Biomedical subjects

Frank L H Brown

Publications and source records attributed to Frank L H Brown.

At least 19 recordsLinked to original sources

PubMed2006

Contributions of Gaussian curvature and nonconstant lipid volume to protein deformation of lipid bilayers.

An elastic model for membrane deformations induced by integral membrane proteins is presented. An earlier theory is extended to account for nonvanishing saddle splay modulus within lipid monolayers and perturbations to lipid volume proximal to the protein. Analytical results are derived for the deformation profile surrounding a single cylindrical protein inclusion, which compare favorably to coarse-grained simulations over a range of protein sizes. Numerical results for multi-protein systems indicate that membrane-mediated interactions between inclusions are strongly affected by Gaussian curvature and display nonpairwise additivity. Implications for the aggregation of proteins are discussed.

Cell Membrane↗

PubMed2006

Single molecule photon counting statistics for quantum mechanical chromophore dynamics.

We extend the generating function technique for calculation of single molecule photon emission statistics (Zheng, Y.; Brown, F. L. H. Phys. Rev. Lett. 2003, 90, 238305) to systems governed by multi-level quantum dynamics. This opens up the possibility to study phenomena that are outside the realm of purely stochastic and mixed quantum-stochastic models. In particular, the present methodology allows for calculation of photon statistics that are spectrally resolved and subject to quantum coherence. Several model calculations illustrate the generality of the technique and highlight quantitative and qualitative differences between quantum mechanical models and related stochastic approximations when they arise. Calculations suggest that studying photon statistics as a function of photon frequency has the potential to reveal more about system dynamics than the usual broadband detection schemes.

Color↗

PubMed2006

Analysis of shape, fluctuations, and dynamics in intermembrane junctions.

A dynamic-elastic model for weakly adhered intermembrane junctions is presented. Helfrich membrane energetics coupled to hydrodynamic modes of the surrounding solvent reproduce the average shape, fluctuations, and dynamics of these junctions as measured experimentally. Comparison between numerical results and experimental data provides the first direct measure of surface tension in these systems (0.01-0.06 dyn/cm). The measurements suggest bilayer-bilayer adhesion energetics as the dominant source of surface tension in the experimental systems.

Computer Simulation↗

PubMed2006

Nonequilibrium membrane fluctuations driven by active proteins.

We extend a model for nonthermal membrane undulations driven by active (adenosine triphosphate-dependent or light-harvesting) membrane proteins [N. Gov, Phys. Rev. Lett. 93, 268104 (2004)]. The present model accounts for the fact that proteins can diffuse laterally across the membrane surface and that individual proteins are expected to exert forces preferentially in one normal direction over the other (due to their orientation within the bilayer). The addition of these effects alters the scaling of fluctuation amplitudes with system size. Additionally, theoretical arguments and dynamic simulations both suggest that, in certain regimes, the probability distribution of fluctuation amplitudes is expected to be non-Gaussian (in contrast to thermal systems).

Biomechanical Phenomena↗

PubMed2006

Generating function methods in single-molecule spectroscopy.

Certain single-molecule measurements record a time series of individual physical events. Examples of such events include the emission of single photons or discrete fluctuations of molecular state (as in fluorescence blinking or spectral diffusion). The generating function formalism is a natural framework for studying these measurements both theoretically and numerically. Kinetic, stochastic, and quantum models for chromophore dynamics may all be extended to generating function calculations, enabling direct comparison to experiment with only slight extensions to familiar theoretical/computational tools.

Fluorescence↗

PubMed2005

A consistent model for thermal fluctuations and protein-induced deformations in lipid bilayers.

We present an elastic Hamiltonian for membrane energetics that captures bilayer undulation and peristaltic deformations over all wavelengths, including the short wavelength protrusion regime. The model implies continuous functional forms for thermal undulation and peristaltic amplitudes as a function of wavelength and predicts previously overlooked relationships between these curves. Undulation and peristaltic spectra display excellent agreement with data from both atomistic and coarse-grained models over all simulated length scales. Additionally, the model accurately predicts the bilayer's response to a cylindrical protein inclusion as observed in coarse-grained simulation. This elastic response provides an explanation for gramicidin ion channel lifetime versus membrane thickness data that requires no fit constants. The physical parameters inherent to this picture may be expressed in terms of familiar material properties associated with lipid monolayers. Inclusion of a finite monolayer spontaneous curvature is essential to obtain fully consistent agreement between theory and the full range of available simulation/experimental data.

Computer Simulation↗

PubMed2005

Implicit solvent simulation models for biomembranes.

Fully atomic simulation strategies are infeasible for the study of many processes of interest to membrane biology, biophysics and biochemistry. We review various coarse-grained simulation methodologies with special emphasis on methods and models that do not require the explicit simulation of water. Examples from our own research demonstrate that such models have potential for simulating a variety of biologically relevant phenomena at the membrane surface.

Biophysical Phenomena↗

PubMed2005

Flexible lipid bilayers in implicit solvent.

A minimalist simulation model for lipid bilayers is presented. Each lipid is represented by a flexible chain of beads in implicit solvent. The hydrophobic effect is mimicked through an intermolecular pair potential localized at the "water"/hydrocarbon tail interface. This potential guarantees realistic interfacial tensions for lipids in a bilayer geometry. Lipids self-assemble into bilayer structures that display fluidity and elastic properties consistent with experimental model membrane systems. Varying molecular flexibility allows for tuning of elastic moduli and area per molecule over a range of values seen in experimental systems.

Biophysics↗

PubMed2005

Dynamic simulations of membranes with cytoskeletal interactions.

We describe a simulation algorithm for the dynamics of elastic membrane sheets over long length and time scales. Our model includes implicit hydrodynamic coupling between membrane and surrounding solvent and allows for arbitrary external forces acting on the membrane surface. In particular, the methodology is well suited to studying membranes in interaction with cytoskeletal filaments. We present results for the thermal undulations of a lipid bilayer attached to a regular network of spectrin filaments as a model for the red blood cell membrane. The dynamic fluctuations of the bilayer over the spectrin network are quantified and used to predict the macroscopic diffusion constant of band 3 on the surface of the red blood cell. We find that thermal undulations likely play a role in the mobility of band 3 in the plane of the erythrocyte membrane.

Algorithms↗

PubMed2005

Composition dependence of bilayer elasticity.

A previously developed molecular level model for homogeneous lipid bilayers [Brannigan and Brown, J. Chem. Phys 120, 1059 (2004)] is extended to allow for multiple lipid species. Monte Carlo simulations (including species exchange moves for efficient sampling) reveal a variety of mixing behaviors in binary systems. Two species are identified that maintain stable, randomly mixed fluid membranes at vanishing tension over all possible binary compositions. The thermal and elastic properties of membranes formed by these lipids are characterized over the full composition range. Equilibrium area at constant tension is nonmonotonic with respect to composition, but consistent with that of a quadratic mixture. In the constant tension ensemble, the bending rigidity of the bilayer is minimized at an intermediate composition. The observed functional form of bending rigidity vs composition is fit to a simple expression motivated by linear elasticity theory; this expression accounts for membrane heterogeneity through a single parameter.

Journal Article↗

PubMed2004

Brownian dynamics in Fourier space: membrane simulations over long length and time scales.

A simulation algorithm for elastic membrane sheets is presented. Overdamped stochastic dynamics including hydrodynamic coupling to surrounding solvent and arbitrary external forces are generated by employing Fourier modes of the sheet as the primary dynamic variables. Simulations over the micron length scale and second time scale are easily achieved. The dynamics of a lipid bilayer attached to an underlying network of cytoskeletal filaments is used to estimate the diffusion constant of membrane-bound proteins on the surface of the red blood cell.

Animals↗

PubMed2004

Single molecule photon emission statistics in the slow modulation limit.

A framework for calculating photon emission statistics for single chromophores perturbed by slow environmental fluctuations is introduced. When internal chromophore dynamics are significantly faster than time scales for environmental modulation it becomes possible to invoke a type of adiabatic approximation, allowing for straightforward calculation of photon counting moments including explicitly quantum effects. Unlike previous exact treatments, the present methodology involves calculation of dynamics reflecting only the modulation characteristics of the environment and quantum dynamics of an isolated chromophore separately, i.e., the complicated intermingling of chromophore quantum dynamics and the environmental modulation are suppressed via the adiabatic approximation. This leads to significant conceptual and computational simplifications. Within its regime of applicability, the present approximation reproduces exact calculations quantitatively. We demonstrate this accuracy explicitly for the case of a two-level chromophore modulated by a number of different stochastic models.

Computer Simulation↗

PubMed2004

The role of molecular shape in bilayer elasticity and phase behavior.

A previously developed molecular level model for lipid bilayers [G. Brannigan and F. L. H. Brown, J. Chem. Phys. 120, 1059 (2004)] is extended to allow for variations in lipid length and simulations under constant surface tension conditions. The dependence of membrane elasticity on bilayer thickness is obtained by adjusting lipid length at constant temperature and surface tension. Additionally, bilayer fluidity at various lipid lengths is quantified by analysis of a length versus temperature phase diagram at vanishing tension. Regions of solid, gel-like (hexatic) and fluid bilayer behavior are established by identification of phase boundaries. The main melting transition is found to be density driven; the melting temperature scales inversely with lipid length since thermal expansion increases with lipid aspect ratio.

Journal Article↗

PubMed2004

Single molecule photon emission statistics for non-Markovian blinking models.

The statistics of photon emission from a single molecule under continuous wave excitation are considered. In particular, we study stochastic model systems where photon emission rates evolve in time with non-Markovian dynamics. Our calculations are based on the recently introduced generalized optical Bloch equation (GBE) formalism, but with numerical complications beyond those seen in previous Markovian stochastic models. A spectral representation is introduced to facilitate the numerical solution of the GBE equations for these more challenging cases.

Journal Article↗

PubMed2004

Solvent-free simulations of fluid membrane bilayers.

A molecular level model for lipid bilayers is presented. Lipids are represented by rigid, asymmetric, soft spherocylinders in implicit solvent. A simple three parameter potential between pairs of lipids gives rise to a rich assortment of phases including (but not limited to) micelles, fluid bilayers, and gel-like bilayers. Monte Carlo simulations have been carried out to verify self-assembly, characterize the phases corresponding to different potential parametrizations, and to quantify the physical properties associated with those parameter sets corresponding to fluid bilayer behavior. The studied fluid bilayers have compressibility moduli in agreement with experimental systems, but display bending moduli at least three times larger than typical biological membranes without cholesterol.

Computer Simulation↗

PubMed2004

Dynamics of pinned membranes with application to protein diffusion on the surface of red blood cells.

We present a theoretical treatment and simulation algorithm for the dynamics of Helfrich elastic membrane surfaces in the presence of general harmonic perturbations and hydrodynamic coupling to the surrounding solvent. In the limit of localized and strong interactions, this harmonic model can be used to pin the membrane to intracellular/intercellular structures. We consider the case of pinning to the cytoskeleton and use such a model to estimate the macroscopic diffusion constant for band 3 protein on the surface of human erythrocytes. Comparison to experimental results suggests that thermal undulations of the membrane surface should play a significant role in protein mobility on the red blood cell.

Adsorption↗

PubMed2003

Single-molecule photon counting statistics via generalized optical Bloch equations.

We derive the generating function for single molecule photon emission events within the context of the stochastically modulated optical Bloch equations. Statistical properties of single molecule photon counting experiments are deduced from a set of coupled differential equations only slightly more complicated than the Bloch equations themselves. This formulation allows for the study of photon bunching and antibunching within a single theoretical framework and provides a description of these behaviors that emphasizes the connection with single molecule experiments. Application is made to the spectroscopy of a chromophore coupled to a single two level system.

Journal Article↗

PubMed2003

Single-molecule kinetics with time-dependent rates: a generating function approach.

A theoretical strategy for calculating the statistical properties of time series generated by single molecule measurements is presented. Emphasis is placed on the case where observable states interconvert via rate "constants" exhibiting stochastic time dependence. Such is the case for measurements of single fluorophores coupled to biomolecules undergoing conformational fluctuations [H. P. Lu, L. Xun, and X. S. Xie, Science 282, 1877 (1998)]]. In contrast to previous studies, we focus on the number of fluorophore blinking events occurring within a given amount of time as our stochastic variable. This formulation allows for an elementary analysis within the generating function framework.

Journal Article↗