Quantifying the kinetic paths of flexible biomolecular recognition

Biomolecular recognition often involves large conformational changes, sometimes even local unfolding. The identification of kinetic pathways has become a central issue in understanding the nature of binding. A new approach is proposed here to study the dynamics of this binding-folding process through the establishment of a path-integral framework on the underlying energy landscape. The dominant kinetic paths of binding and folding can be determined and quantified. The significant coupling between the binding and folding of biomolecules often exists in many important cellular processes. In this case, the corresponding kinetic paths of binding are shown to be intimately correlated with those of folding and the dynamics becomes quite cooperative. This implies that binding and folding happen concurrently. When the coupling between binding and folding is weak (strong), the kinetic process usually starts with significant folding (binding) first, with the binding (folding) later proceeding to the end. The kinetic rate can be obtained through the contributions from the dominant paths. The rate is shown to have a bell-shaped dependence on temperature in the concentration-saturated regime consistent with experiment. The changes of the kinetics that occur upon changing the parameters of the underlying binding-folding energy landscape are studied.

Energy conversion in shape memory alloy heat engine - Part II: Simulation

In this paper, a theoretical model proposed in Part I (Zhu et al., 2001a) is used to simulate the behavior of a twin crank NiTi SMA spring based heat engine, which has been experimentally studied by Iwanaga et al. (1988). The simulation results are compared favorably with the measurements. It is found that (1) output torque and heat efficiency decrease as rotation speed increase; (2) both output torque and output power increase with the increase of hot water temperature; (3) at high rotation speed, higher water temperature improves the heat efficiency. On the contrary, at low rotation speed, lower water temperature is more efficient; (4) the effects of initial spring length may not be monotonic as reported. According to the simulation, output torque, output power and heat efficiency increase with the decrease of spring length only in the low rotation speed case. At high rotation speed, the result might be on the contrary.

Kinetic and Size Control of Polystyrene and Polyacrylic Octadecyl Ester Lattices Via Polymerization in O/W Microemulsions

The kinetic studies of the acrylic octadecyl ester and styrene polymerization in microemulsion systems, (1) cetyl pyridine bromide (CPDB)/t-butanol/styrene/water; (2) CPDB/t-butanol/toluene + acrylic octadecyl ester (1:1, w/v)/ water; (3) cetyl pyridine bromide/styrene/formamide, were made by using dynamic laser light scattering techniques (DLS). The mechanisms of nucleation of latex particles were discussed. The most possible nucleation location of the styrene and acrylic octadecyl ester microlatex particles in aqueous microemulsion system is in aqueous phase via homogeneous nucleation. Meanwhile, parts of microlatex particles are possibly produced via swollen micelles (microemulsions) and monomer droplets nucleation. On the other hand, the most possible nucleation location of the styrene microlatex particles in nonaqueous microemulsion system is inside monomer droplets. The relationship between the amount of monomer and the size of microlatex was also investigated. It has been found that the size of microlatex particles could be controlled by changing the amount of monomer. (C) 2002 Elsevier Science B.V. All rights reserved.

A Study of Composite Beam with Shape Memory Alloy Arbitrarily Embedded under Thermal and Mechanical Loadings

The constitutive relations and kinematic assumptions on the composite beam with shape memory alloy (SMA) arbitrarily embedded are discussed and the results related to the different kinematic assumptions are compared. As the approach of mechanics of materials is to study the composite beam with the SMA layer embedded, the kinematic assumption is vital. In this paper, we systematically study the kinematic assumptions influence on the composite beam deflection and vibration characteristics. Based on the different kinematic assumptions, the equations of equilibrium/motion are different. Here three widely used kinematic assumptions are presented and the equations of equilibrium/motion are derived accordingly. As the three kinematic assumptions change from the simple to the complex one, the governing equations evolve from the linear to the nonlinear ones. For the nonlinear equations of equilibrium, the numerical solution is obtained by using Galerkin discretization method and Newton-Rhapson iteration method. The analysis on the numerical difficulty of using Galerkin method on the post-buckling analysis is presented. For the post-buckling analysis, finite element method is applied to avoid the difficulty due to the singularity occurred in Galerkin method. The natural frequencies of the composite beam with the nonlinear governing equation, which are obtained by directly linearizing the equations and locally linearizing the equations around each equilibrium, are compared. The influences of the SMA layer thickness and the shift from neutral axis on the deflection, buckling and post-buckling are also investigated. This paper presents a very general way to treat thermo-mechanical properties of the composite beam with SMA arbitrarily embedded. The governing equations for each kinematic assumption consist of a third order and a fourth order differential equation with a total of seven boundary conditions. Some previous studies on the SMA layer either ignore the thermal constraint effect or implicitly assume that the SMA is symmetrically embedded. The composite beam with the SMA layer asymmetrically embedded is studied here, in which symmetric embedding is a special case. Based on the different kinematic assumptions, the results are different depending on the deflection magnitude because of the nonlinear hardening effect due to the (large) deflection. And this difference is systematically compared for both the deflection and the natural frequencies. For simple kinematic assumption, the governing equations are linear and analytical solution is available. But as the deflection increases to the large magnitude, the simple kinematic assumption does not really reflect the structural deflection and the complex one must be used. During the systematic comparison of computational results due to the different kinematic assumptions, the application range of the simple kinematic assumption is also evaluated. Besides the equilibrium study of the composite laminate with SMA embedded, the buckling, post-buckling, free and forced vibrations of the composite beam with the different configurations are also studied and compared.

Depth dependence of nanohardness in a CuAlNi single crystal shape memory alloy

Instrumented nanoindentation was employed to study the depth dependence of nanohardness in a CuAlNi single crystal shape memory alloy that exhibits shape memory effect (SME). A Berkovich indenter and a cube comer indenter were used in this study, and the

A Discussion on Modeling Shape Memory Alloy Embedded in A Composite Laminate as Axial Force and Elastic Foundation

In this paper, the possible error sources of the composite natural frequencies due to modeling the shape memory alloy (SMA) wire as an axial force or an elastic foundation and anisotropy are discussed. The great benefit of modeling the SMA wire as an axial force and an elastic foundation is that the complex constitutive relation of SMA can be avoided. But as the SMA wire and graphite-epoxy are rigidly bonded together, such constraint causes the re-distribution of the stress in the composite. This, together with anisotropy, which also reduces the structural stiffness can cause the relatively large error between the experimental data and theoretical results.

Kinetic measurements of cell surface E-selectin/carbohydrate ligand interactions

Selectin/ligand interactions initiate the multistep adhesion and signaling cascades in the recruitment of leukocytes from circulation to inflamed tissues and may also play a role in tumor metastasis. Kinetic properties of these interactions are essential determinants governing blood-borne cells' tethering to and rolling on the vessel wall. Extending our recently developed micropipette method, we have measured the kinetic rates of E-selectin/ligand interactions. Red cells coated with an E-selectin construct were allowed to bind HL-60 or Colo-205 cells bearing carbohydrate ligands. Specific adhesions were observed to occur at isolated points, the frequency of which followed a Poisson distribution. These point attachments were formed at the same rate with both the HL-60 and Colo-205 cells (0.14 +/- 0.04 and 0.13 +/- 0.03 mum(2) s(-1) per unit density of E-selectin, respectively) but dissociated from the former at a rate twice as fast as did from the latter (0.92 +/- 0.23 and 0.44 +/- 0.10 s(-1), respectively). The reverse rates agree well with those measured by the flow chamber. The forward rates are orders of magnitude higher than those of Fc gamma receptors interacting with IgG measured under similar conditions, consistent with the rapid kinetics requirement for the function of E-selectin/ligand binding, which is to capture leukocytes on endothelial surfaces from flow.

A Thermodynamic Constitutive Model for Stress Induced Phase Transformation in Shape Memory Alloys

In this paper a thermodynamic constitutive model is developed for stress induced phase transformation in single crystalline and polycrystalline shape memory alloys (SMAs). Volume fractions of different martensite variants are chosen as internal variables to describe the evolution of microstructure state in the material. This model is then used in prediction the transformation behavior of a SMA (Cu-Al-Zn-Mn) under complex thermomechanical load (including complete and incomplete transformation in mechanical cycling, and proportional/non-proportional loading). (C) 2002 Elsevier Science Ltd. All rights reserved.

Energy Conversion in Shape Memory Alloy Heat Engine Part I: Theory

Shape Memory Alloy (SMA) can be easily deformed to a new shape by applying a small external load at low temperature, and then recovers its original configuration upon heating. This unique shape memory phenomenon has inspired many novel designs. SMA based heat engine is one among them. SMA heat engine is an environment-friendly alternative to extract mechanical energy from low-grade energies, for instance, warm wastewater, geothermal energy, solar thermal energy, etc. The aim of this paper is to present an applicable theoretical model for simulation of SMA-based heat engines. First, a micro-mechanical constitutive model is derived for SMAs. The volume fractions of austenite and martensite variants are chosen as internal variables to describe the evolution of microstructure in SMA upon phase transition. Subsequently, the energy equation is derived based on the first thermodynamic law and the previous SMA model. From Fourier’s law of heat conduction and Newton’s law of cooling, both differential and integral forms of energy conversion equation are obtained.

Kinetic Assessment of Measured Mass Flow Rates and Streamwise Pressure Distributions in Microchannel Gas Flows

Measured mass flow rates and streamwise pressure distributions of gas flowing through microchannels were reported by many researchers. Assessment of these data is crucial before they are used in the examination of slip models and numerical schemes, and in the design of microchannel elements in various MEMS devices. On the basis of kinetic solutions of the mass flow rates and pressure distributions in microchannel gas flows, the measured data available are properly normalized and then are compared with each other. The 69 normalized data of measured pressure distributions are in excellent agreement, and 67 of them are within 1 +/- 0.05. The normalized data of mass flow-rates ranging between 0.95 and 1 agree well with each other as the inlet Knudsen number Kn (i) < 0.02, but they scatter between 0.85 and 1.15 as Kn (i) > 0.02 with, to some extent, a very interesting bifurcation trend.

Theory Of Phase Transformation And Reorientation In Single Crystalline Shape Memory Alloys

A constitutive model, based on an (n + 1)-phase mixture of the Mori-Tanaka average theory, has been developed for stress-induced martensitic transformation and reorientation in single crystalline shape memory alloys. Volume fractions of different martensite lattice correspondence variants are chosen as internal variables to describe microstructural evolution. Macroscopic Gibbs free energy for the phase transformation is derived with thermodynamics principles and the ensemble average method of micro-mechanics. The critical condition and the evolution equation are proposed for both the phase transition and reorientation. This model can also simulate interior hysteresis loops during loading/unloading by switching the critical driving forces when an opposite transition takes place.

Self-consistent kinetic modeling of low-pressure inductively coupled radio-frequency discharges

An efficient method for solving the spatially inhomogeneous Boltzmann equation in a two-term approximation for low-pressure inductively coupled plasmas has been developed. The electron distribution function (EDF), a function of total electron energy and two spatial coordinates, is found self-consistently with the static space-charge potential which is computed from a 2D fluid model, and the rf electric field profile which is calculated from the Maxwell equations. The EDF and the spatial distributions of the electron density, potential, temperature, ionization rate, and the inductive electric field are calculated and discussed. (C) 1996 American Institute of Physics.

Self-consistent kinetic modeling of electron distribution function in a low-pressure inductively coupled plasma

Based upon the spatially inhomogeneous Boltzmann equation in two-term approximation coupled with electromagnetic and fluid model analysis for the recently developed inductively coupled plasma sources, a self-consistent electron kinetic model is developed. The electron distribution function, spatial distributions of the electron density and ionization rate are calculated and discussed.

The kinetic-theory for dilute solid liquid 2-phase flow

On the basis of a brief review of the continuum theory for macroscopic descriptions and the kinetic theory for microscopic descriptions in solid/liquid two-phase flows, some suggestions are presented, i.e. the solid phase may be described by the Boltzmann equation and the liquid phase still be described by conservation laws in the continuum theory. Among them the action force on the particles by the liquid fluid is a coupling factor which connects the phases. For dilute steady solid/liquid two-phase flows, the particle velocity distribution function can be derived by analogy with the procedures in the kinetic theory of gas molecules for the equilibrium state instead of being assumed, as previous investigators did. This done, more detailed information, such as the velocity probability density distribution, mean velocity distribution and fluctuating intensity etc. can be obtained directly from the particle velocity distribution function or from its integration. Experiments have been performed for dilute solid/liquid two-phase flow in a 4 x 6 cm2 sized circulating square pipe system by means of laser Doppler anemometry so that the theories can be examined. The comparisons show that the theories agree very well with all the measured data.