Separation of translational and rotational contributions in solution studies using fluorescence photobleaching recovery

Although fluorescence photobleaching recovery (FPR) experiments are usually interpreted in terms of the translational motions of a fluorescently labeled species, rotational motions can also modulate recovery through the cosine-squared laws for dipolar absorption and emission processes. In a complex interacting system, translational and rotational contributions may both be simultaneously present. We show how these contributions can be separated in solution studies using an FPR setup in which (a) the linear polarization of the low-intensity observation beam and the high-intensity photobleaching pulse can be varied independently, and (b) all emitted fluorescent photons are counted equally. The fluorescence recovery signal obtained with the observation beam polarized at the magic angle, 54.7 degrees, from the bleach polarization direction is independent of label orientation, whereas the anisotropy function formed from a combination of parallel and perpendicular polarizations isolates the orientational recovery. The anisotropy function is identical to that in fluorescence correlation spectroscopy and, for rigid-body rotational diffusion, can be expressed as a sum of five exponential terms.     

Magnetosome dynamics in magnetotactic bacteria.

Diffusive motions of the magnetosomes (enveloped Fe3O4 particles) in the magnetotactic bacterium Aquaspirillum magnetotacticum result in a very broad-line Mössbauer spectrum (T approximately 100 mm/s) above freezing temperatures. The line width increases with increasing temperature. The data are analyzed using a bounded diffusion model to yield the rotational and translational motions of the magnetosomes as well as the effective viscosity of the material surrounding the magnetosomes. The results are [theta 2] l/2 less than 1.5 degrees and [x2] 1/2 less than 8.4 A for the rotational and translational motions, respectively, implying that the particles are fixed in whole cells. The effective viscosity is 10 cP at 295 K and increases with decreasing temperature. Additional Fe3+ material in the cell is shown to be associated with the magnetosomes. Fe2+ material in the cell appears to be associated with the cell envelope.     

Translational and rotational motions of proteins in a protein crowded environment

Fluorescence correlation spectroscopy (FCS) was used to measure the translational diffusion of labeled apomyoglobin (tracer) in concentrated solutions of ribonuclease A and human serum albumin (crowders), as a quantitative model system of protein diffusive motions in crowded physiological environments. The ratio of the diffusion coefficient of the tracer protein in the protein crowded solutions and its diffusion coefficient in aqueous solution has been interpreted in terms of local apparent viscosities, a molecular parameter characteristic for each tracer-crowder system. In all protein solutions studied in this work, local translational viscosity values were larger than the solution bulk viscosity, and larger than rotational viscosities estimated for apomyoglobin in the same crowding solutions. Here we propose a method to estimate local apparent viscosities for the tracer translational and rotational diffusion directly from the bulk viscosity of the concentrated protein solutions. As a result of this study, the identification of protein species and the study of hydrodynamic changes and interactions in model crowded protein solutions by means of FCS and time-resolved fluorescence depolarization techniques may be expected to be greatly simplified.     

An experimental apparatus for the simulation of three-dimensional movements in orthodontics

An apparatus for the study of three-dimensional force systems and the resulting movements during orthodontic treatment is presented. The instrument consists of two force-torque transducers which are capable of recording both forces and torques simultaneously, in all spatial directions. Each sensor has a measuring range of 15 N (450 Nmm) and a resolution of 0.02 N (0.5 Nmm) and is mounted on a set of three translational and three rotational stages driven by stepping motors. Positioning accuracy is in the range of 1 μm and 0.01° respectively. The apparatus is computer controlled and supported by comprehensive software.     

On an exact starting expression for macromolecular hydrodynamic models

A calculational method developed by G. K. Youngren and A. Acrivos [J. Fluid Mech. 75 , 377 (1975)] expresses the fluid forces exerted over the surface of an immersed body in terms of differences between body and fluid motions. As opposed to bead-model approaches, this method starts from an essentially exact hydrodynamic expression, and therefore should be of particular interest to those workers trying to obtain accurate coefficients needed to characterize the diffusive and viscoelastic behavior of macromolecules with complex shapes. However, Youngren and Acrivos's treatment has not been widely adopted nor even used as a proper starting place for higher order bead-model methods. This is probably related to the unfamiliar appearance of their exact expression, which involves two surface integral terms as opposed to the single summation involved in bead models. We show that their expression may be rewritten in the expected analogous form involving one surface integral term whenever stick boundary conditions are applied to a rigid body or a flexible body composed of rigid segments. For spherical segments, we obtain Rotne–Prager-type bead-model results by following typical assumptions. Extensions to deformable particles are considered, in which internal friction can be represented by an arbitrarily viscous internal fluid.     

Oblique circle method for measuring the curvature and twist of mitotic spindle microtubule bundles

The highly ordered spatial organization of microtubule bundles in the mitotic spindle is crucial for its proper functioning. The recent discovery of twisted shapes of microtubule bundles and spindle chirality suggests that the bundles extend along curved paths in three dimensions, rather than being confined to a plane. This, in turn, implies that rotational forces, i.e., torques, exist in the spindle in addition to the widely studied linear forces. However, studies of spindle architecture and forces are impeded by a lack of a robust method for the geometric quantification of microtubule bundles in the spindle. In this work, we describe a simple method for measuring and evaluating the shapes of microtubule bundles by characterizing them in terms of their curvature and twist. By using confocal microscopy, we obtain three-dimensional images of spindles, which allows us to trace the entire microtubule bundle. For each traced bundle, we first fit a plane and then fit a circle lying in that plane. With this robust method, we extract the curvature and twist, which represent the geometric information characteristic for each bundle. As the bundle shapes reflect the forces within them, this method is valuable for the understanding of forces that act on chromosomes during mitosis.     

Motion of groups of atoms in DNA studied by molecular dynamics simulation

The analysis of Molecular Dynamics simulations of two double stranded oligonucleotides is presented in terms of motions of quasi rigid subunits. First, a strategy is presented for grouping atoms submitted to concerted internal motions. The method is based on the analysis of the interatomic distance RMS matrix. It is found that each nucleotide can reasonably be decomposed into 3 or 4 rigid groups of atoms depending on the tolerance of the definition of a rigid body. In the second part, the different kinds of motions of the subunits (deformation, translation and rotation) are studied in terms of correlation using the canonical correlation analysis of data. It is shown that the residual deformation of any subunit does not influence the translational and rotational motions of the others, except perhaps for long time dynamics. Received: 3 October 1997 / Revised version: 22 December 1997 / Accepted: 23 December 1997     

Interaction forces between red cells agglutinated by antibody. I. Theoretical.

A general method of calculating forces, torques, and translational and rotational velocities of rigid, neutrally buoyant spheres suspended in viscous liquids undergoing a uniform shear flow has been given by Arp and Mason (1977). The method is based on the matrix formulation of hydrodynamic resistances in creeping flow by Brenner and O'Neill (1972). We describe the solution of the Brenner-O'Neill force-torque vector equation in terms of the particle and external flow field coordinates and derive expressions for the normal force acting along, and the shear force acting perpendicular to, the axis of the doublet of spheres, the latter explicitly given for the first time. The equations consist of a term comprising force and torque coefficients obtained from the matrices of the hydrodynamic resistances (functions of the distance h between sphere surfaces which have been computed), and terms comprising the orientation of the doublet axis relative to the coordinates of the external flow field and the shear stress (which can be experimentally determined). We have applied the theory to a system of doublets of sphered, hardened human red cells of group A or B antigenic type cross-linked by the corresponding antibody at a fixed interparticle distance. Working from studies of the breakup of doublets of red cells in an accelerating Poiseuille flow, given in the succeeding paper, we are able to compute the hydrodynamic force required to separate the two spheres. Previous work has shown that the theory can be applied to doublets in a variable shear, Poiseuille flow, provided the ratio of particle to tube diameter is small. In calculating the force-torque coefficients it was assumed that the cells are crosslinked by antibody with h = 20 nm.     

A model for insect locomotion in the horizontal plane: Feedforward activation of fast muscles, stability, and robustness

We develop a neuromechanical model for running insects that includes a simplified hexapedal leg geometry with agonist-antagonist muscle pairs actuating each leg joint. Restricting to dynamics in the horizontal plane and neglecting leg masses, we reduce the model to three degrees of freedom describing translational and yawing motions of the body. Muscles are driven by stylized action potentials characteristic of fast motoneurons, and modeled using an activation function and nonlinear length and shortening velocity dependence. Parameter values are based on measurements from depressor muscles and observations of kinematics and dynamics of the cockroach Blaberus discoidalis; in particular, motoneuronal inputs and muscle force levels are chosen to approximately achieve joint torques that are consistent with measured ground reaction forces. We show that the model has stable double-tripod gaits over the animal's speed range, that its dynamics at preferred speeds matches those observed, and that it maintains stable gaits, with low frequency yaw deviations, when subject to random perturbations in foot touchdown and lift-off timing and action potential input timing. We explain this in terms of the low-dimensional dynamics.     

Investigations into the rheological characteristics of bovine amniotic fluid

The rheological characteristics of bovine amniotic fluid have been studied at different shear rates. The viscosity of bovine amniotic fluid at 20°C was found to increase with time at a constant low shear rate during the measurement. Additionally, the viscosity was observed to decrease with increasing shear rate, indicating that a shear thinning behaviour of the fluid was occurring. The log-log plot of shear stress versus shear rate yielded a straight line, consistent with non-Newtonian behaviour of the fluid and characteristic of pseudoplastic liquids. The data of shear stress versus shear rate could be represented by a power law model. The treatment of amniotic fluid with cetylpyridinium chloride (CPC) resulted in the precipitation of a mixture of components, including complex sulphated polysaccharides and extracellular proteoglycans, with the viscosity of the resulting liquid similar to that of water at 20°C. In addition, the viscosity of the CPC-pretreated fluid did not increase with time at constant shear rate and remained constant with the increase in shear rate. The apparent increase in viscosity with time and the shear thinning behaviour of the amniotic fluid can thus be attributed to pseudoplastic liquid behaviour associated with the presence of structurally complex polysaccharides and extracellular proteoglycans. The implications of this fluid viscosity behaviour are discussed in terms of their impact on the operation of packed or expanded (fluidized) chromatographic bed systems when amniotic fluid biofeed-stocks are used as a source of commercially important proteins.     

Interaction forces between red cells agglutinated by antibody. II. Measurement of hydrodynamic force of breakup.

The expressions derived in the previous paper for the respective normal, F3, and shear forces, Fshear, acting along and perpendicular to the axis of a doublet of rigid spheres, were used to determine the hydrodynamic forces required to separate two red cell spheres of antigenic type B crosslinked by the corresponding antibody. Cells were sphered and swollen in isotonic buffered glycerol containing 8 X 10(-5) M sodium dodecyl sulfate, fixed in 0.085% glutaraldehyde, and suspended in aqueous glycerol (viscosity: 15-34 mPa s), containing 0.15 M NaCl and anti-B antibody from human hyperimmune antiserum at concentrations from 0.73 to 3.56 vol%. After incubating and mixing for 12 h, doublets were observed through a microscope flowing in a 178-micron tube by gravity feed between two reservoirs. Using a traveling microtube apparatus, the doublets were tracked in a constantly accelerating flow and the translational and rotational motions were recorded on videotape until breakup occurred. From a frame by frame replay of the tape, the radial position, velocity and orientation of the doublet were obtained and the normal and shear forces of separation at breakup computed. Both forces increased significantly with increasing antiserum concentration, the mean values of F3 increasing from 0.060 to 0.197 nN, and Fshear from 0.023 to 0.072 nN. There was no significant effect of glycerol viscosity on the forces of separation. It was not possible to determine whether the shear or normal force was responsible for doublet separation. Measurements of the mean dimensionless period of rotation, TG, of doublets in suspensions containing 0.73 and 2.40% antiserum undergoing steady flow were also made to test whether the spheres were rigidly linked or capable of some independent rotation. A fairly narrow distribution in TG about the value 15.64, predicted for rigidly-linked doublets, was obtained at both antiserum concentrations.     

Fluid mechanics of the zebrafish embryonic heart trabeculation

Embryonic heart development is a mechanosensitive process, where specific fluid forces are needed for the correct development, and abnormal mechanical stimuli can lead to malformations. It is thus important to understand the nature of embryonic heart fluid forces. However, the fluid dynamical behaviour close to the embryonic endocardial surface is very sensitive to the geometry and motion dynamics of fine-scale cardiac trabecular surface structures. Here, we conducted image-based computational fluid dynamics (CFD) simulations to quantify the fluid mechanics associated with the zebrafish embryonic heart trabeculae. To capture trabecular geometric and motion details, we used a fish line that expresses fluorescence at the endocardial cell membrane, and high resolution 3D confocal microscopy. Our endocardial wall shear stress (WSS) results were found to exceed those reported in existing literature, which were estimated using myocardial rather than endocardial boundaries. By conducting simulations of single intra-trabecular spaces under varied scenarios, where the translational or deformational motions (caused by contraction) were removed, we found that a squeeze flow effect was responsible for most of the WSS magnitude in the intra-trabecular spaces, rather than the shear interaction with the flow in the main ventricular chamber. We found that trabecular structures were responsible for the high spatial variability of the magnitude and oscillatory nature of WSS, and for reducing the endocardial deformational burden. We further found cells attached to the endocardium within the intra-trabecular spaces, which were likely embryonic hemogenic cells, whose presence increased endocardial WSS. Overall, our results suggested that a complex multi-component consideration of both anatomic features and motion dynamics were needed to quantify the trabeculated embryonic heart fluid mechanics.     

The hemodynamic forces acting on thrombi, from incipient attachment of single cells to maturity and embolization

We consider the steady fluid forces acting on a thrombus from the time of first contact of a single cell with a natural or artificial surface, through the attachment process and growth to embolization. For a hemi-spherical or cylindrical attached cell of height less than 1/100-1/20th of the channel width, shear and tensile stresses are solely dependent on viscosity and on the ratio of average fluid velocity to channel width vt/Dt (shear rate). Large values of this ratio reduce adhesion and increase embolization. The average shear stress on such cells is approximately 1-10 Pa (10-100 dyn cm2), the average tensile stress about three times higher. For other shapes and larger protrusions, stress varies with protrusion height as well. Maturing thrombi composed of cell aggregates embedded in a fibrin mesh do not appear to allow significant fluid flow through their porous structure. The interior forces are then due solely to hydrostatic pressure and initially vary directly with vt/Dt and inversely with thrombus height Hp, thus favouring embolization at an early stage and in arterial systems. Rough surfaces are identified as causing an increase in dwell-time and possibly immobilizing an unattached cell due to 'negative lift'.     

Comparison of tRNA motions in the free and ribosomal bound structures

A general method is presented that allows the separation of the rigid body motions from the nonrigid body motions of structural subunits when bound in a complex. The application presented considers the motions of the tRNAs: free, bound to the ribosome and to a synthase. We observe that both the rigid body and nonrigid body motions of the structural subunits are highly controlled by the large ribosomal assembly and are important for the functional motions of the assembly. For the intact ribosome, its major parts, the 30S and the 50S subunits, are found to have counterrotational motions in the first few slowest modes, which are consistent with the experimentally observed ratchet motion. The tRNAs are found to have on average approximately 72-75% rigid body motions and principally translational motions within the first 100 slow modes of the complex. Although the three tRNAs exhibit different apparent total motions, after the rigid body motions are removed, the remaining internal motions of all three tRNAs are essentially the same. The direction of the translational motions of the tRNAs are in the same direction as the requisite translocation step, especially in the first slowest mode. Surprisingly the small intrinsically flexible mRNA has all of its internal motions completely inhibited and shows mainly a rigid-body translation in the slow modes of the ribosome complex. On the other hand, the required nonrigid body motions of the tRNA during translocation reveal that the anticodon-stem-loop, as well as the acceptor arm, of the tRNA enjoy a large mobility but act as rigid structural units. In summary, the ribosome exerts its control by enforcing rigidity in the functional parts of the tRNAs as well as in the mRNA.     

Inverse and forward dynamics: models of multi-body systems

Connected multi-body systems exhibit notoriously complex behaviour when driven by external and internal forces and torques. The problem of reconstructing the internal forces and/or torques from the movements and known external forces is called the 'inverse dynamics problem', whereas calculating motion from known internal forces and/or torques and resulting reaction forces is called the 'forward dynamics problem'. When stepping forward to cross the street, people use muscle forces that generate angular accelerations of their body segments and, by virtue of reaction forces from the street, a forward acceleration of the centre of mass of their body. Inverse dynamics calculations applied to a set of motion data from such an event can teach us how temporal patterns of joint torques were responsible for the observed motion. In forward dynamics calculations we may attempt to create motion from such temporal patterns, which is extremely difficult, because of the complex mechanical linkage along the chains forming the multi-body system. To understand, predict and sometimes control multi-body systems, we may want to have mathematical expressions for them. The Newton-Euler, Lagrangian and Featherstone approaches have their advantages and disadvantages. The simulation of collisions and the inclusion of muscle forces or other internal forces are discussed. Also, the possibility to perform a mixed inverse and forward dynamics calculation are dealt with. The use and limitations of these approaches form the conclusion.     

Rotational diffusion of TEMPONE in the cytoplasm of Chinese hamster lung cells.

The correlation time for rotational diffusion (tau R) of 2,2,6,6-tetramethyl-4-piperidone-N-oxide (TEMPONE) in Chinese hamster lung (V79) cells has been measured. For these cells in an isosmotic solution at 20 degrees C, tau R = 4.18 X 10(-11) s, approximately 3.6 times greater than tau R = 1.17 X 10(-11) s in water. The relationship between tau R and viscosity was investigated in a number of glycerol-water (0-50%) and sucrose-water (20-40%) solutions and a constant Stokes-Einstein volume of 44 A3 was found for TEMPONE in solutions of less than 20% glycerol and sucrose. This gives an average shear viscosity (for rotation of a small molecule) of 0.038 poise for the cytoplasm. When nonsecular terms were used in the calculation of tau R, the activation energies for rotation of TEMPONE in the above solutions correlated well with the activation energies for shear viscosity. The viscosity increases as the cell is shrunk in hypertonic solutions. It also increases with decreasing temperature with an activation energy of 3.7 kcal/mol, about the same as the activation energy for the viscosity of pure water. The rotational correlation times were carefully calculated considering inhomogeneous line broadening, non-Lorentzian line shapes, the need for accurate tensor values and nonsecular terms.     

A model of a radially expanding and contracting lymphangion

The lymphatic system is an extensive vascular network featuring valves and contractile walls that pump interstitial fluid and plasma proteins back to the main circulation. Immune function also relies on the lymphatic system's ability to transport white blood cells. Failure to drain and pump this excess fluid results in edema characterized by fluid retention and swelling of limbs. It is, therefore, important to understand the mechanisms of fluid transport and pumping of lymphatic vessels. Unfortunately, there are very few studies in this area, most of which assume Poiseuille flow conditions. In vivo observations reveal that these vessels contract strongly, with diameter changes of the order of magnitude of the diameter itself over a cycle that lasts typically 2-3s. The radial velocity of the contracting vessel is on the order of the axial fluid velocity, suggesting that modeling flow in these vessels with a Poiseuille model is inappropriate. In this paper, we describe a model of a radially expanding and contracting lymphatic vessel and investigate the validity of assuming Poiseuille flow to estimate wall shear stress, which is presumably important for lymphatic endothelial cell mechanotransduction. Three different wall motions, periodic sinusoidal, skewed sinusoidal and physiologic wall motions, were investigated with steady and unsteady parabolic inlet velocities. Despite high radial velocities resulting from the wall motion, wall shear stress values were within 4% of quasi-static Poiseuille values. Therefore, Poiseuille flow is valid for the estimation of wall shear stress for the majority of the lymphangion contractile cycle.     

The effects of shear flow on protein structure and function

Protein molecules are subjected to potentially denaturing fluid shear forces during processing and in circulation in the body. These complex molecules, involved in numerous biological functions and reactions, can be significantly impaired by molecular damage. There have been many studies on the effects of hydrodynamic shear forces on protein structure and function. These studies are reviewed and the implications to bioprocessing and pathophysiology of certain diseases are discussed.     

Improving joint torque calculations: optimization-based inverse dynamics to reduce the effect of motion errors

The accuracy of joint torques calculated from inverse dynamics methods is strongly dependent upon errors in body segment motion profiles, which arise from two sources of noise: the motion capture system and movement artifacts of skin-mounted markers. The current study presents a method to increase the accuracy of estimated joint torques through the optimization of the angular position data used to describe these segment motions. To compute these angular data, we formulated a constrained nonlinear optimization problem with a cost function that minimizes the difference between the known ground reaction forces (GRFs) and the GRF calculated via a top-down inverse dynamics solution. To evaluate this approach, we constructed idealized error-free reference movements (of squatting and lifting) that produced a set of known “true” motions and associated true joint torques and GRF. To simulate real-world inaccuracies in motion data, these true motions were perturbed by artificial noise. We then applied our approach to these noise-induced data to determine optimized motions and related joint torques. To evaluate the efficacy of the optimization approach compared to traditional (bottom-up or top-down) inverse dynamics approaches, we computed the root mean square error (RMSE) values of joint torques derived from each approach relative to the expected true joint torques. Compared to traditional approaches, the optimization approach reduced the RMSE by 54% to 79%. Average reduction due to our method was 65%; previous methods only achieved an overall reduction of 30%. These results suggest that significant improvement in the accuracy of joint torque calculations can be achieved using this approach.     

Dynamical clustering of red blood cells in capillary vessels

We have modeled the dynamics of a 3-D system consisting of red blood cells (RBCs), plasma and capillary walls using a discrete-particle approach. The blood cells and capillary walls are composed of a mesh of particles interacting with harmonic forces between nearest neighbors. We employ classical mechanics to mimic the elastic properties of RBCs with a biconcave disk composed of a mesh of spring-like particles. The fluid particle method allows for modeling the plasma as a particle ensemble, where each particle represents a collective unit of fluid, which is defined by its mass, moment of inertia, translational and angular momenta. Realistic behavior of blood cells is modeled by considering RBCs and plasma flowing through capillaries of various shapes. Three types of vessels are employed: a pipe with a choking point, a curved vessel and bifurcating capillaries. There is a strong tendency to produce RBC clusters in capillaries. The choking points and other irregularities in geometry influence both the flow and RBC shapes, considerably increasing the clotting effect. We also discuss other clotting factors coming from the physical properties of blood, such as the viscosity of the plasma and the elasticity of the RBCs. Modeling has been carried out with adequate resolution by using 1 to 10 million particles. Discrete particle simulations open a new pathway for modeling the dynamics of complex, viscoelastic fluids at the microscale, where both liquid and solid phases are treated with discrete particles. Figure A snapshot from fluid particle simulation of RBCs flowing along a curved capillary. The red color corresponds to the highest velocity. We can observe aggregation of RBCs at places with the most stagnant plasma flow.