Implicit solvent simulations of DPC micelle formation.

The formation of micelles by dodecylphosphocholine (DPC) is modeled by treating the surfactants in atomic detail and the solvent implicitly, in the spirit of the EEF1 solvation model for proteins. The solvation parameters of the DPC atoms are carried over from those of similar atoms in proteins. A slight adjustment of the parameters for the headgroup was found necessary for obtaining an aggregation number consistent with experiment.

Theory of MRI in the presence of zero to low magnetic fields and tensor imaging field gradients.

Today, all commonly practiced magnetic resonance imaging (MRI) reconstruction methods assume that the magnetic field created by the gradient coils is everywhere truncated by a dominant static uniform magnetic field. However, with the advent of SQUID detected MRI at microtesla fields, the opposite limit attracts attention, i.e.

Voltage-dependent energetics of alamethicin monomers in the membrane.

The implicit membrane model IMM1 is extended to include the effect of transmembrane potential and used to investigate the optimal membrane binding configurations and energies for alamethicin helices. In the absence of voltage, the lowest energy configuration is on the membrane surface with a tilt allowing the N terminus to be fully buried. Slightly higher in energy is an also tilted configuration with the N terminus deeper in the membrane and almost crossing the membrane.

Dielectric spectroscopy of liquid crystalline dispersions.

We describe dielectric spectroscopy measurements on dispersions of two thermotropic liquid crystals (5CB and 8CB) in a poly(dimethylsiloxane) matrix. 5CB exhibits nematic and isotropic phases, while 8CB exhibits smectic, nematic, and isotropic phases. The spectra of the dispersions exhibit a temperature-dependent dielectric relaxation in the interval from 100 to 1000 Hz, with relaxation times that depend strongly on whether the dispersed phase is isotropic, nematic, or smectic.

Thermodynamics of buried water clusters at a protein-ligand binding interface.

The structure of the complex of cyclophilin A (CypA) with cyclosporin A (CsA, 1) shows a cluster of four water molecules buried at the binding interface, which is rearranged when CsA is replaced by (5-hydroxynorvaline)-2-cyclosporin (2). The thermodynamic contributions of each bound water molecule in the two complexes are explored with the inhomogeneous fluid solvation theory and molecular dynamics simulations. Water (WTR) 133 in complex 1 contributes little to the binding affinity, while WTR6 and 7 in complex 2 play an essential role in mediating protein-ligand binding with a hydrogen bond network.

Energetics of the native and non-native states of the glycophorin transmembrane helix dimer.

Using an implicit membrane model (IMM1), we examine whether the structure of the transmembrane domain of Glycophorin A (GpA) could be predicted based on energetic considerations alone. The energetics of native GpA shows that van der Waals interactions make the largest contribution to stability. Although specific electrostatic interactions are stabilizing, the overall electrostatic contribution is close to zero.

Analysis of avian bone response to mechanical loading. Part two: Development of a computational connected cellular network to study bone intercellular communication.

Mechanical loading-induced signals are hypothesized to be transmitted and integrated by connected bone cells before reaching the bone surfaces where adaptation occurs. A computational connected cellular network (CCCN) model is developed to explore how bone cells perceive and transmit the signals through intercellular communication. This is part two of a two-part study in which a CCCN is developed to study the intercellular communication within a grid of bone cells.

Analysis of avian bone response to mechanical loading-Part one: Distribution of bone fluid shear stress induced by bending and axial loading.

Mechanical loading-induced signals are hypothesized to be transmitted and integrated by a bone-connected cellular network (CCN) before reaching the bone surfaces where adaptation occurs. Our objective is to establish a computational model to explore how bone cells transmit the signals through intercellular communication. In this first part of the study the bone fluid shear stress acting on every bone cell in a CCN is acquired as the excitation signal for the computational model.

Estimation of bone permeability using accurate microstructural measurements.

While interstitial fluid flow is necessary for the viability of osteocytes, it is also believed to play a role in bone's mechanosensory system by shearing bone cell membranes or causing cytoskeleton deformation and thus activating biochemical responses that lead to the process of bone adaptation. However, the fluid flow properties that regulate bone's adaptive response are poorly understood. In this paper, we present an analytical approach to determine the degree of anisotropy of the permeability of the lacunar-canalicular porosity in bone.

Optically detected nuclear magnetic resonance at the sub-micron scale.

Nuclear magnetic resonance is arguably one of the most powerful techniques available today to characterize diverse systems. However, the low sensitivity of the standard detection method constrains the applicability of this technique to samples having effective dimensions not less than a few microns. Here, we propose a novel scheme and device for the indirect detection of the nuclear spin signal at a submicroscopic scale.

Structural Determinants of Transmembrane β-Barrels.

The recognition of β-barrel membrane proteins based on their sequence is more challenging than the recognition of α-helical membrane proteins. This goal could benefit from a better understanding of the physical determinants of transmembrane β-barrel structure. To that end, we first extend the IMM1 implicit membrane model in a way that allows the modeling of membrane proteins with an internal aqueous pore.

Mapping bone interstitial fluid movement: displacement of ferritin tracer during histological processing.

Bone interstitial fluid flow is thought to play a fundamental role in the mechanical stimulation of bone cells, either via shear stresses or cytoskeletal deformations. Recent evidence indicates that osteocytes are surrounded by a fiber matrix that may be involved in the mechanotransduction of external stimuli as well as in nutrient exchange. In our previous tracer studies designed to map how different-sized molecules travel through the bone porosities, we found that injected ferritin was confined to blood vessels and did not pass into the mineralized matrix.

Implicit solvent simulations of peptide interactions with anionic lipid membranes.

A recently developed implicit membrane model (IMM1) is supplemented with a Gouy-Chapman term describing counterion-screened electrostatic interactions of a solute with negatively charged membrane lipids. The new model is tested on peptides that bind to anionic membranes. Pentalysine binds just outside the plane of negative charge, whereas Lys-Phe peptides insert their aromatic rings into the hydrophobic core.

Delineating bone's interstitial fluid pathway in vivo.

Although interstitial fluid flow has been suggested to play a role in bone adaptation and metabolism, the constituents and ultrastructure of this interstitial fluid pathway are not well understood. Bone's lacunar-canalicular porosity is generally believed to be a continuous interstitial fluid pathway through which osteocytes sense external mechanical loading as well as obtain nutrients and dispose of wastes. Recent electron microscopy studies have suggested that a fiber matrix surrounds the osteocytic cell processes and fills this pericellular fluid space.