical shift measurements were used to investigate the solubility of the peptide as a function of concentration in methanol and water. This enabled the determination of critical aggregation concentrations, The Solubility was lower in water. In dilute solution, diffusion coefficients revealed the presence of intermediate aggregates in concentrated solution, coexisting with NMR-silent larger aggregates, presumed to be beta-sheets. In water, diffusion coefficients did not change appreciably with concentration, indicating the presence mainly of monomers, coexisting with larger aggregates in more concentrated solution. Concentration-dependent chemical shift measurements indicated a folded conformation for the monomers/intermediate aggregates in dilute methanol, with unfolding at higher concentration. In water, an antiparallel arrangement of strands was indicated by certain ROESY peak correlations. The temperature-dependent solubility of AAKLVFF in methanol was well described by a van't Hoff analysis, providing a solubilization enthalpy and entropy. This pointed to the importance of solvophobic interactions in the self-assembly process. Molecular dynamics Simulations constrained by NOE values from NMR suggested disordered reverse turn structures for the monomer, with an antiparallel twisted conformation for dimers. To model the beta-sheet structures formed at higher concentration, possible model arrangements of strands into beta-sheets with parallel and antiparallel configurations and different stacking sequences were used as the basis for MD simulations; two particular arrangements of antiparallel beta-sheets were found to be stable, one being linear and twisted and the other twisted in two directions. These structures Were used to simulate Circular dichroism spectra. The roles of aromatic stacking interactions and charge transfer effects were also examined. Simulated spectra were found to be similar to those observed experimentally.(in water or methanol) which show a maximum at 215 or 218 nm due to pi-pi* interactions, when allowance is made for a 15-18 nm red-shift that may be due to light scattering effects.

Structure and viscoelasticity of an electrorheological fluid in oscillatory shear: computer simulation investigation

The three-dimensional molecular dynamics simulation method has been used to study the dynamic responses of an electrorheological (ER) fluid in oscillatory shear. The structure and related viscoelastic behaviour of the fluid are found to be sensitive to the amplitude of the strain. With the increase of the strain amplitude, the structure formed by the particles changes from isolated columns to sheet-like structures which may be perpendicular or parallel to the oscillating direction. Along with the structure evolution, the field-induced moduli decrease significantly with an increase in strain amplitude. The viscoelastic behaviour of the structures obtained in the cases of different strain amplitudes was examined in the linear response regime and an evident structure dependence of the moduli was found. The reason for this lies in the anisotropy of the arrangement of the particles in these structures. Short-range interactions between the particles cannot be neglected in determining the viscoelastic behaviour of ER fluids at small strain amplitude, especially for parallel sheets. The simulation results were compared with available experimental data and good agreement was reached for most of them.

Computer simulation study of equilibrium properties of magnetic dipolar fluids

Langevin dynamics simulations are used to investigate the equilibrium magnetization properties and structure of magnetic dipolar fluids. The influence of using different boundary conditions are systematically studied. Simulation results on the initial susceptibility and magnetization curves are compared with theoretical predictions. The effect of particle aggregation is discussed in detail by performing a cluster analysis of the microstructure.

Dynamic simulation studies of structural formation and transition in electro-magneto-rheological fluids

The computer simulation method has been used to study the structural formation and transition of electro-magneto-rheological (EMR) fluids under compatible electric and magnetic fields. When the fields are applied simultaneously and perpendicularly to each other, the particles rapidly arrange into two-dimensional close-packed layer structures parallel to both fields. The layers then combine together to form thicker sheet-like structures, which finally relax into three-dimensional close-packed structures with the help of the thermal fluctuations. On the other hand, if the electric field is applied firstly to induce the body-centered tetragonal (BCT) columns in the system, and then the magnetic field is applied in the perpendicular direction. the BCT to face-centered cubic (FCC) structure transition is observed in very short time. Following that. the structure keeps on evolving due to the demagnetization effect and finally form the three-dimensional close-packed structures.

Simulation of field-induced structural formation and transition in electromagnetorheological suspensions

A computer simulation method has been used to study the three-dimensional structural formation and transition of eleetromagnetorheological (EMR) suspensions under compatible electric and magnetic fields. When the fields are applied simultaneously and perpendicularly to each other, the particles rapidly arrange into single layer structures parallel to both fields. In each layer, there is a two-dimensional hexagonal lattice. The single layers then combine together to form thicker sheetlike structures. With the help of the thermal fluctuations, the thicker structures relax into three-dimensional close-packed structures, which may be face-centered cubic (fcc), hexagonal close-packed (hup) lattices, or, more probably, the mixture of them, depending on the initial configurations and the thermal fluctuations. On the other hand, if the electric field is applied first to induce the body-centered tetragonal (bct) columns in the system, and then the magnetic field is applied in the perpendicular direction, the bet to fee structure transition is observed in a very short time. Following that, the structure keeps on evolving due to the demagnetization effect and finally forms close-packed structures with fee and hcp lattice character. The simulation results are in agreement with the theoretical and experimental results.

Investigating early hominin dispersal patterns: developing a framework for climate data integration

An investigation using the Stepping Out model of early hominin dispersal out of Africa is presented here. The late arrival of early hominins into Europe, as deduced from the fossil record, is shown to be consistent with poor ability of these hominins to survive in the Eurasian landscape. The present study also extends the understanding of modelling results from the original study by Mithen and Reed (2002. Stepping out: a computer simulation of hominid dispersal from Africa. J. Hum. Evol. 43, 433-462). The representation of climate and vegetation patterns has been improved through the use of climate model output. This study demonstrates that interpretative confidence may be strengthened, and new insights gained when climate models and hominin dispersal models are integrated. (C) 2007 Elsevier Ltd. All rights reserved.

The infrared spectrum of silicon difluoride

The infrared spectrum of the stretching fundamentals of SiF2 has been obtained at a resolution of ≈ 0.1 cm−1 using a FTIR spectrometer. The spectrum has been analysed using computer simulation based on a coupled hamiltonian for v1 and v3, giving v1 = 855.01 cm−1 and v3 = 870.40 cm−1. The relative magnitude and sign of the vibrational transition moments has been determined from the ξC13 Coriolis coupling.

The Origins of Lactase Persistence in Europe

Lactase persistence (LP) is common among people of European ancestry, but with the exception of some African, Middle Eastern and southern Asian groups, is rare or absent elsewhere in the world. Lactase gene haplotype conservation around a polymorphism strongly associated with LP in Europeans (-13,910 C/T) indicates that the derived allele is recent in origin and has been subject to strong positive selection. Furthermore, ancient DNA work has shown that the -13,910*T (derived) allele was very rare or absent in early Neolithic central Europeans. It is unlikely that LP would provide a selective advantage without a supply of fresh milk, and this has lead to a gene-culture coevolutionary model where lactase persistence is only favoured in cultures practicing dairying, and dairying is more favoured in lactase persistent populations. We have developed a flexible demic computer simulation model to explore the spread of lactase persistence, dairying, other subsistence practices and unlinked genetic markers in Europe and western Asia's geographic space. Using data on -13,910*T allele frequency and farming arrival dates across Europe, and approximate Bayesian computation to estimate parameters of interest, we infer that the -13,910*T allele first underwent selection among dairying farmers around 7,500 years ago in a region between the central Balkans and central Europe, possibly in association with the dissemination of the Neolithic Linearbandkeramik culture over Central Europe. Furthermore, our results suggest that natural selection favouring a lactase persistence allele was not higher in northern latitudes through an increased requirement for dietary vitamin D. Our results provide a coherent and spatially explicit picture of the coevolution of lactase persistence and dairying in Europe.

Truth in complex adaptive systems models should be based on truth by constructive verification

It is argued that the truth status of emergent properties of complex adaptive systems models should be based on an epistemology of proof by constructive verification and therefore on the ontological axioms of a non-realist logical system such as constructivism or intuitionism. ‘Emergent’ properties of complex adaptive systems (CAS) models create particular epistemological and ontological challenges. These challenges bear directly on current debates in the philosophy of mathematics and in theoretical computer science. CAS research, with its emphasis on computer simulation, is heavily reliant on models which explore the entailments of Formal Axiomatic Systems (FAS). The incompleteness results of Gödel, the incomputability results of Turing, and the Algorithmic Information Theory results of Chaitin, undermine a realist (platonic) truth model of emergent properties. These same findings support the hegemony of epistemology over ontology and point to alternative truth models such as intuitionism, constructivism and quasi-empiricism.

RBF equalizer design using directional evolutionary multi-objective optimization

Whilst radial basis function (RBF) equalizers have been employed to combat the linear and nonlinear distortions in modern communication systems, most of them do not take into account the equalizer's generalization capability. In this paper, it is firstly proposed that the. model's generalization capability can be improved by treating the modelling problem as a multi-objective optimization (MOO) problem, with each objective based on one of several training sets. Then, as a modelling application, a new RBF equalizer learning scheme is introduced based on the directional evolutionary MOO (EMOO). Directional EMOO improves the computational efficiency of conventional EMOO, which has been widely applied in solving MOO problems, by explicitly making use of the directional information. Computer simulation demonstrates that the new scheme can be used to derive RBF equalizers with good performance not only on explaining the training samples but on predicting the unseen samples.

Turbo channel estimation and equalisation for a superposition-based cooperative system

This study investigates the superposition-based cooperative transmission system. In this system, a key point is for the relay node to detect data transmitted from the source node. This issued was less considered in the existing literature as the channel is usually assumed to be flat fading and a priori known. In practice, however, the channel is not only a priori unknown but subject to frequency selective fading. Channel estimation is thus necessary. Of particular interest is the channel estimation at the relay node which imposes extra requirement for the system resources. The authors propose a novel turbo least-square channel estimator by exploring the superposition structure of the transmission data. The proposed channel estimator not only requires no pilot symbols but also has significantly better performance than the classic approach. The soft-in-soft-out minimum mean square error (MMSE) equaliser is also re-derived to match the superimposed data structure. Finally computer simulation results are shown to verify the proposed algorithm.

Nonlinear channel equalizer design using directional evolutionary multi-objective optimization

In this paper, a new equalizer learning scheme is introduced based on the algorithm of the directional evolutionary multi-objective optimization (EMOO). Whilst nonlinear channel equalizers such as the radial basis function (RBF) equalizers have been widely studied to combat the linear and nonlinear distortions in the modern communication systems, most of them do not take into account the equalizers' generalization capabilities. In this paper, equalizers are designed aiming at improving their generalization capabilities. It is proposed that this objective can be achieved by treating the equalizer design problem as a multi-objective optimization (MOO) problem, with each objective based on one of several training sets, followed by deriving equalizers with good capabilities of recovering the signals for all the training sets. Conventional EMOO which is widely applied in the MOO problems suffers from disadvantages such as slow convergence speed. Directional EMOO improves the computational efficiency of the conventional EMOO by explicitly making use of the directional information. The new equalizer learning scheme based on the directional EMOO is applied to the RBF equalizer design. Computer simulation demonstrates that the new scheme can be used to derive RBF equalizers with good generalization capabilities, i.e., good performance on predicting the unseen samples.

Robust blind deconvolution algorithm: variance approximation and series decoupling

An alternative blind deconvolution algorithm for white-noise driven minimum phase systems is presented and verified by computer simulation. This algorithm uses a cost function based on a novel idea: variance approximation and series decoupling (VASD), and suggests that not all autocorrelation function values are necessary to implement blind deconvolution.

How predation and landscape fragmentation affect vole population dynamics

Background: Microtine species in Fennoscandia display a distinct north-south gradient from regular cycles to stable populations. The gradient has often been attributed to changes in the interactions between microtines and their predators. Although the spatial structure of the environment is known to influence predator-prey dynamics of a wide range of species, it has scarcely been considered in relation to the Fennoscandian gradient. Furthermore, the length of microtine breeding season also displays a north-south gradient. However, little consideration has been given to its role in shaping or generating population cycles. Because these factors covary along the gradient it is difficult to distinguish their effects experimentally in the field. The distinction is here attempted using realistic agent-based modelling. Methodology/Principal Findings: By using a spatially explicit computer simulation model based on behavioural and ecological data from the field vole (Microtus agrestis), we generated a number of repeated time series of vole densities whose mean population size and amplitude were measured. Subsequently, these time series were subjected to statistical autoregressive modelling, to investigate the effects on vole population dynamics of making predators more specialised, of altering the breeding season, and increasing the level of habitat fragmentation. We found that fragmentation as well as the presence of specialist predators are necessary for the occurrence of population cycles. Habitat fragmentation and predator assembly jointly determined cycle length and amplitude. Length of vole breeding season had little impact on the oscillations. Significance: There is good agreement between our results and the experimental work from Fennoscandia, but our results allow distinction of causation that is hard to unravel in field experiments. We hope our results will help understand the reasons for cycle gradients observed in other areas. Our results clearly demonstrate the importance of landscape fragmentation for population cycling and we recommend that the degree of fragmentation be more fully considered in future analyses of vole dynamics.