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PubMed2001

MD simulations of homomorphous PNA, DNA, and RNA single strands: characterization and comparison of conformations and dynamics.

MD simulations of homomorphous single-stranded PNA, DNA, and RNA with the same base sequence have been performed in aqueous solvent. For each strand two separate simulations were performed starting from a (i) helical conformation and (ii) random coiled state. Comparisons of the simulations with the single-stranded helices (case i) show that the differences in the covalent nature of the backbones cause significant differences in the structural and dynamical properties of the strands. It is found that the PNA strand maintains its nice base-stacked initial helical structure throughout the 1.5-ns MD simulation at 300 K, while DNA/RNA show relatively larger fluctuations in the structures with a few local unstacking events during -ns MD simulation each. It seems that the weak physical coupling between the bases and the backbone in PNA causes a loss of correlation between the dynamics of the bases and the backbone compared to the DNA/RNA and helps maintain the base-stacked helical conformation. The global flexibility of a single-stranded PNA helix was also found to be lowest, while RNA appears to be the most flexible single-stranded helix. The sugar pucker of several nucleotides in single-stranded DNA and RNA was found to adopt both C2'-endo and C3'-endo conformations for significant times. This effect is more pronounced for single strands in completely coiled states. The simulations with single-stranded coils as the initial structure also indicate that a PNA can adopt a more compact globular structure, while DNA/RNA of the same size adopts a more extended coil structure. This allows even a short PNA in the coiled state to form a significantly stable nonsequentially base-stacked globular structure in solution. Due to the hydrophobic nature of the PNA backbone, it interacts with surrounding water rather weakly compared to DNA/RNA.

Base Sequence↗

PubMed1999

Wear of composite resin veneering materials in a dual-axis chewing simulator.

The attritional wear of human enamel and four different composite resins for the veneering of crowns was evaluated in a dual-axis chewing simulator over up to 1200000 loading cycles. Enamel showed less wear than the composite resins. However, an ultrafine compact-filled composite resin (Targis) showed a wear not statistically significantly different from that of enamel. The other composite resins showed a statistically significantly higher wear than enamel regardless whether microfine, ultrafine midway-filled or ultrafine compact-filled.

Analysis of Variance↗

PubMed2006

Generalized approach for modeling minimally invasive surgery as a stochastic process using a discrete Markov model.

Minimally invasive surgery (MIS) involves a multidimensional series of tasks requiring a synthesis between visual information and the kinematics and dynamics of the surgical tools. Analysis of these sources of information is a key step in defining objective criteria for characterizing surgical performance. The Blue DRAGON is a new system for acquiring the kinematics and the dynamics of two endoscopic tools synchronized with the endoscopic view of the surgical scene. Modeling the process of MIS using a finite state model [Markov model (MM)] reveals the internal structure of the surgical task and is utilized as one of the key steps in objectively assessing surgical performance. The experimental protocol includes tying an intracorporeal knot in a MIS setup performed on an animal model (pig) by 30 surgeons at different levels of training including expert surgeons. An objective learning curve was defined based on measuring quantitative statistical distance (similarity) between MM of experts and MM of residents at different levels of training. The objective learning curve was similar to that of the subjective performance analysis. The MM proved to be a powerful and compact mathematical model for decomposing a complex task such as laparoscopic suturing. Systems like surgical robots or virtual reality simulators in which the kinematics and the dynamics of the surgical tool are inherently measured may benefit from incorporation of the proposed methodology.

Computer Simulation↗

PubMed1994

Physiology, morphology and detailed passive models of guinea-pig cerebellar Purkinje cells.

1. Purkinje cells (PCs) from guinea-pig cerebellar slices were physiologically characterized using intracellular techniques. Extracellular caesium ions were used to linearize the membrane properties of PCs near the resting potential. Under these conditions the average input resistance, RN, was 29 M omega, the average system time constant, tau 0, was 82 ms and the average cable length, LN, was 0.59. 2. Three PCs were fully reconstructed following physiological measurements and staining with horseradish peroxidase. Assuming that each spine has an area of 1 micron 2 and that the spine density over the spiny dendrites is ten spines per micrometre length, the total membrane area of each PC is approximately 150,000 microns 2, of which approximately 100,000 microns 2 is in the spines. 3. Detailed passive cable and compartmental models were built for each of the three reconstructed PCs. Computational methods were devised to incorporate globally the huge number of spines into these models. In all three cells the models predict that the specific membrane resistivity, Rm, of the soma is much lower than the dendritic Rm (approximately 500 and approximately 100,000 omega cm2 respectively). The specific membrane capacitance, Cm, is estimated to be 1.5-2 muF cm-2 and the specific cytoplasm resistivity, Ri, is 250 omega cm. 4. The average cable length of the dendrites according to the model is 0.13 lambda, suggesting that under caesium conditions PCs are electrically very compact. Brief somatic spikes, however, are expected to attenuate 30-fold when spreading passively into the dendritic terminals. A simulated 200 Hz train of fast, 90 mV somatic spikes produced a smooth 12 mV steady depolarization at the dendritic terminals. 5. A transient synaptic conductance increase, with a 1 nS peak at 0.5 ms and a driving force of 60 mV, is expected to produce approximately 20 mV peak depolarization at the spine head membrane. This EPSP then attenuates between 200- and 900-fold into the soma. Approximately 800 randomly distributed and synchronously activated spiny inputs are required to fire the soma. 6. The passive model of the PC predicts a poor resolution of the spatio-temporal pattern of the parallel fibre input. An equally sized, randomly distributed group of approximately 1% of the parallel fibres, activated within a time window of a few milliseconds, would result in approximately the same composite EPSP at the soma.

Animals↗

PubMed2003

Minimally invasive surgery task decomposition--etymology of endoscopic suturing.

The analogy between Minimally Invasive Surgery (MIS) and the human language inspires the decomposition of a surgical task into its primary elements. The frequency of different elements or words" and their sequential associations or "grammar" both hold critical information about the process and outcome of the procedure. Modeling these sequential element expressions using a multi finite states model (Markov model) reveals the grammatical structure of the surgical task and is utilized as one of the key steps in objectively assessing surgical performance. The experimental protocol included 30 surgeons at different levels of training (5xR1,R2,R3,R4,R5, and experts) performing Laparoscopic suturing on an animal model (pig). The kinematics and dynamics of left and right endoscopic tools along with the visual view of the surgical scene were acquired by the Blue DRAGON system. The methodology of decomposing the surgical task is based on a fully connected, finite-states (30 states) Markov model (MM) where the left and right hands are represented by 15 states each. In addition to the MM objective analysis, a scoring protocol was used by an expert surgeon to subjectively assess the subjects' technical performance. An objective learning curve was defined based on measuring quantitative statistical distance (similarity) between MM of experts and MM of residents at different levels of training. The objective learning curve (e.g. statistical distance between MM) was similar to that of the subjective performance analysis. The MM proved to be a powerful and compact mathematical model for decomposing a complex task such as laparoscopic suturing. Systems like surgical robots or virtual reality simulators that inherently measure the kinematics and dynamics of the surgical tool may benefit from inclusion of the proposed methodology for analysis of efficacy and objective evaluation of surgical skills during training.

Endoscopy↗

PubMed2003

Non-arrhenius behavior in the unfolding of a short, hydrophobic alpha-helix. Complementarity of molecular dynamics and lattice model simulations.

The unfolding of the last, C-terminal residue of AcNH(2)-(l-Leu)(11)-NHMe in its alpha-helical form has been investigated by measuring the variation of free energy involved in the alpha(R) to beta conformational transition. These calculations were performed using large-scale molecular dynamics simulations in conjunction with the umbrella sampling method. For different temperatures ranging from 280 to 370 K, the free energy of activation was estimated. Concurrently, unfolding simulations of a homopolypeptide formed by twelve hydrophobic residues were carried out, employing a three-dimensional lattice model description of the peptide, with a temperature-dependent interaction potential. Using a Monte Carlo approach, the lowest free energy conformation, an analogue of a right-handed alpha-helix, was determined in the region where the peptide chain is well ordered. The free energy barrier separating this state from a distinct, compact conformation, analogue to a beta-strand, was determined over a large enough range of temperatures. The results of these molecular dynamics and lattice model simulations are consistent and indicate that the kinetics of the unfolding of a hydrophobic peptide exhibits a non-Arrhenius behavior closely related to the temperature dependence of the hydrophobic effect. These results further illuminate the necessity to include a temperature dependence in potential energy functions designed for coarse-grained models of proteins.

Computer Simulation↗

PubMed1997

Effects of needle tip bevel and aspiration procedure on the morphology and developmental capacity of bovine compact cumulus oocyte complexes.

Effects of the needle tip bevel and the aspiration procedure on the morphology of cumulusoocyte-complexes (COCs) and the developmental capacity of the oocytes after IVF were studied in 2 in vitro oocyte pick-up (OPU) simulations using a disposable ovum pick-up needle guidance system. In Experiment 1, the influence of the length of the needle bevel was investigated using a short and a long bevelled 20-g disposable needle. After being aspirated from slaughterhouse ovaries, the retrieved COCs were divided into 3 categories: 1) oocytes surrounded by a compact cumulus, 2) oocytes with an expanded cumulus, 3) partially naked oocytes. In Experiment 2, the influence of 5 different levels of aspiration vacuum for 3 different needle diameters (18-g, 19-g, 20-g) and 2 different needle bevels (long, short) was tested on the recovery and on the morphology of the cumulus investment of a fixed number of previously scored compact cumulus oocytes complexes (CCOCs), retrieved after slicing slaughterhouse ovaries. The re-retrieved COCs were allocated to Categories 1 and 3. The results show that the length of the needle bevel has a significant effect on oocyte recovery, in favor of the long-bevelled needle. As soon as higher aspiration vacua are used, a decrease of the number of CCOCs can be observed, which is less prominent for the short-bevelled needle compared to the long-bevelled one. The final number of blastocysts is similar for both needle types. In Experiment 2, the disposable needle system proved to be highly effective since nearly 80% of the CCOCs were retrieved. At low aspiration vacuum, up to 90% of the CCOCs withstand the aspiration procedure undamaged. Increasing the aspiration vacuum results in a decrease of the number of CCOCs, which is less pronounced using thinner needles. Averaged over all needle types, the prevalence of blastocysts expressed relative to the number of recovered oocytes decreases with higher aspiration vacuum.

Journal Article↗

PubMed2003

Compact phases of polymers with hydrogen bonding.

We propose an off-lattice model for a self-avoiding homopolymer chain with two different competing attractive interactions, mimicking the hydrophobic effect and the hydrogen-bond formation, respectively. By means of Monte Carlo simulations, we are able to trace out the complete phase diagram for different values of the relative strengths of the two competing interactions. For strong enough hydrogen bonding, the ground state is a helical conformation, whereas with decreasing hydrogen-bonding strength, helices get eventually destabilized at low temperature in favor of more compact conformations resembling beta sheets appearing in the native structures of proteins. For weaker hydrogen bonding helices are not thermodynamically relevant anymore.

Journal Article↗

PubMed2005

An in vivo evaluation of induction of abnormal sperm morphology in mice by landfill leachates.

Although several reports have demonstrated the acutely toxic and genotoxic effects of landfill leachates in microbial organisms, plants and aquatic animals, the effects of pollutants present in these leachates have not been clarified yet in terrestrial animals. This study mainly aimed to evaluate a potential genetic effect of raw and simulated leachates from Orita-Aperin and Oworonsoki landfills in south-west Nigeria by use of the murine sperm-head abnormality test. These landfills neither have a synthetic membrane liner at the bottom, nor a natural layer of compacted soil with the desired hydraulic conductivity, nor a run-off control system. As a result, the leachates produced are discharged into the environment. Samples designated as Orita-Aperin Raw Leachate (OARL), Orita-Aperin Simulated Leachate (OASL), Oworonsoki Raw Leachate (OWRL) and Oworonsoki Simulated Leachate (OWSL) were analyzed in the sperm-head abnormality test at concentrations (v/v) of 1%, 2.5%, 5%, 10% and 25%. Mice were given 0.5 ml sample per day for five consecutive days by intraperitoneal injection. Each dose group comprised seven mice, and a 5-week exposure period was utilized. The data show that the test mixtures induced a dose-dependent, statistically significant increase (P<0.05) in the number of sperm with abnormal morphology. Physico-chemical analysis of the test samples shows that they contained constituents that are capable of inducing mutation in biologic system. The interaction of some of these constituents with the genetic material in the differentiating cells during spermatogenesis may be responsible for these observations. This is relevant in environmental waste management, and for the assessment of the hazardous effects of the chemicals in landfill leachates.

Animals↗

PubMed2004

Understanding the determinants of stability and folding of small globular proteins from their energetics.

The results of minimal model calculations indicate that the stability and the kinetic accessibility of the native state of small globular proteins are controlled by few "hot" sites. By means of molecular dynamics simulations around the native conformation, which describe the protein and the surrounding solvent at the all-atom level, an accurate and compact energetic map of the native state of the protein is generated. This map is further simplified by means of an eigenvalue decomposition. The components of the eigenvector associated with the lowest eigenvalue indicate which hot sites are likely to be responsible for the stability and for the rapid folding of the protein. The comparison of the results of the model with the findings of mutagenesis experiments performed for four small proteins show that the eigenvalue decomposition method is able to identify between 60% and 80% of these (hot) sites.

Amino Acid Sequence↗

PubMed2006

A recommended specification for heavy vehicle rear underrun guards.

A large research program was carried out to evaluate the effectiveness of different heavy vehicle rear underrun guards. Based on the test results, a recommended underrun guard specification was developed to prevent passenger injuries in such accidents. Data obtained from a series of static and full-scale crash tests performed at the Transport Canada Research Center was used in the development of the specification. Four different underrun guard designs were used during the full-scale crash tests. Three different vehicle models representing sub-compact, compact vehicles and light trucks and vans traveling at 48, 56 and 65 km/h relative speeds were used to impact underrun guards head on. The first 10 of the crash tests guard was attached to a simulated trailer while the last one performed using an actual truck. The results obtained from these tests show that a guard built to the minimum requirements of U.S. FMVSS 223 may not be strong enough to prevent passenger compartment intrusion especially in compact and sub-compact automobiles. This paper documents the tests performed, the results obtained and their analyses, and conclusions derived from these analyses. A recommended specification is prepared on the minimum performance that should be required for an effective underrun guard.

Accidents, Traffic↗

PubMed2003

On the choice of a sparse prior.

An emerging paradigm analyses in what respect the properties of the nervous system reflect properties of natural scenes. It is hypothesized that neurons form sparse representations of natural stimuli: each neuron should respond strongly to some stimuli while being inactive upon presentation of most others. For a given network, sparse representations need fewest spikes, and thus the nervous system can consume the least energy. To obtain optimally sparse responses the receptive fields of simulated neurons are optimized. Algorithmically this is identical to searching for basis functions that allow coding for the stimuli with sparse coefficients. The problem is identical to maximizing the log likelihood of a generative model with prior knowledge of natural images. It is found that the resulting simulated neurons share most properties of simple cells found in primary visual cortex. Thus, forming optimally sparse representations is a very compact approach to describing simple cell properties. Many ways of defining sparse responses exist and it is widely believed that the particular choice of the sparse prior of the generative model does not significantly influence the estimated basis functions. Here we examine this assumption more closely. We include the constraint of unit variance of neuronal activity, used in most studies, into the objective functions. We then analyze learning on a database of natural (cat-cam) visual stimuli. We show that the effective objective functions are largely dominated by the constraint, and are therefore very similar. The resulting receptive fields show some similarities but also qualitative differences. Even for coefficient values for which the objective functions are dissimilar, the distributions of coefficients are similar and do not match the priors of the assumed generative model. In conclusion, the specific choice of the sparse prior is relevant, as is the choice of additional constraints, such as normalization of variance.

Algorithms↗

PubMed1999

Progress and perspectives in computational neuroanatomy.

The tremendous increase in processing power of personal computers has recently allowed the construction of highly sophisticated models of neuronal function and behavior. Anatomy plays a fundamental role in supporting and shaping nervous system activity, yet to date most details of such a role have escaped the efforts of experimental and theoretical neuroscientists, mainly because of the problem's complexity. When accurate cellular morphologies are included in electrophysiological computer simulations, quantitative and qualitative effects of dendritic structure on firing properties can be extensively characterized. Complete models of dendritic morphology can be implemented to allow the computer generation of virtual neurons that model the anatomical characteristics of their real counterparts to a great degree of approximation. From a restricted and already available experimental database, stochastic and statistical algorithms can create an unlimited number of non-identical virtual neurons within several mammalian morphological classes, storing them in a compact and parsimonious format. When modeled neurons are distributed in three-dimensional and biologically plausible rules governing axonal navigation and connectivity are added to the simulations, entire portions of the nervous system can be "grown" as anatomically realistic neural networks. These computational constructs are useful to determine the influence of local geometry on system neuroanatomy, and to investigate systematically the mutual interactions between anatomical parameters and electrophysiological activity at the network level. A detailed computer model of a "virtual brain" that was truly equivalent to the biological structure could in principle allow scientists to carry out experiments that could not be performed on real nervous systems because of physical constraints. The computational approach to neuroanatomy is just at its beginning, but has a great potential to enhance the intuition of investigators and to aid neuroscience education. Anat Rec (New Anat): 257:195-207, 1999.

Animals↗

PubMed2004

The folding pathway of ubiquitin from all-atom molecular dynamics simulations.

The folding (unfolding) pathway of ubiquitin is probed using all-atom molecular dynamics simulations. We dissect the folding pathway using two techniques: first, we probe the folding pathway of ubiquitin by calculating the evolution of structural properties over time and second, we identify the rate determining transition state for folding. The structural properties that we look at are hydrophobic solvent accessible surface area (SASA) and Calpha-root-mean-square deviation (rmsd). These properties on their own tell us relatively little about the folding pathway of ubiquitin; however, when plotted against each other, they become powerful tools for dissecting ubiquitin's folding mechanism. Plots of Calpha-rmsd against SASA serve as a phase space trajectories for the folding of ubiquitin. In this study, these plots show that ubiquitin folds to the native state via the population of an intermediate state. This is shown by an initial hydrophobic collapse phase followed by a second phase of secondary structure arrangement. Analysis of the structure of the intermediate state shows that it is a collapsed species with very little secondary structure. In reconciling these observations with recent experimental data, the transition that we observe in our simulations from the unfolded state (U) to the intermediate state (I) most likely occurs in the dead-time of the stopped flow instrument. The folding pathway of ubiquitin is probed further by identification of the rate-determining transition state for folding. The method used for this is essential dynamics, which utilizes a principal component analysis (PCA) on the atomic fluctuations throughout the simulation. The five transition state structures identified in silico are in good agreement with the experimentally determined transition state. The calculation of phi-values from the structures generated in the simulations is also carried out and it shows a good correlation with the experimentally measured values. An initial analysis of the denatured state shows that it is compact with fluctuating regions of nonnative secondary structure. It is found that the compactness in the denatured state is due to the burial of some hydrophobic residues. We conclude by looking at a correlation between folding kinetics and residual structure in the denatured state. A hierarchical folding mechanism is then proposed for ubiquitin.

Computer Simulation↗

PubMed2003

Simulation and analysis of flow patterns around the scleractinian coral Madracis mirabilis (Duchassaing and Michelotti).

Three-dimensional morphologies of Madracis mirabilis were obtained using X-ray computed tomography scanning techniques. The morphologies were used to simulate the flow patterns around the colony. In the simulations, the thin-branching low-flow morph with a relatively larger branch-spacing was compared with the more compact high-flow morph of M. mirabilis. For both morphologies, the inside-colony flow velocities were computed for Reynolds numbers ranging from 154 to 3840. In the high-flow morph, it was found that in the range of investigated Reynolds numbers a stagnant region develops within the colony, whereas in the low-flow morph the stagnant region disappeared. Experiments done under natural conditions suggest that a morph is adapted to a certain external flow velocity and develops a stagnant region below a particular threshold for the external flow velocity. When the external flow velocity exceeds a certain threshold, which is characteristic for the growth form, the core velocity becomes equal to the external velocity. A potential application of a profile of core velocities for a range of Reynolds numbers for a certain morph is the prediction of the optimal external flow velocity for a certain morph, and this can be used to assess the state of the physical (palaeo-) environment.

Animals↗

PubMedDate not supplied

Simulated epicardial potential maps during paced activation reflect myocardial fibrous structure.

Using a three-dimensional propagation model of the human ventricular myocardium, we studied the role of fibrous structure in generating epicardial potential maps. This model represents the myocardium as an anisotropic bidomain with an equal anisotropy ratio, and it incorporates a realistic representation of anatomical features, including epi-endocardial fiber rotation in the compact portion of the wall (compacta) and a distinct fiber arrangement of the trabeculated portion (trabeculata). Activation sequences were elicited at various intramural depths, and maps were calculated throughout a 60 ms sequence. The simulated maps closely resembled those measured by others in the canine heart. During the early stages of activation, a typical map featuring a central minimum flanked by two maxima emerged, with the axis joining these extrema approximately parallel to the fibers near the pacing site, and the axis joining the maxima rotated in the same direction as the fibers for different pacing depths; for endocardial and subendocardial pacing this map changed into one with an oblong positive area. During the later stages of activation, the positive areas of the maps expanded and rotated with the transmural fiber rotation. In concurrence with experiments, we saw a fragmentation and asymmetry of expanding and rotating positive areas. The latter features-apparently caused by the interface between the compacta and trabeculata, variable local thickness of the wall, or local undulations of the vetricular surface-could not be reproduced by more idealized, slab models.

Animals↗

PubMed1998

Tertiary contacts in alpha-lactalbumin at pH 7 and pH 2: a molecular dynamics study.

Molecular dynamics simulations of alpha-lactalbumin were performed under conditions of neutral pH and low pH in order to study the acid-induced molten globule state. Through the use of experimental techniques such as NMR and CD spectroscopy, molten globules have been characterized as being compact intermediates with secondary structure similar to that of the native protein but with tertiary structure that is disordered. The detailed structure of the molten globule state is unknown, however. Through the use of computer simulations we can study the structural changes which occur upon lowering pH. The simulations presented here differ from previous unfolding simulations in two important ways: the electrostatic interactions are treated more accurately than ever before, and artificially high temperatures are not used to force the protein to unfold. Simulations of 880 psec each were run at pH 7 (control simulation) and pH 2. We concentrate on the interesting changes in the tertiary interactions within the protein with lowering of pH. In particular, there is a loss of native tertiary contacts in the beta domain and interdomain region, and a large decrease in interdomain hydrogen bonds.

Computer Simulation↗

PubMed1993

Theoretical probes of conformational fluctuations in S-peptide and RNase A/3'-UMP enzyme product complex.

The dynamic properties of the RNase A/3'-UMP enzyme/product complex and the S-peptide of RNase A have been investigated by molecular dynamics simulations using suitable generalization of ideas introduced to probe the energy landscape in structural glasses. We introduce two measures, namely, the kinetic energy fluctuation metric and the force metric, both of which are used to calculate the time needed for sampling the conformation space of the molecules. The calculation of the fluctuation metric requires a single trajectory whereas the force metric is computed using two independent trajectories. The vacuum MD simulations show that for both systems the time required for kinetic energy equipartitioning is surprisingly long even at high temperatures. We show that the force metric is a powerful means of probing the nature and relative importance of conformational substates which determine the dynamics at low temperatures. In particular the time dependence of the non-bonded force metric is used to demonstrate that at low temperatures the system is predominantly localized in a single cluster of conformational substates. The force metric is used to show that relaxation of long range (in sequence space) interactions must be mediated by a sequence of local dihedral angle transitions. We also argue that the time needed for compact structure formation is intimately related to the time needed for the relaxation of the dihedral angle degrees of freedom. The time for non-bonded interactions, which drive protein molecules to fold under appropriate conditions, to relax becomes extremely long as the temperature is lowered suggesting that the formation of maximally compact structure in proteins must be a very slow process.

Computer Simulation↗