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PubMed2005

4D Monte Carlo simulation of proton beam scanning: modelling of variations in time and space to study the interplay between scanning pattern and time-dependent patient geometry.

When dosimetric effects in time-dependent geometries are studied, usually either the results of individual three-dimensional (3D) calculations are combined or probability-based approaches are applied. These methods may become cumbersome and time-consuming if high time resolution is required or if the geometry is complex. Furthermore, it is difficult to study double-dynamic systems, e.g., to investigate the influence of time-dependent beam delivery (i.e., magnetically moving beam spots in proton beam scanning) on the dose deposition in a moving target. We recently introduced the technique of 4D Monte Carlo dose calculation to model continuously changing geometries. In intensity modulated proton therapy, dose is delivered by individual pristine Bragg curves. Dose spots are positioned in the patient by varying magnetic field and beam energy. If the movement of these dose spots occurs during significant respiratory motion, interplay effects can take place. Because of the inhomogeneity of individual subfields, the consequences of motion can be more severe than in conventional proton therapy. We demonstrate how the technique of 4D Monte Carlo can be used to study interplay effects in proton beam scanning. Time-dependent beam delivery to a changing patient geometry is simulated in a single 4D dose calculation. Interplay effects between respiratory motion and beam scanning speed are demonstrated.

Dose-Response Relationship, Radiation↗
PubMed2006

Computer simulation study of a simple cubatic mesogenic lattice model.

Over the last , the possible existence of a cubatic mesophase, possessing cubic orientational order (i.e., along three mutually orthogonal axes) but no translational one, has been addressed theoretically, and predicted in some cases, where the investigated interaction models involved hard-core repulsion only; on the other hand, no experimental realizations of such a phase are known at the time being. The present paper addresses a very simple cubatic mesogenic lattice model, involving continuous interactions; we consider particles possessing Oh symmetry, whose centers of mass are associated with a three-dimensional simple-cubic lattice; the pair potential is taken to be isotropic in orientation space, and restricted to nearest neighboring sites; let the two orthonormal triads {uj, j=1, 2, 3} and {vk, k=1, 2, 3} define orientations of a pair of interacting particles, and let fjk=vj.uk. The interaction model studied here is defined by the simplest nontrivial (quartic) polynomial in the scalar products f jk, consistent with the assumed symmetry and favoring orientational order; it is, so to speak, the cubatic counterpart of the Lebwohl-Lasher model for uniaxial nematics. The model was investigated by mean field theory and Monte Carlo simulation, and found to produce a low-temperature cubatically ordered phase, undergoing a first order transition to the isotropic phase at higher temperature; the mean field treatment yielded results in reasonable qualitative agreement with simulation.

Journal Article↗
PubMed2004

Planning, implementation and optimization of future space missions using an immersive visualization environment (IVE) machine.

Beginning in 1995, a team of 3-D engineering visualization experts assembled at the Lockheed Martin Space Systems Company and began to develop innovative virtual prototyping simulation tools for performing ground processing and real-time visualization of design and planning of aerospace missions. At the University of Colorado, a team of 3-D visualization experts also began developing the science of 3-D visualization and immersive visualization at the newly founded British Petroleum (BP) Center for visualization, which began operations in October, 2001. BP acquired ARCO in the year 2000 and awarded the 3-D flexible IVE developed by ARCO (beginning in 1990) to the University of Colorado, CU, the winner in a competition among 6 Universities. CU then hired Dr. G. Dorn, the leader of the ARCO team as Center Director, and the other experts to apply 3-D immersive visualization to aerospace and to other University Research fields, while continuing research on surface interpretation of seismic data and 3-D volumes. This paper recounts further progress and outlines plans in Aerospace applications at Lockheed Martin and CU.

Astronauts↗
PubMed2004

How different feature spaces may be represented in cortical maps.

This paper explores how different high-dimensional feature spaces might be represented in cortical maps, subject to continuity and completeness constraints. Spaces explored included products of circular variables (such as orientation), products of linear dimensions encoding scalar features (such as spatial frequency) and products of binary features. Maps were generated using the Kohonen algorithm, with uniform or non-uniform stimulus distributions. A 2D retina was always assumed to be present. Simulations were run with and without annealing. For uniform input distributions, coverage uniformity (Swindale 1991 Biol. Cybern. 65 415-24) was used to measure how well the map was able to represent the feature space. For non-uniform distributions a weighted measure of coverage uniformity was calculated. Good coverage could be achieved for up to five or six cyclic variables but was substantially worse for a similar number of uniformly distributed scalar features. For annealed maps of multi-dimensional stimuli with Gaussian distributions, the distribution of receptive field centres and the distribution of total activity evoked on the cortex matched the stimulus distribution well. For annealed maps of non-uniformly distributed binary features there was an approximately linear relationship between the area of a map devoted to a specific feature and the probability of occurrence of the feature during development. Deviations from uniform retinotopy often led to improved coverage.

Algorithms↗
PubMedDate not supplied

Continuous removal of protein aggregates by annular chromatography.

The removal of polymeric proteins from their monomers is a frequently encountered separation task, especially in the polishing step of therapeutic proteins. Continuous separation of protein polymers from monomers by annular chromatography using size exclusion chromatography has been studied regarding the resolution, recovery, fouling, and productivity and has been compared to conventional chromatography. An IgG preparation rich in aggregates was used as a model protein mixture. Under conditions that maximized the throughput, the polymers could be separated from the monomers, but baseline separation could not be achieved. Baseline separation was also not possible in batch mode using equivalent conditions, which was also confirmed by computer simulation. For separation of the aggregates from the product the entire available separation space (360 degrees ) was indispensable. Therefore only cyclic, discontinuous regeneration could be carried out. Loading was identified as a critical step, since the concentrated protein solution evaded into the headspace instead of migrating into the gel where viscous fingering often occurs in conventional chromatography. The productivity of annular chromatography was two times higher than that of the conventional batch chromatography, and the buffer consumption was reduced to half the conventional value. These two benefits are especially important for protein separation processes that suffer from low loadability, such as size exclusion chromatography. We have demonstrated that size exclusion can be performed on an industrial scale when it is run continuously with the aid of a pressurized annular chromatograph.

Chromatography, Gel↗
PubMed1986

ICU monitoring of ventilation distribution.

The oxygen washin method has been shown to be a practical way to measure functional residual capacity (FRC) in the intensive care unit. The ventilator oxygen concentration is increased and measurements of respiratory flow and oxygen concentration at the mouth are made with the patient monitoring system. No additional personnel, bedside equipment or ventilator attachments are required. A feasibility study was performed to determine if this method could be used to estimate a continuous distribution of ventilation with respect to ventilation to volume ratio VA/V. Due to gas mixing in the ventilator, the inspired oxygen fraction does not increase instantaneously to its new value. An equation was derived which models the lung as 50 discrete compartments and accounts for the transient change in mean inspired oxygen fraction. A digital computer simulation demonstrated good distribution recovery for one and two mode ventilation distributions. Continuous distributions were computed for four post cardiac surgery patients at four levels of positive end expiratory pressure (PEEP). In these patients a linear increase in the amount of ventilation in the normal VA/V range occurred with increasing PEEP, i.e., slow and fast spaces tended to move centrally toward a more normal VA/V range. At zero PEEP 26% of the ventilation occurred in the normal range and this increased to 49% at 15 PEEP. Dead space fraction was poorly estimated and spurious modes occurred in the high VA/V range.

Cardiac Surgical Procedures↗
PubMed2004

Coupled modeling of cement/claystone interactions and radionuclide migration.

The interactions between cement and a clayey host-rock of an underground repository for intermediate-level radioactive waste are studied with the reactive transport code HYTEC for supporting performance assessment. Care is taken in using relevant time scales (100,000 years) and dimensions. Based on a literature review, three hypotheses are considered with respect to the mineralogical composition of the claystone and the neo-formed phases. In the long term, the pH is buffered for all hypotheses and important mineral transformations occur both in cement and the host-rock. The destruction of the primary minerals is localized close to the cement/claystone interface and is characterized by the precipitation of secondary phases with retention properties (illite, zeolite). However, beyond the zone of intense mineral transformations, the pore water chemistry is also disturbed over a dozen meters due to an attenuated but continuous flux of hydroxyl, potassium and calcium ions. Four interdependent mechanisms control the profile in the whole system: diffusion of the alkaline plume, mineralogical buffering, ion exchange and clogging of the pore space at the cement/claystone interface. The migration of a selected group of radionuclides (Cs, Ra, Tc and U) is explicitly integrated in the simulations of the strongly coupled system. Theoretical profiles of distribution coefficient (Kd) and solubility limit values are derived from the simulations, and their sensitivity with respect to the system evolution is estimated.

Aluminum Silicates↗
PubMed2001

Monte Carlo track structure for radiation biology and space applications.

Over the past two decades event by event Monte Carlo track structure codes have increasingly been used for biophysical modelling and radiotherapy. Advent of these codes has helped to shed light on many aspects of microdosimetry and mechanism of damage by ionising radiation in the cell. These codes have continuously been modified to include new improved cross sections and computational techniques. This paper provides a summary of input data for ionizations, excitations and elastic scattering cross sections for event by event Monte Carlo track structure simulations for electrons and ions in the form of parametric equations, which makes it easy to reproduce the data. Stopping power and radial distribution of dose are presented for ions and compared with experimental data. A model is described for simulation of full slowing down of proton tracks in water in the range 1 keV to 1 MeV. Modelling and calculations are presented for the response of a TEPC proportional counter irradiated with 5 MeV alpha-particles. Distributions are presented for the wall and wall-less counters. Data shows contribution of indirect effects to the lineal energy distribution for the wall counters responses even at such a low ion energy.

Algorithms↗
PubMed1989

Intramucosal gastric cysts simulating submucosal cysts.

A total of 2.004 sections from 41 gastrectomy specimens were reviewed for the presence of submucosal cysts. In nine of the gastrectomy specimens, cysts were found protruding into the submucosal space (in one specimen, two such cysts were found). All ten cysts were seen surrounded by the muscularis mucosae, even those without any apparent connection with the mucosa. Deeper cuts of the paraffin blocks demonstrated a continuity between the muscle fibres surrounding the cysts and the muscularis mucosae. A gap in the muscularis mucosae was also demonstrated, through which cysts pushed the muscle fibres into the submucosal area. No specific association between cysts and adenocarcinoma of the stomach was found in the present work.

Atrophy↗
PubMed1992

Dual wavelength spectrophotometry as a diagnostic test of the pulp chamber contents.

The purpose of this in vitro study was to determine the feasibility of using dual wavelength spectrophotometry to identify teeth with pulp chambers that are either empty, filled with fixed pulp tissue, or filled with oxygenated blood. In phase I of the experiment, a human third molar was prepared so that its pulp space could be filled with oxygenated blood and later emptied. In phase II, the lower jaw of a beagle dog was removed and placed in formalin, thereby fixing the pulps of the teeth. The pulp of the right canine was removed via an apical approach, and attachments were placed in a similar position to those on the human tooth, to allow filling and emptying of the pulp space. Cavit was placed over the exposed fixed pulp in the left canine. Ten readings, which were separated by light source and detector removal and replacement, were taken of the right canine pulp space when it was empty or filled with oxygenated blood, or the left canine pulp space when it was filled with fixed tissue. Distinct and reproducible changes were measured for pulp spaces filled with air, tissue, or oxygenated blood. In phase III, simulated pulp testing on a dog tooth model was performed. Blood was introduced into the root canal space, the chamber was rinsed with water and replaced with air, according to a predetermined code. Spectrophotometer readings were recorded. The identification of pulpal contents was correctly determined in all 20 of the predetermined conditions. The findings indicate that continuous wave spectrophotometry may become a useful pulp testing method.

Animals↗
PubMed2004

Scaling behaviors of colloidal aggregates under uniform pressure.

We present a theoretical model for the compaction of a colloidal sediment under uniaxial mechanical pressure in the continuous three-dimensional space. The initial system is formed with aggregated particles dispersed in a fluid, and softly sedimented in a vessel. When a uniform pressure is applied, it evolves irreversibly through successive creation and destruction of bonds between the particles. The rules governing the bonds depend on both geometrical constraints and current stresses. Numerical simulations of such systems exhibit three different scenarios, corresponding, respectively, to the fragile, elastic, and plastic behaviors. In the elastic regime, where most bonds are permanent, the pressure scales as a power law of the volume fraction of particles, with a numerical exponent equal to 4.4. In the plastic regime, where many bonds are broken and many others created, the pressure also scales with volume fraction, but the exponent is much lower, equal to 1.7. These scaling behaviors agree remarkably well with recent experiments realized on the compaction of systems with aggregated silica particles in the oedometer cell. They also can be explained with simple theoretical arguments using a plausible morphology of the resistant paths acting throughout the system. Finally, at very large applied pressures, all these regimes converge to the random close packing of spheres.

Journal Article↗
PubMed2001

Bimanual haptic workstation for laparoscopic surgery simulation.

Realistic laparoscopic surgical simulators will require real-time graphic imaging and tactile feedback. Our research objective is to develop a cost-effective haptic workstation for the simulation of laparoscopic procedures for training and treatment planning. The physical station consists of a custom-built frame into which laparoscopic trocars and surgical tools may be attached/inserted and which are continuously adjustable to various positions and orientations to simulate multiple laparoscopic surgical approaches. Instruments inserted through the trocars are attached to end effectors of two haptic devices and interfaced to a high speed PC with fast graphics capability. The haptic device transduces 3D motion of the two manually operated surgical instruments into slave maneuvers in virtual space. The slave instrument tips probe the simulated organ. Simulations currently in progress include: 1) Surface-only renderings, deformation, and haptic interactions with elements in the gall gladder surgical field; 2) Voxel-based simulations of the bulk manipulation of tissue; 3) laparoscopic herniorrhaphy. This system provides force feed-forward from the grasped tools to the contact tissue in virtual space, with deformation of the tissue by the virtual probe, and force feedback from the deformed tissue to the operator's hands.

Computer Graphics↗
PubMed1995

An automated method for dynamic ligand design.

An automated method for the dynamic ligand design (DLD) for a binding site of known structure is described. The method can be used for the creation of de novo ligands and for the modification of existing ligands. The binding site is saturated with atoms (sp3 carbon atoms in the present implementation) that form molecules under the influence of a potential function that joins atoms to each other with the correct stereochemistry. The resulting molecules are linked to precomputed functional group minimum energy positions in the binding site. The generalized potential function allows atoms to sample a continuous parameter space that includes the Cartesian coordinates and their occupancy and type, e.g., the method allows change of an sp3 carbon into an sp2 carbon or oxygen. A parameter space formulated in this way can then be sampled and optimized by a variety of methods. In this work, molecules are generated by use of a Monte Carlo simulated annealing algorithm. The DLD method is illustrated by its application to the binding site of FK506 binding protein (FKBP), an immunophilin. De novo ligands are designed and modification of the immunosuppressant drug FK506 are suggested. The results demonstrate that the dynamic ligand design approach can automatically construct ligands which complement both the shape and charge distribution of the binding site.

Algorithms↗
PubMed2002

Delivering images to the operating room: a web-based solution.

As radiology departments become filmless, they are discovering that some areas are particularly difficult to deliver images. Many departments have found that the operating room is one such area. There are space constraints and difficulty in manipulating the images by a sterile surgeon. This report describes one method to overcome this obstacle. The author's institution has been using picture archiving and communication system (PACS) for approximately 3 years, and it has been a filmless department for 1 year. The PACS transfers images to a webserver for distribution throughout the hospital. It is accessed by Internet Explorer without any additional software. The authors recently started a pilot program in which they installed dual panel flat screen monitors in 6 operating rooms. The computers are connected to the hospital backbone by ethernet. Graphic cards installed in the computers allow the use of dual monitors. Because the surgeons were experienced in viewing cases on the enterprise web system, they had little difficulty in adapting to the operating room (OR) system. Initial reception of the system is positive. The use of the web system was found to be superior by the surgeons because of the flexibility and manipulation of the images compared with film. Images can be magnified to facilitate viewing from across the room. The ultimate goal of electronic radiology is to replace hardcopy film in all aspects. One area that PACS has difficulty in accomplishing this goal is in the operating room. Most institutions have continued to print film for the OR. The authors have initiated a project that may allow web viewing in the OR. Because of limited space in the OR, an additional computer was undesirable. The CPU tower, keyboard, and mouse were mounted on a frame on the wall. The images were displayed on 2 flat screen monitors, which simulated the viewboxes traditionally used by the surgeons. Interviews with the surgeons have found both positive and negative aspects of the system. Overall impression is good, but the timeliness of the intraoperative films needs to be improved. The author's pilot project of installing a web-based display system in the operating room still is being evaluated. Their initial results have been positive, and if there are no major problems that arise the project will be expanded. These results show that it is possible to provide image delivery to the OR over the intranet that is acceptable to the surgeons.

Computer Systems↗
PubMed2004

Thermal lattice Bhatnagar-Gross-Krook model for flows with viscous heat dissipation in the incompressible limit.

In this paper, by introducing a different distribution function and starting from the Boltzmann equation as well as the Maxwell-Boltzmann distribution, we obtain a Boltzmann Bhatnagar-Gross-Krook (BGK) equation for thermal flows with viscous heat dissipation in the incompressible limit. The continuous thermal BGK model is then discretized over both time and phase space to form a lattice BGK model, which is shown to be consistent with some existing double distribution function lattice BGK models based on macroscopic governing equations. We have also demonstrated that the lattice BGK model derived theoretically in this work can be used to simulate laminar incompressible convention heat transfer with/without viscous heat dissipation.

Journal Article↗
PubMed1995

A spectral network model of pitch perception.

A model of pitch perception, called the spatial pitch network or SPINET model, is developed and analyzed. The model neurally instantiates ideas from the spectral pitch modeling literature and joins them to basic neural network signal processing designs to stimulate a broader range of perceptual pitch data than previous spectral models. The components of the model are interpreted as peripheral mechanical and neural processing stages, which are capable of being incorporated into a larger network architecture for separating multiple sound sources in the environment. The core of the new model transforms a spectral representation of an acoustic source into a spatial distribution of pitch strengths. The SPINET model uses a weighted "harmonic sieve" whereby the strength of activation of a given pitch depends upon a weighted sum of narrow regions around the harmonics of the nominal pitch value, and higher harmonics contribute less to a pitch than lower ones. Suitably chosen harmonic weighting functions enable computer simulations of pitch perception data involving mistuned components, shifted harmonics, and various types of continuous spectra including rippled noise. It is shown how the weighting functions produce the dominance region, how they lead to octave shifts of pitch in response to ambiguous stimuli, and how they lead to a pitch region in response to the octave-spaced Shepard tone complexes and Deutsch tritones without the use of attentional mechanisms to limit pitch choices. An on-center off-surround network in the model helps to produce noise suppression, partial masking, and edge pitch. Finally, it is shown how peripheral filtering and short-term energy measurements produce a model pitch estimate that is sensitive to certain component phase relationships.

Cochlea↗
PubMed1977

Kinetic analysis of iodide transport in dog thyroid slices: perchlorate-induced discharge.

Dog thyroid slices were incubated with methimazole (2 mM) and radioiodide. The medium radioactivity was continuously recorded for 8 h. Multiple data were collected for individual glands to calculate simultaneously by compartmental analysis the influx and efflux rates of iodide from the slices. A two-compartment thyroid model was necessary and sufficient to simulate the transport of inorganic iodide. The two compartments could be defined as the cellular and the luminal spaces, but interferences due to slice thickness, nonuniform follicle sizes, and open follicles were not excluded. Sodium perchlorate (1 mM) inhibited the influx of iodide into the follicles and discharged the trapped radioiode into the medium with increased efflux rates. Our data suggest that perchlorate decreases the inward influx rates by competition and enhances the outward efflux rates by countertransport and support the hypothesis of mobile iodide carriers at the basal and apical membranes of the thyroid cells.

Animals↗
PubMed1984

A model for the distribution and clearance of inert substances in subcutaneous tissue.

The subcutaneous space has received attention in recent years as a route for the continuous administration of drugs and implantation of drug delivery systems. Yet little work has been devoted to an examination of the mass transport (distribution) of drugs in the subcutaneous space and the factors that influence their rate of clearance. A mathematical model is developed to describe the spreading and resorption of substances infused into the subcutaneous space. It simulates radial diffusion and flow in the direction of spreading as well as lateral convection into the systemic circulation. An analytic solution is obtained for the distribution of the substance as a function of time and position in the subcutaneous space. Two independent parameters, v (Péclét no.) and H (generalized Biot no.), are found to control the transport. Examples are presented to illustrate the effects of these parameters on the distribution of substances in the subcutaneous space.

Absorption↗