Jeff Z. Y. Chen

An evaluation of an automated 4D-CT contour propagation tool to define an internal gross tumour volume for lung cancer radiotherapy

BACKGROUND AND PURPOSE To evaluate an automated 4D-CT contouring propagation tool by its impact on the inter- and intra-physician variability in lung tumour delineation. MATERIALS AND METHODS In a previous study, six radiation oncologists contoured the gross tumour volume (GTV) and nodes on 10 phases of the 4D-CT dataset of 10 lung cancer patients to examine the intra- and inter-physician variability. In this study, a model-based deformable image registration algorithm was used to propagate the GTV and nodes on each phase of the same 4D-CT datasets. A blind review of the contours was performed by each physician and edited. Inter- and intra-physician variability for both the manual and automated methods was assessed by calculating the centroid motion of the GTV using the Pearson correlation coefficient and the variability in the internal gross tumour volume (IGTV) overlap using the Dice similarity coefficient (DSC). RESULTS The time for manual delineation was (42.7±18.6)min versus (17.7±5.4)min when the propagation tool was used. A significant improvement in the mean Pearson correlation coefficient was also observed. There was a significant decrease in mean DSC in only 1 out of 10 primary IGTVs and 2 out of 10 nodal IGTVs. Intra-physician variability was not significantly impacted (DSC>0.742). CONCLUSIONS Automated 4D-CT propagation tools can significantly decrease the IGTV delineation time without significantly decreasing the inter- and intra-physician variability.

Asynchronous multicanonical basin hopping method and its application to cobalt nanoclusters

The multicanonical basin hopping (MUBH) method, which uses a multicanonical weight in the basin hopping (BH) Monte Carlo method, was found to be very efficient for global optimization of large-scale systems such as Lennard-Jones clusters containing more than 150 atoms. We have implemented an asynchronous parallel version of the MUBH method using the message passing interface (MPI) to take advantage of the full usage of multiprocessors in either a homogeneous or heterogeneous computational environment. Based on the intrinsic properties of the Monte Carlo method, this MPI implementation used the task parallelism to minimize interthread data communication. For a Co nanocluster consisting of N atoms, we have applied the asynchronous multicanonical basin hopping (AMUBH) method (for 181 < N < or = 200), together with BH (for 2 < or = N < 150) and MUBH (for 150 < or = N < or = 180), to search for the molecular configuration of the global energy minimum. AMUBH becomes the only practical computational scheme for locating the energy minimum within realistic computational time for a relatively large cluster.

Multicanonical basin hopping: A new global optimization method for complex systems

We introduce a new optimization algorithm that combines the basin-hopping method, which can be used to efficiently map out an energy landscape associated with minima, with the multicanonical Monte Carlo method, which encourages the system to move out of energy traps during the computation. As an example of implementing the algorithm for the global minimization of a multivariable system, we consider the Lennard-Jones systems containing 150-185 particles, and find that the new algorithm is more efficient than the original basin-hopping method.

Dependence of folding dynamics and structural stability on the location of a hydrophobic pair in β‐hairpins

We study the dependence of folding time, nucleation site, and stability of a model β‐hairpin on the location of a cross‐strand hydrophobic pair, using a coarse‐grained off‐lattice model with the aid of Monte Carlo simulations. Our simulations have produced 6500 independent folding trajectories dynamically, forming the basis for extensive statistical analysis. Four folding pathways, zipping‐out, middle‐out, zipping‐in, and reptation, have been closely monitored and discussed in all seven sequences studied. A hydrophobic pair placed near the β‐turn or in the middle section effectively speed up folding; a hydrophobic pair placed close to the terminal ends or next to the β‐turn encourages stability of the entire chain. Proteins 2006.

Modified diffusion equation for the wormlike-chain statistics in curvilinear coordinates

One of the essential physical quantities used to study the conformation and structure of polymers is the so-called propagator in polymer theories. On the basis of the wormlike-chain statistical-physics model, we derive the partial diffusion equation that the propagator satisfies, for a curvilinear coordinate system. As it turns out, an additional term exists, that couples the rotating local coordinate frame with an orientation differential operator; this term has not been previously documented. In addition, for a wormlike chain moving on a curved surface, the external-field term needs to be supplemented by a surface curvature energy penalty.

Development of a novel ArcCHECK™ insert for routine quality assurance of VMAT delivery including dose calculation with inhomogeneities

PURPOSE To design a versatile, nonhomogeneous insert for the dose verification phantom ArcCHECK(™) (Sun Nuclear Corp., FL) and to demonstrate its usefulness for the verification of dose distributions in inhomogeneous media. As an example, we demonstrate it can be used clinically for routine quality assurance of two volumetric modulated arc therapy (VMAT) systems for lung stereotactic body radiation therapy (SBRT): SmartArc(®) (Pinnacle(3), Philips Radiation Oncology Systems, Fitchburg, WI) and RapidArc(®) (Eclipse(™), Varian Medical Systems, Palo Alto, CA). METHODS The cylindrical detector array ArcCHECK(™) has a retractable homogeneous acrylic insert. In this work, we designed and manufactured a customized heterogeneous insert with densities that simulate soft tissue, lung, bone, and air. The insert offers several possible heterogeneity configurations and multiple locations for point dose measurements. SmartArc(®) and RapidArc(®) plans for lung SBRT were generated and copied to ArcCHECK(™) for each inhomogeneity configuration. Dose delivery was done on a Varian 2100 ix linac. The evaluation of dose distributions was based on gamma analysis of the diode measurements and point doses measurements at different positions near the inhomogeneities. RESULTS The insert was successfully manufactured and tested with different measurements of VMAT plans. Dose distributions measured with the homogeneous insert showed gamma passing rates similar to our clinical results (∼99%) for both treatment-planning systems. Using nonhomogeneous inserts decreased the passing rates by up to 3.6% in the examples studied. Overall, SmartArc(®) plans showed better gamma passing rates for nonhomogeneous measurements. The discrepancy between calculated and measured point doses was increased up to 6.5% for the nonhomogeneous insert depending on the inhomogeneity configuration and measurement location. SmartArc(®) and RapidArc(®) plans had similar plan quality but RapidArc(®) plans had significantly higher monitor units (up to 70%). CONCLUSIONS A versatile, nonhomogeneous insert was developed for ArcCHECK(™) for an easy and quick evaluation of dose calculations with nonhomogeneous media and for comparison of different treatment planning systems. The device was tested for SmartArc(®) and RapidArc(®) plans for lung SBRT, showing the uncertainties of dose calculations with inhomogeneities. The new insert combines the convenience of the ArcCHECK(™) and the possibility of assessing dose distributions in inhomogeneous media.PURPOSE To design a versatile, nonhomogeneous insert for the dose verification phantom ArcCHECK™ (Sun Nuclear Corp., FL) and to demonstrate its usefulness for the verification of dose distributions in inhomogeneous media. As an example, we demonstrate it can be used clinically for routine quality assurance of two volumetric modulated arc therapy (VMAT) systems for lung stereotactic body radiation therapy (SBRT): SmartArc® (Pinnacle3 , Philips Radiation Oncology Systems, Fitchburg, WI) and RapidArc® (Eclipse™ , Varian Medical Systems, Palo Alto, CA). METHODS The cylindrical detector array ArcCHECK™ has a retractable homogeneous acrylic insert. In this work, we designed and manufactured a customized heterogeneous insert with densities that simulate soft tissue, lung, bone, and air. The insert offers several possible heterogeneity configurations and multiple locations for point dose measurements. SmartArc® and RapidArc® plans for lung SBRT were generated and copied to ArcCHECK™ for each inhomogeneity configuration. Dose delivery was done on a Varian 2100 ix linac. The evaluation of dose distributions was based on gamma analysis of the diode measurements and point doses measurements at different positions near the inhomogeneities. RESULTS The insert was successfully manufactured and tested with different measurements of VMAT plans. Dose distributions measured with the homogeneous insert showed gamma passing rates similar to our clinical results (∼99%) for both treatment-planning systems. Using nonhomogeneous inserts decreased the passing rates by up to 3.6% in the examples studied. Overall, SmartArc® plans showed better gamma passing rates for nonhomogeneous measurements. The discrepancy between calculated and measured point doses was increased up to 6.5% for the nonhomogeneous insert depending on the inhomogeneity configuration and measurement location. SmartArc® and RapidArc® plans had similar plan quality but RapidArc® plans had significantly higher monitor units (up to 70%). CONCLUSIONS A versatile, nonhomogeneous insert was developed for ArcCHECK™ for an easy and quick evaluation of dose calculations with nonhomogeneous media and for comparison of different treatment planning systems. The device was tested for SmartArc® and RapidArc® plans for lung SBRT, showing the uncertainties of dose calculations with inhomogeneities. The new insert combines the convenience of the ArcCHECK™ and the possibility of assessing dose distributions in inhomogeneous media.

Morphologies and phase diagrams of ABC star triblock copolymers confined in a spherical cavity

The morphologies and phase diagrams exhibited by symmetric ABC star triblock copolymer nanoparticles are investigated by using the real-space self-consistent field theory. A variety of three-dimensional morphologies, such as spherically concentric lamellae and ring-like structures, are identified in the triangular phase diagrams for the polymeric nanoparticles, depending on the volume fractions of the components and the interaction between the polymers and the confining spherical surface. We first study a number of examples where the confining radius and degree of interactions between the polymer and the spherical surface are fixed. A neutral surface that has no energetic preference on any ABC component induces ring-like structures in axisymmetry in an orbicular region of the phase diagram, which surrounds the central region where distorted cylinder phases are stable; a spherical surface that attracts one of the three polymer components induces distorted cylinders into the ring-like structures in a central region of the phase diagram; a spherical surface that repels one of the components stabilizes a lamella-like structure in spherical symmetry in a large region of the phase diagrams. We then focus on an example of polygonal tiling morphologies to study the effects due to variations of the spherical radius and the degree of interactions between the polymer and the spherical surface. The results show that the degree of interactions can obviously influence the formation of morphologies but the spherical radius only affects the polygonal tiling morphologies through slightly adjusting their natural arrangement in the neutral surface case.

Development of a novel ArcCHECK{sup Trade-Mark-Sign} insert for routine quality assurance of VMAT delivery including dose calculation with inhomogeneities

PURPOSE To design a versatile, nonhomogeneous insert for the dose verification phantom ArcCHECK(™) (Sun Nuclear Corp., FL) and to demonstrate its usefulness for the verification of dose distributions in inhomogeneous media. As an example, we demonstrate it can be used clinically for routine quality assurance of two volumetric modulated arc therapy (VMAT) systems for lung stereotactic body radiation therapy (SBRT): SmartArc(®) (Pinnacle(3), Philips Radiation Oncology Systems, Fitchburg, WI) and RapidArc(®) (Eclipse(™), Varian Medical Systems, Palo Alto, CA). METHODS The cylindrical detector array ArcCHECK(™) has a retractable homogeneous acrylic insert. In this work, we designed and manufactured a customized heterogeneous insert with densities that simulate soft tissue, lung, bone, and air. The insert offers several possible heterogeneity configurations and multiple locations for point dose measurements. SmartArc(®) and RapidArc(®) plans for lung SBRT were generated and copied to ArcCHECK(™) for each inhomogeneity configuration. Dose delivery was done on a Varian 2100 ix linac. The evaluation of dose distributions was based on gamma analysis of the diode measurements and point doses measurements at different positions near the inhomogeneities. RESULTS The insert was successfully manufactured and tested with different measurements of VMAT plans. Dose distributions measured with the homogeneous insert showed gamma passing rates similar to our clinical results (∼99%) for both treatment-planning systems. Using nonhomogeneous inserts decreased the passing rates by up to 3.6% in the examples studied. Overall, SmartArc(®) plans showed better gamma passing rates for nonhomogeneous measurements. The discrepancy between calculated and measured point doses was increased up to 6.5% for the nonhomogeneous insert depending on the inhomogeneity configuration and measurement location. SmartArc(®) and RapidArc(®) plans had similar plan quality but RapidArc(®) plans had significantly higher monitor units (up to 70%). CONCLUSIONS A versatile, nonhomogeneous insert was developed for ArcCHECK(™) for an easy and quick evaluation of dose calculations with nonhomogeneous media and for comparison of different treatment planning systems. The device was tested for SmartArc(®) and RapidArc(®) plans for lung SBRT, showing the uncertainties of dose calculations with inhomogeneities. The new insert combines the convenience of the ArcCHECK(™) and the possibility of assessing dose distributions in inhomogeneous media.PURPOSE To design a versatile, nonhomogeneous insert for the dose verification phantom ArcCHECK™ (Sun Nuclear Corp., FL) and to demonstrate its usefulness for the verification of dose distributions in inhomogeneous media. As an example, we demonstrate it can be used clinically for routine quality assurance of two volumetric modulated arc therapy (VMAT) systems for lung stereotactic body radiation therapy (SBRT): SmartArc® (Pinnacle3 , Philips Radiation Oncology Systems, Fitchburg, WI) and RapidArc® (Eclipse™ , Varian Medical Systems, Palo Alto, CA). METHODS The cylindrical detector array ArcCHECK™ has a retractable homogeneous acrylic insert. In this work, we designed and manufactured a customized heterogeneous insert with densities that simulate soft tissue, lung, bone, and air. The insert offers several possible heterogeneity configurations and multiple locations for point dose measurements. SmartArc® and RapidArc® plans for lung SBRT were generated and copied to ArcCHECK™ for each inhomogeneity configuration. Dose delivery was done on a Varian 2100 ix linac. The evaluation of dose distributions was based on gamma analysis of the diode measurements and point doses measurements at different positions near the inhomogeneities. RESULTS The insert was successfully manufactured and tested with different measurements of VMAT plans. Dose distributions measured with the homogeneous insert showed gamma passing rates similar to our clinical results (∼99%) for both treatment-planning systems. Using nonhomogeneous inserts decreased the passing rates by up to 3.6% in the examples studied. Overall, SmartArc® plans showed better gamma passing rates for nonhomogeneous measurements. The discrepancy between calculated and measured point doses was increased up to 6.5% for the nonhomogeneous insert depending on the inhomogeneity configuration and measurement location. SmartArc® and RapidArc® plans had similar plan quality but RapidArc® plans had significantly higher monitor units (up to 70%). CONCLUSIONS A versatile, nonhomogeneous insert was developed for ArcCHECK™ for an easy and quick evaluation of dose calculations with nonhomogeneous media and for comparison of different treatment planning systems. The device was tested for SmartArc® and RapidArc® plans for lung SBRT, showing the uncertainties of dose calculations with inhomogeneities. The new insert combines the convenience of the ArcCHECK™ and the possibility of assessing dose distributions in inhomogeneous media.

Computational study of the Trp‐cage miniprotein based on the ECEPP/3 force field

Using a newly developed Monte Carlo global optimization method called basin paving, we have performed an ab initio computation for the structure of Trp‐cage based on the ECEPP/3 force field in vacuo. The lowest energy minimum has been located. Its corresponding configuration is comparable to the native structure of Trp‐cage (PDB code 1L2Y) with a backbone root mean square deviation of 2.24 Å. Proteins 2007.

Determination of structural transitions of atomic clusters from local and global bond orientational order parameters

Designing an effective order parameter for the identification of geometries in atomic clusters is an important step toward understanding the structural transitions occurring in these systems. We propose a method that simultaneously utilizes the local and global bond orientational order parameters for structural transitions. When applied to Lennard-Jones clusters at finite temperature over the size range 30< or =N< or =146, this method identified all the major geometries: icosahedra with Mackay overlayers, icosahedra with anti-Mackay overlayers, decahedra, octahedra, and tetrahedra. From the distributions of these geometries as a function of temperatures on clusters containing 38, 75, and 98 atoms, we are able to interpret all transition types without ambiguity.