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Mean Force (mean + force)
Selected AbstractsPropagation of Tears in Pericardium From Young Bulls: Influence of the SutureARTIFICIAL ORGANS, Issue 3 2010José María García Páez Abstract The tearing of the collagen fibers of biological materials utilized in implants or bioprostheses is an important, and sometimes early cause of the failure of these devices. We studied the force necessary to propagate a tear in a biomaterial, pericardium from young bulls, and the influence of the suture. An Elmendorf pendulum capable of measuring the force necessary to tear a given length of tissue was employed. We analyzed 112 trials (70%) that proved valid after achieving the homogeneity of the samples according to their thickness, thus making the results comparable. Mean forces ranging between 19.87 and 150 N were required to propagate tears measuring from 0.25 to 2.0 cm. In the samples with a 1-cm-long suture, sewn using an edge-to-edge technique, the propagation of the tear required a mean force of 15.75 N when the suture was made of nylon and 28.73 N when Prolene was utilized. When these results were compared with the mean recorded in an unsutured control series (56.76 N), the loss of resistance was significant in both sutured series (P = 0.000 and P = 0.011, respectively). Finally, the equation that relates the force (y) with the length of the tear made in unsutured tissue (x) was also obtained: y = 58.14 + 9.62x2 (R2 = 0.924). The force necessary to produce a microtear, thus estimated, can be utilized as a parameter for comparison. [source] Root canal preparation with FlexMaster: asessment of torque and force in relation to canal anatomyINTERNATIONAL ENDODONTIC JOURNAL, Issue 12 2003W. Hübscher Abstract Aim, To investigate physical parameters of FlexMaster nickel-titanium instruments while preparing curved canals in maxillary molars in vitro. Methodology, A torque-testing platform was used to prepare root canals in 11 extracted human maxillary molars with FlexMaster rotary instruments. Peak torque and force was registered along with numbers of rotations required to shape the canals. Canals were divided into ,wide' and ,constricted' groups depending on canal volumes assessed by microcomputed tomography. Resistance to cyclic fatigue was also tested. Mean scores for each instrument type were calculated and statistically compared using anova and Scheffé post hoc tests. Results, Mean torque varied between 0.1 ± 0.1 and 0.8 ± 0.5 N cm while mean force ranged from 4.2 ± 2.0 to 7.3 ± 3.5 N. Mean numbers of rotations totalled up to 18. All three variables registered showed weak correlations to preoperative canal volumes (P < 0.01) and differed significantly between ,wide' and ,constricted' canals (P < 0.001). Numbers of rotations to fracture in a cyclic fatigue test were between 348 and 1362. Conclusion, FlexMaster instruments generated low torque scores and were highly resistant to cyclic fatigue, whilst three instruments fractured in extremely narrow canals. Consequently, more research is required to limit fracture incidence and to optimize instrumentation guidelines. [source] Models for the adsorption and self-assembly of ethanol and 1-decanethiol on Au(111) surfaces.INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 2 2010A comparative study by computer simulation Abstract Results from computer simulations, based on different models to study theadsorption and self-assembly of the ethanol and 1-decanethiol on gold surfaces, Au(111), are presented. Canonical ensemble Monte Carlo simulations were performed at 298 K using two different force fields. One from DFT calculations, where the gold electrode has an explicit structure (corrugated electrode), and the other representing an electrode, in which the structure is taken into account on an average way (flat electrode). The behavior of the ethanol adsorption on gold surfaces, with and without the 1-decanethiol presence, is analyzed. The introduction of molecular flexibility is also discussed. The relative surface density for the ethanol oxygen, adsorbed on gold, and the density profiles, in different conditions, show that the structure of the surface has a fundamental role on the way the adsorption takes place, not only on the preferential adsorption sites of the surface but also on the ethanol distribution over the electrodes. Potentials of mean force have also been calculated for the two surface models, giving the free energy barriers to the 1-decanethiol crossing of the solvent adsorption layers. The average tilt angle, obtained with a single thiol molecule in the simulation box, presents the values: ,26° for the rigid molecule model and 74° ± 18° for the flexible one. These differences are analyzed. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010 [source] Cover Picture (Isr. J. Chem.ISRAEL JOURNAL OF CHEMISTRY, Issue 3-4 20093-4/2009) Structures of E. coli Adenylate Kinase in the open (4AKE) and closed (1ANK) states with cyanine dye derivatives modeled onto residues 128 and 194 for single-molecule Forster resonance energy transfer (FRET) studies of lid dynamics. The bottom of the figure displays a sample distance-vs.-time trajectory displaying spontaneous lid open,closed transitions on the millisecond timescale. The time-dependent potential of mean force along the lid coordinate measured by single-molecule FRET is also displayed. Further information can be found in Hanson et al., Proc. Natl. Acad. Sci. USA, 104, 18055,18060 (2007). With thanks to Haw Yang. [source] Novel free energy calculations to explore mechanisms and energetics of membrane protein structure and functionJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 11 2009Wonpil Im Abstract Understanding the delicate balance of forces governing helix or ,-hairpin interactions in transmembrane (TM) proteins is central to understanding membrane structure and function. These membrane constituent interactions play an essential role in determining the structure and function of membrane proteins, and protein interactions in membranes, and thus form the basis for many vital processes, including TM signaling, transport of ions and small molecules, energy transduction, and cell,cell recognition. "Why does a single-pass TM helix or ,-hairpin have specific orientations in membranes?" "What are the roles of hydrogen bonds, close packing, and helix-lipid or ,-hairpin-lipid interactions in helix or ,-hairpin associations in membranes?" "How do these interactions change the membrane structures?" "How do TM domains transmit signals across membranes?" These are important membrane biophysical questions that can be addressed by understanding the delicate balance of forces governing helix or ,-hairpin interactions with/in membranes. In this work, we summarize a series of helix/,-hairpin restraint potentials that we have developed, and illustrate their applications that begin to address the complicated energetics and molecular mechanisms of these interactions at the atomic level by calculating the potentials of mean force (PMFs) along reaction coordinates relevant to helix/,-hairpin motions in membranes and dissecting the total PMF into the contributions arising from physically important microscopic forces. © 2009 Wiley Periodicals, Inc. J Comput Chem 2009 [source] Strategies to model the near-solute solvent molecular density/polarizationJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 5 2009Pei-Kun Yang Abstract The solvent molecular distribution significantly affects the behavior of the solute molecules and is thus important in studying many biological phenomena. It can be described by the solvent molecular density distribution, g, and the solvent electric dipole distribution, p. The g and p can be computed directly by counting the number of solvent molecules/dipoles in a microscopic volume centered at r during a simulation or indirectly from the mean force F and electrostatic field E acting on the solvent molecule at r, respectively. However, it is not clear how the g and p derived from simulations depend on the solvent molecular center or the solute charge and if the gF and pE computed from the mean force and electric field acting on the solvent molecule, respectively, could reproduce the corresponding g and p obtained by direct counting. Hence, we have computed g,p,gF, and pE using different water centers from simulations of a solute atom of varying charge solvated in TIP3P water. The results show that gF and pE can reproduce the g and p obtained using a given count center. This implies that rather than solving the coordinates of each water molecule by MD simulations, the distribution of water molecules could be indirectly obtained from analytical formulas for the mean force F and electrostatic field E acting on the solvent molecule at r. Furthermore, the dependence of the g and p distributions on the solute charge revealed provides an estimate of the change in g and p surrounding a biomolecule upon a change in its conformation. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009 [source] Prediction of integral membrane protein type by collocated hydrophobic amino acid pairsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 1 2009Ke Chen Abstract A computational model, IMP-TYPE, is proposed for the classification of five types of integral membrane proteins from protein sequence. The proposed model aims not only at providing accurate predictions but most importantly it incorporates interesting and transparent biological patterns. When contrasted with the best-performing existing models, IMP-TYPE reduces the error rates of these methods by 19 and 34% for two out-of-sample tests performed on benchmark datasets. Our empirical evaluations also show that the proposed method provides even bigger improvements, i.e., 29 and 45% error rate reductions, when predictions are performed for sequences that share low (40%) identity with sequences from the training dataset. We also show that IMP-TYPE can be used in a standalone mode, i.e., it duplicates significant majority of correct predictions provided by other leading methods, while providing additional correct predictions which are incorrectly classified by the other methods. Our method computes predictions using a Support Vector Machine classifier that takes feature-based encoded sequence as its input. The input feature set includes hydrophobic AA pairs, which were selected by utilizing a consensus of three feature selection algorithms. The hydrophobic residues that build up the AA pairs used by our method are shown to be associated with the formation of transmembrane helices in a few recent studies concerning integral membrane proteins. Our study also indicates that Met and Phe display a certain degree of hydrophobicity, which may be more crucial than their polarity or aromaticity when they occur in the transmembrane segments. This conclusion is supported by a recent study on potential of mean force for membrane protein folding and a study of scales for membrane propensity of amino acids. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009 [source] The parameterization and validation of generalized born models using the pairwise descreening approximationJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 14 2004Julien Michel Abstract Generalized Born Surface Area (GBSA) models for water using the Pairwise Descreening Approximation (PDA) have been parameterized by two different methods. The first method, similar to that used in previously reported parameterizations, optimizes all parameters against the experimental free energies of hydration of organic molecules. The second method optimizes the PDA parameters to compensate only for systematic errors of the PDA. The best models are compared to Poisson,Boltzmann calculations and applied to the computation of potentials of mean force (PMFs) for the association of various molecules. PMFs present a more rigorous test of the ability of a solvation model to correctly reproduce the screening of intermolecular interactions by the solvent, than its accuracy at predicting free energies of hydration of small molecules. Models derived with the first method are sometimes shown to fail to compute accurate potentials of mean force because of large errors in the computation of Born radii, while no such difficulties are observed with the second method. Furthermore, accurate computation of the Born radii appears to be more important than good agreement with experimental free energies of solvation. We discuss the source of errors in the potentials of mean force and suggest means to reduce them. Our findings suggest that Generalized Born models that use the Pairwise Descreening Approximation and that are derived solely by unconstrained optimization of parameters against free energies of hydration should be applied to the modeling of intermolecular interactions with caution. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1760,1770, 2004 [source] Implementation of an adaptive umbrella sampling method for the calculation of multidimensional potential of mean force of chemical reactions in solutionJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 14 2003Ramkumar Rajamani Abstract We describe the implementation of an adaptive umbrella sampling method, making use of the weighted histogram analysis method, for computing multidimensional potential of mean force for chemical reaction in solution. The approach is illustrated by investigating the effect of aqueous solution on the free energy surface for the proton transfer reaction of [H3N,H,NH3]+ using a combined quantum mechanical and molecular mechanical AM1/TIP3P potential. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1775,1781, 2003 [source] Statistical thermodynamics of internal rotation in a hindering potential of mean force obtained from computer simulationsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 10 2003Vladimir Hnizdo Abstract A method of statistical estimation is applied to the problem of one-dimensional internal rotation in a hindering potential of mean force. The hindering potential, which may have a completely general shape, is expanded in a Fourier series, the coefficients of which are estimated by fitting an appropriate statistical,mechanical distribution to the random variable of internal rotation angle. The function of reduced moment of inertia of an internal rotation is averaged over the thermodynamic ensemble of atomic configurations of the molecule obtained in stochastic simulations. When quantum effects are not important, an accurate estimate of the absolute internal rotation entropy of a molecule with a single rotatable bond is obtained. When there is more than one rotatable bond, the "marginal" statistical,mechanical properties corresponding to a given internal rotational degree of freedom are educed. The method is illustrated using Monte Carlo simulations of two public health relevant halocarbon molecules, each having a single internal-rotation degree of freedom, and a molecular dynamics simulation of an immunologically relevant polypeptide, in which several dihedral angles are analyzed. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1172,1183, 2003 [source] Structural basis for preferential binding of non- ortho -substituted polychlorinated biphenyls by the monoclonal antibody S2B1JOURNAL OF MOLECULAR RECOGNITION, Issue 4 2005Jean-Luc Pellequer Abstract Polychlorinated biphenyls (PCBs) are a family of 209 isomers (congeners) with a wide range of toxic effects. In structural terms, they are of two types: those with and those without chlorines at the ortho positions (2, 2,, 6 and 6,). Only 20 congeners have no ortho chlorines. Three of these are bound by the aryl hydrocarbon receptor and are one to four orders of magnitude more toxic than all others. A monoclonal antibody, S2B1, and its recombinant Fab have high selectivity and nanomolar binding affinities for two of the most toxic non- ortho -chlorinated PCBs, 3,4,3,,4,-tetrachlorobiphenyl and 3,4,3,,4,,5,-pentachlorobiphenyl. To investigate the basis for these properties, we built a three-dimensional structure model of the S2B1 variable fragment (Fv) based on the high-resolution crystallographic structures of antibodies 48G7 and N1G9. Two plausible conformations for the complementarity-determining region (CDR) H3 loop led to two putative PCB-binding pockets with very different shapes (models A and B). Docking studies using molecular mechanics and potentials of mean force (PMF) indicated that model B was most consistent with the selectivity observed for S2B1 in competition ELISAs. The binding site in model B had a deep, narrow pocket between VL and VH, with a slight constriction at the top that opened into a wider pocket between CDRs H1 and H3 on the antibody surface. This binding site resembles those of esterolytic antibodies that bind haptens with phenyl rings. One phenyl ring of the PCB fits into the deep pocket, and the other ring is bound in the shallower one. The bound PCB is surrounded by the side chains of TyrL91, TyrL96 and TrpH98, and it has a ,-cation interaction with ArgL46. The tight fit of the binding pocket around the ortho positions of the bound PCBs indicates that steric hindrance of ortho chlorines in the binding site, rather than induced conformational change of the PCBs, is responsible for the selectivity of S2B1. Copyright © 2005 John Wiley & Sons, Ltd. [source] The effects of partial and total interosseous membrane transection on load sharing in the cadaver forearmJOURNAL OF ORTHOPAEDIC RESEARCH, Issue 4 2001Michael F. Shepard This study was performed to examine the effects of partial and total transection of the interosseous membrane (IOM) on load transfer in the forearm. Twenty fresh frozen forearms were instrumented with custom designed load cells placed in the proximal radius and distal ulna. Simultaneous measurements of load cell forces, radial head displacement relative to the capitellum, and local tension within the central band of the IOM were made as the wrist was loaded to 134 N with the forearm at 90° of elbow flexion and in neutral pronation supination. For valgus elbow alignment (radial head contacting the capitellum), mean force carried by the distal ulna was 7.1% of the applied wrist force and mean force transferred from radius to ulna through the IOM was 4.4%. For varus elbow alignment (mean 2.0 mm gap between the radial head and capitellum), mean distal ulna force was 28% and mean IOM force was 51%. Section of the proximal and distal one-thirds of the IOM had no significant effect upon mean distal ulnar force or mean IOM force. Total IOM section significantly increased mean distal ulnar force for varus elbow alignment in all wrist positions tested. The mean level of applied wrist force necessary to close the varus gap (89 N) decreased significantly after both partial IOM section (71 N) and total IOM section (25 N). The IOM became loaded only when the radius displaced proximally relative to the ulna, closing the gap between the radius and capitellum. As the radius displaced proximally, the wrist becomes increasingly ulnar positive, which in turn leads to direct loading of the distal ulna. This shift of force to the distal ulna could present clinically as ulnar sided wrist pain or as ulnar impaction after IOM injury. © 2001 Orthopaedic Research Society. Punlished by Elsevier Science Ltd. All rights reserved. [source] Continuous peripheral nerve block catheter tip adhesion in a rat modelACTA ANAESTHESIOLOGICA SCANDINAVICA, Issue 6 2006C. C. Buckenmaier III Background:, Continuous peripheral nerve block (CPNB) has been used effectively in combat casualties from Iraq and Afghanistan to provide surgical anesthesia and extended duration analgesia during evacuation and convalescence. Little information is available concerning catheter tip tissue reaction with prolonged use. Methods:, Forty-eight male Sprague-Dawley rats were assigned (12 per group) to one of four catheter tip designs provided by Arrow International: group A, 20-gauge catheter with three side-holes and a bullet-shaped tip; group B, 19-gauge StimuCathÔ catheter with coiled omni-port end with hemispherical distal tip; group C, 19-gauge catheter with single end-hole in conducting tip; group D, 19-gauge catheter with closed conducting tip with four side-holes. Following laparotomy, a randomly assigned catheter tip was sutured to the parietal peritoneal wall with the tip extending between experimental injuries created on the abdominal wall and cecum. After 7 days in situ, the catheter tips were removed from the adhesion mass using a force gauge, and the grams of force needed for removal were recorded. Results:, The mean force ± standard deviation values were 1.09 ± 1.21 g for group A, 21.20 ± 30.15 g for group B, 0.88 ± 1.47 g for group C and 1.60 ± 2.50 g for group D. The variation of each catheter group mean force compared with that of group B was significant (P < 0.05). There was no significant difference in adhesion force between groups A, C and D. Conclusions:, These results suggest that the manufactured design of a CPNB catheter tip can contribute to the adhesion of the tip in an intense inflammatory environment. This finding may have important clinical implications for CPNB catheters left in place for extended periods of time. [source] Influence of standardized mobilization on the posteroanterior stiffness of the lumbar spine in asymptomatic subjectsPHYSIOTHERAPY RESEARCH INTERNATIONAL, Issue 3 2001Dr Garry Allison Abstract Background and Purpose Spinal mobilization is commonly used to relieve pain and assist recovery of mobility in individuals with low back pain. Fundamental to this concept is the belief that spinal mobilization will influence the mechanical properties of the symptomatic motion segment. The objective of the present study was to examine the segmental effects of a standardized mobilization procedure on the posteroanterior (PA) stiffness of the lumbar spine. Method Audio and visual feedback was used to train a physiotherapist to perform PA mobilization at a consistent load and frequency. After training, twenty-four subjects without low back pain were recruited for the intervention phase of the study. The spinal posteroanterior mobilization (SPAM) apparatus was used to measure the PA stiffness of the lumbar spine at three measurement sites (L1, L3 and L5). The trained physiotherapist then applied the standardized PA mobilization technique via the L3 spinous process for two minutes. Following mobilization, PA stiffness was measured three times at the three locations. Results The physiotherapist was able to apply a standardized mobilization with a mean force of 146 N (standard deviation (SD) 8 N) at a frequency of 1.5 Hz. The first trial on each assessment demonstrated a pre-condition effect. Two minutes' PA mobilization resulted in no significant change in the PA stiffness of the lumbar spine at the level to which the mobilization was applied, or at the L1 and L5 segments. The 95% confidence intervals (CI) of the difference in PA stiffness before and after testing included zero at each measurement site. Conclusions Clinicians should pre-condition the spine when assessing PA stiffness both before and after interventions. A standardized mobilization of 150 N at 1.5 Hz for two minutes had no segmental effect on spinal PA stiffness. Subsequent studies need to consider other mechanisms that may contribute to the changes that occur after PA spinal mobilization. Copyright © 2001 Whurr Publishers Ltd. [source] Quantitative prediction of protein,protein binding affinity with a potential of mean force considering volume correctionPROTEIN SCIENCE, Issue 12 2009Yu Su Abstract Quantitative prediction of protein,protein binding affinity is essential for understanding protein,protein interactions. In this article, an atomic level potential of mean force (PMF) considering volume correction is presented for the prediction of protein,protein binding affinity. The potential is obtained by statistically analyzing X-ray structures of protein,protein complexes in the Protein Data Bank. This approach circumvents the complicated steps of the volume correction process and is very easy to implement in practice. It can obtain more reasonable pair potential compared with traditional PMF and shows a classic picture of nonbonded atom pair interaction as Lennard-Jones potential. To evaluate the prediction ability for protein,protein binding affinity, six test sets are examined. Sets 1,5 were used as test set in five published studies, respectively, and set 6 was the union set of sets 1,5, with a total of 86 protein,protein complexes. The correlation coefficient (R) and standard deviation (SD) of fitting predicted affinity to experimental data were calculated to compare the performance of ours with that in literature. Our predictions on sets 1,5 were as good as the best prediction reported in the published studies, and for union set 6, R = 0.76, SD = 2.24 kcal/mol. Furthermore, we found that the volume correction can significantly improve the prediction ability. This approach can also promote the research on docking and protein structure prediction. [source] Propagation of Tears in Pericardium From Young Bulls: Influence of the SutureARTIFICIAL ORGANS, Issue 3 2010José María García Páez Abstract The tearing of the collagen fibers of biological materials utilized in implants or bioprostheses is an important, and sometimes early cause of the failure of these devices. We studied the force necessary to propagate a tear in a biomaterial, pericardium from young bulls, and the influence of the suture. An Elmendorf pendulum capable of measuring the force necessary to tear a given length of tissue was employed. We analyzed 112 trials (70%) that proved valid after achieving the homogeneity of the samples according to their thickness, thus making the results comparable. Mean forces ranging between 19.87 and 150 N were required to propagate tears measuring from 0.25 to 2.0 cm. In the samples with a 1-cm-long suture, sewn using an edge-to-edge technique, the propagation of the tear required a mean force of 15.75 N when the suture was made of nylon and 28.73 N when Prolene was utilized. When these results were compared with the mean recorded in an unsutured control series (56.76 N), the loss of resistance was significant in both sutured series (P = 0.000 and P = 0.011, respectively). Finally, the equation that relates the force (y) with the length of the tear made in unsutured tissue (x) was also obtained: y = 58.14 + 9.62x2 (R2 = 0.924). The force necessary to produce a microtear, thus estimated, can be utilized as a parameter for comparison. [source] An in vitro assessment of the strength of porcelain veneers dependent on tooth preparationJOURNAL OF ORAL REHABILITATION, Issue 12 2000P. Hahn The treatment of teeth using veneer restorations combines aesthetic and functional improvements with a low destructive technique. Different kinds of tooth preparation techniques are described in the literature for this kind of restoration. This in vitro study aimed to examine the influence of the incisal preparation on the loadability of teeth restored with porcelain laminate veneers. Thirty-six selected mandibular incisors were randomly assigned to three groups with 12 teeth per group. In the first group, only the facial surface was prepared. In the second group, the preparation included a rounded incisal edge and a distinct chamfer lingually. The third group served as an unprepared control. Empress® veneers were then fabricated and cemented with a low viscous luting composite material. After 120 days storage in Ringer's solution, the specimens were loaded incisally to the point of failure. Statistical analysis of the results showed significant differences between the series (P=0·0103). Group 2 (with preparation of the incisal edge) exhibited the lowest fracture resistance (466±99 N) (N, mean forces). When prepared only facially, the teeth restored with Empress® veneers reached the strength of unprepared teeth. Compared with the biting force described for incisors in the literature, the in vitro loadability reached in this investigation seems to jusitify the clinical use of both preparation designs tested. [source] | |||||||||||||