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.     

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%.     

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.     

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.     

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.     

Numerical simulation of collapsible-tube flows with sinusoidal forced oscillations

Collapsible-tube flow with self-excited oscillations has been extensively investigated. Though physiologically relevant, forced oscillation coupled with self-excited oscillation has received little attention in this context. Based on an ODE model of collapsible-tube flow, the present study applies modern dynamics methods to investigate numerically the responses of forced oscillation to a limit-cycle oscillation which has topological characteristics discovered in previous unforced experiments. A devil's staircase and period-doubling cascades are presented with forcing frequency and amplitude as control parameters. In both cases, details are provided in a bifurcation diagram. Poincaré sections, a frequency spectrum and the largest Lyapunov exponents verify the existence of chaos in some circumstances. The thin fractal structure found in the strange attractors is believed to be a result of high damping and low stiffness in such systems.     

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.     

Mitochondrial network of skeletal muscle fiber

Highly specialized muscle fibers require a unique spatial organization of the mitochondrial network. Mitochondrial morphology is largely determined by the fusion and fission of these organelles. This review summarizes the current concepts of mitochondrial dynamics mechanisms and structural features of the mitochondrial network in striated muscle tissue. The role of mitochondria and their dynamics in muscle fiber physiology are also discussed.     

Fractional exponential decay in the capture of ligands by randomly distributed traps in one dimension

In many biophysical and biochemical experiments one observes the decay of some ligand population by an appropriate system of traps. We analyse this decay for a one-dimensional system of randomly distributed traps, and show that one can distinguish three different regimes. The decay starts with a fractional exponential of the form exp[−(t/t ₀)^1/2], which changes into a fractional exponential of the form exp[−(t/t ₁)^1/3] for long times, which in its turn changes into a pure exponential time dependence, i.e. exp[−t/t ₂] for very long times. With these three regimes, we associate three time scales, related to the average trap density and the diffusion constant characterizing the motion of the ligands.     

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.     

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.     

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.     

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.