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Douglas Henderson

Publications and source records attributed to Douglas Henderson.

15 recordsLinked to original sources
PubMed2006

The effect of protein dielectric coefficient on the ionic selectivity of a calcium channel.

Calcium-selective ion channels are known to have carboxylate-rich selectivity filters, a common motif that is primarily responsible for their high Ca(2+) affinity. Different Ca(2+) affinities ranging from micromolar (the L-type Ca channel) to millimolar (the ryanodine receptor channel) are closely related to the different physiological functions of these channels. To understand the physical mechanism for this range of affinities given similar amino acids in their selectivity filters, we use grand canonical Monte Carlo simulations to assess the binding of monovalent and divalent ions in the selectivity filter of a model Ca channel. We use a reduced model where the electolyte is modeled by hard-sphere ions embedded in a continuum dielectric solvent, while the interior of protein surrounding the channel is allowed to have a dielectric coefficient different from that of the electrolyte. The induced charges that appear on the protein/lumen interface are calculated by the induced charge computation method [Boda et al., Phys. Rev. E 69, 046702 (2004)]. It is shown that decreasing the dielectric coefficient of the protein attracts more cations into the pore because the protein's carboxyl groups induce negative charges on the dielectric boundary. As the density of the hard-sphere ions increases in the filter, Ca(2+) is absorbed into the filter with higher probability than Na(+) because Ca(2+) provides twice the charge to neutralize the negative charge of the pore (both structural carboxylate oxygens and induced charges) than Na(+) while occupying about the same space (the charge/space competition mechanism). As a result, Ca(2+) affinity is improved an order of magnitude by decreasing the protein dielectric coefficient from 80 to 5. Our results indicate that adjusting the dielectric properties of the protein surrounding the permeation pathway is a possible way for evolution to regulate the Ca(2+) affinity of the common four-carboxylate motif.

Calcium↗
PubMed2005

Computer simulation of macroion layering in a wedge film.

The layering of macroions confined to a wedge slit formed by two uncharged hard walls is studied using a canonical Monte Carlo method combined with a simulation cell that contains both wedge-shaped slit and bath regions. The macroion solution is modeled within a one-component fluid approach that in an effective way incorporates the double layer repulsion due to simple electrolyte ions as well as the discrete nature of an aqueous solvent. The layer formation under a wedge confinement is analyzed by carrying out separate simulation runs for a set of consecutive wedge segments designed to represent a single wedge slit. As the wedge thickness progressively increases, the sequence of regions along the wedge film with distinct features of macroion layering has been established. This sequence comprises (i) a wedge region of the thickness smaller than the macroion diameter that is free of macroions; (ii) a region with a one-dimensional macroion chain along the wedge corner at a wedge thickness of a one macroion diameter; (iii) a region comprising a low-ordered macroion monolayer that extends until the wedge thickness slightly above two macroion diameters; (iv) a region comprising a pair of well-defined two-dimensional configurations of macroions segregated on each of the wedge walls; and (v) a free-of-macroions wedge region between two surface monolayers that now originates from an electrostatic repulsion imposed by the surface macroions, which is followed by (vi) a well-defined macroion monolayer film between two surface monolayers, a less defined bilayer film, a three-layer film, and so on up to the bulk solution. Once formed, the macroion surface monolayers persist for all remaining wedge thicknesses up to the bulk, forming in such a way effective charged wedge boundaries. Such a formation of the macroion surface monolayers on the uncharged confining walls is related to the haloing mechanism for regulating the stability in colloidal suspensions [Tohver et al. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 8951] and is discussed as well. Finally, the estimated boundary of the free of macroion region between surface monolayers correlates well with the location of the boundary of the so-called "vacuum" phase that has been observed experimentally in an aqueous suspension of charged polystyrene spheres bounded by electrostatically repulsive glass walls [Pieransky et al. Phys. Rev. Lett. 1983, 50, 900].

Adsorption↗
PubMed2005

Hard-sphere radial distribution function again.

A theoretically based closed-form analytical equation for the radial distribution function, g(r), of a fluid of hard spheres is presented and used to obtain an accurate analytic representation. The method makes use of an analytic expression for the short- and long-range behaviors of g(r), both obtained from the Percus-Yevick equation, in combination with the thermodynamic consistency constraint. Physical arguments then leave only three parameters in the equation of g(r) that are to be solved numerically, whereas all remaining ones are taken from the analytical solution of the Percus-Yevick equation.

Algorithms↗
PubMed2005

Feasibility study of helical tomotherapy for total body or total marrow irradiation.

Total body radiation (TBI) has been used for many years as a preconditioning agent before bone marrow transplantation. Many side effects still plague its use. We investigated the planning and delivery of total body irradiation (TBI) and selective total marrow irradiation (TMI) and a reduced radiation dose to sensitive structures using image-guided helical tomotherapy. To assess the feasibility of using helical tomotherapy, (A) we studied variations in pitch, field width, and modulation factor on total body and total marrow helical tomotherapy treatments. We varied these parameters to provide a uniform dose along with a treatment times similar to conventional TBI (15-30 min). (B) We also investigated limited (head, chest, and pelvis) megavoltage CT (MVCT) scanning for the dimensional pretreatment setup verification rather than total body MVCT scanning to shorten the overall treatment time per treatment fraction. (C) We placed thermoluminescent detectors (TLDs) inside a Rando phantom to measure the dose at seven anatomical sites, including the lungs. A simulated TBI treatment showed homogeneous dose coverage (+/-10%) to the whole body. Doses to the sensitive organs were reduced by 35%-70% of the target dose. TLD measurements on Rando showed an accurate dose delivery (+/-7%) to the target and critical organs. In the TMI study, the dose was delivered conformally to the bone marrow only. The TBI and TMI treatment delivery time was reduced (by 50%) by increasing the field width from 2.5 to 5.0 cm in the inferior-superior direction. A limited MVCT reduced the target localization time 60% compared to whole body MVCT. MVCT image-guided helical tomotherapy offers a novel method to deliver a precise, homogeneous radiation dose to the whole body target while reducing the dose significantly to all critical organs. A judicious selection of pitch, modulation factor, and field size is required to produce a homogeneous dose distribution along with an acceptable treatment time. In addition, conformal radiation to the bone marrow appears feasible in an external radiation treatment using image-guided helical tomotherapy.

Bone Marrow↗
PubMed2004

Spreading of nanofluids driven by the structural disjoining pressure gradient.

This paper discusses the role of the structural disjoining pressure exerted by nanoparticles on the spreading of a liquid film containing these particles. The origin of the structural disjoining pressure in a confined geometry is due to the layering of the particles normal to the confining plane and has already been traced to the net increase in the entropy of the system in previous studies. In a recent paper, Wasan and Nikolov (Nature, 423 (2003) 156) pointed out that the structural component of the disjoining pressure is strong enough to move a liquid wedge; this casts a new light on many applications-most notably, detergency. While the concept of spreading driven by the disjoining pressure is not new, the importance of the structural disjoining pressure arises from its long-range nature (as compared to the van der Waals' force), making it an important component of the overall force balance near the contact line. In this paper, we report on a parametric study of the spreading phenomena by examining the effects of nanoparticle size, concentration and polydispersity on the displacement of an oil-aqueous interface with the aqueous bulk containing nanoparticles. The solution of the extended Laplace-Young equations for the profile of the meniscus yields the position of the nominal contact line under the action of the structural disjoining pressure. Simulations show that the displacement of the contact line is greater with a high nanoparticle volume fraction, small particles for the same volume fraction, monodispersed (in size) particles rather than polydispersed particles and when the resisting capillary pressure is small, i.e., when the interfacial tension is low and/or the radius of the dispersed phase drop/bubble is large.

Journal Article↗
PubMed2004

CT-based analysis of dose homogeneity in total body irradiation using lateral beam.

A computed tomography (CT) based treatment planning system for total body irradiation (TBI) is presented and compared with the commonly practiced lateral treatment delivery. The TBI regimen has been proved to be an essential conditional regimen for patients undergoing bone marrow transplantation. The advantage of the TBI regimen with bone marrow transplantation (BMT) in hematological malignancies can be offset by toxicities arising from TBI in posttransplant complications. With the increasing survival rates, the evaluation of long-term side effects and quality of life has become an important area of research interest. There have been several treatment techniques developed over the decades designed to achieve accurate dose delivery and dose homogeneity. This paper reports on the verification of the dose delivery for a basic lateral technique using thermoluminescent dosimeters (TLDs) placed in an anthropomorphic phantom and its correlation with CT-based treatment planning. CT-based treatment plans on several patients were used to evaluate the doses delivered to the whole body and critical organs. A large variation in doses delivered to the whole body was demonstrated, with some parts of the bone marrow failing to receive the prescribed dose and some critical organs, such as the lungs, receiving excessive doses. Placing the arms at the sides only partially compensates for the increased transmission of the lungs because the arms only shadow part of the lung. This study shows that CT-based treatment planning for TBI provides precise and accurate dose calculations and allows for the correlation of clinical outcomes with the doses actually delivered to various organs.

Body Burden↗
PubMed2004

Interaction between a macrosphere and a flat wall mediated by a hard-sphere colloidal suspension.

The interaction between the macrosphere and the flat wall immersed in a binary fluid comprising small and large (size ratio around 1:10) hard spheres has been investigated. We find that the presence of the highly size-asymmetric particles qualitatively modifies the induced excluded-volume interaction between the macrosphere and the flat wall compared to that observed in a single-component suspending fluid comprised of only large or only small species. The role in the interaction between a macrosphere and a flat wall played by species of the fine component that usually is approximated by a continuum medium (primitive description of a bidisperse fluid) is emphasized. Particularly, we show that taking into account the smaller component of a bidisperse suspending fluid modifies significantly the macrosphere-wall depletion attraction that is predicted when only large particles are taken into account. The depletion attraction force created by the presence of small fluid particles enhances the adsorption of large particles and their structuring on the wall.

Journal Article↗
PubMed2004

Applied field nonequilibrium molecular dynamics simulations of ion exit from a beta-barrel model of the L-type calcium channel.

We present results of applied field nonequilibrium molecular dynamics simulations (AF NEMD) of a minimal beta-barrel model channel intended to represent an L-type calcium channel that suggests a possible relationship between glutamate side chain conformational changes and ion flux in calcium channels. The beta-barrel is used to provide a scaffolding for glutamate side chains and a confinement for electrolyte of dimensions similar to the expected channel structure. It was preloaded with ions to explore relative rates of ion exit for different occupancy configurations. Our simulations with an asymmetrical flexible selectivity filter represented by four glutamate side chains (EEEE), one of which differs in initial dihedrals from the other three, indicate a plausible mechanism for the observed anomalous mole fraction effect seen in calcium channels. Apparent rates of electric field-induced exit from channels preloaded with three Na+ ions are much higher than for channels with one Ca2+ followed by two Na+ ions, consistent with the common notion that Ca2+ block of Na+ current is due to competition between the Ca2+ and Na+ ions for the negatively charged (EEEE) locus. In our model, the Ca2+ ion ligates simultaneously to the four negatively charged glutamate side chains and sterically blocks the permeation pathway. Ca2+-relief of Ca2+-block is suggested by a much higher rate of exit for channels preloaded with three Ca2+ ions than for channels with two Ca2+ ions.

Algorithms↗
PubMed2004

Computing induced charges in inhomogeneous dielectric media: application in a Monte Carlo simulation of complex ionic systems.

The efficient calculation of induced charges in an inhomogeneous dielectric is important in simulations and coarse-grained models in molecular biology, chemical physics, and electrochemistry. We present the induced charge computation (ICC) method for the calculation of the polarization charges based on the variational formulation of Allen et al. [Phys. Chem. Chem. Phys. 3, 4177 (2001)]. We give a different solution for their extremum condition that produces a matrix formulation. The induced charges are directly calculated by solving the linear matrix equation Ah=c, where h contains the discretized induced charge density, c depends only on the source charges-the ions moved in the simulation-and the matrix A depends on the geometry of dielectrics, which is assumed to be unchanged during the simulation. Thus, the matrix need be inverted only once at the beginning of the simulation. We verify the efficiency and accuracy of the method by means of Monte Carlo simulations for two special cases. In the simplest case, a single sharp planar dielectric boundary is present, which allows comparison with exact results calculated using the method of electrostatic images. The other special case is a particularly simple case where the matrix A is not diagonal: a slab with two parallel flat boundaries. Our results for electrolyte solutions in these special cases show that the ICC method is both accurate and efficient.

Journal Article↗
PubMed2004

Molecular-dynamics simulation of the effect of ions on a liquid-liquid interface for a partially miscible mixture.

Molecular-dynamics simulations were performed to model the effect of added salt ions on the liquid-liquid interface in a partially miscible system. Simulations of the interface between saturated phases of a model 1-hexanol+water system show a bilayer structure of 1-hexanol molecules at the interface with -OH heads of the first layer directed into the water phase and the opposite orientation for the second layer. The alignment of the polar -OH groups at the interface stabilizes a charge separation of sodium and chloride ions when salt is introduced into the aqueous phase, producing an electrical double layer. Chloride ions aggregate nearer the interface and sodium ions move toward the bulk water phase, consistent with the explanation that the -OH alignment presents a region of partial positive charges to which the hydrated chloride atoms are attracted. Ions near the interface were found to be less solvated than those in the bulk phase. An electric field was also applied to drive ions through the interface. Ions crossing the interface tended to shed water molecules as they entered the hexanol bilayer, leaving a trail of water molecules. Stabilization and facilitated transport of the ion by interactions with the second layer of hexanol molecules appeared to be an important step in the mechanism of sodium ion transport.

Journal Article↗
PubMed2004

Phase separation in mixtures of Yukawa and charged Yukawa particles from Gibbs ensemble Monte Carlo simulations and the mean spherical approximation.

The phase equilibrium of mixtures of Yukawa and charged Yukawa particles is studied by means of Gibbs ensemble Monte Carlo (GEMC) simulation method and the mean spherical approximation (MSA). The strength of the Coulomb energy compared to that of the Yukawa attraction is characterized by a coupling constant. For low coupling constants a classical vapor--liquid phase separation appears with a good agreement between GEMC and the MSA. For high coupling constant, a phase separation between a salt poor and a salt rich phase occurs that resembles the phase equilibrium behavior of the solvent primitive model.

Journal Article↗
PubMed2004

Attraction-driven disorder in a hard-core colloidal monolayer.

Monte Carlo simulation techniques were employed to explore the effect of short-range attraction on the orientational ordering in a two-dimensional assembly of monodisperse spherical particles. We find that if the range of square-well attraction is approximately 15% of the particle diameter, the dense attractive fluid shows the same ordering behavior as the same density fluid composed of purely repulsive hard spheres. Fluids with an attraction range larger than 15% show an enhanced tendency to crystallization, while disorder occurs for fluids with an attractive range shorter than 15% of the particle diameter. A possible link with the existence of "repulsive" and "attractive" states in dense colloidal systems is discussed.

Journal Article↗
PubMed2002

Expression of telomerase reverse transcriptase (TERT) in malignant mesotheliomas.

To evaluate the usefulness of determinations of telomerase activity for distinguishing malignant from benign mesothelial lesions, immunohistochemical (using a rabbit polyclonal antibody and the peroxidase method; n = 68) and in situ hybridization (using sense and antisense oligonucleotide probes; n = 46) studies were made on malignant mesotheliomas (epithelioid, 39; sarcomatoid, 18, including 2 of the desmoplastic type; and biphasic, 11) and 19 benign mesothelial lesions (benign mesothelial hyperplasia, 3; and reactive pleuritis, 16). In addition, biochemical studies of telomerase activity were made in 9 of the malignant mesotheliomas. Telomerase activity was detected histochemically in all but one of the malignant mesotheliomas, but only in one (pleuritis) of the benign lesions, in which it was present only in activated lymphocytes. Antisense hybridization signals indicated the presence of telomerase mRNA mainly in the cytoplasm of the malignant cells. Sense probes gave negative results. Biochemical determinations revealed a strong telomerase activity in the 9 malignant mesotheliomas examined. This study demonstrates the usefulness of immunohistochemical staining for the evaluation of mesotheliomas. The required immunostaining can be performed using paraffin sections of formalin-fixed tissues.

DNA-Binding Proteins↗
PubMed2001

Density Functional Study of a Simple Membrane Using the Solvent Primitive Model.

The model membrane, whose surfaces are maintained at the differing surface potentials, V(1) and V(2), on its inner and outer surfaces, that has been studied previously is extended to include explicit solvent molecules. The solvent primitive model, where the solvent molecules are treated as hard spheres, is used. In this study, the electrolyte can interact with the membrane both electrostatically and by means of a short-range van der Waals-like potential that can be attractive or repulsive. The bulk fluid beyond the outer surface is a four-component electrolyte consisting of the hard sphere solvent, two species of cations, and one species of anions. The membrane is impermeable to one of the cation species so that the fluid in the membrane and beyond the inner surface is a three-component electrolyte. Previously, we studied this model membrane by computer simulation and density functional theory (DFT) and found this theory to be quite accurate. Here we report further results, obtained using DFT, from which results can be obtained much more easily than from simulations. The density profiles of the electrolyte near the membrane and the charge-potential relationship of the membrane surfaces under a wider variety of conditions than is possible by simulation are studied. The presence of the solvent molecules leads to a greater excluded volume. As a result, the density profiles are oscillatory, whereas they are monotonic when a molecular model for the solvent is not used. The potential versus charge relationship is strongly influenced by the solvent density. In addition to the electrostatic interactions, the effect of a van der Waals interaction on the solvent molecules is considered. Copyright 2001 Academic Press.

Journal Article↗