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PubMedDate not supplied

Using difference intervals for time-varying isosurface visualization.

We present a novel approach to out-of-core time-varying isosurface visualization. We attempt to interactively visualize time-varying datasets which are too large to fit into main memory using a technique which is dramatically different from existing algorithms. Inspired by video encoding techniques, we examine the data differences between time steps to extract isosurface information. We exploit span space extraction techniques to retrieve operations necessary to update isosurface geometry from neighboring time steps. Because only the changes between time steps need to be retrieved from disk, I/O bandwidth requirements are minimized. We apply temporal compression to further reduce disk access and employ a point-based previewing technique that is refined in idle interaction cycles. Our experiments on computational simulation data indicate that this method is an extremely viable solution to large time-varying isosurface visualization. Our work advances the state-of-the-art by enabling all isosurfaces to be represented by a compact set of operations.

Journal Article↗

PubMedDate not supplied

Dendritic integration in ganglion cells of the mudpuppy retina.

Computer simulations were carried out to evaluate the influence of varying the membrane resistance (Rm) on the dendritic integration capacity of three classes of ganglion cells in the mudpuppy (Necturus maculosus) retina. Three broadly different morphological classes of ganglion cells were selected for this study and represent the range of dendritic tree sizes found in the ganglion cell population of this species. Simulations were conducted on anatomical data obtained from cells stained with horseradish peroxidase; each cell was traced, using a computer as an entry device and later converted to a compartmental (electrical) representation of the cell. Computer-simulation analysis used a time-variant conductance change which was similar in waveform to light-activated bipolar cell input. The simulated membrane resistance for each cell varied between 5000 and 100,000 omega cm2, and conductance changes were introduced into different regions of the soma-dendritic tree to evaluate dendritic integration efficiency. When higher values of Rm are used, even the largest cells become electronically compact and attenuation of voltage responses is minimized from distal to soma regions. Responses were less attenuated from proximal to distal regions of the cell because of the favorable impedance matching, and because less current is required to polarize small "sealed" dendritic terminations. Steady-state responses integrate more effectively than transient responses, particularly when Rm is high, since transient responses were more attenuated by the membrane capacitance. The possibility that Rm is a dynamic property of retinal ganglion cells is discussed in view of the functional organization of dendritic integration efficiency as Rm fluctuates from low to high values.

Animals↗

PubMed2006

A molecular dynamics study of the effect of Ca2+ removal on calmodulin structure.

Calmodulin is a small (148 residues), ubiquitous, highly-conserved Ca(2+) binding protein serving as a modulator of many calcium-dependent processes. In this study, we followed, by means of molecular dynamics, the structural stability of the protein when one of its four bound Ca(2+) ions is removed, and compared it to a simulation of the fully Ca(2+) bound protein. We found that the removal of a single Ca(2+) ion from the N-lobe of the protein, which has a lower affinity for the ion, is sufficient to initiate a considerable structural rearrangement. Although the overall structure of the fully 4 Ca(2+) bound protein remained intact in the extended conformation, the Ca(2+)-removed protein changed its conformation into a compact state. The observation that the 3 Ca(2+) loaded protein assumes a compacted solution state is in accord with experimental observation that the NSCP protein, which binds only three Ca(2+) ions, is natively in a compact state. Examination of the folding dynamics reveals a cooperation between the C-lobe, N-lobe, and the interdomain helix that enable the conformation change. The forces driving this conformational change are discussed.

Animals↗

PubMed2005

Molecular simulations for the conformational assessment of a porphyrin-fullerene dyad in different environments.

Conformational space of a porphyrin-fullerene dyad with the donor and acceptor connected by a relatively flexible linker is studied by molecular dynamics simulations in both non-polar and polar solvents, as well as in vacuum. The most probable conformations obtained from the vacuum MD simulations were optimized with semi-empirical (SE) and density functional theory (DFT) methods and the extent of the structural changes is assessed. The computational results indicate the co-existence of different conformers in both polar and nonpolar solvents showing agreement with experimental results. The most probable vacuum conformations at 300 K are similar to the ones at 0 K, while the structures most often observed in the solvents show less compact conformations. Optimization with SE and DFT calculations leads to structures, which represent relatively well the folded conformations in solvent, which validates the electronic structure calculations relevant to describing photoinduced electron-transfer in H2P-O34-C60.

Computer Simulation↗

PubMed2025

Molecular dynamics simulations reveal subtle consequences of H3K9 and H3K27 tri-methylation on chromatin constituents.

Epigenetic modifications of histone tails are key mechanisms of genome regulation. In particular, tri-methylation of lysines (K) 9 and K27 of the histone H3 tail is important for genome silencing. In this work, we explore, using all-atom molecular dynamics simulations, the effect of these two epigenetic marks on the structure and interactions of the H3 tail in several contexts: isolated tails, nucleosomes, chromatosomes, and stacked nucleosomes. Overall, we find that although the isolated tails do not show significant conformational changes upon methylation, a more flexible and extended H3 tail compared to the native tail results in the nucleosome systems, with K9 methylation effects more pronounced. This change could facilitate the interaction of the tail with protein readers like heterochromatin protein 1 or Polycomb group. We also observe that both methylations increase the interactions of the H3 tail with the linker DNA in the context of the chromatosome, producing a chromatosome with tighter linker DNA, which could favor chromatin compaction. For stacked nucleosomes mimicking i±2 zigzag interactions, methylation of either K9 or K27 reduces the interactions of one of the H3 tails with its parental nucleosome and increases its interactions with the nonparental nucleosome, which could also help compact the chromatin fiber. In the three nucleosome-containing systems, we observe an asymmetry between the two tails, especially in the chromatosome, where one tail extends to interact with the linker DNA. This asymmetry modulates the effect that methylation has on each tail. Thus, overall, methylations of K9 and K27 have a subtle but notable impact on the H3 tail structure and its interactions within the chromatin fiber. These results help explain how this epigenetic modification compacts chromatin fibers and promotes longer-range interactions; these changes also guide how to approximate these effects in coarse-grained chromatin models.

Histones↗

PubMed2004

Structural similarity of E. coli 5S rRNA in solution and within the ribosome.

The article presents translational and rotational diffusion coefficients of 5S rRNA determined experimentally by the method of dynamic light scattering (DLS) and its comparison with the values predicted for different models of this molecule. The tertiary structure of free 5S rRNA was proposed on the basis of the atomic structures of the 5S rRNA from E. coli and H. marismortui extracted from the ribosome. A comparison of the values of DT, tauR, and Rg predicted for different models with experimental results for the free molecule in solution suggests that free 5S rRNA is less compact than that in the complex with ribosomal proteins. In general, the molecules of 5S rRNA consist of three domains: a short one and two longer ones. As follows from a comparison of the results of our simulations with experimental values, in the molecule in solution the two closest helical fragments of the longer domains remain collinear, whereas the short domain takes a position significantly deviated from them.

Base Sequence↗

PubMed1990

Determination of the conformation of Lewis blood group oligosaccharides by simulation of two-dimensional nuclear Overhauser data.

Through control of both the nmr probe temperature and of the solvent viscosity, phase-sensitive two-dimensional 1H nuclear Overhauser data (NOESY) at 300 and 500 MHz are obtained with excellent signal-to-noise ratios for Lewis blood group penta- and hexasaccharides isolated from human milk. Relatively long mixing times are required to produce measurable NOE intensities in these oligosaccharides, which makes a full relaxation matrix analysis necessary. By measurements of selective T1 for a few isolated 1H resonances, it was possible to generate a simulation of the complete NOESY spectrum at arbitrary mixing time for comparison with the experimental data. From an exhaustive search of the conformational space, it was found that only a small range of glycosidic dihedral angles of the nonreducing terminal Lewis blood group determinant fragments of the milk oligosaccharides LNF-2 and LND-1 produce simulated spectra agreeing within experimental error to the data. Conformational energy calculations reveal that each of these conformations is also one of minimum energy. It is concluded that the Lewis(a) and Lewis(b) oligosaccharides adopt relatively compact rigid structures in solution, as shown by the observation of cross peaks between protons in nonadjacent residues. Like the blood group A and H oligosaccharides, there exists only a small dependence of the conformation for Lewis(a) and Lewis(b) oligosaccharides on solvent. The apparent lack of dependence of conformation of these oligosaccharides on DMSO in D2O suggests that modification of solvent viscosity with mixtures of DMSO:D2O may provide a useful general strategy of NOESY studies of oligosaccharides.

Carbohydrate Conformation↗

PubMed2001

Compression forces and amount of outer coating layer affecting the time-controlled disintegration of the compression-coated tablets prepared by direct compression with micronized ethylcellulose.

The influence of compression force to inner core tablet or to outer coating layer of the compression-coated tablet on the function of time-controlled disintegration was investigated. The inner core tablet was directly compacted by sodium diclofenac (model drug) and ethylcellulose (EC) with 4.6-microm particle size was used as an outer coating layer. The immersion time of the compression-coated tablet previously soaked in pH 1.2 solution to simulate the residence time of the tablet in the GI tract affecting the dissolution behavior of the compression-coated tablet was also investigated. The effect of the amount of the outer coating layer used on the drug release was examined. The results indicate that sodium diclofenac released from these compression-coated tablets exhibited a longer lag of a period about 16.3 h in both distilled water and pH 6.8 buffer solution, followed by a different drug release behavior. The lag time was independent of the pH of dissolution medium, and the immersion time in pH 1.2 solution. After that lag time, the outer shell of the compression-coated tablets broke into two halves to make a rapid drug release. However, the drug release behavior of the soaked tablet in pH 6.8 buffer solution was dependent on the immersion time. The compression force < 200 kg/cm(2) to the inner core tablet influenced the release behavior of drug less, but > 200 kg/cm(2) might delay the lag time. The lag time of the compression-coated tablets was linearly correlated with the compression force to the outer coating layer (r = 0.9896). We also found that the more the amount of outer coating layer added, the longer the lag time obtained. The study demonstrates that the time-controlled disintegration of the compression-coated tablet was effectively controlled by the compression force applied and the amount of outer coating layer added.

Cellulose↗

PubMed2006

Characterizing the conformational ensemble of monomeric polyglutamine.

Studies of synthetic polyglutamine peptides in vitro have established that polyglutamine peptides aggregate via a classic nucleation and growth mechanism. Chen and colleagues [Proc Natl Acad Sci U S A 2002;99:11884-11889] have found that monomeric polyglutamine, which is a disordered statistical coil in solution, is the critical nucleus for aggregation. Therefore, nucleation of beta-sheet-rich aggregates requires an initial disorder to order transition, which is a highly unfavorable thermodynamic reaction. The questions of interest to us are as follows: What are the statistical fluctuations that drive beta-sheet formation in monomeric polyglutamine? How do these fluctuations vary with chain length? And why is this process thermodynamically unfavorable, that is, why is monomeric polyglutamine disordered? To answer these questions we use multiple molecular dynamics simulations to provide quantitative characterization of conformational ensembles for two short polyglutamine peptides. We find that the ensemble for polyglutamine is indeed disordered. However, the disorder is inherently different from that of denatured proteins and the average compactness and magnitude of conformational fluctuations increase with chain length. Most importantly, the effective concentration of sidechain primary amides around backbone units is inherently high and peptide units are solvated either by hydrogen bonds to sidechains or surrounding water molecules. Due to the multiplicity of backbone solvation modes the probability associated with any specific backbone conformation is small, resulting in a conformational entropy bottleneck which makes beta-sheet formation in monomeric polyglutamine thermodynamically unfavorable.

Algorithms↗

PubMed1998

Determination of the three-dimensional solution structure of Raphanus sativus antifungal protein 1 by 1H NMR.

Raphanus sativus Antifungal Protein 1 (Rs-AFP1) is a 51 amino acid residue plant defensin isolated from radish (Raphanus sativus L.) seeds. The three-dimensional structure in aqueous solution has been determined from two-dimensional 1H NMR data recorded at 500 MHz using the DIANA/REDAC calculation protocols. Experimental constraints consisted of 787 interproton distances extracted from NOE cross-peaks, 89 torsional constraints from 106 vicinal interproton coupling constants and 32 stereospecific assignments of prochiral protons. Further refinement by simulated annealing resulted in a set of 20 structures having pairwise root-mean-square differences of 1.35(+/- 0.35) A over the backbone heavy atoms and 2.11(+/- 0.46) A over all heavy atoms. The molecule adopts a compact globular fold comprising an alpha-helix from Asn18 till Leu28 and a triple-stranded beta-sheet (beta 1 = Lys2-Arg6, beta 2 = His33-Tyr38 and beta 3 = His43-Pro50). The central strand of this beta-sheet is connected by two disulfide bridges (Cys21-Cys45 and Cys25-Cys47) to the alpha-helix. The connection between beta-strand 2 and 3 is formed by a type VIa beta-turn. Even the loop (Pro7 to Asn17) between beta-strand 1 and the alpha-helix is relatively well defined. The structure of Raphanus sativus Antifungal Protein 1 features all the characteristics of the "cysteine stabilized alpha beta motif". A comparison of the complete structure and of the regions important for interaction with the fungal receptor according to a mutational study, is made with the structure of gamma-thionin, a plant defensin that has no antifungal activity. It is concluded that this interaction is both electrostatic and specific, and some possible scenarios for the mode of action are given.

Amino Acid Sequence↗

PubMed1994

Solution structure of PMP-D2, a 35-residue peptide isolated from the insect Locusta migratoria.

The three-dimensional solution structure of PMP-D2, a 35 amino acid peptide isolated from the insect Locusta migratoria, has been determined from two-dimensional 1H NMR spectroscopy data. The structure calculations were performed from 222 NOE-derived interproton distances and 11 dihedral angles calculated from the JHN-H alpha coupling constants, using either a combination of distance geometry and restrained simulated annealing or by restrained simulated annealing alone. PMP-D2 contains three disulfide bridges that have been assigned from NMR data and structure calculations and independently confirmed using chemical and enzymatic methods. The core region of PMP-D2 adopts a compact globular fold, stabilized by hydrophobic interactions, which consists of a short three-stranded antiparallel beta-sheet involving residues 8-11, 15-19, and 25-29. Back-calculation of the NOESY spectra was used to validate the final structures. Analysis of the CD spectra of PMP-D2 under various conditions of ionic strength and in the presence of organic solvents demonstrates the high stability of this molecule. PMP-D2 was recently shown to inhibit Ca2+ currents. This activity is discussed based on the comparison of PMP-D2 three-dimensional structure with the recently established three-dimensional structure of the Ca2+ channel blocker omega-conotoxin GVIA.

Amino Acid Sequence↗

PubMed2003

Algorithm and performance of a clinical IMRT beam-angle optimization system.

This paper describes the algorithm and examines the performance of an intensity-modulated radiation therapy (IMRT) beam-angle optimization (BAO) system. In this algorithm successive sets of beam angles are selected from a set of predefined directions using a fast simulated annealing (FSA) algorithm. An IMRT beam-profile optimization is performed on each generated set of beams. The IMRT optimization is accelerated by using a fast dose calculation method that utilizes a precomputed dose kernel. A compact kernel is constructed for each of the predefined beams prior to starting the FSA algorithm. The IMRT optimizations during the BAO are then performed using these kernels in a fast dose calculation engine. This technique allows the IMRT optimization to be performed more than two orders of magnitude faster than a similar optimization that uses a convolution dose calculation engine. Any type of optimization criterion present in the IMRT system can be used in this BAO system. An objective function based on clinically-relevant dose-volume (DV) criteria is used in this study. This facilitates the comparison between a BAO plan and the corresponding plan produced by a planner since the latter is usually optimized using a DV-based objective function. A simple prostate case and a complex head-and-neck (HN) case were used to evaluate the usefulness and performance of this BAO method. For the prostate case we compared the BAO results for three, five and seven coplanar beams with those of the same number of equispaced coplanar beams. For the HN case we compare the BAO results for seven and nine non-coplanar beams with that for nine equispaced coplanar beams. In each case the BAO algorithm was allowed to search up to 1000 different sets of beams. The BAO for the prostate cases were finished in about 1-2 h on a moderate 400 MHz workstation while that for the head-and-neck cases were completed in 13-17 h on a 750 MHz machine. No a priori beam-selection criteria have been used in achieving this performance. In both the prostate and the head-and-neck cases, BAO is shown to provide improvements in plan quality over that of the equispaced beams. The use of DV-based objective function also allows us to study the dependence of the improvement of plan quality offered by BAO on the DV criteria used in the optimization. We found that BAO is especially useful for cases that require strong DV criteria. The main advantages of this BAO system are its speed and its direct link to a clinical IMRT system.

Algorithms↗

PubMed2002

Exact and efficient discrete random walk method for time-dependent two-dimensional environments.

We present an exact method for speeding up random walk in two-dimensional complicated lattice environments. To this end, we derive the discrete two-dimensional probability distribution function for a diffusing particle starting at the center of a square of linear size s. This is used to propagate random walkers from the center of the square to sites which are nearest neighbors to its perimeter sites, thus saving O(s(2)) steps in numerical simulations. We discuss in detail how this method can be implemented efficiently. We examine its performance in the diffusion limited aggregation model which produces fractal structures, and in a one-sided step-growth model producing compact, fingerlike structures. We show that in both cases, the square propagator method reduces the computational effort by a factor proportional to the linear system size as compared to standard random walk.

Journal Article↗

PubMed2004

Synthetic view of two-dimensional aggregation.

Extensive Monte Carlo simulations using short-range and medium-range interactions reveal the existence of quasisteady out-of-equilibrium phases in two-dimensional (2D) atom or cluster aggregation at different coverages namely fractal-type, dendrites, compact islands with faceted or rough boundaries, as well as gas or fluid phases. Different aggregation processes are identified. For medium-range effective pair potentials such as the one used for copper atoms, 2D liquid droplets are found.

Journal Article↗

PubMed2002

Cooperative origin of low-density domains in liquid water.

We study clusters formed by water molecules possessing large enough tetrahedrality with respect to their nearest neighbors. Using Monte Carlo simulation of SPC/E water and Voronoi tessellation, we find that regions of lower density than the bulk are formed by accretion of molecules into clusters exceeding a minimum size. Clusters are predominantly linear objects and become less compact as they grow until they reach a size beyond which further accretion is not accompanied by a density decrease. The results suggest that the formation of "icelike" regions in liquid water is cooperative.

Journal Article↗

PubMed2004

Magneto-optical nonreciprocal phase shift in garnet/silicon-on-insulator waveguides.

We demonstrate the integration of a single-crystal magneto-optical film onto thin silicon-on-insulator (SOI) waveguides by use of direct wafer bonding. Simulations show that the high confinement and asymmetric structure of SOI allows an enhancement of approximately 3x over the nonreciprocal phase shift achieved in previous designs; this value is confirmed by our measurements. Our structure will allow compact magneto-optical nonreciprocal devices, such as isolators, integrated on a silicon waveguiding platform.

Journal Article↗

PubMed1998

Polysaccharide film-coating process for freely swellable hydrogels.

In order to control the drug release from coated hydrogels by preventing membrane fractures, an intramembrane freely swellable matrix device was designed by enclosing a void space between a crosslinked poly(vinyl alcohol) (PVA) matrix and a calcium alginate membrane. The highly swellable PVA matrix loaded with diltiazem hydrochloride was obtained by means of a simplified procedure of the polymer crosslinking reaction using glutaraldehyde in solution with ammonium persulfate. The undried swollen matrix was coated with a calcium alginate membrane employing an ionotropic gelation of sodium alginate induced by calcium ions. The subsequent drying process generated a void space separating the inner core from the membrane. The resulting calcium alginate membrane, which was uniform and compact in the structure, increased in thickness according to the coating time. Coating times exceeding 5 min allowed modification of the drug release profile providing, after a short burst period, sustained and constant rate phases in both simulated gastric fluid and simulated intestinal fluid. Because the inner hydrogel expanded freely inside the device, the unstressed and intact membrane could act as the rate-controlling factor in the drug release process. Owing to the pH-dependent behavior of the membrane, most of the drug was delivered in intestinal fluid. Therefore, the device proposed could be advantageously used for drug targeting to the small intestine.

Drug Delivery Systems↗

PubMed2002

Combining location and expression data for principled discovery of genetic regulatory network models.

We develop principled methods for the automatic induction (discovery) of genetic regulatory network models from multiple data sources and data modalities. Models of regulatory networks are represented as Bayesian networks, allowing the models to compactly and robustly capture probabilistic multivariate statistical dependencies between the various cellular factors in these networks. We build on previous Bayesian network validation results by extending the validation framework to the context of model induction, leveraging heuristic simulated annealing search algorithms and posterior model averaging. Using expression data in isolation yields results inconsistent with location data so we incorporate genomic location data to guide the model induction process. We combine these two data modalities by allowing location data to influence the model prior and expression data to influence the model likelihood. We demonstrate the utility of this approach by discovering genetic regulatory models of thirty-three variables involved in S. cerevisiae pheromone response. The models we automatically generate are consistent with the current understanding regarding this regulatory network, but also suggest new directions for future experimental investigation.

Bayes Theorem↗