Visual Analysis of Biomolecular Surfaces

Surface models of biomolecules have become crucially important for the study and understanding of interaction between biomolecules and their environment. We argue for the need for a detailed understanding of biomolecular surfaces by describing several applications in computational and structural biology. We review methods used to model, represent, characterize, and visualize biomolecular surfaces focusing on the role that geometry and topology play in identifying features on the surface. These methods enable the development of efficient computational and visualization tools for studying the function of biomolecules.

Stability of the viscous flow of a fluid through a flexible tube

The stability of the Hagen-Poiseuille flow of a Newtonian fluid in a tube of radius R surrounded by an incompressible viscoelastic medium of radius R < r < HR is analysed in the high Reynolds number regime. The dimensionless numbers that affect the fluid flow are the Reynolds number Re = (rho VR/eta), the ratio of the viscosities of the wall and fluid eta(r) = (eta(s)/eta), the ratio of radii H and the dimensionless velocity Gamma = (rho V-2/G)(1/2). Here rho is the density of the fluid, G is the coefficient of elasticity of the wall and V is the maximum fluid velocity at the centre of the tube. In the high Reynolds number regime, an asymptotic expansion in the small parameter epsilon = (1/Re) is employed. In the leading approximation, the viscous effects are neglected and there is a balance between the inertial stresses in the fluid and the elastic stresses in the medium. There are multiple solutions for the leading-order growth rate s((0)), all of which are imaginary, indicating that the fluctuations are neutrally stable, since there is no viscous dissipation of energy or transfer of energy from the mean flow to the fluctuations due to the Reynolds stress. There is an O(epsilon(1/2)) correction to the growth rate, s((1)), due to the presence of a wall layer of thickness epsilon(1/2)R where the viscous stresses are O(epsilon(1/2)) smaller than the inertial stresses. An energy balance analysis indicates that the transfer of energy from the mean flow to the fluctuations due to the Reynolds stress in the wall layer is exactly cancelled by an opposite transfer of equal magnitude due to the deformation work done at the interface, and there is no net transfer from the mean flow to the fluctuations. Consequently, the fluctuations are stabilized by the viscous dissipation in the wall layer, and the real part of s(1) is negative. However, there are certain values of Gamma and wavenumber k where s((1)) = 0. At these points, the wall layer amplitude becomes zero because the tangential velocity boundary condition is identically satisfied by the inviscid flow solution. The real part of the O(epsilon) correction to the growth rate s((2)) turns out to be negative at these points, indicating a small stabilizing effect due to the dissipation in the bulk of the fluid and the wall material. It is found that the minimum value of s((2)) increases proportional to (H-1)(-2) for (H-1) much less than 1 (thickness of wall much less than the tube radius), and decreases proportional to H-4 for H much greater than 1. The damping rate for the inviscid modes is smaller than that for the viscous wall and centre modes in a rigid tube, which have been determined previously using a singular perturbation analysis. Therefore, these are the most unstable modes in the flow through a flexible tube

Stability of the viscous flow of a fluid through a flexible tube

The stability of Hagen-Poiseuille flow of a Newtonian fluid of viscosity eta in a tube of radius R surrounded by a viscoelastic medium of elasticity G and viscosity eta(s) occupying the annulus R < r < HR is determined using a linear stability analysis. The inertia of the fluid and the medium are neglected, and the mass and momentum conservation equations for the fluid and wall are linear. The only coupling between the mean flow and fluctuations enters via an additional term in the boundary condition for the tangential velocity at the interface, due to the discontinuity in the strain rate in the mean flow at the surface. This additional term is responsible for destabilizing the surface when the mean velocity increases beyond a transition value, and the physical mechanism driving the instability is the transfer of energy from the mean flow to the fluctuations due to the work done by the mean flow at the interface. The transition velocity Gamma(t) for the presence of surface instabilities depends on the wavenumber k and three dimensionless parameters: the ratio of the solid and fluid viscosities eta(r) = (eta(s)/eta), the capillary number Lambda = (T/GR) and the ratio of radii H, where T is the surface tension of the interface. For eta(r) = 0 and Lambda = 0, the transition velocity Gamma(t) diverges in the limits k much less than 1 and k much greater than 1, and has a minimum for finite k. The qualitative behaviour of the transition velocity is the same for Lambda > 0 and eta(r) = 0, though there is an increase in Gamma(t) in the limit k much greater than 1. When the viscosity of the surface is non-zero (eta(r) > 0), however, there is a qualitative change in the Gamma(t) vs. k curves. For eta(r) < 1, the transition velocity Gamma(t) is finite only when k is greater than a minimum value k(min), while perturbations with wavenumber k < k(min) are stable even for Gamma--> infinity. For eta(r) > 1, Gamma(t) is finite only for k(min) < k < k(max), while perturbations with wavenumber k < k(min) or k > k(max) are stable in the limit Gamma--> infinity. As H decreases or eta(r) increases, the difference k(max)- k(min) decreases. At minimum value H = H-min, which is a function of eta(r), the difference k(max)-k(min) = 0, and for H < H-min, perturbations of all wavenumbers are stable even in the limit Gamma--> infinity. The calculations indicate that H-min shows a strong divergence proportional to exp (0.0832 eta(r)(2)) for eta(r) much greater than 1.

Stability of the flow of a fluid through a flexible tube at high Reynolds number

The stability of the Hagen-Poiseuille flow of a Newtonian fluid in a tube of radius R surrounded by an incompressible viscoelastic medium of radius R < r < HR is analysed in the high Reynolds number regime. The dimensionless numbers that affect the fluid flow are the Reynolds number Re = (ρVR / η), the ratio of the viscosities of the wall and fluid ηr = (ηs/η), the ratio of radii H and the dimensionless velocity Γ = (ρV2/G)1/2. Here ρ is the density of the fluid, G is the coefficient of elasticity of the wall and Vis the maximum fluid velocity at the centre of the tube. In the high Reynolds number regime, an asymptotic expansion in the small parameter ε = (1/Re) is employed. In the leading approximation, the viscous effects are neglected and there is a balance between the inertial stresses in the fluid and the elastic stresses in the medium. There are multiple solutions for the leading-order growth rate do), all of which are imaginary, indicating that the fluctuations are neutrally stable, since there is no viscous dissipation of energy or transfer of energy from the mean flow to the fluctruations due to the Reynolds strees. There is an O(ε1/2) correction to the growth rate, s(1), due to the presence of a wall layer of thickness ε1/2R where the viscous stresses are O(ε1/2) smaller than the inertial stresses. An energy balance analysis indicates that the transfer of energy from the mean flow to the fluctuations due to the Reynolds stress in the wall layer is exactly cancelled by an opposite transfer of equal magnitude due to the deformation work done at the interface, and there is no net transfer from the mean flow to the fluctuations. Consequently, the fluctuations are stabilized by the viscous dissipation in the wall layer, and the real part of s(1) is negative. However, there are certain values of Γ and wavenumber k where s(l) = 0. At these points, the wail layer amplitude becomes zero because the tangential velocity boundary condition is identically satisfied by the inviscid flow solution. The real part of the O(ε) correction to the growth rate s(2) turns out to be negative at these points, indicating a small stabilizing effect due to the dissipation in the bulk of the fluid and the wall material. It is found that the minimum value of s(2) increases [is proportional to] (H − 1)−2 for (H − 1) [double less-than sign] 1 (thickness of wall much less than the tube radius), and decreases [is proportional to] (H−4 for H [dbl greater-than sign] 1. The damping rate for the inviscid modes is smaller than that for the viscous wall and centre modes in a rigid tube, which have been determined previously using a singular perturbation analysis. Therefore, these are the most unstable modes in the flow through a flexible tube.