Aspects of model building applied to the C-terminal domain of the L12 protein from chloroplast ribosomes: a molecular dynamics study

A 170 picosecond molecular dynamics trajectory has been calculated starting from a model-built structure of chloroplast CTF. Local conformational changes occur during the equilibration period. Thereafter, a dynamically stable structure is attained. The conformational changes involve a turn connecting two structural subdomains which has an amino acid insertion and several substitutions with respect to the E. coli sequence. Potential energy minimisation alone fails to detect such a change. The overall folding and atomic positional fluctuations are very similar to those found in MD simulations of the E. coli molecule. The combined use of computer graphics based model building and MD calculations has lead to a thermally stable putative structure for the chloroplast CTF.     

Computational fluid dynamics study of common stent models inside idealised curved coronary arteries

The haemodynamic behaviour of blood inside a coronary artery after stenting is greatly affected by individual stent features as well as complex geometrical properties of the artery including tortuosity and curvature. Regions at higher risk of restenosis, as measured by low wall shear stress (WSS < 0.5 Pa), have not yet been studied in detail in curved stented arteries. In this study, three-dimensional computational modelling and computational fluid dynamics methodologies were used to analyse the haemodynamic characteristics in curved stented arteries using several common stent models. Results in this study showed that stent strut thickness was one major factor influencing the distribution of WSS in curved arteries. Regions of low WSS were found behind struts, particularly those oriented at a large angle relative to the streamwise flow direction. These findings were similar to those obtained in studies of straight arteries. An uneven distribution of WSS at the inner and outer bends of curved arteries was observed where the WSS was lower at the inner bend. In this study, it was also shown that stents with a helical configuration generated an extra swirling component of the flow based on the helical direction; however, this extra swirl in the flow field did not cause significant changes on the distribution of WSS under the current setup.     

Aspects of the molecular structure and dynamics of neuropeptide Y.

Human neuropeptide Y (hNPY) and the Q34-->P34 mutant (P34-hNPY) have been characterized by CD spectroscopy. hNPY self-associates in aqueous solution with a dimerization constant in the micromolar range. The self-association correlates with an increase in secondary-structure content which was studied as a function of concentration, temperature and pH. The effects of temperature were measured in water (5-84 degrees C) and in ethanediol/water (2 : 1) (-90 degrees to +90 degrees C). A single-residue mutation, Q34-->P34, affects the pH, thermal and self-association properties of NPY. The CD results are correlated with photochemically induced dynamic nuclear polarization NMR experiments which show that the tyrosines at the interface between two monomer units present limited accessibility to a photoreactive dye. An equilibrium state is described, involving a PP-fold monomer form and a handshake dimer form, that accommodates the physicochemical properties of NPY.     

Optimal control applied to native-invasive population dynamics

This article presents a model for population interactions between an invasive and a native species, where the effect of disturbance in the system (such as flooding) is modeled as a control variable in the growth terms. The motivating example is cottonwood-salt cedar competition, with flooding being detrimental at low and high levels and being advantageous at medium levels, which led us to consider quadratic growth functions of the control. An objective functional is formulated to maximize the native species while minimizing the cost of implementing the control. A new existence result for an optimal control with these quadratic growth functions is given. Numerical results are examined for various parameter values. The results provide suggestions for managing the disturbance regime when invasive species are present.     

Atomic solvation parameters applied to molecular dynamics of proteins in solution.

A solvation energy function for use in the molecular simulation of proteins is proposed. It is based on the accessible surface areas of atoms in the protein and on atomic solvation parameters derived from empirical vapor-to-water free energies of transfer of amino acid side-chain analogs. The energy function and its derivatives were added to the CHARMM molecular simulation program (Brooks, B.R., Bruccoleri, R.E., Olafson, B.D., States, D.J., Swaminathan, S., & Karplus, M., 1983, J. Comput. Chem. 4(2), 187-217). The effect of the added energy term was evaluated by 110 ps of molecular dynamics on the 26-residue protein melittin. The melittin monomer and tetramer were studied both with and without the added term. With the added energy term the monomer partially unfolded, while the secondary structure of the tetramer was preserved, in agreement with reported experiments (Brown, L.R., Lauterwein, J., & Wuethrich, K., 1980, Biochim. Biophys. Acta 622(2), 231-244; Lauterwein, J., Brown, L.R., & Wuethrich, K., 1980, Biochim. Biophys. Acta 622(2), 219-230).     

The characteristics method applied to the study of muscle dynamics

In two-state sliding filament models of muscle contraction a partial differential equation must be solved to find the cross-bridge distribution functionn(x, t). In this paper the analytical form of this function is obtained by integration along the characteristic line and special cases are presented in which the explicit expression forn(x, t) can be completely determined. These analytical solutions provide a direct mathematical connection between the microscopic contraction parameters contained in the kinetic theories and macroscopic muscle dynamics and are thus used to investigate what parameters influence the transient contractile tension in typical experimental conditions. The results of this investigation are consistent with relevant aspects of muscle physiology.     

MRI-based quantification of outflow boundary conditions for computational fluid dynamics of stenosed human carotid arteries

Accurate assessment of wall shear stress (WSS) is vital for studies on the pathogenesis of atherosclerosis. WSS distributions can be obtained by computational fluid dynamics (CFD) using patient-specific geometries and flow measurements. If patient-specific flow measurements are unavailable, in- and outflow have to be estimated, for instance by using Murray’s Law. It is currently unknown to what extent this law holds for carotid bifurcations, especially in cases where stenoses are involved. We performed flow measurements in the carotid bifurcation using phase-contrast MRI in patients with varying degrees of stenosis. An empirical relation between outflow and degree of area stenosis was determined and the outflow measurements were compared to estimations based on Murray’s Law. Furthermore, the influence of outflow conditions on the WSS distribution was studied.For bifurcations with an area stenosis smaller than 65%, the outflow ratio of the internal carotid artery (ICA) to the common carotid artery (CCA) was 0.62±0.12 while the outflow ratio of the external carotid artery (ECA) was 0.35±0.13. If the area stenosis was larger than 65%, the flow to the ICA decreased linearly to zero at 100% area stenosis. The empirical relation fitted the flow data well (R²=0.69), whereas Murray’s Law overestimated the flow to the ICA substantially for larger stenosis, resulting in an overestimation of the WSS. If patient-specific flow measurements of the carotid bifurcation are unavailable, estimation of the outflow ratio by the presented empirical relation will result in a good approximation of calculated WSS using CFD.     

The importance of blood rheology in patient-specific computational fluid dynamics simulation of stenotic carotid arteries

Biomechanics and Modeling in Mechanobiology - The initiation and progression of atherosclerosis, which is the main cause of cardiovascular diseases, correlate with local haemodynamic factors such...     

Tissue pressures and fluid dynamics in the kidney.

The kidney has several characteristics which make renal pressures and fluid dynamics unique when compared to other organs. Renal blood flow is roughly 100 times that of skeletal muscle. The renal circulation consists of two distinct capillary beds in series: a high pressure system in the glomerulus that favors filtration and a low pressure system in the peritubule network that favors reabsorption. The hydrostatic pressure in the glomerular capillary is 4-6 times higher than the hydrostatic pressure in the peritubule capillary so that approximately 25% of the plasma is filtered. The bulk of the filtrate is subsequently reabsorbed by the peritubule capillary network. Micropuncture techniques have been used to obtain quantitative measurements of the pressures and fluid dynamics of the peritubule microcirculation. The net force for uptake of all the fluid reabsorbed by a single proximal tubule up to the point of micropuncture is 21 mm Hg acting over a capillary bed with a permeability surface area product of 2 nl/min per mm Hg. In contrast to subcutaneous tissue and muscle, the renal interstitial fluid pressure is positive. The consequence of a positive interstitial fluid pressure is that normal lymph flow is relatively high and changes in interstitial fluid pressure have relatively little effects on lymph flow.     

The Krylov-Bogoliubov-Mitropolskii method applied to models of population dynamics

In this study the possibility of applying the asymptotic method of Krylov-Bogoliubov-Mitropolskii to problems of population dynamics is shown. Especially a general Volterra-Gause-Witt type model for prey-predator interaction is investigated. A discussion on the results obtained is given for the general model and for a particular case as well.     

The small mass assumption applied to the multibody dynamics of motor proteins

This paper presents a multibody dynamics approach to the modeling, simulation and analysis of motor protein dynamic behavior. Usually proteins are modeled as a collection of a small number of particles, oftentimes only two particles, with spring-like connections between them. However, these simple particle models potentially omit interactions and dynamics between the unmodeled particles and the environment that may be important. Multibody dynamics models can be used to address this issue. However, widely used techniques for analyzing particle models may not be applicable to multibody models. Herein the validity of the small mass assumption, which is central to the analysis of particle models, is examined in detail using a simplified multibody model of the molecular motor protein Myosin V.     

Aspects of population dynamics in Halimione portulacoides communities

Summary Studies on sample plots inHalimione portulacoides communities show that environmental disturbances, either natural or induced by man, start a sequence of partly overlapping density maxima inSuaeda maritima, Aster tripolium andPuccinellia maritima successively, before the originalHalimione community totally recovers. When succession time before recovering is long enough, there are tendencies in redundancy of this sequence stressing the unilinear character of the succession. Minor environmental impacts induce a longer time-lag period of theSuaeda density maximum, suggesting threshold values of these impacts for the species to maintain minimal population densities or to become locally extinct. This sequence of interim species starting after an environmental disturbance, suggests also a gradient character in various biological attributes, for instance in life-time, propagation, nutrient and genetic plasticity strategies. The mechanism described can therefore be interpreted as a complex of mostly well-adapted and well-integrated inherent species strategies capable of absorbing environmental shocks. It is suggested that in the salt-marsh ccosystem the pattern of spatial variation in densities and that of temporal variation in fluctuations of the three species populations under natural conditions reflect corresponding patterns of environmental disturbances in the vegetation taking into account a timelag associated with the magnitude of the impact concerned.Contribution to the Symposium on Plant species and plant communities held at Nijmegen, 11–12 November 1976, on the occasion of the 60th birthday of Professor Victor Westhoff.Nomenclature follows Heukels-van Ooststroom. Flora van Nederland, 18e druk, 1975. Wolters-Noodhoff, Groningen.The authors are greatly indebted to Dr K.F. Vaas (Yerseke) for reviewing the English text.Communication Nr. 160.     

Comparative study of the fluid dynamics of bottom spray fluid bed coaters

Fluid dynamics of pellets processed in bottom spray traditional Wurster coating and swirl accelerated air (precision) coating were compared with the intent to understand and facilitate improvements in the coating processes. Fluid dynamics was described by pellet mass flow rate (MFR) obtained using a pellet collection system and images captured using high speed photography. Pellet flow within the partition column was found to be denser and slower in Wurster coating than in precision coating, suggesting a higher tendency of agglomeration during the coating process. The influence of partition gap and load on the MFR indicated that the mechanism of transport of pellets into the coating zone in precision coating depended on a strong suction, whereas in Wurster coating, pellets were transported by a combination of peripheral fluidization, gravity, and weak suction pressure. In precision coating, MFR was found to increase uniformly with air flow rate and atomizing pressure, whereas MFR in Wurster coating did not correlate as well with air flow rate and atomizing pressure. This demonstration showed that transport in precision coating was air dominated. In conclusion, fluid dynamics in precision coating was found to be air dominated and dependent on pressure differential, thus it is more responsive to changes in operational variables than Wurster coating.     

Pulsatile flow of Casson's fluid through stenosed arteries with applications to blood flow

The effects of non-Newtonian nature of blood and pulsatility on flow through a stenosed tube have been investigated. A perturbation method is used to analyse the flow. It is of interest to note that the thickness of the viscous flow region is non-uniform (changing with axial distance). An analytic relation between viscous flow region thickness and red cell concentration has been obtained. It is important to mention that some researchers have obtained an approximate solution for the flow rate-pressure gradient equation (assuming the ratio between the yield stress and the wall shear to be very small in comparison to unity); in the present analysis, we have obtained an exact solution for this non-linear equation without making that assumption. The approximate and exact solutions compare well with one of the exact solutions. Another important result is that the mean and steady flow rates decrease as the yield stress theta increases. For the low values of the yield stress, the mean flow rate is higher than the steady flow rate, but for high values of the yield stress, the mean flow rate behaviour is of opposite nature. The critical value of the yield stress at which the flow rate behaviour changes from one type to another has been determined. Further, it seems that there exists a value of the yield stress at which flow stops for both the flows (steady and pulsatile). It is observed that the flow stop yield value for pulsatile flow is lower than the steady flow. The most notable result of pulsatility is the phase lag between the pressure gradient and flow rate, which is further influenced by the yield stress and stenosis. Another important result of pulsatility is the mean resistance to flow is greater than its steady flow value, whereas the mean value of the wall shear for pulsatile flow is equal to steady wall shear. Many standard results regarding Casson and Newtonian fluids flow, uniform tube flow and steady flow can be obtained as the special cases of the present analysis. Finally, some applications of this theoretical analysis have been cited.