Growth of lipid vesicle structures: From surface fractals to mass fractals
Sandalo Roldan-Vargas, Ramon Barnadas-Rodriguez, Alberto Martin-Molina, Manuel Quesada-Perez, Joan Estelrich et al.
We study fractal vesicle aggregates whose morphology is conditioned by the interaction between the lipid vesicle membranes and calcium and magnesium ions. These morphologies are probed by means of static light scattering using a cross-correlation scheme that avoids the multiple intracluster scatteri ... [Phys. Rev. E 78, 010902 (2008)] published Wed Jul 23, 2008.
DMLC IMRT delivery to targets moving in 2D in Beam's Eye View
Dharanipathy Rangaraj, Geethpriya Palaniswaamy, and Lech Papiez
The goal of this article is to present the algorithm for DMLC leaf control capable of delivering IMRT to tumors that experience motion in two dimensions in the beams eye view (BEV) plane. The generic, two-dimensional (2D) motion of the projection of the rigid target on BEV plane can be divided into ... [Med. Phys. 35, 3765 (2008)] published Wed Jul 23, 2008.
An image-based rat model for Monte Carlo organ dose calculations
Li Wu, Guozhi Zhang, Qingming Luo, and Qian Liu
An anatomically realistic rat model was developed from color images of successive cryosections of a mature SpragueDawley rat. Images were obtained, by digital scanning, of 9475 slices with thickness of 0.02 mm. A total of 13 major organs and tissues were selected, and models of these organs and tiss ... [Med. Phys. 35, 3759 (2008)] published Wed Jul 23, 2008.
A novel MR-guided interventional device for 3D circumferential access to breast tissue
Matthew Smith, Xu Zhai, Ray Harter, Gale Sisney, Mai Elezaby et al.
MRI is rapidly growing as a tool for image-guided procedures in the breast such as needle localizations, biopsy, and cryotherapy. The ability of MRI to resolve small (<1 cm) lesions allows earlier detection and diagnosis than with ultrasound. Most MR-guidance methods perform a two-dimensional compr ... [Med. Phys. 35, 3779 (2008)] published Wed Jul 23, 2008.
Magnetic resonance acoustic radiation force imaging
Nathan McDannold and Stephan E. Maier
Acoustic radiation force impulse imaging is an elastography method developed for ultrasound imaging that maps displacements produced by focused ultrasound pulses systematically applied to different locations. The resulting images are stiffness weighted and yield information about local mechanical ti ... [Med. Phys. 35, 3748 (2008)] published Wed Jul 23, 2008.
Formation of fast spirals on heterogeneities of an excitable medium
G. B. Makkes van der Deijl and A. V. Panfilov
We study the process of formation of spiral waves in a heterogeneous excitable medium under external stimulation, using numerical and analytical methods. We show that in an excitable medium with several heterogeneities with respect to refractory period, fast rotating spiral waves can be generated. T ... [Phys. Rev. E 78, 012901 (2008)] published Tue Jul 22, 2008.
Spike-triggered averages for passive and resonant neurons receiving filtered excitatory and inhibitory synaptic drive
Laurent Badel, Wulfram Gerstner, and Magnus J. E. Richardson
A path-integral approach is developed for the analysis of spike-triggered average quantities in neurons with voltage-gated subthreshold currents. Using a linearization procedure to reduce the models to the generalized integrate-and-fire form, analytical expressions are obtained in an experimentally ... [Phys. Rev. E 78, 011914 (2008)] published Tue Jul 22, 2008.
Fluctuation theorem and large deviation function for a solvable model of a molecular motor
D. Lacoste, A. W.C. Lau, and K. Mallick
We study a discrete stochastic model of a molecular motor. This discrete model can be viewed as a minimal ratchet model. We extend our previous work on this model, by further investigating the constraints imposed by the fluctuation theorem on the operation of a molecular motor far from equilibrium. ... [Phys. Rev. E 78, 011915 (2008)] published Tue Jul 22, 2008.
Effect of sensory blind zones on milling behavior in a dynamic self-propelled particle model
Jonathan P. Newman and Hiroki Sayama
Emergent pattern formation in self-propelled particle (SPP) systems is extensively studied because it addresses a range of swarming phenomena that occur without leadership. Here we present a dynamic SPP model in which a sensory blind zone is introduced into each particle's zone of interaction. Using ... [Phys. Rev. E 78, 011913 (2008)] published Tue Jul 22, 2008.
Erratum: Coexistence of amplitude and frequency modulations in intracellular calcium dynamics [Phys. Rev. E [bold 77], 030903(R) (2008)]
Maurizio De Pitta, Vladislav Volman, Herbert Levine, Giovanni Pioggia, Danilo De Rossi et al.
... [Phys. Rev. E 78, 019902 (2008)] published Tue Jul 22, 2008.
Quantitative detection of DNA labeled with magnetic nanoparticles using arrays of MgO-based magnetic tunnel junction sensors
Weifeng Shen, Benaiah D. Schrag, Matthew J. Carter, and Gang Xiao
We have demonstrated the detection of 2.5 [mu]M target DNA labeled with 16 nm FeO nanoparticles (NPs) using arrays of magnetic tunnel junction sensors with (001)-oriented MgO barrier layers. A MTJ sensor bridge was designed to detect the presence of magnetic NPs bonded with target DNA. A raw signa ... [Appl. Phys. Lett. 93, 033903 (2008)] published Tue Jul 22, 2008.
High-numerical-aperture-based virtual point detectors for photoacoustic tomography
Changhui Li and Lihong V. Wang
The focal point of a high-numerical-aperture (NA) ultrasonic transducer can be used as a virtual point detector. This virtual point detector detects omnidirectionally over a wide acceptance angle. It also combines a large active transducer surface and a small effective virtual detector size. Thus th ... [Appl. Phys. Lett. 93, 033902 (2008)] published Tue Jul 22, 2008.
Subpicoliter droplet generation based on a nozzle-free acoustic transducer
Chuang-Yuan Lee, Wei Pang, Hongyu Yu, and Eun Sok Kim
This letter reports picoliter liquid droplet generation using an orifice-free acoustic ejector operating at its harmonic frequencies. For an acoustic ejector working at the thickness-mode resonance, the droplet size is primarily determined by the acoustic wavelength, which is proportional to the pie ... [Appl. Phys. Lett. 93, 034104 (2008)] published Tue Jul 22, 2008.
Segmentation of Brain Immunohistochemistry Images Using Clustering of Linear Centroids and Regional Shapes
Hai-Shan Wu, Jacinta Murray, and Susan Morgello
A generalized clustering algorithm utilizing the geometrical shapes of clusters for segmentation of colored brain immunohistological images is presented. To simplify the computation, the dimension of vectors composed from the pixel RGB components is reduced from three to two by applying a de-correla ... [J. Imaging Sci. Technol. 52, 040502 (2008)] published Tue Jul 22, 2008.
Optical imaging analysis of microscopic radiation dose gradients in Gafchromic EBT film using a digital microscope
Brian M. Keller, Chris Peressotti, and Jean-Philippe Pignol
By providing superior localization and immobilization, stereotactic radiosurgery (SRS) is capable of delivering millimeter spheres of dose to intracranial targets with submillimeter precision. Several authors have proposed new SRS solutions to dramatically reduce beam penumbra to hundreds of microns ... [Med. Phys. 35, 3740 (2008)] published Tue Jul 22, 2008.
Anniversary Paper: Development of x-ray computed tomography: The role of Medical Physics and AAPM from the 1970s to present
Xiaochuan Pan, Jeffrey Siewerdsen, Patrick J. La Riviere, and Willi A. Kalender
The AAPM, through its members, meetings, and its flagship journal Medical Physics, has played an important role in the development and growth of x-ray tomography in the last 50 years. From a spate of early articles in the 1970s characterizing the first commercial computed tomography (CT) scanners th ... [Med. Phys. 35, 3728 (2008)] published Tue Jul 22, 2008.
Digital data acquisition and analysis of striated muscle diffraction patterns with a direct memory access microprocessor system
Kenneth P. Roos, Ronald J. Baskin, Richard L. Lieber, James W. Cline, and Paul J. Paolini
A microprocessor based data acquisition computing system has been developed to examine dynamic changes in light diffraction patterns from single skeletal muscle fibers. A significant improvement in digital data acquisition rate compared to previous designs has been achieved by utilizing a fast dedic ... [Rev. Sci. Instrum. 51, 762 (2008)] published Tue Jul 22, 2008.
Detection of cathodoluminescence of Giemsa stain and its applications
S. Basu
Giemsa stain shows an intense and durable cathodoluminescence (CL) when studied at 2030 kV with a quartz transmission light pipephotomultiplier system in a scanning electron microscope. Clear CL images of Giemsa-stained chromatin, nuclei, and chromosomes were recorded at low electron does (approxima ... [Rev. Sci. Instrum. 51, 435 (2008)] published Tue Jul 22, 2008.
Mechanochemical action of the dynamin protein
Martin Lenz, Jacques Prost, and Jean-Francois Joanny
Dynamin is a ubiquitous GTPase that tubulates lipid bilayers and is implicated in many membrane severing processes in eukaryotic cells. Setting the grounds for a better understanding of this biological function, we develop a generalized hydrodynamics description of the conformational change of large ... [Phys. Rev. E 78, 011911 (2008)] published Mon Jul 21, 2008.
Effective potential of longitudinal interactions between microtubule protofilaments
M. Neek-Amal, N. Hamedani Radja, and M. R. Ejtehadi
An effective potential for longitudinal interactions between adjacent protofilaments in a microtubule is introduced. Our proposed interaction potential is a periodic and continuous function of the offset between two protofilaments, which also incorporates the bending energy of protofilaments. This p ... [Phys. Rev. E 78, 011912 (2008)] published Mon Jul 21, 2008.
Information capacity of genetic regulatory elements
Gasper TkaCik, Curtis G. Callan, Jr., and William Bialek
Changes in a cell's external or internal conditions are usually reflected in the concentrations of the relevant transcription factors. These proteins in turn modulate the expression levels of the genes under their control and sometimes need to perform nontrivial computations that integrate several i ... [Phys. Rev. E 78, 011910 (2008)] published Mon Jul 21, 2008.
Design and integration of an all-in-one biomicrofluidic chip
Liyu Liu, Wenbin Cao, Jingbo Wu, Weijia Wen, Donald Choy Chang et al.
We demonstrate a highly integrated microfluidic chip with the function of DNA amplification. The integrated chip combines giant electrorheological-fluid actuated micromixer and micropump with a microheater array, all formed using soft lithography. Internal functional components are based on polydime ... [Biomicrofluidics 2, 034103 (2008)] published Mon Jul 21, 2008.
Critical Dynamics of Vesicle Stretching Transition in Elongational Flow
Vasiliy Kantsler, Enrico Segre, and Victor Steinberg
We present results on the stretching of single tubular vesicles in an elongation flow toward dumbbell shapes, and on their relaxation. A critical strain rate epsilon-dot exists; for strain rates epsilon-dot
Thermal denaturation of a native protein via spinodal decomposition in the framework of first-passage-time analysis
Y. S. Djikaev and Eli Ruckenstein
In this paper we present a kinetic model for the thermal unfolding of a native protein. Due to a sufficiently large temperature increase or decrease, the rate with which a cluster of native residues within a protein emits residues becomes larger than the rate of absorption of residues from the unfol ... [Phys. Rev. E 78, 011909 (2008)] published Fri Jul 18, 2008.
Integrated biophotonics approach for noninvasive and multiscale studies of biomolecular and cellular biophysics
Qianru Yu, Michael Proia, and Ahmed A. Heikal
In the crowded cellular milieu, biological processes require coordinated intermolecular interactions, conformational changes, and molecular transport that span a wide range of spatial and temporal scales. This complexity requires an integrated, noninvasive, multiscale experimental approach. Here, we ... [J. Biomed. Opt. 13, 041315 (2008)] published Fri Jul 18, 2008.
Raman microscopy for dynamic molecular imaging of living cells
Keisaku Hamada, Katsumasa Fujita, Nicholas Isaac Smith, Minoru Kobayashi, Yasushi Inouye et al.
We demonstrate dynamic imaging of molecular distribution in unstained living cells using Raman scattering. By combining slit-scanning detection and optimizing the excitation wavelength, we imaged the dynamic molecular distributions of cytochrome c, protein beta sheets, and lipids in unstained HeLa c ... [J. Biomed. Opt. 13, 044027 (2008)] published Fri Jul 18, 2008.
Optical properties of mutant versus wild-type mouse skin measured by reflectance-mode confocal scanning laser microscopy (rCSLM)
Ravikant Samatham, Steven L. Jacques, and Paul Campagnola
Separation of the two optical scattering properties, the scattering coefficient ([mu]) and the anisotropy of scattering (g), has been experimentally difficult in tissues. A new method for measuring these properties in tissues uses reflectance-mode confocal scanning laser microscopy (rCSLM). Experime ... [J. Biomed. Opt. 13, 041309 (2008)] published Fri Jul 18, 2008.
Quasi-simultaneous optical coherence tomography and confocal imaging
Irina Trifanov, Michael Hughes, Adrian Gh. Podoleanu, and Richard B. Rosen
A new approach of acquiring quasi-simultaneous optical coherence tomography (OCT) and confocal images is presented. The two images are generated using different principles, OCT and confocal microscopy. When the system is used to image the retina, the two images have depth resolutions, at present, of ... [J. Biomed. Opt. 13, 044015 (2008)] published Fri Jul 18, 2008.
Aggregation of red blood cells in suspension: study by light-scattering technique at small angles
Cristian V. L. Pop and Silvia Neamtu
Red blood cells (RBCs) in the presence of plasma proteins or other macromolecules have a tendency to form aggregates. Light-scattering technique was used to investigate the RBC aggregation process. A highly diluted suspension of RBCs was illuminated with a 632.8-nm HeNe laser. Angular-resolved measu ... [J. Biomed. Opt. 13, 041308 (2008)] published Fri Jul 18, 2008.
Test of the Gouy-Chapman Theory for a Charged Lipid Membrane against Explicit-Solvent Molecular Dynamics Simulations
Myunggi Yi, Hugh Nymeyer, and Huan-Xiang Zhou
A wealth of experimental data has verified the applicability of the Gouy-Chapman (GC) theory to charged lipid membranes. Surprisingly, a validation of GC by molecular dynamics (MD) simulations has been elusive. Here, we report a test of GC against extensive MD simulations of an anionic lipid bilayer ... [Phys. Rev. Lett. 101, 038103 (2008)] published Fri Jul 18, 2008.
Evaluation of dose prediction errors and optimization convergence errors of deliverable-based head-and-neck IMRT plans computed with a superposition/convolution dose algorithm
I. B. Mihaylov and J. V. Siebers
The purpose of this study is to evaluate dose prediction errors (DPEs) and optimization convergence errors (OCEs) resulting from use of a superposition/convolution dose calculation algorithm in deliverable intensity-modulated radiation therapy (IMRT) optimization for head-and-neck (HN) patients. Thi ... [Med. Phys. 35, 3722 (2008)] published Fri Jul 18, 2008.
A novel PET tumor delineation method based on adaptive region-growing and dual-front active contours
Hua Li, Wade L. Thorstad, Kenneth J. Biehl, Richard Laforest, Yi Su et al.
To more accurately and precisely delineate a tumor in a 3D PET image, we proposed a novel, semi-automatic, two-stage method by utilizing an adaptive region-growing algorithm and a dual-front active contour model. First, a rough region of interest (ROI) is manually drawn by a radiation oncologist tha ... [Med. Phys. 35, 3711 (2008)] published Fri Jul 18, 2008.
Inference of the solvation energy parameters of amino acids using maximum entropy approach
Trinh X. Hoang, Flavio Seno, Antonio Trovato, Jayanth R. Banavar, and Amos Maritan
We present a novel technique, based on the principle of maximum entropy, for deriving the solvation energy parameters of amino acids from the knowledge of the solvent accessible areas in experimentally determined native state structures as well as high quality decoys of proteins. We present the resu ... [J. Chem. Phys. 129, 035102 (2008)] published Thu Jul 17, 2008.
Inference of the solvation energy parameters of amino acids using maximum entropy approach
Trinh X. Hoang, Flavio Seno, Antonio Trovato, Jayanth R. Banavar, and Amos Maritan
We present a novel technique, based on the principle of maximum entropy, for deriving the solvation energy parameters of amino acids from the knowledge of the solvent accessible areas in experimentally determined native state structures as well as high quality decoys of proteins. We present the resu ... [J. Chem. Phys. 129, 035102 (2008)] published Thu Jul 17, 2008.
Quantum mechanical methods applied to excitation energy transfer: A comparative analysis on excitation energies and electronic couplings
A. Munoz-Losa, C. Curutchet, I. Fdez. Galvan, and B. Mennucci
We present a comparative study on the influence of the quantum mechanical (QM) method (including basis set) on the evaluation of transition energies, transition densities and dipoles, and excitation energy transfer (EET) electronic couplings for a series of chromophores (and the corresponding pairs) ... [J. Chem. Phys. 129, 034104 (2008)] published Thu Jul 17, 2008.
Ontogenetic tumor growth and evolution equations
G. Dattoli, P. L. Ottaviani, and S. Pagnutti
We review the theory of ontogenetic tumor growth by discussing different evolution equations which account for the relevant dynamics. It is shown that most of the equations proposed can be treated from a unitary point of view. We extend the West ontogenetic evolution model to cancer growth and show ... [J. Appl. Phys. 104, 024701 (2008)] published Thu Jul 17, 2008.
Rigid model-based 3D segmentation of the bones of joints in MR and CT images for motion analysis
Jiamin Liu, Jayaram K. Udupa, Punam K. Saha, Dewey Odhner, Bruce E. Hirsch et al.
There are several medical application areas that require the segmentation and separation of the component bones of joints in a sequence of images of the joint acquired under various loading conditions, our own target area being joint motion analysis. This is a challenging problem due to the proximit ... [Med. Phys. 35, 3637 (2008)] published Thu Jul 17, 2008.
Quantification of carotid vessel wall and plaque thickness change using 3D ultrasound images
Bernard Chiu, Micaela Egger, J. David Spence, Grace Parraga, and Aaron Fenster
Quantitative measurements of carotid plaque burden progression or regression are important in monitoring patients and in evaluation of new treatment options. 3D ultrasound (US) has been used to monitor the progression or regression of carotid artery plaques. This paper reports on the development and ... [Med. Phys. 35, 3691 (2008)] published Thu Jul 17, 2008.
The extraction of true profiles for TPS commissioning and its impact on IMRT patient-specific QA
Guanghua Yan, Christopher Fox, Chihray Liu, and Jonathan G. Li
The aim of this work is to investigate the clinical impact of detector size effect on patient specific intensity-modulated radiation therapy (IMRT) quality assurance (QA). Two photon beam models, BM6 and BM4, were commissioned using photon beam profiles measured with a 6 mm diameter and a 4 mm diame ... [Med. Phys. 35, 3661 (2008)] published Thu Jul 17, 2008.
A Monte Carlo study on the effect of seed design on the interseed attenuation in permanent prostate implants
Hossein Afsharpour, Michel D'Amours, Benoit Cote, Jean-Francois Carrier, Frank Verhaegen et al.
Standard algorithms for postimplant analysis of transperineal interstitial permanent prostate brachytherapy (TIPPB) are based on AAPM Task Group 43 formalism (TG-43), which makes use of a world entirely made of water. This entails an assignment of the prostate, surrounding organs at risk, as well as ... [Med. Phys. 35, 3671 (2008)] published Thu Jul 17, 2008.
Automated breast mass detection in 3D reconstructed tomosynthesis volumes: A featureless approach
Swatee Singh, Georgia D. Tourassi, Jay A. Baker, Ehsan Samei, and Joseph Y. Lo
The purpose of this study was to propose and implement a computer aided detection (CADe) tool for breast tomosynthesis. This task was accomplished in two stagesa highly sensitive mass detector followed by a false positive (FP) reduction stage. Breast tomosynthesis data from 100 human subject cases w ... [Med. Phys. 35, 3626 (2008)] published Thu Jul 17, 2008.
Novel approach for the Monte Carlo calculation of free-air chamber correction factors
Ernesto Mainegra-Hing, Nick Reynaert, and Iwan Kawrakow
A self-consistent approach for the Monte Carlo calculation of free-air chamber (FAC) correction factors needed to convert the chamber reading into the quantity air-kerma at the point of measurement is introduced, and its implementation in the new EGSnrc user code egs_fac is discussed. To validate th ... [Med. Phys. 35, 3650 (2008)] published Thu Jul 17, 2008.
Clinical prototype of a plastic water-equivalent scintillating fiber dosimeter array for QA applications
Frederic Lacroix, Louis Archambault, Luc Gingras, Mathieu Guillot, A. Sam Beddar et al.
A clinical prototype of a scintillating fiber dosimeter array for quality assurance applications is presented. The array consists of a linear array of 29 plastic scintillation detectors embedded in a water-equivalent plastic sheet coupled to optical fibers used to guide optical photons to a charge c ... [Med. Phys. 35, 3682 (2008)] published Thu Jul 17, 2008.
Consequences of modern anthropometric dimensions for radiographic techniques and patient radiation exposures
Chintan Shah, A. Kyle Jones, and Charles E. Willis
Radiographic techniques are devised on the basis of anatomic dimensions. Inaccurate dimensions can cause radiographs to be exposed inappropriately and patient radiation exposures to be calculated incorrectly. The source of anatomic dimensions in common usage dates back to 1948. The objective of this ... [Med. Phys. 35, 3616 (2008)] published Thu Jul 17, 2008.
Novel Mechanical Actuation of a Modular Laparoscopic Surgical Tool
David J. Miller and Carl A. Nelson
A functional analysis of current laparoscopic surgical technology prompted a redesign of the tools in order to provide multiple functionalities within a single tool. With this redesign came the need for a number of novel mechanisms to actuate and deploy functional tips to the surgical site from thei ... [J. Med. Devices 2, 031002 (2008)] published Thu Jul 17, 2008.
Differential postural effects of plantar-flexor muscles fatigue under normal, altered and improved vestibular and neck somatosensory conditions. (arXiv:0807.3608v1 [q-bio.NC])
ePrint arXiv http://arXiv.org/
Waiting time models of cancer progression. (arXiv:0807.3638v1 [q-bio.PE])
ePrint arXiv http://arXiv.org/
Effects of intersegmental transfers on target location by proteins. (arXiv:0807.3639v1 [q-bio.SC])
ePrint arXiv http://arXiv.org/
Markov invariants, plethysms, and phylogenetics (the long version). (arXiv:0711.3503v4 [q-bio.PE] UPDATED)
ePrint arXiv http://arXiv.org/
Phylogenetic estimation with partial likelihood tensors. (arXiv:0807.3387v1 [q-bio.QM] CROSS LISTED)
ePrint arXiv http://arXiv.org/