Distinct conformational properties determined by implicit and explicit representation of protein-solvent interactions. An analytical and computer simulation study

In the protein folding problem, solvent-mediated forces are commonly represented by intra-chain pairwise contact energy. Although this approximation has proven to be useful in several circumstances, it is limited in some other aspects of the problem. Here we show that it is possible to achieve two models to represent the chain-solvent system. one of them with implicit and other with explicit solvent, such that both reproduce the same thermodynamic results. Firstly, lattice models treated by analytical methods, were used to show that the implicit and explicitly representation of solvent effects can be energetically equivalent only if local solvent properties are time and spatially invariant. Following, applying the same reasoning Used for the lattice models, two inter-consistent Monte Carlo off-lattice models for implicit and explicit solvent are constructed, being that now in the latter the solvent properties are allowed to fluctuate. Then, it is shown that the chain configurational evolution as well as the globule equilibrium conformation are significantly distinct for implicit and explicit solvent systems. Actually, strongly contrasting with the implicit solvent version, the explicit solvent model predicts: (i) a malleable globule, in agreement with the estimated large protein-volume fluctuations; (ii) thermal conformational stability, resembling the conformational hear resistance of globular proteins, in which radii of gyration are practically insensitive to thermal effects over a relatively wide range of temperatures; and (iii) smaller radii of gyration at higher temperatures, indicating that the chain conformational entropy in the unfolded state is significantly smaller than that estimated from random coil configurations. Finally, we comment on the meaning of these results with respect to the understanding of the folding process. (C) 2009 Elsevier B.V. All rights reserved.

XSophe-Sophe-XeprView (R). A computer simulation software suite (v. 1.1.3) for the analysis of continuous wave EPR spectra

The XSophe-Sophe-XeprView((R)) computer simulation software suite enables scientists to easily determine spin Hamiltonian parameters from isotropic, randomly oriented and single crystal continuous wave electron paramagnetic resonance (CW EPR) spectra from radicals and isolated paramagnetic metal ion centers or clusters found in metalloproteins, chemical systems and materials science. XSophe provides an X-windows graphical user interface to the Sophe programme and allows: creation of multiple input files, local and remote execution of Sophe, the display of sophelog (output from Sophe) and input parameters/files. Sophe is a sophisticated computer simulation software programme employing a number of innovative technologies including; the Sydney OPera HousE (SOPHE) partition and interpolation schemes, a field segmentation algorithm, the mosaic misorientation linewidth model, parallelization and spectral optimisation. In conjunction with the SOPHE partition scheme and the field segmentation algorithm, the SOPHE interpolation scheme and the mosaic misorientation linewidth model greatly increase the speed of simulations for most spin systems. Employing brute force matrix diagonalization in the simulation of an EPR spectrum from a high spin Cr(III) complex with the spin Hamiltonian parameters g(e) = 2.00, D = 0.10 cm(-1), E/D = 0.25, A(x) = 120.0, A(y) = 120.0, A(z) = 240.0 x 10(-4) cm(-1) requires a SOPHE grid size of N = 400 (to produce a good signal to noise ratio) and takes 229.47 s. In contrast the use of either the SOPHE interpolation scheme or the mosaic misorientation linewidth model requires a SOPHE grid size of only N = 18 and takes 44.08 and 0.79 s, respectively. Results from Sophe are transferred via the Common Object Request Broker Architecture (CORBA) to XSophe and subsequently to XeprView((R)) where the simulated CW EPR spectra (1D and 2D) can be compared to the experimental spectra. Energy level diagrams, transition roadmaps and transition surfaces aid the interpretation of complicated randomly oriented CW EPR spectra and can be viewed with a web browser and an OpenInventor scene graph viewer.

Erosion/productivity modelling of maize farming in the Philippine uplands part II: Simulation of alternative farming methods

A version of the Agricultural Production Systems Simulator (APSIM) capable of simulating the key agronomic aspects of intercropping maize between legume shrub hedgerows was described and parameterised in the first paper of this series (Nelson et al., this issue). In this paper, APSIM is used to simulate maize yields and soil erosion from traditional open-field farming and hedgerow intercropping in the Philippine uplands. Two variants of open-field farming were simulated using APSIM, continuous and fallow, for comparison with intercropping maize between leguminous shrub hedgerows. Continuous open-field maize farming was predicted to be unsustainable in the long term, while fallow open-field farming was predicted to slow productivity decline by spreading the effect of erosion over a larger cropping area. Hedgerow intercropping was predicted to reduce erosion by maintaining soil surface cover during periods of intense rainfall, contributing to sustainable production of maize in the long term. In the third paper in this series, Nelson et al. (this issue) use cost-benefit analysis to compare the economic viability of hedgerow intercropping relative to traditional open-field farming of maize in relatively inaccessible upland areas. (C) 1998 Elsevier Science Ltd. All rights reserved.

Computer simulations of coupled problems in geological and geochemical systems

The finite element method is used to simulate coupled problems, which describe the related physical and chemical processes of ore body formation and mineralization, in geological and geochemical systems. The main purpose of this paper is to illustrate some simulation results for different types of modelling problems in pore-fluid saturated rock masses. The aims of the simulation results presented in this paper are: (1) getting a better understanding of the processes and mechanisms of ore body formation and mineralization in the upper crust of the Earth; (2) demonstrating the usefulness and applicability of the finite element method in dealing with a wide range of coupled problems in geological and geochemical systems; (3) qualitatively establishing a set of showcase problems, against which any numerical method and computer package can be reasonably validated. (C) 2002 Published by Elsevier Science B.V.

A 2D numerical model for simulating the physics of fault systems

Simulations provide a powerful means to help gain the understanding of crustal fault system physics required to progress towards the goal of earthquake forecasting. Cellular Automata are efficient enough to probe system dynamics but their simplifications render interpretations questionable. In contrast, sophisticated elasto-dynamic models yield more convincing results but are too computationally demanding to explore phase space. To help bridge this gap, we develop a simple 2D elastodynamic model of parallel fault systems. The model is discretised onto a triangular lattice and faults are specified as split nodes along horizontal rows in the lattice. A simple numerical approach is presented for calculating the forces at medium and split nodes such that general nonlinear frictional constitutive relations can be modeled along faults. Single and multi-fault simulation examples are presented using a nonlinear frictional relation that is slip and slip-rate dependent in order to illustrate the model.

Numerical simulation of double-diffusion driven convective flow and rock alteration in three-dimensional fluid-saturated geological fault zones

Numerical methods are used to simulate the double-diffusion driven convective pore-fluid flow and rock alteration in three-dimensional fluid-saturated geological fault zones. The double diffusion is caused by a combination of both the positive upward temperature gradient and the positive downward salinity concentration gradient within a three-dimensional fluid-saturated geological fault zone, which is assumed to be more permeable than its surrounding rocks. In order to ensure the physical meaningfulness of the obtained numerical solutions, the numerical method used in this study is validated by a benchmark problem, for which the analytical solution to the critical Rayleigh number of the system is available. The theoretical value of the critical Rayleigh number of a three-dimensional fluid-saturated geological fault zone system can be used to judge whether or not the double-diffusion driven convective pore-fluid flow can take place within the system. After the possibility of triggering the double-diffusion driven convective pore-fluid flow is theoretically validated for the numerical model of a three-dimensional fluid-saturated geological fault zone system, the corresponding numerical solutions for the convective flow and temperature are directly coupled with a geochemical system. Through the numerical simulation of the coupled system between the convective fluid flow, heat transfer, mass transport and chemical reactions, we have investigated the effect of the double-diffusion driven convective pore-fluid flow on the rock alteration, which is the direct consequence of mineral redistribution due to its dissolution, transportation and precipitation, within the three-dimensional fluid-saturated geological fault zone system. (c) 2005 Elsevier B.V. All rights reserved.

Finite Element Analysis of 2 Immediate Loading Systems in Edentulous Mandible: Rigid and Semirigid Splinting of Implants

Purpose: The objective of this study was to evaluate the stress on the cortical bone around single body dental implants supporting mandibular complete fixed denture with rigid (Neopronto System-Neodent) or semirigid splinting system (Barra Distal System-Neodent). Methods and Materials: Stress levels on several system components were analyzed through finite element analysis. Focusing on stress concentration at cortical bone around single body dental implants supporting mandibular complete fixed dentures with rigid ( Neopronto System-Neodent) or semirigid splinting system ( Barra Distal System-Neodent), after axial and oblique occlusal loading simulation, applied in the last cantilever element. Results: The results showed that semirigid implant splinting generated lower von Mises stress in the cortical bone under axial loading. Rigid implant splinting generated higher von Mises stress in the cortical bone under oblique loading. Conclusion: It was concluded that the use of a semirigid system for rehabilitation of edentulous mandibles by means of immediate implant-supported fixed complete denture is recommended, because it reduces stress concentration in the cortical bone. As a consequence, bone level is better preserved, and implant survival is improved. Nevertheless, for both situations the cortical bone integrity was protected, because the maximum stress level findings were lower than those pointed in the literature as being harmful. The maximum stress limit for cortical bone (167 MPa) represents the threshold between plastic and elastic state for a given material. Because any force is applied to an object, and there is no deformation, we can conclude that the elastic threshold was not surpassed, keeping its structural integrity. If the force is higher than the plastic threshold, the object will suffer permanent deformation. In cortical bone, this represents the beginning of bone resorption and/or remodeling processes, which, according to our simulated loading, would not occur. ( Implant Dent 2010; 19:39-49)

Set-valued Markov chains and negative semitrajectories of discretized dynamical systems

Computer simulation of dynamical systems involves a phase space which is the finite set of machine arithmetic. Rounding state values of the continuous system to this grid yields a spatially discrete dynamical system, often with different dynamical behaviour. Discretization of an invertible smooth system gives a system with set-valued negative semitrajectories. As the grid is refined, asymptotic behaviour of the semitrajectories follows probabilistic laws which correspond to a set-valued Markov chain, whose transition probabilities can be explicitly calculated. The results are illustrated for two-dimensional dynamical systems obtained by discretization of fractional linear transformations of the unit disc in the complex plane.

Control of nitrate recirculation flow in predenitrification systems

The control of the nitrate recirculation flow in a predenitrification system is addressed. An elementary mass balance analysis on the utilisation efficiency of the influent biodegradable COD (bCOD) for nitrate removal indicates that the control problem can be broken down into two parts: maintaining the anoxic zone anoxic (i.e. nitrate is present throughout the anoxic zone) and maximising the usage of influent soluble bCOD for denitrification. Simulation studies using the Simulation Benchmark developed in the European COST program show that both objectives can be achieved by maintaining the nitrate concentration at the outlet of the anoxic zone at around 2 mgN/L. This setpoint appears to be robust towards variations in the influent characteristics and sludge kinetics.

Simulation of insect movement with respect to plant architecture and morphogenesis

Developments in computer and three dimensional (3D) digitiser technologies have made it possible to keep track of the broad range of data required to simulate an insect moving around or over the highly heterogeneous habitat of a plant's surface. Properties of plant parts vary within a complex canopy architecture, and insect damage can induce further changes that affect an animal's movements, development and likelihood of survival. Models of plant architectural development based on Lindenmayer systems (L-systems) serve as dynamic platforms for simulation of insect movement, providing ail explicit model of the developing 3D structure of a plant as well as allowing physiological processes associated with plant growth and responses to damage to be described and Simulated. Simple examples of the use of the L-system formalism to model insect movement, operating Lit different spatial scales-from insects foraging on an individual plant to insects flying around plants in a field-are presented. Such models can be used to explore questions about the consequences of changes in environmental architecture and configuration on host finding, exploitation and its population consequences. In effect this model is a 'virtual ecosystem' laboratory to address local as well as landscape-level questions pertinent to plant-insect interactions, taking plant architecture into account. (C) 2002 Elsevier Science B.V. All rights reserved.

Using crop simulation to generate genotype by environment interaction effects for sorghum in water-limited environments

Multi-environment trials (METs) used to evaluate breeding lines vary in the number of years that they sample. We used a cropping systems model to simulate the target population of environments (TPE) for 6 locations over 108 years for 54 'near-isolines' of sorghum in north-eastern Australia. For a single reference genotype, each of 547 trials was clustered into 1 of 3 'drought environment types' (DETs) based on a seasonal water stress index. Within sequential METs of 2 years duration, the frequencies of these drought patterns often differed substantially from those derived for the entire TPE. This was reflected in variation in the mean yield of the reference genotype. For the TPE and for 2-year METs, restricted maximum likelihood methods were used to estimate components of genotypic and genotype by environment variance. These also varied substantially, although not in direct correlation with frequency of occurrence of different DETs over a 2-year period. Combined analysis over different numbers of seasons demonstrated the expected improvement in the correlation between MET estimates of genotype performance and the overall genotype averages as the number of seasons in the MET was increased.

Conditional simulation of random fields by successive residuals

This paper presents a new approach to the LU decomposition method for the simulation of stationary and ergodic random fields. The approach overcomes the size limitations of LU and is suitable for any size simulation. The proposed approach can facilitate fast updating of generated realizations with new data, when appropriate, without repeating the full simulation process. Based on a novel column partitioning of the L matrix, expressed in terms of successive conditional covariance matrices, the approach presented here demonstrates that LU simulation is equivalent to the successive solution of kriging residual estimates plus random terms. Consequently, it can be used for the LU decomposition of matrices of any size. The simulation approach is termed conditional simulation by successive residuals as at each step, a small set (group) of random variables is simulated with a LU decomposition of a matrix of updated conditional covariance of residuals. The simulated group is then used to estimate residuals without the need to solve large systems of equations.

Simulation of the load-unload response ratio and critical sensitivity in the lattice solid model

The Load-Unload Response Ratio (LURR) method is an intermediate-term earthquake prediction approach that has shown considerable promise. It involves calculating the ratio of a specified energy release measure during loading and unloading where loading and unloading periods are determined from the earth tide induced perturbations in the Coulomb Failure Stress on optimally oriented faults. In the lead-up to large earthquakes, high LURR values are frequently observed a few months or years prior to the event. These signals may have a similar origin to the observed accelerating seismic moment release (AMR) prior to many large earthquakes or may be due to critical sensitivity of the crust when a large earthquake is imminent. As a first step towards studying the underlying physical mechanism for the LURR observations, numerical studies are conducted using the particle based lattice solid model (LSM) to determine whether LURR observations can be reproduced. The model is initialized as a heterogeneous 2-D block made up of random-sized particles bonded by elastic-brittle links. The system is subjected to uniaxial compression from rigid driving plates on the upper and lower edges of the model. Experiments are conducted using both strain and stress control to load the plates. A sinusoidal stress perturbation is added to the gradual compressional loading to simulate loading and unloading cycles and LURR is calculated. The results reproduce signals similar to those observed in earthquake prediction practice with a high LURR value followed by a sudden drop prior to macroscopic failure of the sample. The results suggest that LURR provides a good predictor for catastrophic failure in elastic-brittle systems and motivate further research to study the underlying physical mechanisms and statistical properties of high LURR values. The results provide encouragement for earthquake prediction research and the use of advanced simulation models to probe the physics of earthquakes.

Simulation supplements field studies to determine no-till dryland corn population recommendations for semiarid western Nebraska

In a 2-yr multiple-site field study conducted in western Nebraska during 1999 and 2000, optimum dryland corn (Zea mays L.) population varied from less than 1.7 to more than 5.6 plants m(-2), depending largely on available water resources. The objective of this study was to use a modeling approach to investigate corn population recommendations for a wide range of seasonal variation. A corn growth simulation model (APSIM-maize) was coupled to long-term sequences of historical climatic data from western Nebraska to provide probabilistic estimates of dryland yield for a range of corn populations. Simulated populations ranged from 2 to 5 plants m(-2). Simulations began with one of three levels of available soil water at planting, either 80, 160, or 240 mm in the surface 1.5 m of a loam soil. Gross margins were maximized at 3 plants m(-2) when starting available water was 160 or 240 mm, and the expected probability of a financial loss at this population was reduced from about 10% at 160 mm to 0% at 240 mm. When starting available water was 80 mm, average gross margins were less than $15 ha(-1), and risk of financial loss exceeded 40%. Median yields were greatest when starting available soil water was 240 mm. However, perhaps the greater benefit of additional soil water at planting was reduction in the risk of making a financial loss. Dryland corn growers in western Nebraska are advised to use a population of 3 plants m(-2) as a base recommendation.