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PubMed2004

Comparison of spectroscopic potentials and an a priori analytical function. The potential energy curve of the ground state of the sodium dimer, X1Sigmag(+) Na2.

The results of a "universal" potential energy function, one that incorporates electronegativity and Slater's effective nuclear charge into a Morse-type function, are compared to spectroscopically derived potential energy curves of the X1Sigmag(+) state of Na2. The function is a priori in that it does not require prior knowledge of the actual potential and has no adjustable parameters. Criteria used to evaluate the performance of the function are comparisons of predicted versus spectroscopic energies at Rydberg-Klein-Rees (RKR) procedure turning points, predicted distances at measured energies versus RKR distances, and eigenvalues derived from the a priori potential versus spectroscopically deduced energy levels. The a priori function describes the Na2 potential with deviations approaching the magnitude of those found among some spectroscopic potentials from different sources. By examining the behavior of the "spectroscopic" parameter of the Morse function, irregularities are found in five of the seven spectroscopic potentials examined. A new procedure is demonstrated for correcting irregularities on the inner branch of spectroscopic potentials at high extents of dissociation and for extending reliably the potential in this region beyond the domain of the measurements.

Journal Article↗

PubMed1991

Cellular cytotoxic function and potential in acute myelogenous leukaemia.

Twenty-seven adult AML patients (13 with active disease and 14 in complete remission) were investigated for their cellular cytotoxic potential and function. All AML patients, whether with active disease or in complete remission, showed increased percentage of CD3+ lymphocytes expressing the cytotoxicity-linked cytoplasmic serine esterase, suggesting a higher than normal cytotoxic potential. However, when the cytotoxic function in these patients were analysed in terms of the natural killer and lectin-dependent cellular cytotoxicity, all AML patients, whether with active disease or in complete remission, had impaired target cell lytic activity. This paradox of cytotoxicity is most likely due to the immunosuppressive effect of the serum factor elaborated by leukaemia myeloblasts.

Adult↗

PubMed2002

A method for optimizing potential-energy functions by a hierarchical design of the potential-energy landscape: application to the UNRES force field.

A method for optimizing potential-energy functions of proteins is proposed. The method assumes a hierarchical structure of the energy landscape, which means that the energy decreases as the number of native-like elements in a structure increases, being lowest for structures from the native family and highest for structures with no native-like element. A level of the hierarchy is defined as a family of structures with the same number of native-like elements (or degree of native likeness). Optimization of a potential-energy function is aimed at achieving such a hierarchical structure of the energy landscape by forcing appropriate free-energy gaps between hierarchy levels to place their energies in ascending order. This procedure is different from methods developed thus far, in which the energy gap and/or the Z score between the native structure and all non-native structures are maximized, regardless of the degree of native likeness of the non-native structures. The advantage of this approach lies in reducing the number of structures with decreasing energy, which should ensure the searchability of the potential. The method was tested on two proteins, PDB ID codes and, with an off-lattice united-residue force field. For, the search of the conformational space with the use of the conformational space annealing method and the newly optimized potential-energy function found the native structure very quickly, as opposed to the potential-energy functions obtained by former optimization methods. After even incomplete optimization, the force field obtained by using located the native-like structures of two peptides, and betanova (a designed three-stranded beta-sheet peptide), as the lowest-energy conformations, whereas for the 46-residue N-terminal fragment of staphylococcal protein A, the native-like conformation was the second-lowest-energy conformation and had an energy 2 kcal/mol above that of the lowest-energy structure.

Algorithms↗

PubMed2000

The 5' part of the mouse immunoglobulin kappa locus as a continuously cloned structure.

Five contigs of the 5' part of the immunoglobulin kappa locus (F. Röschenthaler et al., Eur. J. Immunol. 1999. 29: 2065 - 2071) have been linked by cosmid clones prepared from bacterial artificial chromosomes (BACs) and by PCR. One of the previously defined contigs which contains three pseudogenes (Z7) was shown by fluorescence in situ hybridization to be located near the kappa locus on chromosome 6, but not within the locus; the three Vkappa genes are therefore now classified as orphons. A Vkappa9 / 10 gene, which was sequenced previously, was now localized within the locus, and two additional Vkappa genes were identified, a potentially functional Vkappa24 gene and a pseudogene of the Vkappa9 / 10 family. This brings the number of localized and sequenced Vkappa genes in the locus to 140; 75 of them are functional, 21 potentially functional and 44 pseudogenes. The 5' part of the kappa locus is now one contig of 1.88 megabase (Mb); it comprises 82 Vkappa genes. Other contigs of the locus are 65 kb, 105 kb and 1.04 Mb in size and contain 2, 5 and 51 Vkappa genes, respectively. The contigs are separated by three gaps of 10 - 40 kb each. Detailed restriction maps and other structural details of the kappa locus are deposted in the Internet at http://www.med. uni-muenchen.de / biochemie / zachau / kappa.htm.

Animals↗

PubMed2004

Inclusion of signal analysis in a hybrid medical decision support system.

OBJECTIVES: Signal analysis has played an important role in cardiac diagnosis, both as a separate entity and in conjunction with clinical parameters. Hybrid systems are an effective method for developing higher-order decision models in which biomedical signal data can be incorporated. METHODS: The hybrid system components include a knowledge-based system that utilizes approximate reasoning techniques, a neural network model based on a potential function approach to supervised learning that uses the general class of Cohen orthogonal functions as potential functions, and a signal analysis component that relies on continuous chaotic modeling to produce a degree of variability in the time series. The hybrid system is illustrated in an application for differentiation among different types of dementia. RESULTS: Application of this method to cardiac diagnosis shows that chaotic parameters alone contribute significantly to correct classification while the addition of clinical parameters increases the sensitivity, specificity, and accuracy. Applications to electroencephalogram analysis indicate that the second-order difference plots display significant differences for the different types of EEG waves identifiable by frequency, both in shape and degree of dispersion. Hence the identification of these waves, and the duration of their occurrence, may provide suitable variables for chaotic analysis. CONCLUSIONS: Results from studies in cardiology demonstrate that using chaotic measures for ECG analysis provide useful information for classification. Sensitivity, specificity, and accuracy are increased if these methods are combined with other clinical parameters in a hybrid system. This approach has been extended to new applications based on EEG analysis combined with other relevant information.

Computer Simulation↗

PubMed1992

Functional interhemispheric asymmetries at birth as demonstrated by somatosensory evoked potentials.

Functional cerebral hemispheric asymmetries detectable at birth have been suggested by a number of neuroanatomic, neuroradiologic, and clinical neurophysiologic modalities. The aim of this study was to determine whether functional interhemispheric asymmetries can be identified using electrophysiologic measures. As part of a prospective study, somatosensory evoked potentials following median nerve stimulation were recorded in nine healthy full-term newborns on day 2 or 3 of life, and somatosensory evoked potentials were repeated at 2 and 6 months of age. These children were subsequently examined at 1 and 3 years of age by a pediatric neurologist and all had normal examinations. Handedness was determined at 3 years by questioning the parent and by clinical observation. Three of nine were left-handers. All three left-handers had clearly identifiable neonatal N19 parietal potentials over the right hemisphere. Following right median nerve stimulation, contralateral parietal potentials were absent on two of the three and questionable in the third. Asymmetries were not clearly present in right-handers although only one showed an increased maturation of the right hemisphere relative to the left. At 2 months of age, interhemispheric differences were no longer clearly evident. This data suggests that preferential hemispheric asymmetries are masked by 2 months of age. This differential rate of development demonstrated by neonatal somatosensory evoked potentials may be an early indicator of ultimate handedness.

Cerebral Cortex↗

PubMed2006

Soft sticky dipole-quadrupole-octupole potential energy function for liquid water: an approximate moment expansion.

A new, efficient potential energy function for liquid water is presented here. The new model, which is referred here as the soft sticky dipole-quadrupole-octupole (SSDQO) model, describes a water molecule as a Lennard-Jones sphere with point dipole, quadrupole, and octupole moments. It is a single-point model and resembles the hard-sphere sticky dipole potential model for water by Bratko et al. [J. Chem. Phys. 83, 6367 (1985)] and the soft sticky dipole model by Ichiye and Liu [J. Phys. Chem. 100, 2723 (1996)] except now the sticky potential consists of an approximate moment expansion for the dimer interaction potential, which is much faster than the true moment expansion. The object here is to demonstrate that the SSDQO potential energy function can accurately mimic the potential energy function of a multipoint model using the moments of that model. First, the SSDQO potential energy function using the dipole, quadruple, and octupole moments from SPC/E, TIP3P, or TIP5P is shown to reproduce the dimer potential energy functions of the respective multipoint model. In addition, in Monte Carlo simulations of the pure liquid at room temperature, SSDQO reproduces radial distribution functions of the respective model. However, the Monte Carlo simulations using the SSDQO model are about three times faster than those using the three-point models and the long-range interactions decay faster for SSDQO (1/r(3) and faster) than for multipoint models (1/r). Moreover, the contribution of each moment to the energetics and other properties can be determined. Overall, the simplicity, efficiency, and accuracy of the SSDQO potential energy function make it potentially very useful for studies of aqueous solvation by computer simulations.

Journal Article↗

PubMed1999

Determination of the Effective Ground State Potential Energy Function of Ozone from High-Resolution Infrared Spectra.

The effective ground state potential energy function of the ozone molecule near the C(2v) equilibrium configuration was obtained in a least-squares fit to the largest sample of experimental, high-resolution vibration-rotation data used for this purpose so far. The fitting is based on variational calculations carried out with the extended Morse Oscillator Rigid Bender Internal Dynamics model. The potential function is expanded in Morse-type functions of the stretching variables and in cosine of the bending angle. The present calculation produces results in significantly better agreement with experiment than previous determinations of the potential energy surface, and the energies predicted with the new surface are sufficiently accurate to be useful for the assignment of new high-resolution spectra. The rms (root-mean-square) deviation of the fit of rovibrational data up to J = 5 is 0.02 cm(-1). For the set of all 60 band centers of the (16)O(3) molecule included in the Atlas of Ozone Line Parameters, the rms deviation is 0.025 cm(-1), and for all band centers determined so far from high-resolution spectra, including those recently observed and assigned in Reims corresponding to highly excited stretching and bending vibrations (v(1) + v(2) + v(3) = 6), the rms deviation is 0.1 cm(-1). The "dark states" that produce resonance perturbations in the observed bands are described with experimental accuracy up to the (v(1)v(2)v(3)) = (080) state. Extrapolation tests demonstrate the predictive power of the potential function obtained: rotational extrapolation up to J = 10 for the 11 lowest vibrational states results in an rms deviation of 0.06cm(-1). Also, vibrational energies measured by low-resolution Raman spectroscopy (which were not included in the input data for the fit) are calculated within the experimental accuracy (rms = 1.6 cm(-1)) of the experimental values up to the dissociation limit. The statistical analysis suggests that the accuracy of the equilibrium geometry and force constants of the molecule is considerably improved relative to previous determinations. The long-range behavior of the fitted potential at the dissociation limit O(3) --> O(2) + O shows very good agreement with experimental data. The new potential energy surface was used to predict the band centers of the isotopomers (17)O(3) and (18)O(3). Copyright 1999 Academic Press.

Journal Article↗

PubMed2005

Analytic potential energy functions for simulating aluminum nanoparticles.

Potential energy functions (PEFs) parametrized to bulk data are shown to perform poorly for small aluminum nanoparticles and clusters. In contrast, PEFs parametrized to a limited set of cluster and bulk data, but no nanoparticle data, perform well for nanoparticles. This validates a practical scheme for developing PEFs for nanoscale systems. Building on these findings, we optimized five PEFs by minimizing the error in the fit over a broad data set. Two of these PEFs have errors of less than or equal to 0.08 eV/atom for each of three categories of system sizes, i.e., for small clusters, for nanoparticles, and for bulk potential energies.

Journal Article↗

PubMed2026

Exploring the ecological drivers of bacteriophage diversity and functional viral potential in the skin of the axolotl Ambystoma altamirani.

Bacteriophages play important roles in shaping microbial community dynamics across diverse environments. In the amphibian skin, most microbiome studies have focused on bacteria and their interactions with the fungus Batrachochytrium dendrobatidis (Bd), leaving other microbial components, including viruses, largely unexplored. Here, we present the first characterization of the viral community in the amphibian skin microbiome, focusing on ecological drivers of bacteriophage diversity and functional potential in the axolotl Ambystoma altamirani. Using public shotgun metagenomes, we found that the viral fraction was dominated by bacteriophages of the class Caudoviricetes. Bacteriophage diversity was significantly associated with local physicochemical parameters at the time of sampling, and showed a strong positive correlation with bacterial diversity, whereas no significant associations were detected with the presence of Bd. In addition, seasonality influenced the composition and properties of bacteria-bacteriophage co-abundance networks. Functional annotation of assembled bacteriophage sequences revealed a diverse functional potential, including putative auxiliary metabolic genes, superinfection exclusion, toxin-antitoxin, and virulence factors. Overall, these findings highlight the ecological relevance of bacteriophages in amphibian skin microbiomes and underscore the need for further studies on their role in the amphibian host's health.

Animals↗

PubMed2005

S0 ring-puckering potential energy function for coumaran.

With the aid of a reported inversion splitting value, the far-infrared spectrum resulting from the ring-puckering vibration of coumaran has been reassigned and the one-dimensional potential energy function has been determined. The barrier to planarity is 155 +/- 4 cm(-1) and the dihedral angle is 25 degrees . These results agree well with the millimeter wave spectra values of 152 cm(-1) and 23 degrees , which utilized different data and a different type of potential function for the calculations. The MP2/cc-pvtz ab initio values of 238 cm(-1) and 26.5 degrees agree more poorly. If the benzene ring is assumed to remain rigid, the calculated barrier drops to 204 cm(-1). The puckering potential functions for the ring-flapping and ring-twisting vibrationally excited states were also determined and the barriers were found to be 149 and 156 cm(-1), respectively.

Journal Article↗

PubMed1995

Potential energy functions.

When energy is a critical quantity, accurate biomolecular simulations rest in substantial part on accurate potential energy functions (force fields). Improvements in methodology for determining parameters--particularly, in the systematic use of computational data obtained from quantum chemical calculations--and enhancements in functional form are leading to better potential energy functions. New calculations have been developed for water (including calculations that incorporate electronic polarizability to take account of the degree to which a molecule can be polarized), proteins, nucleic acids, carbohydrates, lipids, and general organic molecules. Most notably, two new biomolecular force fields have recently been derived and significant redeterminations of the parameters of two existing biomolecular force fields have been carried out. Some progress has also been made in incorporating polarizability into potential energy functions for molecules in general and in improving the treatment of metal-ligand interactions in systems of biomolecular interest.

Electrochemistry↗

PubMed1998

A flexible algorithm for construction of 3-D vessel networks for use in thermal modeling.

A new algorithm for the construction of artificial blood vessel networks is presented. The algorithm produces three-dimensional (3-D) geometrical representations of both arterial and venous networks. The key ingredient of the algorithm is a 3-D potential function defined in the tissue volume. This potential function controls the paths by which points are connected to existing vessels, thereby producing new vessel segments. The potential function has no physiological interpretation, but, by adjustment of parameters governing the potential, it is possible to produce networks that have physiologically meaningful geometrical properties. If desired, the veins can be generated counter current to the arteries. Furthermore, the potential function allows fashioning of the networks to the presence of bone or air cavities. The resulting networks can be used for thermal simulations of hyperthermia treatment.

Algorithms↗

PubMed2006

[Noise image segmentation based on generalized fuzzy Gibbs random field].

In order to segment the blurred image with large noise, the authors propose a new Bayesian image segmentation method based on generalized fuzzy Gibbs random field. Based on the generalized fuzzy set, the new method introduces generalized fuzzy membership into Gibbs potential function and the potential function is redefined to obtain the new segmentation model. The optimal processing is executed through iterative conditional modes (ICM). The experiment results showed that the new approach could effectively segment the degenerated images.

Algorithms↗

PubMed1975

A new approach to empirical intermolecular and conformational potential energy functions. I. Description of model and derivation of parameters.

An empirical potential energy function based on the interactions of the electrons and nuclei in molecules has been developed and tested. The potential energy of interaction is approximated by the sum of the coulombic interactions between all point charge centers (electrons and nuclei), an exponential repulsion to represent electron-electron overlap repulsion, and an R(-6) (R = distance) attraction to simulate dispersion and other attractive energies between the heavy atom fragments of the molecules. The parameters of the potential energy function have been determined from experimental gas-phase and crystal data.The results indicate that both intramolecular and intermolecular interaction energies can be treated with the same set of parameters. In comparison to other empirical interaction potentials now in use, there are fewer independent parameters, there is no need for intrinsic torsional potentials to obtain the correct rotational barriers, and there is no need for special hydrogen bonding functions to account for the directionality and energetics of hydrogen bonding.

Journal Article↗

PubMed1978

Response of delayed (K+) channels to the time-dependent clamping functions in squid giant axon. II. Descending ramps, hyperbolae, and exponentials.

Squid giant axons are voltage-clamped with decaying ramp, hyperbolic, and exponential potential functions to determine an input potential function that generates parametric current density vs. membrane potential (I-V) plots best approximating the I-V curves generated from the steady state delayed (K+) current densities at a series of step clamp potentials. The optimum potential function must produce consistent I-V plots over an extended range of decay periods. A five-millisecond step clamp at the largest depolarizing potential in the experiment insures identical initial conditions for all potential functions. Although all parametric I-V curves are sensitive to K+ accumulation in the periaxonal space, the alteration of the I-V curves due to this accumulation is minimized for the hyperbolic and exponential decay functions. The advantages of these functions for the rapid generation of I-V curves are discussed.

Animals↗

PubMed2003

The SAAP force field. A simple approach to a new all-atom protein force field by using single amino acid potential (SAAP) functions in various solvents.

A simple strategy to compose a new all-atom protein force field (named as the SAAP force field), which utilizes the single amino acid potential (SAAP) functions obtained in various solvents by ab initio molecular orbital calculation applying the isodensity polarizable continuum model (IPCM), is presented. We considered that the total energy function of a protein force field (E(TOTAL)) is divided into three components; a single amino acid potential term (E(SAAP)), an interamino acid nonbonded interaction term (E(INTER)), and a miscellaneous term (E(OTHERS)), which is ignored (or considered to be constant) at the current version of the force field. The E(INTER) term consists of electrostatic interactions (E(ES')) and van der Waals interactions (E(LJ')). Despite simplicity, the SAAP force field implicitly involves the correlation among individual terms of the Lifson's potential function within a single amino acid unit and can treat solvent effects unambiguously by choosing the SAAP function in an appropriate solvent and the dielectric constant (D) of medium. Application of the SAAP force field to the Monte Carlo simulation of For-Ala(2)-NH(2) in vacuo reasonably reproduced the results of the extensive conformational search by ab initio molecular orbital calculation. In addition, the preliminary Monte Carlo simulations for For-Gly(10)-NH(2) and For-Ala(10)-NH(2) showed reversible transitions from the extended to the pseudosecondary structures in water (D = 78.39) as well as in ether (D = 4.335). The result suggested that the new approach is efficient for fast modeling of protein structures in various environments. Decomposition analysis of the total energy function (E(TOTAL)) by using the SAAP force field suggested that conformational propensities of single amino acids (i.e., the E(SAAP) term) may play definitive roles on the topologies of protein secondary structures.

Alanine↗

PubMed2003

Packing helices in proteins by global optimization of a potential energy function.

An efficient method has been developed for packing alpha-helices in proteins. It treats alpha-helices as rigid bodies and uses a simplified Lennard-Jones potential with Miyazawa-Jernigan contact-energy parameters to describe the interactions between the alpha-helical elements in this coarse-grained system. Global conformational searches to generate packing arrangements rapidly are carried out with a Monte Carlo-with-minimization type of approach. The results for 42 proteins show that the approach reproduces native-like folds of alpha-helical proteins as low-energy local minima of this highly simplified potential function.

Protein Structure, Secondary↗