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PubMed2006

Calculation of vertical correlation probability in Ge/Si(001) shallow island quantum dot multilayer systems.

We investigate the behavior of the island vertical pairing probability in multilayer systems of Ge island quantum dots (QDs) in Si(001). By combining a simple kinetic rate model with our previously reported atomistic simulation results on the nature of the stress field from buried shallow Ge islands having {105}-oriented sidewalls, we derive an analytical expression for correlation probability as a function of the parameters characterizing the multi-QD systems. The approach is based upon continuum mechanochemical potential model, which allows one to introduce necessary elements of the kinetics of island formation in a simple way. We compare the model predictions with available experimental data and find that the model provides a satisfactory description of the coupling probability. The correlation probability behavior as a function of capping layer thickness, Ge island size, interisland distance, and Ge adatom diffusion length is investigated within the framework of the developed model.

Computer Simulation↗

PubMed2004

Calculating expectations with time-dependent perturbations in quantum Monte Carlo.

We show that a small perturbation periodic in imaginary time can be used to compute expectation values of nondifferential operators that do not commute with the Hamiltonian within the framework of quantum diffusion Monte Carlo. Some results for the harmonic oscillator and the helium atom are presented showing the validity of the proposed method.

Journal Article↗

PubMed2006

An ab initio study of the fcc and hcp structures of helium.

The hexagonal close packed (hcp) and face centered cubic (fcc) structures of helium are studied by using a new ab initio computational model for large complexes comprising small subsystems. The new model is formulated within the framework of the energy incremental scheme. In the calculation of intra- and intersystem energies, model systems are introduced. To each subsystem associated is a set of partner subsystems defined by a vicinity criterion. In the independent calculations of intra- and intersystem energies, the calculations are performed on model subsystems defined by the subsystems considered and their partner subsystems. A small and a large basis set are associated with each subsystem. For partner subsystems in a model system, the small basis set is adopted. By introducing a particular decomposition scheme, the intermolecular potential is written as a sum of effective one-body potentials. The binding energy per atom in an infinite crystal of atoms is the negative value of this one-body potential. The one-body potentials for hcp and fcc structures are calculated for the following nearest neighbor distances (d0): 4.6, 5.1, 5.4, 5.435, 5.5, 5.61, and 6.1 a.u. The equilibrium distance is 5.44 a.u. for both structures. The equilibrium dimer distance is 5.61 a.u. For the larger distances, i.e., d0 > 5.4 a.u., the difference of the effective one-body potentials for the two structures is less than 0.2 microE(h). However, the hcp structure has the lowest effective one-body potential for all the distances considered. For the smallest distance the difference in the effective one-body potential is 3.9 microE(h). Hence, for solid helium, i.e., helium under high pressure, the hcp structure is the preferred one. The error in the calculated effective one-body potential for the distance d0 = 5.61 a.u. is of the order of 1 microE(h) (approximately 0.5%).

Journal Article↗

PubMed1991

Humanized antibodies for antiviral therapy.

Antibody therapy holds great promise for the treatment of cancer, autoimmune disorders, and viral infections. Murine monoclonal antibodies are relatively easy to produce but are severely restricted for therapeutic use by their immunogenicity in humans. Production of human monoclonal antibodies has been problematic. Humanized antibodies can be generated by introducing the six hypervariable regions from the heavy and light chains of a murine antibody into a human framework sequence and combining it with human constant regions. We humanized, with the aid of computer modeling, two murine monoclonal antibodies against herpes simplex virus gB and gD glycoproteins. The binding, virus neutralization, and cell protection results all indicate that both humanized antibodies have retained the binding activities and the biological properties of the murine monoclonal antibodies.

Amino Acid Sequence↗

PubMed1988

Effect of excluded volume on topological properties of circular DNA.

We have performed computer simulations of closed polymer chains with allowance for the excluded volume effects within the framework of the free-joint model. The probability of knot formation, the linking probability of a pair of chains and the variance in the writhing number proved to be significantly affected by the excluded volume effects. This is true even for DNA with completely screened charges for which the b/d ratio (where b is the Kuhn statistical length and d is the diameter of the double helix) is as large as 50. Allowance for the electrostatic repulsion (change of the DNA effective diameter d) further increases the effects. The most dramatic dependence on d is found for the probability of knot formation. The data on the dependence of the variance of writhing, mean value of (WR)2, on d indicate that the DNA superhelix energy should be significantly ionic strength-dependent. Special calculations have shown that the free-joint model underestimates the mean value of (Wr)2 value by about 20% as compared with the wormlike model.

DNA, Circular↗

PubMed2006

Decoupling functional mechanisms of adaptive encoding.

In a natural setting, adaptive mechanisms constantly modulate the encoding properties of sensory neurons in response to changes in the external environment. Recent experiments have revealed that adaptation affects both the spatiotemporal integration properties and baseline membrane potential of sensory neurons. However, the precise functional role of adaptation remains an open question, due in part to contradictory experimental results. Here, we develop a framework to characterize adaptive encoding, including a cascade model with a time-varying receptive field (reflecting spatiotemporal integration properties) and offset (reflecting baseline membrane potential), and a recursive technique for tracking changes in the model parameters during a single stimulus/response trial. Simulated and experimental responses from retinal neurons are used to track adaptive changes in receptive field structure and offset during nonstationary stimulation. Due to the nonlinear nature of spiking neurons, the parameters of the receptive field and offset must be estimated simultaneously, or changes in the offset (or even in the statistical distribution of the stimulus) can mask, confound, or create the illusion of adaptive changes in the receptive field. Our analysis suggests that these confounding effects may be at the root of the inconsistency in the literature and shows that seemingly conflicting experimental results can be reconciled within our framework.

Adaptation, Physiological↗

PubMed2006

On counting position weight matrix matches in a sequence, with application to discriminative motif finding.

MOTIVATION AND RESULTS: The position weight matrix (PWM) is a popular method to model transcription factor binding sites. A fundamental problem in cis-regulatory analysis is to "count" the occurrences of a PWM in a DNA sequence. We propose a novel probabilistic score to solve this problem of counting PWM occurrences. The proposed score has two important properties: (1) It gives appropriate weights to both strong and weak occurrences of the PWM, without using thresholds. (2) For any given PWM, this score can be computed while allowing for occurrences of other, a priori known PWMs, in a statistically sound framework. Additionally, the score is efficiently differentiable with respect to the PWM parameters, which has important consequences for designing search algorithms. The second problem we address is to find, ab initio, PWMs that have high counts in one set of sequences, and low counts in another. We develop a novel algorithm to solve this "discriminative motif-finding problem", using the proposed score for counting a PWM in the sequences. The algorithm is a local search technique that exploits derivative information on an objective function to enhance speed and performance. It is extensively tested on synthetic data, and shown to perform better than other discriminative as well as non-discriminative PWM finding algorithms. It is then applied to cis-regulatory modules involved in development of the fruitfly embryo, to elicit known and novel motifs. We finally use the algorithm on genes predictive of social behavior in the honey bee, and find interesting motifs. AVAILABILITY: The program is available upon request from the author.

Algorithms↗

PubMed2006

Indelign: a probabilistic framework for annotation of insertions and deletions in a multiple alignment.

MOTIVATION: A quantitative study of molecular evolutionary events such as substitutions, insertions and deletions from closely related genomes requires (1) an accurate multiple sequence alignment program and (2) a method to annotate the insertions and deletions that explain the 'gaps' in the alignment. Although the former requirement has been extensively addressed, the latter problem has received little attention, especially in a comprehensive probabilistic framework. RESULTS: Here, we present Indelign, a program that uses a probabilistic evolutionary model to compute the most likely scenario of insertions and deletions consistent with an input multiple alignment. It is also capable of modifying the given alignment so as to obtain a better agreement with the evolutionary model. We find close to optimal performance and substantial improvement over alternative methods, in tests of Indelign on synthetic data. We use Indelign to analyze regulatory sequences in Drosophila, and find an excess of insertions over deletions, which is different from what has been reported for neutral sequences. AVAILABILITY: The Indelign program may be downloaded from the website http://veda.cs.uiuc.edu/indelign/ SUPPLEMENTARY INFORMATION: Supplementary material is available at Bioinformatics online.

Algorithms↗

PubMed2003

Defining neuroscience nursing practice: the 2001 role delineation study.

Studies that provided a blueprint for the Certified Neuroscience Registered Nurse (CNRN) examination were conducted in 1987, 1992, and 1997. In 2000, the American Board of Neuroscience Nursing (ABNN) formed a task force to re-examine the previous role delineation survey, obtain information to define current neuroscience nursing practice, and provide content validity for future CNRN examinations. Previous role delineation studies conducted by ABNN and a review of the literature provided the background for the study. The theoretical framework was the Nursing Intervention Classification (NIC) taxonomy and the methodology was a survey design. Computer Adaptive Technologies, Inc. (CAT), assisted the task force with survey development and data analysis. The survey, a three-part questionnaire, was mailed to 1,505 CNRNs and returned by 453 participants.

Certification↗

PubMed2000

Frustrated heisenberg magnets: A nonperturbative approach

Frustrated magnets are a notorious example of where usual perturbative methods fail. Using a nonperturbative Wilson-like approach, we get a coherent picture of the physics of frustrated Heisenberg magnets everywhere between d = 2 and d = 4. We recover all known perturbative results in a single framework and find the transition to be weakly of first order in d = 3. We compute effective exponents that are in good agreement with numerical and experimental data.

Journal Article↗

PubMed2000

Efficient total energy calculations from self-energy models.

We propose a new method for calculating total energies of systems of interacting electrons, which requires little more computational resources than standard density-functional theories. The total energy is calculated within the framework of many-body perturbation theory by using an efficient model of the self-energy, that nevertheless retains the main features of the exact operator. The method shows promising performance when tested against quantum Monte Carlo results for the linear response of the homogeneous electron gas and structural properties of bulk silicon.

Journal Article↗

PubMed2005

Alignment of continuous video onto 3D point clouds.

We propose a general framework for aligning continuous (oblique) video onto 3D sensor data. We align a point cloud computed from the video onto the point cloud directly obtained from a 3D sensor. This is in contrast to existing techniques where the 2D images are aligned to a 3D model derived from the 3D sensor data. Using point clouds enables the alignment for scenes full of objects that are difficult to model; for example, trees. To compute 3D point clouds from video, motion stereo is used along with a state-of-the-art algorithm for camera pose estimation. Our experiments with real data demonstrate the advantages of the proposed registration algorithm for texturing models in large-scale semiurban environments. The capability to align video before a 3D model is built from the 3D sensor data offers new practical opportunities for 3D modeling. We introduce a novel modeling-through-registration approach that fuses 3D information from both the 3D sensor and the video. Initial experiments with real data illustrate the potential of the proposed approach.

Algorithms↗

PubMedDate not supplied

Stylized and abstract painterly rendering system using a multiscale segmented sphere hierarchy.

This paper presents a novel system framework for interactive, three-dimensional, stylized, abstract painterly rendering. In this framework, the input models are first represented using 3D point sets and then this point-based representation is used to build a multiresolution bounding sphere hierarchy. From the leaf to root nodes, spheres of various sizes are rendered into multiple-size strokes on the canvas. The proposed sphere hierarchy is developed using multiscale region segmentation. This segmentation task assembles spheres with similar attribute regularities into a meaningful region hierarchy. These attributes include colors, positions, and curvatures. This hierarchy is very useful in the following respects: 1) it ensures the screen-space stroke density, 2) controls different input model abstractions, 3) maintains region structures such as the edges/boundaries at different scales, and 4) renders models interactively. By choosing suitable abstractions, brush stroke, and lighting parameters, we can interactively generate various painterly styles. We also propose a novel scheme that reduces the popping effect in animation sequences. Many different stylized images can be generated using the proposed framework.

Algorithms↗

PubMed2005

Barley morphology, genetics and hormonal regulation of internode elongation modelled by a relational growth grammar.

A multiscaled ecophysiological model of barley (Hordeum vulgare) development is presented here. The model is based on the new formalism of relational growth grammars (RGG), an extension of L-systems, and implemented using the new modelling language XL. It is executable in the interactive modelling platform GroIMP. The model consists of a set of morphogenetic rules, combined with a metabolic regulatory network, which simulates the biosynthesis of gibberellic acid (GA1). GA1 and two of its metabolic precursors are transported along the developing simulated structure. Local concentrations of GA1 determine internode elongation. Furthermore, virtual barley individuals are chosen interactively from a population, based on genotype, and (sexual or asexual) reproduction is simulated. Genotype and phenotype of the population are visualized. Seven Mendelian genes have been implemented in the model so far; some of these directly influence the GA-regulation network. The model exemplifies and validates the new formalism and modelling language. RGG have the capability to represent genetic, metabolic and morphological aspects of plant development and reproduction, all within the same framework.

Computer Simulation↗

PubMed2002

A dual-energy subtraction technique for microcalcification imaging in digital mammography--a signal-to-noise analysis.

Breast cancer may manifest as microcalcifications (microCs) in x-ray mammography. However, the detection and visualization of microCs are often obscured by the overlapping tissue structures. The dual-energy subtraction imaging technique offers an alternative approach for imaging and visualizing microCs. With this technique, separate high- and low-energy images are acquired and their differences are used to "cancel" out the background tissue structures. However, the subtraction process could increase the statistical noise level relative to the calcification contrast. Therefore, a key issue with the dual-energy subtraction imaging technique is to weigh the benefit of removing the cluttered background tissue structure over the drawback of reduced signal-to-noise ratio in the subtracted microC images. In this report, a theoretical framework for calculating the (quantum) noise in the subtraction images is developed and the numerical computations are described. We estimate the noise levels in the dual-energy subtraction signals under various imaging conditions, including the x-ray spectra, microC size, tissue composition, and breast thickness. The selection of imaging parameters is optimized to evaluate the feasibility of using a dual-energy subtraction technique for the improved detection and visualization of microCs. We present the results and discuss its dependence on imaging parameters.

Breast↗

PubMed2004

How enzymes work: analysis by modern rate theory and computer simulations.

Advances in transition state theory and computer simulations are providing new insights into the sources of enzyme catalysis. Both lowering of the activation free energy and changes in the generalized transmission coefficient (recrossing of the transition state, tunneling, and nonequilibrium contributions) can play a role. A framework for understanding these effects is presented, and the contributions of the different factors, as illustrated by specific enzymes, are identified and quantified by computer simulations. The resulting understanding of enzyme catalysis is used to comment on alternative proposals of how enzymes work.

Catalysis↗

PubMed2001

Software and speech--a review of software in phonology therapy.

A review of software was carried out to evaluate to what extent particular titles could be used within a phonological therapy programme using a psycholinguistic approach for children aged between four and seven years. Some of the software had been developed specifically for speech and language therapists working with children's phonological impairments. Other titles were from the education market and aimed at developing children's literacy skills. This paper describes how these software programmes could be used to address phonological impairments through developing the sub-skills described within the psycholinguistic framework.

Humans↗

PubMed2000

A data preprocessing framework for supporting probability-learning in dynamic decision modeling in medicine.

Data preprocessing is needed when real-life clinical databases are used as the data sources to learn the probabilities for dynamic decision models. Data preprocessing is challenging as it involves extensive manual effort and time in developing the data operation scripts. This paper presents a framework to facilitate automated and interactive generation of the problem-specific data preprocessing scripts. The framework has three major components: 1) A model parser that parses the decision model definition, 2) A graphical user interface that facilitates the interaction between the user and the system, and 3) A script generator that automatically generates the specific database scripts for the data preprocessing. We have implemented a prototype system of the framework and evaluated its effectiveness via a case study in the clinical domain. Preliminary results demonstrate the practical promise of the framework.

Artificial Intelligence↗