bluuebunny/crossref_metadata_2025_split huggingface dataset:
Recent advances in polymer molecular dynamics simulation and data analysis
Authors: Tuzun Robert E. , Noid Donald W. , Sumpter Bobby G. , Wozny Christopher E. 
Published: April 2003

AbstractSignificant advances in molecular simulation methodology over the past decade have greatly reduced the traditional size‐timescale bottleneck in molecular dynamics calculations. The development of the geometric statement function method allows for systems up to several hundred thousand atoms to be simulated for up to several nanoseconds in reasonable times on standard workstations. For constant energy simulations, the use of symplectic integrators ensures accurate dynamics, even at long simulation times, without velocity or other artificial rescaling schemes. Finally, new methods of frequency estimation allow for accurate vibrational mode frequency calculations even in the presence of chaotic motion on time scales twenty times shorter than the standard fast Fourier transform, with an additional improvement in the sensitivity of the results when initial dynamics conditions are carefully chosen.
Local relaxation of polymers in dense media: Cooperative kinematics theory and applications
Authors: Bahar Ivet 
Published: April 2003

AbstractCooperative kinematics (CK) theory and its recent applications are presented. CK theory has been developed as an efficient approach for predicting the mechanism of segmental relaxation processes in bulk polymers. The theory aims at determining the most probable changes in atomic coordinates, occurring collectively in response to a given, external or localized, structural perturbation. The basic postulate is the minimization of the energy change involved in the overall conformational motion, which naturally yields the optimal pathway of cooperative relaxation. Attention has been confined here to the collective motions accompanying the rotational transitions of backbone bonds in polyethylene (PE) and polybutadiene (PB). The strong dependence of the mechanism of motions on the geometry of the repeat unit and on chain connectivity is emphasized. The differences in the types of correlated transitions operating in different structures, the effective conformational energy changes triggered by bond rotational jumps, and the correlation lengths for particular bond isomerizations are analyzed. The reorientations of CH bond vectors in cis‐ and trans‐PB are also examined to explain the shorter correlation time of cis units, compared to trans, detected by NMR. A good agreement between various CK predictions and results from molecular dynamics (MD) simulations is obtained. The fact that CK calculations are at least two orders of magnitude faster than MD simulations invites attention to the utility of the CK method as an efficient tool for elucidating the pathway of motion in complex systems.
Atomistic simulations of phenoxy ring flips in the glassy region of a semicrystalline polyimide
Authors: Natarajan Upendra , Mattice Wayne L. 
Published: April 2003

AbstractA quasi‐static atomistic simulation methodology is used to study the 180° (π) flip motion of phenoxy rings in the amorphous glass of a semicrystalline polyimide. The π‐flip is carried out for the rings in various local microenvironments in the polymer. Results show that the activation energy distribution for the flip covers a broad range of values. The energetics, short and long scale matrix movements, and the interrelation between cooperativity and polymer structure are also studied. The results are in qualitative agreement with previous simulation and experimental work on other glassy polymers such as bisphenol‐A polycarbonate and polystyrene. The nature of the movement of the amorphous matrix, in response to the ring flip, is far reaching with greater atomic displacements closer to the phenoxy ring. Intermolecular van der Waals and electrostatic interactions contribute significantly to the energy changes associated with the ring flip. Cooperativity is observed for torsion angles along the repeat unit containing the flipped ring. The mean value of the activation energy compares reasonably well to the experimental value for the flip that has been observed previously through solid‐state NMR experiments.
Liquid‐crystalline ordering in solutions of polyelectrolytes
Authors: Nyrkova Irina A. , Shusharina Nadezhda P. , Khokhlov Alexei R. 
Published: April 2003

AbstractThe isotropic‐nematic phase transition in solutions of stiff‐chain polyelectrolytes is considered on the basis of the Onsager approach for the limiting cases of charged rods and persistent macrolecules. We plotted a full family of phase diagrams for orientational transitions in solutions of polyelectrolytes with any charge density as a function of the low‐molecular‐weight salt concentration. It is shown that charging of macromolecules can lead not only to the renormalization of the chain diameter (discussed by Onsager) or to the twisting effect (predicted by Odijk et al.), but in some cases also to a variety of other regimes, including transitions with very narrow phase separation regions, or with a second orientational transition to a highly oriented nematic phase upon the increase of polymer concentration.
Polymer‐mode‐coupling theory of the slow dynamics of entangled macromolecular fluids
Authors: Schweizer Kenneth S. , Fuchs Matthias , Szamel G. , Guenza Marina , Tang Hai 
Published: April 2003

AbstractA microscopic statistical dynamical theory of the slow dynamics of entangled macromolecular fluids has been formulated at the level of effective generalized Langevin equations‐of‐motion of a tagged polymer. A novel macromolecular version of mode‐coupling theory is employed to approximately capture the cooperative motions of entangled polymers induced by the long range, self‐similiar interchain correlations. Polymer integral equation methods are used to determine the required equilibrium structural input. Entanglements arise due to time and space correlations of the excluded volume forces exerted by the surrounding matrix on a tagged macromolecule. A spatially resolved description of entanglement constraint amplitudes relates the fluctuating forces to fluid structure. Constraint relaxation proceeds via three parallel processes: probe center‐of‐mass translation and shape fluctuations, and collective matrix relaxation. Asymptotic scaling law predictions for the molecular weight and concentration dependences of transport coefficients and relaxation times of chain polymer solutions and melts are in qualitative agreement with the phenomenological reptation theory. Predictions for finite frequency properties such as anomalous diffusion, and shear stress and dielectric relaxation, are derived. Enhanced, power law dissipation for properties controlled by conformational relaxation is predicted, with the corresponding frequency scaling exponents in good agreement with experiments but differing from reptation behavior. For experimentally accessible chain lengths strong finite size corrections for the transport coefficients arise due to entanglement constraint porosity and constraint release. Successful quantitative applications to many experimental data sets suggest the theory provides a unified microscopic understanding of the non‐asymptotic scaling laws observed for the viscosity, dielectric relaxation time, and solution self and tracer diffusion constants. Generalization to fractal macromolecular architectures allows semi‐quantitative treatment of ring and spherical microgel melts, and tracer diffusion in gels. A theory for the influence of concentration fluctuations in entangled polymer blends and diblock copolymers has also been developed. Self‐diffusion in blends is quantitatively suppressed due to dynamical constraints associated with domain formation. Much stronger suppression of diffusion and chain relaxation is predicted near and well below the order‐disorder transition of diblock copolymer melts due to microdomain formation. New dynamical scaling laws are predicted, and quantitative agreement of the theory with recent measurements on polyolefin diblocks is demonstrated. Limitations of the theory, open problems, and possible future directions are discussed.
A monte carlo lattice study of living polymers in a confined geometry
Authors: Rouault Yannick , Milchev Andrey 
Published: April 2003

AbstractWe investigate the changes in the average chain length of a solution of semi‐flexible living polymers between two hard repulsive walls as the width of the slit, D, is varied. Two different Monte Carlo models, that of the ‘slithering snake’ and of the ‘independent monomer states’ are employed in order to simulate a polydisperse system of chain molecules confined in a gap which is either closed (with fixed total density), or open and in contact with an external reservoir. It appears that the mean chain length L in a state of equilibrium polymerization depends essentially on the geometry constraints for sufficiently small D. We find that in the case of an open slit the mean length L(D) decreases with D → 0 for flexible chains whereas it grows if the chains are sufficiently stiff. As the width of a closed gap D is decreased, in a three‐dimensional gap L(D) gradually decreases for absolutely flexible chains whereas for semi‐rigid chains it goes through a minimum at D = 2 and then grows again for D = 1. In two dimensions, in a closed strip the average chain length L(D) for both flexible and rigid macromolecules goes through a sharp minimum and then grows steeply in compliance with a predicted divergence for semi‐rigid polymers as D → 0. We attribute the observed discrepancies of our numeric experiments with some recent analytic predictions to the ordering effect of container walls on the polymer solution when chain stiffness and excluded volume interactions are taken into account.
Nonlinear least squares fitting applied to copolymerization modeling
Authors: Van Herk Alex M. , Dröge Thomas 
Published: April 2003

AbstractThe choice of the statistical method to determine the reactivity ratios in copolymerization modeling is shown to be very important. Problems in literature, as well as possible pitfalls when using available statistical programs that are in itself correct are pointed out. These problems mainly involve (knowledge of) the error structure, as the error structure determines the weighting scheme of the data points in fitting procedures. A simple, robust, statistically correct non‐linear least squares (NLLS) method is reintroduced which is based on the visualization of the sum of squares of residuals in the so‐called sum of squares space (SSS). The advantages of this method include the fact that the method is easy to understand and can be implemented in simple computer programs, as well as the fact that the method allows important aspects of the error structure to be incorporated. Furthermore, in the SSS the joint confidence interval (JCI) with exact shape can be constructed. The exact shape of the JCI is not always ellipsoidal and following a normal distribution, depending on the linearity of the fitted equations. This can sometimes lead to wrong conclusions.
Iatrogenic complications and risks of nerve conduction studies and needle electromyography
Authors: Al‐Shekhlee Amer , Shapiro Barbara E. , Preston David C. 
Published: April 2003

AbstractElectrodiagnostic procedures are routinely performed in patients with a variety of neuromuscular disorders. These studies are generally well tolerated and rarely thought to be associated with any significant side effects. However, needle electromyography is an invasive procedure and under certain situations has the potential to be associated with iatrogenic complications, including bleeding, infection, nerve injury, pneumothorax, and other local trauma. Similar complications are possible if needles are used for either stimulating or recording. In addition, like all other electrical devices and monitoring equipment connected to patients, electrodiagnostic testing carries the risk of stray leakage currents that under certain circumstances can result in electrical injury, especially in patients in the intensive care setting. Similarly, certain precautions are required during nerve conduction studies (NCS) in patients with pacemakers and other similar cardiac devices. In this review, we address the known and theoretical complications of NCS and needle electrode examination, and the possible methods to avoid such hazards. Muscle Nerve 27: 517–526, 2003
Gentamicin fails to increase dystrophin expression in dystrophin‐deficient muscle
Authors: Dunant Patrick , Walter Maggie C. , Karpati George , Lochmüller Hanns 
Published: April 2003

AbstractA recent report that aminoglycoside antibiotics restored the expression of functional dystrophin to skeletal muscles of mdx mice, a model of Duchenne muscular dystrophy (DMD), raised hopes that DMD may be treatable by a conventional drug. Subsequently, several human trials were initiated for evaluating gentamicin therapy in selected DMD patients. An increase of dystrophin expression was not detected in one human trial that was fully reported. Here, we report that we were unable to replicate previously published beneficial results by gentamicin treatment in the mdx mouse. Therefore, we believe that additional animal experimentation is required to further evaluate the possibility of in vivo aminoglycoside therapy of DMD. Muscle Nerve 27: 624–627, 2003
Clinical and genetic analysis of CMT1B in a Nigerian family
Authors: Kakar R. , Ma W. , Dutra A. , Seltzer W.K. , Grewal R.P. 
Published: April 2003

AbstractWe report a Nigerian family with a late‐onset autosomal dominant neuropathy consistent with Charcot‐Marie‐Tooth disease. Electrophysiological examination of the index patient confirmed a severe demyelinating neuropathy with secondary axonal features. Sequence analysis of the myelin protein zero (MPZ) gene identified a C‐to‐G transversion at nucleotide position 234, resulting in a serine‐to‐tryptophan mutation in codon 78 (S78W) of the translated protein. The presence of this novel missense mutation suggests a diagnosis of Charcot‐Marie‐Tooth disease type 1B. Our study confirms the worldwide distribution of this disorder and extends the genetic spectrum of mutations in the MPZ gene. Muscle Nerve 27: 628–630, 2003
Dendritic cells in hyperplastic thymuses from patients with myasthenia gravis
Authors: Nagane Yuriko , Utsugisawa Kimiaki , Obara Daiji , Yamagata Munehisa , Tohgi Hideo 
Published: April 2003

AbstractTo investigate the role of dendritic cells (DCs) in the hyperplastic myasthenia gravis (MG) thymus, we studied the frequency and distribution of three mature DC phenotypes (CD83+CD11c+, CD86+CD11c+, and HLA‐DR+CD11c+) in samples from patients with MG whose symptoms dramatically improved following thymectomy and in non‐MG control thymuses. In hyperplastic MG thymuses, mature DCs were much more numerous in nonmedullary areas, such as the subcapsular/outer cortex; around the germinal centers; and in extralobular connective tissue, particularly around blood vessels. Mature DCs strongly coexpressed CD44 and appeared to be components of a CD44–highly positive (CD44high) cell population migrating from the vascular system. Furthermore, in the hyperplastic MG thymus, the expression of secondary lymphoid‐tissue chemokine (SLC) markedly increased especially around extralobular blood vessels, where the CD44high cell population accumulated. These findings suggest that DCs may migrate into the hyperplastic thymus from the vascular system via mechanisms that involve CD44 and SLC. DCs may present self‐antigens, thereby promoting the priming and/or boosting of potentially autoreactive T cells against the acetylcholine receptor. Muscle Nerve 27: 582–589, 2003
Ischemic injury and repair process after transection in hypothyroid rat muscles
Authors: Ozawa Junya , Kawamata Seiichi , Kurosaki Tomoyuki , Iwamizu Yusuke , Matsuura Natsue , Abiko Sachiko , Kai Satoru 
Published: April 2003

AbstractHindlimb ischemia for 4 h, followed by reperfusion, resulted in necrosis of most soleus muscle in euthyroid rats, whereas only slight damage occurred in hypothyroid rats. Muscle repair after transection of the tibialis anterior muscle of hypothyroid rats showed delayed debris removal, initial retardation of myotube formation, and a higher incidence of aberrant sarcomeres in newly formed muscle fibers by electron microscopy. The protective mechanism against ischemia in hypothyroid muscles can probably be attributed to decreased degradation of high‐energy phosphates, reduced formation of substrates for xanthine oxidase during ischemia, and attenuated generation of harmful oxygen free radicals during reperfusion. Initial delay of myotube formation seems to reflect retarded proliferation of muscle precursor cells. Prolonged occurrence of aberrant sarcomeres in hypothyroidism is perhaps due to a delay or imbalance in the synthesis of proteins that assemble sarcomeres. These findings demonstrate the significant roles of thyroid hormones in ischemic injury and muscle repair. Muscle Nerve 27: 595–603, 2003
Force impairment in calpain 3–deficient mice is not correlated with mechanical disruption
Authors: Fougerousse Françoise , Gonin Patrick , Durand Muriel , Richard Isabelle , Raymackers Jean‐Marc 
Published: April 2003

AbstractDefects in human calpain 3 are responsible for limb‐girdle muscular dystrophy type 2A, an autosomal‐recessive disorder characterized mainly by late‐onset proximal muscular atrophy. A corresponding murine model has previously been generated by gene targeting. In this report, muscular activity of calpain 3–deficient (capn3−/−) mice was evaluated at different ages. Growth curves showed a progressive global muscular atrophy. Histological examination throughout the lifespan of mice confirmed the dystrophic lesions. Whole animal tests showed only a mild significant impairment of the forelimbs. Studies of the mechanical properties of selected isolated fast‐ and slow‐twitch muscles demonstrated that slow‐twitch muscles were significantly weaker in capn3−/− mice than in wild‐type mice. Three different tests showed that there was no membrane disruption, suggesting a nonmechanical etiology of capn3−/− mice dystrophy. These findings are consistent with a mechanism involving signaling systems. Muscle Nerve 27: 616–623, 2003
Comparison of tension‐free vaginal taping versus modified burch colposuspension on urethral obstruction: A randomized controlled trial
Authors: Wang Alex C. , Chen Min‐Chi 
Published: April 2003

AbstractAimsTo determine whether the tension‐free vaginal tape (TVT) procedure affects the mechanics of voiding in women with genuine stress incontinence (GSI).MethodsBetween July of 1997 and July of 1999, 116 women with GSI in the absence of pelvic prolapse underwent a randomized controlled study of TVT vs. modified Burch colposuspension. The trial was conducted by using a standardized protocol, including strict criteria for excluding preexisting bladder outlet obstruction (BOO). Urodynamic studies including free flowmetry, filling (provocative) and voiding cystometry, and 1‐hour pad test were performed before and at least 1 year after the operation. The Blaivas and Groutz nomogram was used as another criteria to assess the pre‐ and postoperative BOO.ResultsEighteen women were excluded from the study as a result of having preexisting BOO and an additional 8 were lost to follow‐up. The comparison between pre‐ and postoperative variables for each procedure revealed that maximal flow rate of noninvasive uroflowmetry was significantly lower after operation in both groups (P = 0.009, P = 0.010, respectively). Detrusor pressure at maximal flow and urethral resistance were significantly higher and micturition volumes significantly lower after operation in the Burch group (P < 0.001, P < 0.001, P = 0.029, respectively). The difference between pre‐ and postoperative distribution of the obstruction nomogram of the Burch group was significantly different (P = 0.023).ConclusionsBased on strict exclusion criteria for preoperative BOO, our findings strongly suggest that with a median 22 months (range, 12 to 36 months) of follow‐up, a properly performed tension‐free vaginal tape procedure does not cause urethral obstruction. Neurourol. Urodynam. 22:185–190, 2003. © 2003 Wiley‐Liss, Inc.
Falsely elevated postvoid residual urine in pregnant women
Authors: Tan Thai Lian , Logue Elizabeth , Griffiths Derek , Resnick Neil M. 
Published: April 2003

AbstractPortable ultrasound assessment of postmicturition bladder for residual urine volume is rapid, accurate, and precise. However, other cystic pelvic pathologic conditions may present as a false‐positive finding on the ultrasound. We describe two cases in which the residual urine was falsely detected as being elevated due to unsuspected pregnancy. Neurourol. Urodynam. 22:261–262, 2003. © 2003 Wiley‐Liss, Inc.
Voiding urgency and detrusor contractility in women with overactive bladders
Authors: Cucchi A. , Siracusano S. , Guarnaschelli C. , Rovereto B. 
Published: April 2003

AbstractAimsTo check whether the contractility of overactive bladders would be affected by voiding urgency.MethodsWe urodynamically studied 100 women: 20 normal controls (group 1), 60 patients with idiopathic detrusor overactivity (DO), and 20 with neurogenic DO from intracerebral lesions. The idiopathic DO groups 2A (n = 20), 2B (n = 20), and 3 (n = 20) had moderate, severe, and no voiding urgency, respectively. The neurogenic DO group 4 had severe urgency. The delay time of urgent void at cystometry (2 minutes or more or, respectively, less than 2 minutes) defined moderate or severe urgency. Detrusor contractility was defined by the maximum bladder external voiding power (WFmax).ResultsWFmax was higher in the idiopathic DO patients than in the controls, had the highest values in group 2B, and did not differ significantly between groups 1–4 and 2A–3.ConclusionsWe inferred from our data that idiopathic DO suggests a facilitation of voiding contractions and that such facilitation might be centrally amplified by severe urgency. This amplifying effect would probably be impaired in cases of neurogenic DO from intracerebral lesions. Neurourol. Urodynam. 22:223–226, 2003. © 2003 Wiley‐Liss, Inc.