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At least 1,207 records · Page 67Linked to original sources
PubMed2003

Numerical framework models of single proton conduction through gramicidin.

A framework model of single-proton conduction through gramicidin was previously designed to incorporate potentials of mean force and diffusion coefficients computed by the molecular dynamics simulations of Pom s and Roux (1). The resulting diffusion model was solved analytically using the lumped state approximation (LSA), allowing a detailed comparison to be made with conductance data from gramicidin A and two Trp--> Phe analogs (2). The comparison included a sensitivity analysis which required over 1 million current evaluations. A numerical method for constructing framework models is now introduced which involves finding the steady states of random walks using a trapezoid rule closely related to the rule for numerical integration. The method is described and then applied directly to the LSA. Convergence of the results to the analytical solution is seen as the number of random walk sites increase. The numerical method is then used to construct a more elaborate framework model which avoids the LSA. This is also in very good agreement with the analytical solution under the experimental conditions, confirming the accuracy of the LSA. The numerical method remains fast enough to allow an extensive comparison with conductance data.

Computer Simulation↗
PubMed2026

Quantifying the control laws governing terminal attack in lions.

Intercepting an evasive, maneuvering target is among the most computationally demanding tasks a predator performs: in the terminal phase of a chase, it must continuously convert sensory information about the target into steering and speed commands, subject to its own biomechanical limits. How terrestrial predators solve this in real time has remained difficult to quantify. Here, we combine drone videography with AI-based markerless pose estimation to reconstruct the kinematics of 67 lion (Panthera leo) attacks on a mechanized lure programmed to move unpredictably. Lion steering is described by a combination of proportional navigation and proportional pursuit, which is a mixed guidance law previously identified only in the aerial pursuit of Harris's hawks (Parabuteo unicinctus), and speed is regulated within a defined kinematic envelope during turns, which declines at close range where the cost of overshooting is greatest. These findings reveal shared guidance principles across aerial and terrestrial pursuit, thus providing a quantitative framework for comparing pursuit strategies across species.

computational ethology↗
PubMed1992

Combining cognitive learning theory and computer assisted instruction for deaf learners.

This study investigated the effects of implementing cognitive learning theory principles in computer assisted instruction of educational psychology concepts. A total of 19 preservice deaf teachers participated in the study. We used a pre-post design to measure the learning and attitude changes of the teachers. The results of the analysis of pretests and posttests of cognitive outcomes indicated that significant learning occurred as a result of the computer-based instruction. Also, the majority of the students reacted positively to the quality of the lessons. The results also suggest that applying an appropriate theoretical framework to the design of instruction offers an avenue for meaningfully addressing the appropriate use of technology.

Adult↗
PubMed2005

VisANT: data-integrating visual framework for biological networks and modules.

VisANT is a web-based software framework for visualizing and analyzing many types of networks of biological interactions and associations. Networks are a useful computational tool for representing many types of biological data, such as biomolecular interactions, cellular pathways and functional modules. Given user-defined sets of interactions or groupings between genes or proteins, VisANT provides: (i) a visual interface for combining and annotating network data, (ii) supporting function and annotation data for different genomes from the Gene Ontology and KEGG databases and (iii) the statistical and analytical tools needed for extracting topological properties of the user-defined networks. Users can customize, modify, save and share network views with other users, and import basic network data representations from their own data sources, and from standard exchange formats such as PSI-MI and BioPAX. The software framework we employ also supports the development of more sophisticated visualization and analysis functions through its open API for Java-based plug-ins. VisANT is distributed freely via the web at http://visant.bu.edu and can also be downloaded for individual use.

Computer Graphics↗
PubMed2003

Contact damage in model dental multilayers: an investigation of the influence of indenter size.

This paper presents a combined experimental and computational study of the influence of indenter ball size on contact damage in model multilayered structures with equivalent elastic properties to bonded dentin/crown structures. Following a brief description of restored tooth structures, prior work on the development of model dental multilayered structures is reviewed. The effects of indentation ball size are investigated within a combined experimental and computational/analytical framework. The observed cracking patterns at the onset of crack nucleation are shown to be associated with principal stress contours computed using finite element analysis. The implications of the results are discussed for the design of dental multilayers that are more resistant to crack nucleation and propagation.

Journal Article↗
PubMed2002

Augmented reality in spine surgery: critical appraisal and status of development.

In spinal surgery, computer assistance in the operating room is gaining fast-paced acceptance, but it would be simplistic to imagine that added technology is systematically beneficial to the patient. As surgeons are not experts in computer technology, there is a tendency to abandon the evaluation to the market and say the best will emerge. Based on our experience with the development of our own system and confronted with the emergence of new systems adopting solutions we had rejected, we propose a framework to compare various systems between them. Similar evaluation protocols are in use for surgical implants, the same should be done for computer assistance.

Humans↗
PubMed1998

Conformational interconversions in peptide beta-turns: analysis of turns in proteins and computational estimates of barriers.

The two most important beta-turn features in peptides and proteins are the type I and type II turns, which differ mainly in the orientation of the central peptide unit. Facile conformational interconversion is possible, in principle, by a flip of the central peptide unit. Homologous crystal structures afford an opportunity to structurally characterize both possible conformational states, thus allowing identification of sites that are potentially stereochemically mobile. A representative data set of 250 high-resolution (</=2.0 A), non-homologous protein crystal structures and corresponding variant and homologous entries, obtained from the Brookhaven Protein Data Bank, was examined to identify turns that are assigned different conformational types (type I/type II) in related structures. A total of 55 examples of beta-turns were identified as possible candidates for a stereochemically mobile site. Of the 55 examples, 45 could be classified as a potential site for interconversion between type I and type II beta-turns, while ten correspond to flips from type I' to type II' structures. As a further check, the temperature factors of the central peptide unit carbonyl oxygen atom of the 55 examples were examined. The analysis reveals that the turn assignments are indeed reliable. Examination of the secondary structures at the flanking positions of the flippable beta-turns reveals that seven examples occur in the loop region of beta-hairpins, indicating that the formation of ordered secondary structures on either side of the beta-turn does not preclude local conformational variations. In these beta-turns, Pro (11 examples), Lys (nine examples) and Ser (seven examples) were most often found at the i+1 position. Glycine was found to occur overwhelmingly at position i+2 (28 examples), while Ser (seven examples) and Asn (six examples) were amongst the most frequent residues. Activation energy barriers for the interconversion between type I and type II beta-turns were computed using the peptide models Ac-Pro-Aib-NHMe and Ac-Pro-Gly-NHMe within the framework of the AM1 semi-empirical molecular orbital procedure. In order to have a uniform basis for comparison and to eliminate the distracting influence of the deviation of backbone dihedral angles from that expected for ideal beta-turns, the dihedral angles phii+1 and psii+2 were fixed at the ideal values (phii+1=-60 degrees and psii+2=0 degrees). The other two angles (psii+1 and phii+2) were varied systematically to go from type II to type I beta-turn structures. The computational results suggest that there exists one stereospecific, concerted flip of the central peptide unit involving correlated single bond rotation that can occur with an activation barrier of the order of 3 kcal/mol. The results presented here suggest that conformational variations in beta-turns are observed in protein crystal structures and such changes may be an important dynamic feature in solution.

Models, Chemical↗
PubMed2002

A structural EM algorithm for phylogenetic inference.

A central task in the study of molecular evolution is the reconstruction of a phylogenetic tree from sequences of current-day taxa. The most established approach to tree reconstruction is maximum likelihood (ML) analysis. Unfortunately, searching for the maximum likelihood phylogenetic tree is computationally prohibitive for large data sets. In this paper, we describe a new algorithm that uses Structural Expectation Maximization (EM) for learning maximum likelihood phylogenetic trees. This algorithm is similar to the standard EM method for edge-length estimation, except that during iterations of the Structural EM algorithm the topology is improved as well as the edge length. Our algorithm performs iterations of two steps. In the E-step, we use the current tree topology and edge lengths to compute expected sufficient statistics, which summarize the data. In the M-Step, we search for a topology that maximizes the likelihood with respect to these expected sufficient statistics. We show that searching for better topologies inside the M-step can be done efficiently, as opposed to standard methods for topology search. We prove that each iteration of this procedure increases the likelihood of the topology, and thus the procedure must converge. This convergence point, however, can be a suboptimal one. To escape from such "local optima," we further enhance our basic EM procedure by incorporating moves in the flavor of simulated annealing. We evaluate these new algorithms on both synthetic and real sequence data and show that for protein sequences even our basic algorithm finds more plausible trees than existing methods for searching maximum likelihood phylogenies. Furthermore, our algorithms are dramatically faster than such methods, enabling, for the first time, phylogenetic analysis of large protein data sets in the maximum likelihood framework.

Algorithms↗
PubMed2006

Impact of depression on utilization patterns of oral hypoglycemic agents in patients newly diagnosed with type 2 diabetes mellitus: a retrospective cohort analysis.

BACKGROUND: Oral hypoglycemic agents (OHAs) are an important component in the management of type 2 diabetes mellitus (DM). Large-scale studies have demonstrated that tight glycemic control with such agents can reduce the frequency and severity of long-term DM-related complications. OBJECTIVES: The main goal of this study was to examine the impact of depression on utilization patterns of OHAs in patients newly diagnosed with type 2 DM. A secondary objective was to estimate the impact of depression on discontinuation and modification of pharmacotherapy for DM in these patients. METHODS: Patients newly diagnosed with type 2 DM during a 3-year period (1998-2000) were identified from a Medicaid claims database. Presence of preexisting depression was determined on the basis of International Classification of Diseases, Ninth Revision, Clinical Modification diagnosis codes. The patient cohort was followed up until they received their first prescription for an OHA (1998-2001); this date was treated as the index date for the study. Utilization patterns (ie, discontinuation, augmentation, switching, non-modification) for OHAs were computed for a 12-month follow-up period after the index date. A multivariate framework was used to estimate the impact of depression on utilization patterns, controlling for confounders such as demographics, comorbidity, provider interaction, drug regimen complexity, and DM severity. RESULTS: A total of 1237 newly diagnosed type 2 DM patients were identified (depressed, n=446; nondepressed, n=791). A higher number of depressed patients (23.32%) switched or augmented therapy compared with nondepressed patients (16.18%). Also, a higher fraction of depressed patients (39.46%) discontinued OHA therapy compared with nondepressed patients (32.87%). Results of a multinomial logistic regression indicated that, controlling for covariates, patients with depression were 1.72 times more likely to switch (P=0.046) and 1.89 times more likely to augment therapy (P=0.004) compared with nondepressed patients. Logistic regression analysis also indicated that, controlling for confounding covariates, patients with depression were 1.72 times more likely to modify initial OHA therapy compared with patients without depression (P=0.003). CONCLUSION: Depression was significantly associated with utilization patterns of OHAs in these patients newly diagnosed with type 2 DM, thus possibly affecting their disease management.

Administration, Oral↗
PubMed2005

The Noble cardiac ventricular electrophysiology models in CellML.

We present a review of the cardiac ventricular cell electrophysiology models developed by Prof. Denis Noble and colleagues as an example of how models may be published using a web-based CellML publication framework. The models reviewed have been marked-up in CellML and then used to compute all results presented here. The models are freely available from a website as are the specific numerical experiments discussed in this review and the tools used to perform the simulations.

Animals↗
PubMed1984

Initiation of DNA replication in bacteria: analysis of an autorepressor control model.

The precise mechanism by which the initiation of chromosome replication in bacteria is controlled has not yet been established, and several theoretical models have been proposed in an attempt to provide a conceptual framework for the accumulated experimental evidence. The present article contains a detailed quantitative analysis, using computer simulation, of the control model first put forward schematically by Sompayrac & Maaløe in 1973, in which a single operon codes for both the initiator protein and an autorepressor. By comparing the predictions of the model with what is known about the physiology and molecular biology of Escherichia coli under different growth conditions, we are able to delineate the characteristics that such a control system would need to possess in order to be capable of regulating chromosome replication: the control operon has to lie fairly near the origin of replication and contain a moderate to strong promoter and an operator that competes for its repressor with other equally specific binding sites along the chromosome in an interaction that is somewhat weaker than usual; in addition, the messenger molecules encoded for by the repressor gene must have a relatively ineffective ribosome binding site and not too long a halflife.

Binding, Competitive↗
PubMedDate not supplied

Structural analysis of ricin and implications for inhibitor design.

Ricin is a potent cytotoxin with experimental and clinical uses; it has also been used as a poison. There is considerable interest in identifying or designing inhibitors of the toxin that could be administered as antidotes. The X-ray structure of ricin A-chain is known and a plausible mechanism of action has been proposed. This provides a structural and chemical framework around which inhibitors could be designed; such a structure-based project is underway. Computer programs such as DOCK, GRID, SYBYL, and CHEMX have been used to map the ricin A-chain binding site and to search for potential inhibitors. Inhibitor candidates can be assayed kinetically in a protein synthesis assay and binding can be observed crystallographically. Taken together, a workable search algorithm has been developed and initial tests indicate that at least one ricin A-chain inhibitor, pteroic acid, has been identified.

Animals↗
PubMed2001

Dynamic optimization of chemical processes using ant colony framework.

Ant colony framework is illustrated by considering dynamic optimization of six important bench marking examples. This new computational tool is simple to implement and can tackle problems with state as well as terminal constraints in a straightforward fashion. It requires fewer grid points to reach the global optimum at relatively very low computational effort. The examples with varying degree of complexities, analyzed here, illustrate its potential for solving a large class of process optimization problems in chemical engineering.

Journal Article↗
PubMed1997

Avoiding premature closure in sequential diagnosis.

An important aspect of diagnostic reasoning is the ability to recognise when there is sufficient evidence to enable a working diagnosis to be made and thus avoid the unnecessary risks and costs of further testing. On the other hand, the reasoner must be careful to avoid the error, known as premature closure, of accepting a diagnosis before it is fully verified. In the absence of a more rigorous approach to verification, a pragmatic approach adopted in many programs for sequential diagnosis is to discontinue testing when the probability of the leading hypothesis reaches an arbitrary threshold. Experimental results are presented to illustrate the potential unreliability of this approach. A more reliable way to avoid premature closure is to discontinue testing only when the lower bound for the probability of the leading hypothesis reaches an acceptably high level. For example, a lower bound of 70% means that its probability can never be less than 70% regardless of any evidence that further testing may reveal. Another reason to discontinue testing may be that further evidence can at best increase the probability of the leading hypothesis by a small amount. For example, if the probability of the leading hypothesis is 72%, with a lower bound of 65% and an upper bound of 75%, further testing may be difficult to justify. As these examples illustrate, a termination strategy informed by upper and lower bounds for the probability of the leading hypothesis may help to avoid both premature closure and undue prolongation of the testing process. Finding upper and lower bounds for the probability of a diagnostic hypothesis as each new piece of evidence is obtained is feasible by existing techniques only when the number of remaining tests is small. However, new techniques are presented which can often produce a dramatic reduction in the computational effort required to find the upper and lower bounds. Based on the independence Bayesian framework, the theory presented extends a probabilistic model of hypothetico-deductive reasoning designed to enable programs for sequential diagnosis in medicine to emulate the reasoning processes of human diagnosticians.

Abdomen, Acute↗
PubMed2001

Natural J-coupling analysis: interpretation of scalar J-couplings in terms of natural bond orbitals.

The natural J-coupling (NJC) method presented here analyzes the Fermi contact portion of J-coupling in the framework of finite perturbation theory applied to ab initio/density function theory (DFT) wave functions, to compute individual and pairwise orbital contributions to the net J-coupling. The approach is based on the concepts and formalisms of natural bond orbital (NBO) methods. Computed coupling contributions can be classified as Lewis (individual orbital contributions corresponding to the natural Lewis structure of the molecule), delocalization (resulting from pairwise donor-acceptor interactions), and residual repolarization (corresponding to correlation-like interactions). This approach is illustrated by an analysis of the angular and distance dependences of the contributions to vicinal (3)J(HH) couplings in ethane and to the long-range (6)J(HH) couplings in pentane. The results indicate that approximately 70% or more of the net J-coupling is propagated by steric exchange antisymmetry interactions between Lewis orbitals (predominantly sigma bonding orbitals). Hyperconjugative sigma to sigma delocalization interactions account for the remainder of the coupling. Calculated pairwise-steric and hyperconjugative-delocalization energies provide a means for relating coupling mechanisms to molecular energetics. In this way, J-coupling contributions can be related directly to the localized features of the molecular electronic structure in order to explain measured J-coupling patterns and to predict J-coupling trends that have yet to be measured.

Hydrogen Bonding↗
PubMed2006

Correlation of polarizabilities with Van der Waals interactions in pi-systems.

This work aims to (i) provide a semiquantitative relationship that can be used to estimate the binding energy, equilibrium separation, and potential energy surface (PES) for supermolecules consisting of benzene and small polycyclic aromatic hydrocarbons (PAHs) in parallel configuration and (ii) give a qualitative description of pi-pi interactions between PAHs. We compute the one-dimensional PES of benzene translated parallel to various PAHs within the framework of second-order Møller-Plesset (MP2) perturbation theory. For PAHs of small MW difference, we observe a linear correlation between the binding energy and the number of carbon atoms in the supermolecule. The PES of these supermolecules is fit to an (exp-6) function whose variables are subsequently used to derive a mass-centered potential energy function as a function of the number of carbon atoms in the supermolecule. The linear dependence of the binding energy in the supermolecular series examined here can be directly correlated to the average polarizability product of the supermolecule. Last, we consider the supermolecular series of benzene with n-polyacenes to study the convergence of pi-pi interactions between PAHs when their size is considerably different.

Anthracenes↗
PubMed2006

Nanoparticles in solutions of adsorbing polymers: pair interactions, percolation, and phase behavior.

We study the polymer adsorption characteristics, pair-interaction potentials, and phase and percolation behavior in nanoparticle-polymer mixtures. We propose a "saturable" adsorption model to capture the effect of the finite surface saturation capacity for adsorption, and use polymer self-consistent field theory in combination with a McMillan-Mayer framework [McMillan, W. G., Jr.; Mayer, J. E. J. Chem. Phys. 1945, 13, 276] to compute the pair-interaction potentials. Our results demonstrate novel size effects that distinguish the adsorption characteristics of nanoparticles from that of larger particles. Specifically, we predict that the nanoparticle regime is characterized by a significant adsorbance of polymers, albeit distributed predominantly in the form of tails. We also demonstrate that an interplay between the surface saturation, polymer-to-particle size ratios, and the polymer concentrations governs the overall effective interactions between nanoparticles in the presence of an adsorbing polymer. We use simple, mean-field models to relate these characteristics to the phase and percolation behavior in such systems. Our results show that the percolation thresholds for smaller particles are significantly smaller (and, overall, correspond only to a few volume percent) compared to that of the larger particles. Further, with a decrease in the size of the particles, we also predict a considerable increase in the miscibility of the polymer-particle mixtures. Our results are qualitatively in accord with many experimental observations in the nanoparticle regime.

Journal Article↗