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PubMed2001

Rapid dynamics of the microtubule binding of ensconsin in vivo.

Microtubule-associated proteins (MAPs) are proteins that reversibly bind to and regulate microtubule dynamics and functions in vivo. We examined the dynamics of binding of a MAP called ensconsin (E-MAP-115) to microtubules in vivo. We used 5xGFP-EMTB, a construct in which the microtubule-binding domain of ensconsin (EMTB) is fused to five copies of green fluorescent protein (GFP), as a reporter molecule amenable to the use of fluorescent speckle microscopy. Fluorescent speckle microscopy (FSM) sequences and kymograph analyses showed rapid dynamics of speckles comprised of 5xGFP-EMTB in untreated cells. By contrast, in detergent-lysed cytoskeletons, speckles were not dynamic. Since detergent-lysed cytoskeletons differ from living cells in that they lack both ATP and dynamic microtubules, we used azide treatment to substantially reduce the level of ATP in living cells and we used Taxol to halt microtubule dynamics. Both treatments slowed the dynamics of 5xGFP-EMTB speckles observed by FSM. We also used fluorescence recovery after photobleaching (FRAP) to quantify the half-time of binding and dissociation of the 5xGFP-EMTB chimera and to compare this half-time to that of the full-length MAP molecule. In untreated cells, the t(g) of either 5xGFP-EMTB or full-length GFP-ensconsin was similarly rapid (approximately 4 seconds), while in ATP-reduced and Taxol-treated cells, t(g) was increased to 210 seconds and 40 seconds, respectively. In detergent-extracted cells no recovery was seen. Consistent with the rapid dynamics of 5xGFP-EMTB measured with fluorescent speckle microscopy and FRAP, we estimated that the affinity of the MAP for microtubules is approximately 40 microM in untreated living cells, compared with approximately 1 microM in vitro. However, K(D,app) was not significantly changed in the presence of azide and was increased to 110 microM in the presence of Taxol. To test whether changes in the phosphorylation state of cellular proteins might be responsible for altering the dynamics of ensconsin binding, we used FSM to monitor staurosporine-treated cells. Staurosporine treatment substantially halted dynamics of 5xGFP-EMTB speckles along MTs. Our results show that ensconsin is highly dynamic in its association with microtubules, and its microtubule association can be altered by in vivo phosphorylation events.

Animals↗

PubMed2001

[Dynamic MR imaging of liver lesions with superparamagnetic iron oxide (SH-U-555A)].

Dynamic MRI with SH-U-555 (SPIO) was evaluated. Dynamic MRI was performed for 17 patients with 22 lesions. Dynamic study with T2*-weighted imaging (T2* dynamic) and T1-weighted imaging (T1 dynamic) were performed in 8 cases (10 lesions) and 9 cases (12 lesions), respectively. T2* dynamic MR images were obtained before and 30, 90, 180, 270, 360, and 450 seconds and 31 minutes after the intravenous injection of SPIO, and T1 dynamic MR images were obtained before and 0, 40, 80, 120, 180, 240, 300, 360, 420, and 480 seconds and 28 minutes after the injection of SPIO. The signal intensity of each lesion was measured before and after the injection of SPIO. The enhancement ratio of the lesions was calculated and evaluated. The enhancement ratio of hypervascular lesions decreased rapidly in the first phase of T2* dynamic MRI, while that of hypovascular lesions decreased gradually. The enhancement ratio of hypervascular lesions increased in the first phase of T1 dynamic MRI and decreased gradually, while that of hypovascular lesions lacked the increase in the first phase, in contrast to hypervascular lesions. However, the changing of signal intensity could not be recognized on images with T2* dynamic and T1 dynamic study. In conclusion, quantitative analysis using the enhancement ratio made it possible to anticipate lesion vascularity.

Adult↗

PubMed2003

Suppression of centromere dynamics by Taxol in living osteosarcoma cells.

Taxol potently blocks mitosis at the transition from metaphase to anaphase, leading to apoptosis in many types of tumor cells. However, the precise mechanism of action of Taxol is not understood. Here we have tested the hypothesis that a primary mechanism of action of Taxol involves suppression of spindle microtubule dynamics. We have used centromere-binding protein B coupled to green fluorescent protein as a marker for the kinetochores and centromeres of chromosomes and analyzed the effects of low Taxol concentrations on the dynamics of centromeres during metaphase of mitosis in living human osteosarcoma (U2OS) cells by quantitative time-lapse confocal microscopy. In the absence of Taxol, the centromere pairs on attached sister chromatids alternately stretch apart and relax back together approximately 1.2 times/min due to tension on the kinetochores produced by the spindle microtubules (referred to here as centromere dynamics). We found that 50-100 nM Taxol significantly suppressed centromere dynamics. For example, Taxol reduced the mean separation distance between the sister centromeres from 0.73 to 0.65 microm, a distance equivalent to that observed in the complete absence of microtubules. The frequency of transitions between stretching and relaxing was also significantly diminished by Taxol (by 27%-35%). The suppressive effects of Taxol on centromere dynamics were associated with maximal accumulation of cells at mitosis (63%), a >90% block of the metaphase/anaphase transition, and complete inhibition of cell proliferation. The data strongly support the idea that the inhibition of centromere dynamics by Taxol prevents silencing of the mitotic spindle surveillance (checkpoint) mechanism. Because Taxol strongly suppresses microtubule dynamics, the data also indicate that centromere dynamics can be accounted for by microtubule dynamics and may not require significant energetic contributions from microtubule motors. The strict correlation between the degree of suppression of centromere dynamics by Taxol and the degree of mitotic block strongly indicates that the primary mechanism responsible for the mitotic block by Taxol in U2OS cells involves suppression of the polymerization dynamics of kinetochore microtubules.

Antineoplastic Agents, Phytogenic↗

PubMed2003

Suppression of microtubule dynamics by discodermolide by a novel mechanism is associated with mitotic arrest and inhibition of tumor cell proliferation.

Discodermolide is a new microtubule-targeted drug in Phase I clinical trials that inhibits tumor growth and induces G(2)-M cell cycle arrest. It is effective against paclitaxel-resistant cell lines and acts synergistically in combination with paclitaxel. Suppression of microtubule dynamics by microtubule-targeted drugs has been hypothesized to be responsible for their ability to inhibit mitotic progression and cell proliferation. To determine whether discodermolide blocks mitosis by an effect on microtubule dynamics, we analyzed the effects of discodermolide on microtubule dynamics in living A549 human lung cancer cells during interphase at concentrations that block mitosis and inhibit cell proliferation. We found that discodermolide (7-166 nM) significantly suppressed microtubule dynamic instability. At the IC(50) for proliferation (7 nM discodermolide, 72 h), overall dynamicity was reduced by 23%. The principal parameters of dynamic instability suppressed by discodermolide were the microtubule shortening rate and length shortened. In addition, discodermolide markedly increased the frequency of rescued catastrophes. At the discodermolide concentration that resulted in 50% of maximal mitotic block (83 nM, 20 h), most microtubules were completely non-dynamic, no anaphases occurred, and all spindles were abnormal. The dynamicity of the remaining dynamic microtubules was reduced by 62%. The results indicate that a principal mechanism of inhibition of cell proliferation and mitotic block by discodermolide is suppression of microtubule dynamics. Importantly, the results indicate significant additional stabilizing effects of discodermolide on microtubule dynamics as compared with those of paclitaxel that may in turn reflect differences in their binding sites and their effects on tubulin conformation.

Alkanes↗

PubMed2005

Statistical methods for HIV dynamic studies in AIDS clinical trials.

Studies of HIV dynamics in AIDS research are very important for understanding pathogenesis of HIV infection and for assessing the potency of antiviral therapies. Since the viral dynamic results from clinical data were first published by Ho et al. and Wei et al., the study of HIV-1 dynamics in vivo has drawn a great attention from AIDS clinicians and researchers. Although the important findings from HIV dynamic studies have been published in many prestigious scientific journals, statistical methods for estimating viral dynamic parameters have not been paid enough attention by HIV dynamic investigators. The estimation methods in many viral dynamic studies are very crude and inefficient. In this paper, we review the statistical methods and mathematical models for HIV dynamic data analysis developed in recent years. We also address some practical issues and share our experiences in the design and analysis of viral dynamic studies. Some principles and guidelines for the design and analysis of viral dynamic studies are provided. The methodologies reviewed in this paper are also applicable to studies of other viruses such as hepatitis B virus or hepatitis C virus. We also pose some challenging statistical problems in this area in order to stimulate further study by the statistical research community.

Acquired Immunodeficiency Syndrome↗

PubMed2006

Evaluating the long-term metacommunity dynamics of tree hole mosquitoes.

Four different conceptual models of metacommunities have been proposed, termed "patch dynamics," "species sorting", "mass effect", and "neutral". These models simplify thinking about metacommunities and improve our understanding of the role of spatial dynamics both in structuring communities and in determining local and regional diversity. We tested whether mosquito communities inhabiting water-filled tree holes in southeastern Florida, U.S.A., displayed any of the characteristics and dynamics predicted by the four models. The densities of the five most common species in 3-8 tree holes were monitored every two weeks during 1978-2003. We tested relationships between habitat variables and species densities, spatial synchrony, the presence of life history trade-offs, and species turnover. Dynamics showed strong elements of species sorting, but with considerable turnover, as predicted by the patch dynamics model. Consistent with patch dynamics, there was substantial asynchrony in dynamics for different tree holes, substantial species turnover in space and time, and an occupancy/colonization trade-off. Substantial correlations of density and occupancy with tree hole volume were consistent with the species-sorting model, but unlike this model, species did not have permanent refuges. No evidence of mass effects was found, and correlations between habitat variables and dynamics were inconsistent with neutral models. Our results did not match a single model and therefore caution against overly simplifying metacommunity dynamics by using one dynamical characteristic to select a particular metacommunity perspective.

Animals↗

PubMed1998

Microtubule dynamics in serum-starved and serum-stimulated Swiss 3T3 mouse fibroblasts: implications for the relationship between serum-induced contractility and microtubules.

It has been established that cell contractility can be stimulated with low or depolymerizing doses of microtubule (MT) poisons. In addition, low doses of nocodazole and vinblastine have recently been shown to decrease MT dynamics in vivo. In this study, investigated whether there is a direct, or reciprocal feedback-type relationship between contractility and microtubule dynamics, by examining MT dynamic behavior in live cells under conditions where contractility is known to be altered. Quiescent, serum-starved Swiss 3T3 mouse fibroblasts have been shown to be weakened in their contractility; serum stimulation increases cell contractility and causes the formation of stress fibers and adhesion plaques. Growing (control), quiescent (Go), and serum-stimulated cells were injected with rhodamine-tubulin, and MT dynamics were determined by analysis of MT length changes obtained from digitized images of the extreme periphery of the cells, where the MT ends were readily apparent. The MTs in quiescent cells were less dynamic than those in control cells: the growth and shortening rates were reduced by 30% and 45%, respectively. Dynamicity decreased by 47%, and the MTs spent more time in pause. After serum stimulation, MT growth rate, dynamicity, and time spent in pause returned to control cell levels. Although the shortening rate increased by 28%, it remained significantly lower than in control cells. In this system, the serum-induced increase in contractility was accompanied by an increase in MT dynamics. However, increased contractility stimulated with low doses of MT poisons is known to be accompanied by a decrease in MT dynamics. These results suggest that the relationship between MT dynamics and contractility is an indirect one.

3T3 Cells↗

PubMed1999

Static and dynamic balance function in spasmodic torticollis.

The consequences of abnormal head posture on static and dynamic balance skill were studied in a group of 10 patients with idiopathic spasmodic torticollis (ST). In static conditions, body sway was assessed using a conventional force platform with eyes open and with eyes closed. Standardized dynamic balance conditions were produced using a rocking platform; lateral and anteroposterior dynamic balance skills were assessed by measuring linear displacement both of the body base and of the head. Dynamic tests were repeated 6 weeks after botulinum toxin treatment in all patients. Patients' results were compared with those obtained from 10 control subjects. In static conditions, ST patients did not differ from control subjects, but in dynamic conditions, balance parameters were greater in the patient group than in the control group. This was true for the lateral direction and for dynamic balance parameters recorded both before and after botulinum toxin treatment. Eye closure significantly increased dynamic balance parameters in both groups. However, the effect of eye closure was greater in the patient group than the control group, especially for lateral sway, suggesting that patients used vision to compensate for the dynamic balance disturbance induced by the spasmodic torticollis. Despite a significant improvement of head posture in all patients after botulinum toxin treatment, no significant changes in dynamic balance parameters were observed between the first and second test. The possible origins of the dynamic balance disturbance observed in ST patients are discussed.

Adult↗

PubMed2003

Concurrent validity of the Berg Balance Scale and the Dynamic Gait Index in people with vestibular dysfunction.

BACKGROUND AND PURPOSE: The Berg Balance Scale is a reliable and valid measure that is used to assess characteristics of balance. The Dynamic Gait Index is a relatively new measure that has been used to record dynamic gait tasks in people with vestibular dysfunction. The purpose of the present study was to determine the concurrent validity of the Dynamic Gait Index with the Berg Balance Scale in people with vestibular disorders. METHOD: A retrospective review of the charts of people who met the criteria of having completed both the Berg Balance Scale and the Dynamic Gait Index during their first physiotherapy visit. Seventy patients (19 male, 51 female) were identified through the retrospective review of the charts of people referred for vestibular rehabilitation with varying diagnoses of vestibular and balance dysfunction. All were seen at a tertiary medical centre in an outpatient physiotherapy setting. Their age range was from 14 to 88 years (mean 65 years). RESULTS: Correlation between the scores on the Dynamic Gait Index and the Berg Balance Scale was moderate but significant by use of the Spearman rank order correlation (r = 0.71; p < 01). No difference was found between scores on the Dynamic Gait Index or Berg Balance Scale based on gender or diagnosis. A significant difference was identified on the Berg Balance Scale between older and younger people with vestibular disorders. Using previously established criteria to determine increased risk of falling, the Berg Balance Scale and the Dynamic Gait Index agreed 63% of the time. CONCLUSIONS: The moderate correlation between the Dynamic Gait Index and the Berg Balance Scale establishes the concurrent validity of the Dynamic Gait Index in people with vestibular dysfunction. Both these measures provide valuable information to clinicians about patients' functional balance capabilities. However, the lack of perfect correlation indicates that the tests measure different aspects of balance. The Dynamic Gait Index appears to be a more sensitive assessment tool in identifying people with vestibular disorders who are at increased risk for falling, based on currently published criteria.

Adolescent↗

PubMed2006

Dynamic cervical change: is real-time sonographic cervical shortening predictive of preterm delivery in patients with symptoms of preterm labor?

OBJECTIVES: To determine prospectively if dynamic cervical change (spontaneous real-time cervical shortening) is predictive of preterm delivery at < 37 weeks' gestation in patients with symptoms of preterm labor. METHODS: This was a prospective study of patients at 23-34 weeks' gestation who were symptomatic for preterm labor. Patients underwent a 10-min real-time sonographic cervical length assessment with measurements taken at 1-min intervals. The presence or absence of dynamic cervical change, defined as real-time changes in cervical length observable to the naked eye of the sonologist during the examination, was recorded. Gestational age at delivery was obtained from medical records. Preterm delivery was defined as delivery at < 37 weeks' gestation. Dynamic cervical change and initial and minimum cervical lengths were assessed for prediction of preterm delivery. RESULTS: Seventy-six patients were enrolled, and 66 were available for outcome analysis. Thirty-one patients (47%) exhibited dynamic cervical change. Patients with dynamic change had shorter initial cervical lengths (27 mm vs. 36 mm, P = 0.001), shorter minimum cervical lengths (20 vs. 33 mm, P < 0.001) and larger changes in cervical length during the examination period (10 vs. 4 mm, P < 0.001). In the subgroup of patients with an initial cervical length > 30 mm, those with dynamic change delivered earlier than did those without dynamic change (36.8 vs. 38.6 weeks, P = 0.02), and a higher percentage delivered preterm (27% vs. 11%, odds ratio (OR), 3.0 (0.5-17.0)). Multivariate analysis showed that minimum cervical length was a better predictor of preterm delivery than was initial cervical length. CONCLUSIONS: Dynamic cervical change occurs frequently in association with shortened cervical length. In patients with longer initial cervical lengths, dynamic change may increase the risk for preterm delivery. When dynamic change is noted in a patient with preterm labor symptoms, use of the minimum cervical length observed may be better compared with initial cervical length for determining preterm delivery risk.

Adult↗

PubMed1997

Torsion-angle molecular dynamics as a new efficient tool for NMR structure calculation.

Molecular dynamics in torsion-angle space was applied to nuclear magnetic resonance structure calculation using nuclear Overhauser effect-derived distances and J-coupling-constant-derived dihedral angle restraints. Compared to two other commonly used algorithms, molecular dynamics in Cartesian space and metric-matrix geometry combined with Cartesian molecular dynamics, the method shows increased computational efficiency and success rate for large proteins, and it shows a dramatically increased radius of convergence for DNA. The torsion-angle molecular dynamics algorithm starts from an extended strand conformation and proceeds in four stages: high-temperature torsion-angle molecular dynamics, slow-cooling torsion-angle molecular dynamics, Cartesian molecular dynamics, and minimization. Tests were carried out using experimental NMR data for protein G, interleukin-8, villin 14T, and a 12 base-pair duplex of DNA, and simulated NMR data for bovine pancreatic trypsin inhibitor. For villin 14T , a monomer consisting of 126 residues, structure determination by torsion-angle molecular dynamics has a success rate of 85%, a more than twofold improvement over other methods. In the case of the 12 base-pair DNA duplex, torsion-angle molecular dynamics had a success rate of 52% while Cartesian molecular dynamics and metric-matrix distance geometry always failed.

Algorithms↗

PubMed2001

Evidence for a dynamic-dominance hypothesis of handedness.

Handedness is a prominent behavioral phenomenon that emerges from asymmetrical neural organization of human motor systems. However, the aspects of motor performance that correspond to handedness remain largely undetermined. A recent study examining interlimb differences in coordination of reaching demonstrated dominant arm advantages in controlling limb segment inertial dynamics (Sainburg and Kalakanis 2000). Based on these findings, I now propose the dynamic-dominance hypothesis, which states that the essential factor that distinguishes dominant from nondominant arm performance is the facility governing the control of limb dynamics. The purpose of this study is to test two predictions of this hypothesis: 1) adaptation to novel intersegmental dynamics, requiring the development of new dynamic transforms, should be more effective for the dominant arm; 2) there should be no difference in adapting to visuomotor rotations performed with the dominant as compared with the nondominant arm. The latter prediction is based on the idea that visual information about target position is translated into an internal reference frame prior to transformation of the movement plan into dynamic properties, which reflect the forces required to produce movement. To test these predictions, dominant arm adaptation is compared to nondominant arm adaptation during exposure to novel inertial loads and to novel visuomotor rotations. The results indicate substantial interlimb differences in adaptation to novel inertial dynamics, but equivalent adaptation to novel visuomotor rotations. Inverse dynamic analysis revealed better coordination of dominant arm muscle torques across both shoulder and elbow joints, as compared with nondominant arm muscle torques. As a result, dominant arm movements were produced with a fraction of the mean squared muscle torque computed for nondominant arm movements made at similar speeds. These results support the dynamic-dominance hypothesis, indicating that interlimb asymmetries in control arise downstream to visuomotor transformations, when dynamic variables that correspond to the forces required for motion are specified.

Adaptation, Physiological↗

PubMed2005

Modeling the influence of dynamic zoning of forest harvesting on ecological succession in a northern hardwoods landscape.

Dynamic zoning (systematic alteration in the spatial and temporal allocation of even-aged forest management practices) has been proposed as a means to change the spatial pattern of timber harvest across a landscape to maximize forest interior habitat while holding timber harvest levels constant. Simulation studies have established that dynamic zoning strategies produce larger tracts of interior, closed canopy forest, thus increasing the value of these landscapes for interior-dependent wildlife. We used the simulation model LANDIS to examine how the implementation of a dynamic zoning strategy would change trajectories of ecological succession in the Great Divide Ranger District of the Chequamegon-Nicolet National Forest in northern Wisconsin over 500 years. The components of dynamic zoning strategies (number of zones in a scenario and the length of the hiatus between successive entries into zones) and their interaction had highly significant impacts on patterns of forest succession. Dynamic zoning scenarios with more zones and shorter hiatus lengths increased the average amount of the forest dominated by early successional aspen (Populus sp.). Dynamic zoning scenarios with two zones produced more late successional mature northern hardwoods than scenarios with four zones. Dynamic zoning scenarios with very short (30 years) or very long (120 years) hiatus lengths resulted in more late successional mature northern hardwoods than scenarios with intermediate hiatus lengths (60 and 90 years). However, none of the dynamic scenarios produced as much late successional mature northern hardwoods as the static alternative. Furthermore, the amounts of all habitat types in all dynamic zoning scenarios fluctuated greatly in time and space relative to static alternatives, which could negatively impact wildlife species that require a stable amount of habitat above some minimum critical threshold. Indeed, implementing dynamic zoning scenarios of different designs would have both positive and negative effects on wildlife species and for other objectives of forest management.

Animals↗

PubMed2005

Dynamic CE-MRA for endoleak classification after endovascular aneurysm repair.

AIM: To evaluate the value of dynamic contrast enhanced magnetic resonance angiography (CE-MRA) for classification of endoleaks after endovascular aneurysm repair (EVAR). MATERIALS AND METHODS: Twenty-eight patients, between 2 days and 54 months after EVAR, were evaluated with CTA, MRI and dynamic CE-MRA. The additional diagnostic value of the dynamic 3D CE-MRA was evaluated by determining the ability of the dynamic series in pinpointing the site of inflow of an endoleak. RESULTS: An endoleak was detected in 23 patients. Seventeen of the 23 dynamic series were technically successful (no disturbing artifacts limiting the diagnostic value). Using MRI our findings were: 2 type I, 6 type II, 1 type III, no type IV endoleaks and in 14 cases classification could not be made. The classification results for MRI plus the dynamic CE-MRA were: 2 type I, 12 type II, 1 type III, no type IV endoleaks and in eight cases classification could not be made. In six cases the dynamic MRA allowed classification of the endoleak, which was not possible with the non-dynamic images alone (p=0.091, Fisher exact). CONCLUSION: This pilot study shows that dynamic CE-MRA can have additional value in the classification of endoleaks. Dynamic CE-MRA might obviate the need for diagnostic digital subtraction angiography and aid planning for intervention.

Aged↗

PubMed2002

Spurious dynamics in somatosensory cortex.

Cortical networks are dynamical systems whose task is to process information. However, in addition to 'intended' dynamical behaviors, the sheer complexity of a cortical network's structure-regardless of its precise details-should generate additional 'unintended' dynamical behaviors. Dynamics observed in cortical network models and in the somatosensory cortex suggest that such spurious dynamical behaviors are likely to be pervasive but relatively simple, contributing to-rather than dominating-a network's response to stimuli. Spurious dynamics may be responsible for a variety of experimentally observed intriguing features of cortical dynamics. Because of their distributed origins and emergent nature, such dynamical features, while clearly identifiable, will resist attempts at identifying specific mechanisms to explain them. We describe some of the spurious dynamical phenomena associated with somatosensory cortical response to brushing stimulation, to illustrate how spurious dynamics can affect neurons' functional properties, cortical stimulus representation and, ultimately, perception.

Algorithms↗

PubMed2001

Comparison of aqueous molecular dynamics with NMR relaxation and residual dipolar couplings favors internal motion in a mannose oligosaccharide.

An investigation has been performed to assess how aqueous dynamical simulations of flexible molecules can be compared against NMR data. The methodology compares state-of-the-art NMR data (residual dipolar coupling, NOESY, and (13)C relaxation) to molecular dynamics simulations in water over several nanoseconds. In contrast to many previous applications of residual dipolar coupling in structure investigations of biomolecules, the approach described here uses molecular dynamics simulations to provide a dynamic representation of the molecule. A mannose pentasaccharide, alpha-D-Manp-(1-->3)-alpha-D-Manp-(1-->3)-alpha-D-Manp-(1-->3)-alpha-D-Manp-(1-->2)-D-Manp, was chosen as the model compound for this study. The presence of alpha-linked mannan is common to many glycopeptides, and therefore an understanding of the structure and the dynamics of this molecule is of both chemical and biological importance. This paper sets out to address the following questions. (1) Are the single structures which have been used to interpret residual dipolar couplings a useful representation of this molecule? (2) If dynamic flexibility is included in a representation of the molecule, can relaxation and residual dipolar coupling data then be simultaneously satisfied? (3) Do aqueous molecular dynamics simulations provide a reasonable representation of the dynamics present in the molecule and its interaction with water? In summary, two aqueous molecular dynamics simulations, each of 20 ns, were computed. They were started from two distant conformations and both converged to one flexible ensemble. The measured residual dipolar couplings were in agreement with predictions made by averaging the whole ensemble and from a specific single structure selected from the ensemble. However, the inclusion of internal motion was necessary to rationalize the relaxation data. Therefore, it is proposed that although residual dipolar couplings can be interpreted as a single-structure, this may not be a correct interpretation of molecular conformation in light of other experimental data. Second, the methodology described here shows that the ensembles from aqueous molecular dynamics can be effectively tested against experimental data sets. In the simulation, significant conformational motion was observed at each of the linkages, and no evidence for intramolecular hydrogen bonds at either alpha(1-->2) or alpha(1-->3) linkages was found. This is in contrast to simulations of other linkages, such as beta(1-->4), which are often predicted to maintain intramolecular hydrogen bonds and are coincidentally predicted to have less conformational freedom in solution.

Carbohydrate Sequence↗

PubMed2005

Dynamics of nanoscopic water: vibrational echo and infrared pump-probe studies of reverse micelles.

The dynamics of water in nanoscopic pools 1.7-4.0 nm in diameter in AOT reverse micelles were studied with ultrafast infrared spectrally resolved stimulated vibrational echo and pump-probe spectroscopies. The experiments were conducted on the OD hydroxyl stretch of low-concentration HOD in the H2O, providing a direct examination of the hydrogen-bond network dynamics. Pump-probe experiments show that the vibrational lifetime of the OD stretch mode increases as the size of the reverse micelle decreases. These experiments are also sensitive to hydrogen-bond dissociation and reformation dynamics, which are observed to change with reverse micelle size. Spectrally resolved vibrational echo data were obtained at several frequencies. The vibrational echo data are compared to data taken on bulk water and on a 6 M NaCl solution, which is used to examine the role of ionic strength on the water dynamics in reverse micelles. Two types of vibrational echo measurements are presented: the vibrational echo decays and the vibrational echo peak shifts. As the water nanopool size decreases, the vibrational echo decays become slower. Even the largest nanopool (4 nm, approximately 1000 water molecules) has dynamics that are substantially slower than bulk water. It is demonstrated that the slow dynamics in the reverse micelle water nanopools are a result of confinement rather than ionic strength. The data are fit using time-dependent diagrammatic perturbation theory to obtain the frequency-frequency correlation function (FFCF) for each reverse micelle. The results are compared to the FFCF of water and show that the largest differences are in the slowest time scale dynamics. In bulk water, the slowest time scale dynamics are caused by hydrogen-bond network equilibration, i.e., the making and breaking of hydrogen bonds. For the smallest nanopools, the longest time scale component of the water dynamics is approximately 10 times longer than the dynamics in bulk water. The vibrational echo data for the smallest reverse micelle displays a dependence on the detection wavelength, which may indicate that multiple ensembles of water molecules are being observed.

Deuterium↗

PubMed2004

"Cooperativity blockage" in the mixed alkali effect as revealed by molecular-dynamics simulations of alkali metasilicate glass.

The relaxation dynamics of a complex interacting system can be drastically changed when mixing with another component having different dynamics. In this work, we elucidate the effect of the less mobile guest ions on the dynamics of the more mobile host ions in mixed alkali glasses by molecular-dynamics (MD) simulations. One MD simulation was carried out on lithium metasilicate glass with the guest ions created by freezing some randomly chosen lithium ions at their initial locations at 700 K. A remarkable slowing down of the dynamics of the majority mobile Li ions was observed both in the self-part of the density-density correlation function, Fs(k,t), and in the mean-squared displacements. On the other hand, there is no significant change in the structure. The motion of the Li ions in the unadulterated Li metasilicate glass is dynamically heterogeneous. In the present work, the fast and slow ions were divided into two groups. The number of fast ions, which shows faster dynamics (Levy flight) facilitated by cooperative jumps, decreases considerably when small amount of Li ions are frozen. Consequently there is a large overall reduction of the mobility of the Li ions. The result is also in accordance with the experimental finding in mixed alkali silicate glasses that the most dramatic reduction of ionic conductivity occurs in the dilute foreign alkali limit. Similar suppression of the cooperative jumps is observed in the MD simulation data of mixed alkali system, LiKSiO3. Naturally, the effect found here is appropriately described as "cooperativity blockage." Slowing down of the motion of Li ions also was observed when a small number of oxygen atoms chosen at random were frozen. The effect is smaller than the case of freezing some the Li ions, but it is not negligible. The cooperativity blockage is also implemented by confining the Li metasilicate glass inside two parallel walls formed by freezing Li ions in the same metasilicate glass. Molecular-dynamics simulations were performed on the dynamics of the Li ions in the confined glass. Slowing down of the dynamics is largest near the wall and decreases monotonically with distance away from the wall.

Journal Article↗