Population growth with randomly distributed jumps

 The growth of populations with continuous deterministic and random jump components is treated. Three special models in which random jumps occur at the time of events of a Poisson process and admit formal explicit solutions are considered: A) Logistic growth with random disasters having exponentially distributed amplitudes; B) Logistic growth with random disasters causing the removal of a uniformly distributed fraction of the population size; and C) Exponential decay with sudden increases (bonanzas) in the population and with each increase being an exponentially distributed fraction of the current population. Asymptotic and numerical methods are employed to determine the mean extinction time for the population, qualitatively and quantitatively. For Model A, this time becomes exponentially large as the carrying capacity becomes much larger than the mean disaster size. Implications for colonizing species for Model A are discussed. For Models B and C, the practical notion of a small, but positive, effective extinction level is chosen, and in these cases the expected extinction time rises rapidly with population size, yet at less than an e xponentially large order. Received 21 June 1996; received in revised form 17 February 1997     

Image correlation spectroscopy of randomly distributed disks

Image correlation spectroscopy (ICS) has been widely used to quantify spatiotemporal distributions of fluorescently labelled cell membrane proteins and receptors. When the membrane proteins are randomly distributed, ICS may be used to estimate protein densities, provided the proteins behave as point-like objects. At high protein area fraction, however, even randomly placed proteins cannot obey Poisson statistics, because of excluded area. The difficulty can arise if the protein effective area is quite large, or if proteins form large complexes or aggregate into clusters. In these cases, there is a need to determine the correct form of the intensity correlation function for hard disks in two dimensions, including the excluded area effects. We present an approximate but highly accurate algorithm for the computation of this correlation function. The correlation function was verified using test images of randomly distributed hard disks of uniform intensity convolved with the microscope point spread function. This algorithm can be readily modified to compute exact intensity correlation functions for any probe geometry, interaction potential, and fluorophore distribution; we show how to apply it to describe a random distribution of large proteins labeled with a single fluorophore.     

A self-scalable distributed network simulation environment based on cloud computing

While parameter sweep simulations can help undergraduate students and researchers to understand computer networks, their usage in the academia is hindered by the significant computational load they convey. This paper proposes DNSE3, a service oriented computer network simulator that, deployed in a cloud computing infrastructure, leverages its elasticity and pay-per-use features to compute parameter sweeps. The performance and cost of using this application is evaluated in several experiments applying different scalability policies, with results that meet the demands of users in educational institutions. Additionally, the usability of the application has been measured following industry standards with real students, yielding a very satisfactory user experience.     

Controlling network structure in degradable thiol-acrylate biomaterials to tune mass loss behavior

Degradable thiol-acrylate materials were synthesized from the mixed-mode polymerization of a diacrylate poly(ethylene glycol) (PEG) monomer with thiol monomers of varying functionalities to control the final network structure, ultimately influencing the material's degradation behavior and properties. The influence of the concentration of thiol groups and monomer functionality on the mass loss profiles were examined experimentally and theoretically. Mass loss behavior was also predicted for networks with varying extents of cyclization, PEG molecular weight, and backbone chain length distributions. Experimental results indicate that increasing the thiol concentration from 10 to 50 mol % shifted the reverse gelation time from 35 to 8 days and the extent of mass loss at reverse gelation from 75 to 40%. Similarly, decreasing the thiol functionality from 4 to 1 shifted the reverse gelation time from 18 to 8 days and the mass loss extent at reverse gelation from 70 to 45%.     

On the storage capacity of an associative memory with randomly distributed storage elements

In an associative memory with randomly distributed storage elements at least 0.05 bit per storage element can be stored.     

Full-system simulation of distributed memory multicomputers

In this paper we discuss environments for the full-system simulation of multicomputers. These environments are composed of a large collection of modules that simulate the compute nodes and the network, plus additional linking elements that perform communication and synchronization. We present our own environment, in which we integrate Simics with INSEE. We reuse as many Simics modules as possible to reduce the effort of hardware modeling, and also to simulate standard machines running unmodified operating systems. This way we avoid the error-prone effort of developing drivers and libraries. The environment we propose in this paper enables us to show some of the difficulties we found when integrating diverse tools, and how we were able to overcome them. Furthermore we show some important details to have into account in order to do a valid full-system simulation of multicomputers, mostly related with synchronization and timing. Thus, a trade-off has to be found between simulation speed and accuracy of results.     

Numerical simulation of cross-country skiing

A program for numerical simulation of a whole ski race, from start to finish, is developed in MATLAB. The track is modelled by a set of cubical splines in two dimensions and can be used to simulate a track in a closed loop or with the start and finish at different locations. The forces considered in the simulations are gravitational force, normal force between snow and skis, drag force from the wind, frictional force between snow and ski and driving force from the skier. The differential equations of motion are solved from start to finish with the Runge-Kutta method. Different wind situations during the race can be modelled, as well as different glide conditions on different parts of the track. It is also possible to vary the available power during the race. The simulation program's output is the total time of the race, together with the forces and speed during different parts of the race and intermediate times at selected points. Some preliminary simulations are also presented.     

Axoplasmic proteins of the squid giant nerve fiber with particular reference to the fibrous protein

1. Axoplasm of squid giant nerve fibers is examined with the ultracentrifuge and electrophoresis apparatus and several distinct components demonstrated. 2. One of these components, a protein called axon filaments, is isolated by fractional extraction followed by differential ultracentrifugation and redissolving in glycine solution. Axon filaments are monodisperse by ultracentrifugation. Their physical chemical properties have been studied. 3. The existence of a reversible transformation of axon filaments into a particle of lower molecular weight and lower asymmetry has been demonstrated.     

RandomPOD--a new method and device for advanced wear simulation of orthopaedic biomaterials

A 16-station wear simulator of the pin-on-disc type, called RandomPOD, was designed, built, and validated. The primary area of application of the RandomPOD is wear studies of orthopaedic biomaterials. The type of relative motion between the bearing surfaces, generally illustrated as shapes of slide tracks, has been found to have a strong effect on the type and amount of wear produced. The computer-controlled RandomPOD can be programmed to produce virtually any slide track shape and load profile. In the present study, the focus is on the biomechanically realistic random variation in the track shape and load. In the reference test, the established combination of circular translation and static load was used. In addition, the combinations of random motion/static load, and circular translation/random load were included. The pins were conventional ultra-high molecular weight polyethylene (UHMWPE), the discs were polished CoCr, and the lubricant was diluted calf serum. The UHMWPE wear factor resulting from random motion was significantly higher than that resulting from circular translation. This was probably caused by the fact that in the random motion the direction of sliding changed more than in circular translation with the same sliding distance. The type of load, random vs. static, was unimportant with respect to the wear factor produced. The principal advantage of using the present random track is that possible unrealistic wear phenomena related to the use of fixed track shapes can be avoided.     

Numerical simulation of the cardiovascular system

In this article, we aim at giving a non-technical overview of some mathematical models currently used in the numerical simulation of the cardiovascular system. A hierarchy of models for blood flows in large arteries is briefly described as well as an electromechanical model for the heart. We discuss some possible applications of the numerical simulations of such models, for example the optimization of prostheses. We also address the issue of the data assimilation for the calibration of the models.     

Numerical simulation of aldolase tetramer stability

A theoretical study of aldolase tetramer stability, conducted by finite difference Poisson-Boltzmann (FDPB) and modified Tanford-Kirkwood (MTK) techniques using the atomic coordinates of human aldolase, is described. A method for calculating the interaction energy between subunits is proposed. An analysis of the contribution of different energy terms to the stability and oligomeric equilibria (monomer ⇔ dimer ⇔ tetramer) of aldolase is made. It is shown that the loss of solvation energy and electrostatic interactions at very high and low pH-s destabilise the oligomers. These energy terms are compensated over a wide pH range by the stabilization energy due to hydrophobic interactions. It is shown that the aldolase tetramer is energetically more preferable than other oligomers in the pH range from 5 to 11. Subunit-subunit interactions within the tetramer suggest one dimeric form to be the most stable of the possible sub-parts. For this reason the tetramer can be thought of as a “dimer of dimers”. A comparison between our theoretical results and available experimental data shows that the dissociation of the aldolase tetramer below pH 3–4 cooperatively leads to acid denaturation. A second dissociation is predicted to occur at high pH (>12) in addition to the well known acidic dissociation. The analysis suggests that a mutation of His20 or Arg257 to a neutral residue could decrease the pH of the acidic dissociation by approximately 1 pH unit. Received: 16 February 1998 / Revised version: 8 April 1998 / Accepted: 19 April 1998     

The ingi and RIME non-LTR retrotransposons are not randomly distributed in the genome of Trypanosoma brucei

The ingi (long and autonomous) and RIME (short and nonautonomous) non--long-terminal repeat retrotransposons are the most abundant mobile elements characterized to date in the genome of the African trypanosome Trypanosoma brucei. These retrotransposons were thought to be randomly distributed, but a detailed and comprehensive analysis of their genomic distribution had not been performed until now. To address this question, we analyzed the ingi/RIME sequences and flanking sequences from the ongoing T. brucei genome sequencing project (TREU927/4 strain). Among the 81 ingi/RIME elements analyzed, 60% are complete, and 7% of the ingi elements (approximately 15 copies per haploid genome) appear to encode for their own transposition. The size of the direct repeat flanking the ingi/RIME retrotransposons is conserved (i.e., 12-bp), and a strong 11-bp consensus pattern precedes the 5'-direct repeat. The presence of a consensus pattern upstream of the retroelements was confirmed by the analysis of the base occurrence in 294 GSS containing 5'-adjacent ingi/RIME sequences. The conserved sequence is present upstream of ingis and RIMEs, suggesting that ingi-encoded enzymatic activities are used for retrotransposition of RIMEs, which are short nonautonomous retroelements. In conclusion, the ingi and RIME retroelements are not randomly distributed in the genome of T. brucei and are preceded by a conserved sequence, which may be the recognition site of the ingi-encoded endonuclease.     

The reconstruction of structure from electron micrographs of randomly oriented particles

A new method for enhancing and reconstructing the three dimensional structure of randomly oriented particles from their electron micrographs is developed. The method requires as an input many pictures of randomly oriented identical particles. The analysis is based on the calculation and accumulation of the spatial correlation of the densities on the electron micrographs, from which the spherical harmonic coefficients of the structure can be found. The process of enhancement of the spatial correlation and the averaging out of background noise enables reconstructions by use of pictures with low signal-to-noise ratio. The theory is presented and implemented in a computer program package. Simulated electron micrographs of ellipses, rods and a model of hexameric glutamate dehydrogenase are analyzed to demonstrate reconstructions using the computer programs.     

Numerical simulation of cardiovascular dynamics with different types of VAD assistance

A variety of methods by which mechanical circulatory support (MCS) can be provided have been described. However, the haemodynamic benefits of the different methods have not been adequately quantified. The aim of this paper is to compare the haemodynamic effects of six forms of MCS by numerical simulation. Three types of ventricular assist device (VAD) are studied: positive displacement; impeller and a novel reciprocating-valve design. Similarly, three pumping modes are modelled: constant flow; counterpulsation and copulsation. The cardiovascular system is modelled using an approach developed previously, using the concentrated parameter method by considering flow resistance, vessel elasticity and inertial effects of blood in individual conduit segments. The dynamic modelling of displacement and impeller pumps is represented by VAD inlet/outlet flow-rate changes. The dynamics of the reciprocating-valve pump is modelled with a specified displacement profile. Results show that in each simulation, the physiological variables of mean arterial pressure and systemic flow are adequately maintained. Modulation of the impeller pump flow profile produces a small (5 mmHg) oscillatory component to arterial pressure, whereas the displacement and reciprocating-valve pumps generate substantial arterial pressure and flow pulsatility. The impeller pump requires the least power input, the reciprocating valve pump slightly more, and the displacement pump the most. The in parallel configuration of the impeller and displacement pump designs with respect to the left ventricle provides near complete unloading and can cause the aortic valve to remain closed throughout the entire cardiac cycle with the attendant risk of aortic valve leaflet fusion following prolonged support. The in series configuration of the reciprocating-valve pump avoids this shortcoming but activation must be carefully synchronized to the cardiac cycle to allow adequate coronary perfusion. The reciprocating-valve pump is associated with haemodynamic advantages and a favourable power consumption.     

Photo-cross-linked hydrogels with polysaccharide-poly(amino acid) structure: new biomaterials for pharmaceutical applications

The aim of this work has been the preparation and characterization of novel hydrogels with polysaccharide-poly(amino acid) structure having suitable physicochemical properties for pharmaceutical applications. In the first step, hyaluronic acid (HA) and alpha,beta-poly(N-2-hydroxyethyl)-DL-aspartamide (PHEA) have been derivatized with methacrylic anhydride (AMA), thus obtaining HA-AMA and PHM derivatives, respectively. In the second step, aqueous solutions of both these derivatives have been irradiated at 313 nm to obtain chemical hydrogels. The hydrogel obtained by irradiating for 15 min an aqueous solution containing 4% w/v of HA-AMA and 4% w/v of PHM resulted in the highest yield. Its swelling ability was dependent on the pH and nature of the external medium. Besides, this hydrogel undergoes a partial hydrolysis, especially in the presence of enzymes, such as esterase or hyaluronidase, but the entity of this degradation is lower than that observed for a hydrogel based on HA-AMA alone. The ability of this hydrogel to entrap drug molecules has been evaluated by using thrombin as a model drug. In vitro release studies and a platelet aggregation test demonstrated that the HA-AMA/PHM hydrogel is able to release thrombin in the active form, thus suggesting its suitability for the treatment of hemorrhages.     

Numerical simulation of cardiovascular dynamics with healthy and diseased heart valves

This paper presents a new concentrated parameter model for cardiovascular dynamics that includes an innovative model of heart valve dynamics, which is embedded in the overall model of the four chambers of the heart and the systemic and pulmonary circulation loops. The heart chambers are described with a variable elastance model, and the systemic and pulmonary loops are described with modified Windkessel models. In modelling the heart valve dynamics, the various factors that influence the valve motion are examined, and the governing differential equation for valve motion is derived. The heart valve model includes the influence of the blood pressure effect, the friction effect from the tissue, and from blood motion. As improvement from previous works, the contribution of the blood vortex effect in the vicinity of the valve leaflets to valve motion is specially considered. The proposed model is then used in simulation of healthy and certain pathological conditions such as mitral valve stenosis and aortic regurgitation. The predicted results agree well with results illustrated in cardiology textbooks.