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At least 631 records · Page 35Linked to original sources
PubMed2006

Revisiting the geometry of nd10 (n+1)s0 [M(H2O)]p+ complexes using four-component relativistic DFT calculations and scalar relativistic correlated CSOV energy decompositions (M(p+) = Cu+, Zn2+, Ag+, Cd2+, Au+, Hg2+).

Hartree-Fock and DFT (B3LYP) nonrelativistic (scalar relativistic pseudopotentials for the metallic cation) and relativistic (molecular four-component approach coupled to an all-electron basis set) calculations are performed on a series of six nd10 (n+1)s0 [M(H2O)]p+ complexes to investigate their geometry, either planar C2v or nonplanar C(s). These complexes are, formally, entities originating from the complexation of a water molecule to a metallic cation: in the present study, no internal reorganization has been found, which ensures that the complexes can be regarded as a water molecule interacting with a metallic cation. For [Au(H2O)]+ and [Hg(H2O)]2+, it is observed that both electronic correlation and relativistic effects are required to recover the C(s) structures predicted by the four-component relativistic all-electron DFT calculations. However, including the zero-point energy corrections makes these shallow C(s) minima vanish and the systems become floppy. In all other systems, namely [Cu(H2O)]+, [Zn(H2O)]2+, [Ag(H2O)]+, and [Cd(H2O)]2+, all calculations predict a C2v geometry arising from especially flat potential energy surfaces related to the out-of-plane wagging vibration mode. In all cases, our computations point to the quasi-perfect transferability of the atomic pseudopotentials considered toward the molecular species investigated. A rationalization of the shape of the wagging potential energy surfaces (i.e., single well vs. double well) is proposed based on the Constrained Space Orbital Variation decompositions of the complexation energies. Any way of stabilizing the lowest unoccupied orbital of the metallic cation is expected to favor charge-transfer (from the highest occupied orbital(s) of the water ligand), covalence, and, consequently, C(s) structures. The CSOV complexation energy decompositions unambiguously reveal that such stabilizations are achieved by means of relativistic effects for [Au(H2O)]+, and, to a lesser extent, for [Hg(H2O)]2+. Such analyses allow to numerically quantify the rule of thumb known for Au+ which, once again, appears as a better archetype of a relativistic cation than Hg2+. This observation is reinforced due to the especially high contribution of the nonadditive correlation/relativity terms to the total complexation energy of [Au(H2O)]+.

Cadmium↗
PubMed1991

The electrostatic potential of Escherichia coli dihydrofolate reductase.

Escherichia coli dihydrofolate reductase (DHFR) carries a net charge of -10 electrons yet it binds ligands with net charges of -4 (NADPH) and -2 (folate or dihydrofolate). Evaluation and analysis of the electrostatic potential of the enzyme give insight as to how this is accomplished. The results show that the enzyme is covered by an overall negative potential (as expected) except for the ligand binding sites, which are located inside "pockets" of positive potential that enable the enzyme to bind the negatively charged ligands. The electrostatic potential can be related to the asymmetric distribution of charged residues in the enzyme. The asymmetric charge distribution, along with the dielectric boundary that occurs at the solvent-protein interface, is analogous to the situation occurring in superoxide dismutase. Thus DHFR is another case where the shape of the active site focuses electric fields out into solution. The positive electrostatic potential at the entrance of the ligand binding site in E. coli DHFR is shown to be a direct consequence of the presence of three positively charged residues at positions 32, 52, and 57--residues which have also been shown recently to contribute significantly to electronic polarization of the ligand folate. The latter has been postulated to be involved in the catalytic process. A similar structural motif of three positively charged amino acids that gives rise to a positive potential at the entrance to the active site is also found in DHFR from chicken liver, and is suggested to be a common feature in DHFRs from many species. It is noted that, although the net charges of DHFRs from different species vary from +3 to -10, the enzymes are able to bind the same negatively charged ligands, and perform the same catalytic function.

Amino Acids↗
PubMed1994

An improved pair potential to recognize native protein folds.

We present a novel method to improve a simple pair potential of mean force, derived from experimentally determined protein structures, in such a way that it recognizes native protein folds with high reliability. This improvement is based on the use of mutation data matrices to overcome difficulties arising from the poor statistics of small sample sizes. A set of 167 protein chains taken from the Brookhaven Protein Structure Data Base, selected from high-resolution structures and avoiding homologous proteins, is used for generation of the potential set. The potential describes interresidue pair energies depending on distance and sequential separation, and is calculated using the Boltzmann equation. Its performance is evaluated by jackknife tests that try to identify the native fold for a given sequence among a large number of possible threadings on all structures in the set without allowing for gaps. Up to 94% of the protein chains are correctly assigned to their native folds, so that all proper single-chain domains are recognized.

Computer Simulation↗
PubMed1994

Molecular dynamics simulation of the docking of substrates to proteins.

A simple method is described to perform docking of substrates to proteins or probes to receptor molecules by a modification of molecular dynamics simulations. The method consists of a separation of the center-of-mass motion of the substrate from its internal and rotational motions, and a separate coupling to different thermal baths for both types of motion of the substrate and for the motion of the receptor. Thus the temperatures and the time constants of coupling to the baths can be arbitrarily varied for these three types of motion, allowing either a frozen or a flexible receptor and allowing control of search rate without disturbance of internal structure. In addition, an extra repulsive term between substrate and protein was applied to smooth the interaction. The method was applied to a model substrate docking onto a model surface, and to the docking of phosphocholine onto immunoglobulin McPC603, in both cases with a frozen receptor. Using translational temperatures of the substrate in the range of 1300-1700 K and room temperature for the internal degrees of freedom of the substrate, an efficient nontrapping exploratory search ("helicopter view") is obtained which visits the correct binding sites. Low energy conformations can then be further investigated by separate search or by dynamic simulated annealing. In both cases the correct minima were identified. The possibility to work with flexible receptors is discussed.

Antibodies↗
PubMed1995

Automatic identification of discrete substates in proteins: singular value decomposition analysis of time-averaged crystallographic refinements.

The singular value decomposition (SVD) provides a method for decomposing a molecular dynamics trajectory into fundamental modes of atomic motion. The right singular vectors are projections of the protein conformations onto these modes showing the protein motion in a generalized low-dimensional basis. Statistical analysis of the right singular vectors can be used to classify discrete configurational substates in the protein. The configuration space portraits formed from the right singular vectors can also be used to visualize complex high-dimensional motion and to examine the extent of configuration space sampling by the simulation.

Computer Simulation↗
PubMed1988

Confidence interval estimation of a rate and the choice of sample size.

The problem of estimating a rate or proportion is considered. Four methods for constructing an approximate confidence interval are discussed and compared via a simulation study. The most accurate method is found. Also, for each method a sharp upper bound (dependent only on the sample size) is given for the length of the confidence interval. By choosing an appropriate sample size this bound enables the practitioner to achieve a prespecified maximum length for the confidence interval without knowing the population rate. The striking result is that the most accurate method has the smallest bound, thus requiring the least sample units.

Computer Simulation↗
PubMed2001

Ants and agents: a process algebra approach to modelling ant colony behaviour.

Process algebras are widely used in the analysis of distributed computer systems. They allow formal reasoning about how the various components of a system contribute to its overall behaviour. In this paper we show how process algebras can be usefully applied to understanding social insect biology, in particular to studying the relationship between algorithmic behaviour of individual insects and the dynamical behaviour of their colony. We argue that process algebras provide a useful formalism for understanding this relationship, since they combine computer simulation, Markov chain analysis and mean-field methods of analysis. Indeed, process algebras can provide a framework for relating these three methods of analysis to each other and to experiments. We illustrate our approach with a series of graded examples of modelling activity in ant colonies.

Animals↗
PubMed1991

Molecular structure matching by simulated annealing. III. The incorporation of null correspondences into the matching problem.

This paper extends an application of the method of simulated annealing for molecular matching so that the best common subsets of atom positions can be identified. Null correspondences are introduced into the difference distance matrix to enable poorly matched positions to be ignored in minimizing the objective function. The efficiency of the algorithm in finding correct subsets is rigorously tested.

Algorithms↗
PubMed1992

Reversible metabolism of vitamin K-vitamin K epoxide: modeling considerations and limitations.

Due to the cyclical natural of the vitamin K-vitamin K epoxide system, a two-compartment reversible metabolism model was used to describe this interconversion. In attempting to apply this model to the vitamin K-vitamin K epoxide cycle using literature data from dogs, interconversion and elimination clearances were obtained which are not physiologic. Consequently, the assumptions of the model were reexamined with respect to their validity. One critical assumption of the two-compartment model for interconversion is that it can only be applied in the absence of flow limitations. To determine what effect flow limitations may exert on the vitamin K and vitamin K epoxide apparent blood clearances, a model separating the liver from the blood compartment was proposed assuming the interconversion and metabolism of vitamin K and its epoxide occurred only within the liver. Simulated data suggested that if the reversible metabolic clearance values exceeded the distribution clearance terms, all the apparent clearances calculated using blood concentration-time data were in error. It is suggested that a two-compartment interconversion model might be too simplistic for the vitamin K-vitamin K epoxide cycle where the reversible metabolism is efficient and the distributional clearance may be rate limiting.

Animals↗
PubMed2001

Models of central pattern generators for quadruped locomotion. I. Primary gaits.

In this paper we continue the analysis of a network of symmetrically coupled cells modeling central pattern generators for quadruped locomotion proposed by Golubitsky, Stewart, Buono, and Collins. By a cell we mean a system of ordinary differential equations and by a coupled cell system we mean a network of identical cells with coupling terms. We have three main results in this paper. First, we show that the proposed network is the simplest one modeling the common quadruped gaits of walk, trot, and pace. In doing so we prove a general theorem classifying spatio-temporal symmetries of periodic solutions to equivariant systems of differential equations. We also specialize this theorem to coupled cell systems. Second, this paper focuses on primary gaits; that is, gaits that are modeled by output signals from the central pattern generator where each cell emits the same waveform along with exact phase shifts between cells. Our previous work showed that the network is capable of producing six primary gaits. Here, we show that under mild assumptions on the cells and the coupling of the network, primary gaits can be produced from Hopf bifurcation by varying only coupling strengths of the network. Third, we discuss the stability of primary gaits and exhibit these solutions by performing numerical simulations using the dimensionless Morris-Lecar equations for the cell dynamics.

Animals↗
PubMed2001

Models of central pattern generators for quadruped locomotion. II. Secondary gaits.

We continue the analysis of the network of symmetrically coupled cells modeling central pattern generators (CPG) for quadruped locomotion proposed by Golubitsky, Stewart, Buono and Collins by studying secondary gaits. Secondary gaits are modeled by output signals from the CPG where each cell emits one of two different output signals along with exact phase shifts. Examples of secondary gaits are transverse gallop, rotary gallop, and canter. We classify secondary gaits that bifurcate when the Poincaré map of a primary gait has a real eigenvalue crossing the unit circle. In particular, we show that periodic solutions modeling transverse gallop and rotary gallop bifurcate from primary gaits. Moreover, we find gaits from period-doubling bifurcations and analyze plausible footfall patterns. Numerical simulations are performed using the Morris-Lecar equations as cell dynamics.

Animals↗
PubMed2001

Structured population on two patches: modeling dispersal and delay.

We derive from the age-structured model a system of delay differential equations to describe the interaction of spatial dispersal (over two patches) and time delay (arising from the maturation period). Our model analysis shows that varying the immature death rate can alter the behavior of the homogeneous equilibria, leading to transient oscillations around an intermediate equilibrium and complicated dynamics (in the form of the coexistence of possibly stable synchronized periodic oscillations and unstable phase-locked oscillations) near the largest equilibrium.

Age Factors↗
PubMed2004

Ultrasound-estimated bladder weight in healthy children.

Bladder weight in healthy children was determined ultrasonographically using a modified formula that takes into account the different shapes of the urinary bladder. Ultrasonographic examination of the bladder was performed on 92 healthy children (56 boys, 36 girls) with a 5-MHz transducer. Bladders were categorized into five groups according to shape, and three bladder diameters were measured. Ultrasound-estimated bladder weight (UEBW) was calculated according to the formula modified for bladder shape. Correction coefficients were used: 0.55 for round shape, 0.79 for ellipsoid, 0.92 for cuboid, 0.62 for triangular, and 0.78 for undefined shape. Twenty-three children had a round bladder (25%), 22 cuboid (24%), 21 ellipsoid (22.8%), 25 triangular (27.2%), and 1 child had an undefined bladder shape. Using linear regression analysis, a formula was derived for the calculation of normal values of the UEBW by age: UEBW (in grams) = A x 0.995 + 8.405 ( A=age in years). For simplicity in clinical use, the formula was modified to UEBW= A + 8.4. A statistically significant correlation was observed between UEBW and age ( r=0.78, p<0.05). UEBW correlates significantly with children's age. This simple formula is proposed for noninvasive calculation of normal UEBW by age that may be used for the objective and quantitative assessment of the degree of bladder wall hypertrophy. Further studies are needed to evaluate the potential of this method in the detection of pathological bladder conditions.

Adolescent↗
PubMed1988

Analysis of chromium-51 release assay data using personal computer spreadsheet software.

The Chromium-51 release assay is a widely used technique to assess the lysis of labeled target cells in vitro. We have developed a simple technique to analyze data from Chromium-51 release assays using the widely available LOTUS 1-2-3 spreadsheet software. This package calculates percentage specific cytotoxicity and lytic units by linear regression. It uses all data points to compute the linear regression and can determine if there is a statistically significant difference between two lysis curves. The system is simple to use and easily modified, since its implementation requires neither knowledge of computer programming nor custom designed software. This package can help save considerable time when analyzing data from Chromium-51 release assays.

Chromium Radioisotopes↗
PubMed1989

Three-dimensional reconstruction of human limbs from tomographic views.

The recently developed medical imaging technique of tomography can be used with amazing success to learn about the interior of a human body. Each tomograph, however, is limited to only one section of the specific human limb. A series of tomographs taken at irregular intervals and various angles would provide three-dimensional information of the interior of the limb. Currently available 3-D surface display algorithms have limitations, particularly when applied to clinically important image data requiring fast and flexible interactive analysis. In addition to the problem of computation time is the cost of specialized hardware. A new algorithm has been designed for use with three-dimensional medical images which attempts to overcome these limitations. A computer graphics system is described which reconstructs three-dimensional images from tomographic sectional data. This 3-D surface algorithm can be exploited in planning reconstructive bone surgery. An example which illustrates the versatility and speed of the new algorithm is presented.

Algorithms↗
PubMed1990

Determination of first and second derivatives of progress curves in the case of unknown experimental error.

The first and second derivatives of progress curves are obtained from the cubic spline function. The new approach is based on a development of the splining quality test which was used for estimating the precision of the splining. The proposed method is used on a computer with a FORTRAN 77 program. The method may also be applied for an approximate estimation of experimental error.

Computer Simulation↗
PubMed1987

On the solution of equations for feel-better hemodialysis.

In this paper, a scheme for "feel better" or optimal hemodialysis (OPTHD) based on a two-compartmental model has been proposed. Contrary to the conventional constant blood flow dialysis (CVTHD), this scheme suggests that the blood flow rate should vary in stages in order to avoid or minimize the disequilibrium syndromes during dialysis. A set of equations for computing the intracellular and extracellular solute concentrations during the OPTHD operation is developed and the computed results are illustrated. Comparing to the CVTHD, the OPTHD has the advantages of operating at a lower and smoother solute concentration difference between compartments for the same length of dialysis time, or it may achieve the same specific degree of blood cleansing within a shorter period of dialysis time.

Computer Simulation↗