Large deforming buoyant embolus passing through a stenotic common carotid artery: a computational simulation

Arterial embolism is responsible for the death of lots of people who suffers from heart diseases. The major risk of embolism in upper limbs is that the ruptured particles are brought into the brain, thus stimulating neurological symptoms or causing the stroke. We presented a computational model using fluid-structure interactions (FSI) to investigate the physical motion of a blood clot inside the human common carotid artery. We simulated transportation of a buoyant embolus in an unsteady flow within a finite length tube having stenosis. Effects of stenosis severity and embolus size on arterial hemodynamics were investigated. To fulfill realistic nonlinear property of a blood clot, a rubber/foam model was used. The arbitrary Lagrangian-Eulerian formulation (ALE) and adaptive mesh method were used inside fluid domain to capture the large structural interfacial movements. The problem was solved by simultaneous solution of the fluid and the structure equations. Stress distribution and deformation of the clot were analyzed and hence, the regions of the embolus prone to lysis were localized. The maximum magnitude of arterial wall shear stress during embolism occurred at a short distance proximal to the throat of the stenosis. Through embolism, arterial maximum wall shear stress is more sensitive to stenosis severity than the embolus size whereas role of embolus size is more significant than the effect of stenosis severity on spatial and temporal gradients of wall shear stress downstream of the stenosis and on probability of clot lysis due to clot stresses while passing through the stenosis.     

Nonlinear terms produced by passing amplitude-modulated sinusoids through a hair cell transducer function

We derive mathematically the output of Corey and Hudspeth's hair cell transducer function for the following cases: (1) the input is a single carrier whose output is modulated by the sum of two sinusoids; (2) the input is the sum of two carriers, each of which is amplitude-modulated by a single sinusoid. The theoretical results are similar to the results of an experiment in which field potentials were recorded from the human scalp while one ear was stimulated with auditory waveform (1) and with auditory waveform (2) of the cases above.     

Numerical simulation of blood and interstitial flow through a solid tumor

A theoretical framework is presented for describing blood flow through the irregular vasculature of a solid tumor. The tumor capillary bed is modeled as a capillary tree of bifurcating segments whose geometrical construction involves deterministic and random parameters. Blood flow along the individual capillaries accounts for plasma leakage through the capillary walls due to the transmural pressure according to Sterling’s law. The extravasation flow into the interstitium is described by Darcy’s law for a biological porous medium. The pressure field developing in the interstitium is computed by solving Laplace’s equation subject to derived boundary conditions at the capillary vessel walls. Given the arterial, venous, and tumor surface pressures, the problem is formulated as a coupled system of integral and differential equations arising from the interstitium and capillary flow transport equations. Numerical discretization yields a system of linear algebraic equations for the interstitial and capillary segment pressures whose solution is found by iterative methods. Results of numerical computations document the effect of the interstitial hydraulic and vascular permeability on the fractional plasma leakage. Given the material properties, the fractional leakage reaches a maximum at a particular grade of the bifurcating vascular tree.     

Numerical simulation of the electrophoretic transport of a biopolymer through a synthetic nano-pore

We employed a hybrid approach to study numerically the translocation of a biopolymer through an artificial nano-pore driven by an external electric field in the presence of an explicit solvent. The motion of the polymer is simulated by the 3D Langevin dynamics technique. The hydrodynamic interactions (HI) between the polymer and the fluid are taken into account by the lattice Boltzmann equation. Our polymer chain model representing the double-stranded DNA was first validated by comparing the diffusion coefficient obtained from the numerical results with the experimental and theoretical results. Then, we conducted numerical simulations of the biopolymer's translocation process by applying a theoretical formula for the net electrophoretic force acting on the part of the polymer residing in the pore. We compared quantitatively the translocation times and the velocities of different DNA lengths with the corresponding experimental results. Our simulation results are in good agreement with the experimental ones when the HI are considered explicitly.     

Numerical simulation of air flow through a biofilter with heterogeneous porous media

Based on the ideal biofilter model, numerical simulation using lattice Boltzmann method is carried out to investigate the effect of Darcy number and porosity on removal efficiency of low headloss biofilter. The generalized Navier-Stokes model (Brinkman-Forchheimer-extended Darcy model) is applied making several assumptions. It is found that the Darcy number has determinant influence on the removal efficiency, and the effect of porosity on removal efficiency is very weak at lower Darcy numbers but very strong at higher Darcy numbers. It was found there was strong evidence of flow heterogeneity in the biofilter (Chitwood, D.E., Devinny, J.S., Reynolds Jr., F.E., 1999. Evaluation of a two-stage biofilter for treatment of POTW waste air. Environ. Prog. 18, 212-221). In this study we have found the biofilter performance can be improved by adjusting local Darcy number of the porous media in the biofilter.     

脂质筏--病原微生物出入细胞的一种门户

脂质筏是富含胆固醇和鞘磷脂的一种特殊膜结构,脂质筏形成的膜微区具有更低的膜流动性,呈现有序液相。脂质筏参与包括跨膜信号转导、物质内吞、脂质及蛋白定向分选在内的多种重要细胞生物学过程。分布于脂筏的分子主要有两种形式的蛋白修饰：与糖基磷脂酰肌醇(GPI)相连,或被肉豆蔻酸酰化／软脂酸酯酰化。一系列GPI-锚固蛋白被鉴定为多种不同的细菌、细菌毒素和病毒的受体。越来越多的研究发现,不同类型和种属来源的细菌、细菌毒素、原虫及病毒利用细胞质膜表面的脂筏结构介导其入胞,完成跨细胞转运、胞内复制或感染周期,一些病毒还利用脂筏完成其病毒颗粒的组装和出芽过程。通过对病原微生物如何利用脂筏介导其内吞及内吞入胞后在胞内的转运的研究,有利于我们更好地认识病原微生物与宿主细胞之间的相互作用,从而有可能发展更有效的抗感染策略。     

Numerical simulation of the mechanics of a yeast cell under high hydrostatic pressure

The mechanical effects of the compression of a yeast cell (Saccharomyces cerevisiae) under high hydrostatic pressure used for the processing of food and food ingredients are modelled and simulated with the finite-element method. The cell model consists of a cell wall, cytoplasm a lipid filled vacuole and the nucleus. Material parameters have been taken from literature or have been derived from thermodynamic relationships of water and lipids under high hydrostatic pressure. The model has been validated for a pressure load up to 250 MPa. Comparison of the volume reduction to in situ experimental observations reveals very good agreement. Dimensional analysis of the governing equations shows that transient pressure application in a high-pressure food process does not enhance structural inactivation (mechanical damage), unless pressure oscillation frequencies of 700 MHz are applied. The deformation of the cell under pressure deviates strongly from isotropic volume reduction. Especially, organelle membranes exhibit large effective strain values. Hydrostatic stress conditions are preserved in the interior part of the cell. A pressure load of 400 MPa, which is critical upon disruption of cell organelle membranes, generates an effective strain up to 80%. In the cell wall, the stress state is heterogeneous. Von-Mises stress reaches the critical value upon failure of the cell wall of 70+/-4 MPa at a pressure load between 415 and 460 MPa.     

Effects of inner solution viscosity and membrane stiffness on erythrocyte deformability on passing through a microchannel: prediction by two-dimensional simulation

We studied erythrocyte deformability in an effort to develop diagnostic methods based on its measurement and thus aid in the development of therapies for circulatory diseases. In the reported work, we performed two-dimensional numerical simulations of blood flow through a microchannel (MC) to evaluate erythrocyte deformability, applying the immersed boundary method to simulate erythrocyte movement and deformation. To evaluate deformability, MC transit capacity and shape recoverability were considered, defined as the time required to pass through the MC and the time constant during the shape-recovery process after exiting the MC, respectively. The simulation results showed that the erythrocyte MC transit time increased when the viscosity of the inner solution or the stiffness of the membrane increased. The time constant for erythrocyte shape recovery increased as the inner solution viscosity increased. In contrast, the time constant decreased as the erythrocyte membrane stiffness increased. These time-constant trends were in agreement with a theoretical equation derived using the Kelvin model and with previous experimental results. This diagnostic method of measuring erythrocyte shape recoverability and MC transit capacity is anticipated to have clinical application.     

Mobility of protozoa through narrow channels

Microbes in the environment are profoundly affected by chemical and physical heterogeneities occurring on a spatial scale of millimeters to micrometers. Physical refuges are critical for maintaining stable bacterial populations in the presence of high predation pressure by protozoa. The effects of microscale heterogeneity, however, are difficult to replicate and observe using conventional experimental techniques. The objective of this research was to investigate the effect of spatial constraints on the mobility of six species of marine protozoa. Microfluidic devices were created with small channels similar in size to pore spaces in soil or sediment systems. Individuals from each species of protozoa tested were able to rapidly discover and move within these channels. The time required for locating the channel entrance from the source well increased with protozoan size and decreased with channel height. Protozoa of every species were able to pass constrictions with dimensions equal to or smaller than the individual's unconstrained cross-sectional area. Channel geometry was also an important factor affecting protozoan mobility. Linear rates of motion for various species of protozoa varied by channel size. In relatively wide channels, typical rates of motion were 300 to 500 microm s(-1) (or about 1 m per hour). As the channel dimensions decreased, however, motilities slowed more than an order of magnitude to 20 microm s(-1). Protozoa were consistently observed to exhibit several strategies for successfully traversing channel reductions. The empirical results and qualitative observations resulting from this research help define the physical limitations on protozoan grazing, a critical process affecting microbes in the environment.     

Passage times for polymer translocation pulled through a narrow pore

We study the passage times of a translocating polymer of length N in three dimensions, while it is pulled through a narrow pore with a constant force F applied to one end of the polymer. At small to moderate forces, satisfying the condition FN(nu)/k(B)T less, similar 1, where nu approximately 0.588 is the Flory exponent for the polymer, we find that tau(N), the mean time the polymer takes to leave the pore, scales as N(2+nu) independent of F, in agreement with our earlier result for F = 0. At strong forces, i.e., for, FN(nu)/k(B)T > 1, the behavior of the passage time crosses over to tau(N) approximately N(2)/F. We show here that these behaviors stem from the polymer dynamics at the immediate vicinity of the pore-in particular, the memory effects in the polymer chain tension imbalance across the pore.     

Investigating the efficiency of the single backcrossing breeding strategy through computer simulation

A strategy combining single backcrossing with selected bulk breeding has been successfully used in wheat improvement at CIMMYT to introgress rust resistant genes from donor parents to elite adapted cultivars. In this research, the efficiency of this breeding strategy was compared to other crossing and selection strategies through computer simulation. Results indicated this breeding strategy has advantages in retaining or improving the adaptation of the recurrent parents, and at the same time transferring most of the desired donor genes in a wide range of scenarios. Two rounds of backcrossing have advantages when the adaptation of donor parents is much poorer than that of the adapted parents, but the advantage of three rounds of backcrossing over two rounds is minimal. We recommend using the single backcrossing breeding strategy (SBBS) when three conditions are met: (1) multiple genes govern the phenotypic traits to be transferred from donor parents to adapted parents, (2) the donor parents have some favorable genes that may contribute to the improvement of adaptation in the recipient parents, and (3) conventional phenotypic selection is being applied, or individual genotypes cannot be precisely identified. We envisage that all three conditions commonly exist in modern breeding programs, and therefore believe that SBBS could be applied widely. However, we do not exclude the use of repeated backcrossing if the transferred genes can be precisely identified by closely linked molecular markers, and the donor parents have extremely poor adaptation.     

Analyzing cell fate control by cytokines through continuous single cell biochemistry

Cytokines are important regulators of cell fates with high clinical and commercial relevance. However, despite decades of intense academic and industrial research, it proved surprisingly difficult to describe the biological functions of cytokines in a precise and comprehensive manner. The exact analysis of cytokine biology is complicated by the fact that individual cytokines control many different cell fates and activate a multitude of intracellular signaling pathways. Moreover, although activating different molecular programs, different cytokines can be redundant in their biological effects. In addition, cytokines with different biological effects can activate overlapping signaling pathways. This prospect article will outline the necessity of continuous single cell biochemistry to unravel the biological functions of molecular cytokine signaling. It focuses on potentials and limitations of recent technical developments in fluorescent time‐lapse imaging and single cell tracking allowing constant long‐term observation of molecules and behavior of single cells. J. Cell. Biochem. 108: 343–352, 2009. © 2009 Wiley‐Liss, Inc.     

Anomalous caudal vena cava passing through the vertebral canal in a calf

A 15-day-old female Holstein-Friesian calf with an anomalous caudal vena cava was examined macroscopically, roentgenologically, and histologically. The calf, weighing 43 kg, had severe scoliosis. A common renal vein merged into a single venous trunk formed by the union of the left and right common iliac veins. The trunk entered the vertebral canal through the left intervertebral foramen formed by the last (13th) thoracic and the first lumbar vertebrae. The trunk continued along the ventral side of the narrowing spinal cord inside the canal, and then ran out the left intervertebral foramen formed by the 8th and 9th thoracic vertebrae and emptied via the right azygos vein into the cranial vena cava. In contrast, the hepatic vein passed through the foramen vena cava independently of the trunk and entered the right atrium directly. The pathogenesis of the present anomaly may be explained as follows: The right subcardinal vein, failing to make connection with the liver, shunted directly into the right azygos vein derived from the right supracardinal vein. The body axis began to curve before ossification of the vertebrae occurred. Consequently, the developing right supracardinal vein, located close to the spinal cord, is thought to have become enclosed in the vertebrae with the spinal cord during the early fetal stages.     

The role of tracking in the perception of objects, moving toward each other in a narrow vertical slit line

It has been shown by means of calculation and device modeling that the observed subjective pressure of two objects moving toward one another behind a narrow vertical slit corresponds to the pressure of objects retinal projections, induced in its turn by a slowed down tracing. 180e turn of one of the moving objects is also explained by tracing.     

Extrinsic noise passing through a Michaelis-Menten reaction: A universal response of a genetic switch

The study of biochemical pathways usually focuses on a small section of a protein interactions network. Two distinct sources contribute to the noise in such a system: intrinsic noise, inherent in the studied reactions, and extrinsic noise generated in other parts of the network or in the environment. We study the effect of extrinsic noise entering the system through a nonlinear uptake reaction which acts as a nonlinear filter. Varying input noise intensity varies the mean of the noise after the passage through the filter, which changes the stability properties of the system. The steady-state displacement due to small noise is independent on the kinetics of the system but it only depends on the nonlinearity of the input function.For monotonically increasing and concave input functions such as the Michaelis-Menten uptake rate, we give a simple argument based on the small-noise expansion, which enables qualitative predictions of the steady-state displacement only by inspection of experimental data: when weak and rapid noise enters the system through a Michaelis-Menten reaction, then the graph of the system's steady states vs. the mean of the input signal always shifts to the right as noise intensity increases.We test the predictions on two models of lac operon, where TMG/lactose uptake is driven by a Michaelis-Menten enzymatic process. We show that as a consequence of the steady state displacement due to fluctuations in extracellular TMG/lactose concentration the lac switch responds in an asymmetric manner: as noise intensity increases, switching off lactose metabolism becomes easier and switching it on becomes more difficult.     

Growth of a single cell

A theory of growth of a cell which takes up nutrients by diffusion or active transport is discussed. The main conclusion is that the volume should grow at least as fast as the third power of the time. Existing experimental evidence is not a conclusive test of the theory, and further experiments to test it are proposed.