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At least 217 records · Page 12Linked to original sources
PubMed2006

Electrostatic, steric, and hydration interactions favor Na(+) condensation around DNA compared with K(+).

Condensation of monovalent counterions around DNA influences polymer properties of the DNA chain. For example, the Na(+) ions show markedly stronger propensity to induce multiple DNA chains to assemble into compact structures compared with the K(+) ions. To investigate the similarities and differences in the sodium and potassium ion condensation around DNA, we carried out a number of extensive all-atom molecular dynamics simulations of a DNA oligomer consisting of 16 base pairs, [d(CGAGGTTTAAACCTCG)](2), in explicit water. We found that the Na(+) ions penetrate the DNA interior and condense around the DNA exterior to a significantly larger degree compared with the K(+) ions. We have provided a microscopic explanation for the larger Na(+) affinity toward DNA that is based on a combination of steric, electrostatic, and hydration effects. Unexpectedly, we found that the Cl(-) co-ions provide more efficient electrostatic screening for the K(+) ions than for the Na(+) ions, contributing to the larger Na(+) condensation around DNA. To examine the importance of the discrete nature of water and ions, we also computed the counterion distributions from the mean-field electrostatic theory, demonstrating significant disagreements with the all-atom simulations. Prior experimental results on the relative extent of the Na(+) and K(+) condensation around DNA were somewhat contradictory. Recent DNA compaction experiments may be interpreted to suggest stronger Na(+) condensation around DNA compared to K(+), which is consistent with our simulations. We also provide a simple interpretation for the experimentally observed increase in DNA electrophoretic mobility in the alkali metal series, Li(+) < Na(+) < K(+) < Rb(+). We compare the DNA segment conformational preferences in various buffers with the proposed NMR models.

DNA↗
PubMed2002

Particle in cell simulation of laser-accelerated proton beams for radiation therapy.

In this article we present the results of particle in cell (PIC) simulations of laser plasma interaction for proton acceleration for radiation therapy treatments. We show that under optimal interaction conditions protons can be accelerated up to relativistic energies of 300 MeV by a petawatt laser field. The proton acceleration is due to the dragging Coulomb force arising from charge separation induced by the ponderomotive pressure (light pressure) of high-intensity laser. The proton energy and phase space distribution functions obtained from the PIC simulations are used in the calculations of dose distributions using the GEANT Monte Carlo simulation code. Because of the broad energy and angular spectra of the protons, a compact particle selection and beam collimation system will be needed to generate small beams of polyenergetic protons for intensity modulated proton therapy.

Computer Simulation↗
PubMed1997

Ab initio protein folding simulations with genetic algorithms: simulations on the complete sequence of small proteins.

Ab-initio folding simulations have been performed on three small proteins using a genetic algorithm- (GA-) based search method which operates on an all atom representation. Simulations were also performed on a number of small peptides expected to be independent folding units. The present genetic algorithm incorporates the results of developments made to the method first tested in CASP1. Additional operators have been introduced into the search in order to allow the simulation of longer sequences and to avoid the simulation of longer sequences and to avoid premature free energy convergence. Secondary structure information derived from a consensus of eight methods and Monte Carlo simulations on sets of homologous sequences has been used to bias the starting populations used in the GA simulations. For the fragment simulations, the results generally have approximately correct local structure, but tend to be too compact, leading to poor RMS error values. One of the three small protein structures has the topology and most of the general organization correct, although many of the details are incorrect.

Algorithms↗
PubMed1998

Simulations of the structural and dynamical properties of denatured proteins: the "molten coil" state of bovine pancreatic trypsin inhibitor.

The dynamic nature of denatured, unfolded proteins makes it difficult to characterize their structures experimentally. To complement experiment and to obtain more detailed information about the structure and dynamic behavior of the denatured state, we have performed eleven 2.5 ns molecular dynamics simulations of reduced bovine pancreatic trypsin inhibitor (BPTI) at high temperature in water and a control simulation at 298 K, for a total of 30 ns of simulation time. In a neutral pH environment (acidic residues ionized), the unfolded protein structures were compact with an average radius of gyration 9% greater than the native state. The compact conformations resulted from the transient formation of non-native hydrophobic clusters, turns and salt bridges. However, when the acidic residues were protonated, the protein periodically expanded to a radius of gyration of 18 to 20 A. The early steps in unfolding were similar in the different simulations until passing through the major transition state of unfolding. Afterwards, unfolding proceeded through one of two general pathways with respect to secondary structure: loss of the C-terminal helix followed by loss of beta-structure or the opposite. To determine whether the protein preferentially sampled particular conformational substates in the denatured state, pairwise Calpha root-mean-square deviations were measured between all structures, but similar structures were found between only two trajectories. Yet, similar composite properties (secondary structure content, side-chain and water contacts, solvent accessible surface area, etc.) were observed for the structures that unfolded through different pathways. Somewhat surprisingly, the unfolded structures are in agreement with both past experiments suggesting that reduced BPTI is a random coil and more recent experiments providing evidence for non-random structure, demonstrating how ensembles of fluctuating structures can give rise to experimental observables that are seemingly at odds.

Aprotinin↗
PubMed2003

Cellular automata model simulating complex spatiotemporal structure of wide jams.

According to the empirical observation of highway traffic, inside wide moving jams there is a complex spatiotemporal structure: jam is not compact and relatively large values of the time and the distance headway are visible. We present a cellular automata model by introducing "jam headway" and "jammed status" to simulate that complex structure. Using computer simulations, the fundamental diagram, the space-time plots, the time series of the density in the jams, and the 1-min average data of this model are analyzed. It is shown that compared to other existing models, this model can display the experimental characteristics of the wide moving jams.

Journal Article↗
PubMed2004

Formation of partially ordered oligomers of amyloidogenic hexapeptide (NFGAIL) in aqueous solution observed in molecular dynamics simulations.

A combined total of more than 600.0 ns molecular dynamics simulations with explicit solvent have been carried on systems containing either four peptides or a single peptide to investigate the early-stage aggregation process of an amyloidogenic hexapeptide, NFGAIL (residues 22-27 of the human islet amyloid polypeptide). Direct observation of the aggregation process was made possible by placing four peptides in a box of water with an effective concentration of 158 mg/ml to enhance the rate of aggregation. Partially ordered oligomers containing multistrand beta-sheets were observed which could be the precursory structures leading to the amyloid-forming embryonic nuclei. Comparative simulations on a single peptide suggested that the combined effect of higher peptide concentration and periodic boundary condition promoted compact monomers and the short-range interpeptide interactions favored the beta-extended conformation. Of particular interest was the persistent fluctuation of the size of the aggregates throughout the simulations, suggesting that dissociation of peptides from the disordered aggregates was an obligatory step toward the formation of ordered oligomers. Although 95% of peptides formed oligomers and 44% were in beta-extended conformations, only 16% of peptides formed multistrand beta-sheets. The disordered aggregates were mainly stabilized by hydrophobic interactions while cross-strand main-chain hydrogen bonds manifested the ordered oligomers. The transition to the beta-extended conformation was mildly cooperative due to short-range interactions between beta-extended peptides. Taken together, we propose that the role of hydrophobic interaction in the early stage of aggregation is to promote disordered aggregates and disfavor the formation of ordered nuclei and dissociation of the disordered oligomers could be the rate-limiting step at the initiation stage.

Amyloid↗
PubMed2003

Modelling study on the protective role of OH radical scavengers and DNA higher-order structures in induction of single- and double-strand break by gamma-radiation.

PURPOSE: To quantify the protective effects of (non-histonic) OH-radical scavengers and DNA higher-order structures in induction of single- (ssbs) and double-strand breaks (dsbs) by gamma-rays. MATERIALS AND METHODS: Spatial distributions of energy depositions by gamma-rays in liquid water were modelled with the track structure modules of the biophysical simulation code PARTRAC. Such distributions were superimposed on different DNA structure models (e.g. linear DNA, SV40 'minichromosomes' and compact chromatin), and direct energy depositions in the sugar-phosphate were considered as potential (direct) ssbs. The diffusion and interaction of the main chemical species produced in liquid water radiolysis were explicitly simulated, and reactions of *OH with the sugar-phosphate were considered as potential (indirect) ssbs. Two ssb on opposite DNA strands within 10 base pairs were considered as one dsb. Yields of ssb and dsb Gy(-1) Dalton(-1) in different DNA target structures were calculated as a function of the *OH mean lifetime, whose inverse value was taken as representative of the scavenging capacity of the DNA environment. RESULTS AND CONCLUSIONS: A further validation of the models implemented in the PARTRAC code has been provided, thus allowing a better understanding of the mechanisms underlying DNA damage. More specifically, the protection due to *OH scavengers was separately quantified with respect to that due to histones and chromatin folding, which could be 'switched off' in the simulations. As expected, for a given value of the environment scavenging capacity, linear DNA was more susceptible to strand breakage than SV40 minichromosomes, which in turn showed higher damage yields with respect to cellular DNA due to the larger accessibility offered to *OH. Furthermore, by increasing the scavenging capacity, the break yields decreased in all structures and tended to coincide with direct damage yields. Very good agreement was found with available experimental data. Comparisons with data on 'nucleoid' DNA (i.e. unfolded and histone-depleted DNA) also suggested that the experimental procedures used to obtain such structures might lower the environment scavenging capacity owing to the loss of cellular scavengers.

DNA↗
PubMed2003

The 3-D model: comparison of parameters obtained from and by simulating different tableting machines.

The aim of this study is to apply 3-D modeling to data obtained from different tableting machines and for different compression wheels on a linear rotary tableting machine replicator. A new analysis technique to interpret these data by 3-D parameter plots is presented. Tablets were produced on an instrumented eccentric tableting machine and on a linear rotary tableting machine replicator. The materials used were dicalcium phosphate dihydrate (DCPD), spray-dried lactose, microcrystalline cellulose (MCC), hydroxypropyl methylcellulose (HPMC), and theophylline monohydrate. Tableting was performed to different maximum relative densities (rho (rel, max)). Force, time, and displacement were recorded during compaction. The 3-D data plots were prepared using pressure, normalized time, and porosity according to Heckel. A twisted plane was fitted to these data according to the 3-D modeling technique. The resulting parameters were analyzed in a 3-D parameter plot. The results show that the 3-D modeling technique can be applied to compaction cycles from different tableting machines as different as eccentric and rotary tableting machines (simulated). The relation of the data to each other is the same even when the absolute values are different. This is also true for different compression wheels used on the linear rotary tableting machine replicator. By using compression wheels of different sizes on this simulator, mainly time plasticity changes. By using bigger compression wheels for simulation, the materials deform slower at lower densification and they deform faster at higher densification. For brittle materials, the stages of higher densification are influenced; for plastically deforming materials, the stages of lower and higher densification can be influenced.

Computer Simulation↗
PubMed2007

Improved dissipative particle dynamics simulations of lipid bilayers.

The authors introduce a new parameterization for the dissipative particle dynamics simulations of lipid bilayers. In this parameterization, the conservative pairwise forces between beads of the same type in two different hydrophobic chains are chosen to be less repulsive than the water-water interaction, but the intrachain bead interactions are the same as the water-water interaction. For a certain range of parameters, the new bilayer can only be stretched up to 30% before it ruptures. Membrane tension, density profiles, and the in-plane lipid diffusion coefficient of the new bilayer are discussed in detail. They find two kinds of finite size effects that influence the membrane tension: lateral finite size effects, for which larger membranes rupture at a smaller stretch, and transverse finite size effects, for which tensionless bilayers are more compact in larger systems. These finite size effects become rather small when the simulation box is sufficiently large.

Computer Simulation↗
PubMed2003

Molecular dynamics simulation studies of cytochrome b5 from outer mitochondrial and microsomal membrane.

Two forms of cytochrome b(5) have been identified, associated with the outer membrane of liver mitochondria (OM cyt b(5)) and with the membrane of the endoplasmic reticulum (microsomal, Mc cyt b(5)). These proteins have very similar structures, but differ significantly in physical properties, with the OM cyt b(5) exhibiting a more negative reduction potential, higher stability, and stronger interactions with the heme. We perform molecular dynamics simulations to probe the structures and fluctuations of the two proteins in solution, to help explain the observed physical differences. We find that the structures of the two proteins, highly similar in the crystal, differ in position of a surface loop involving residues 49-51 in solution. Hydrophobic residues Ala-18, Ile-32, Leu-36, and Leu-47 tend to cluster together on the surface of rat OM cyt b(5), blocking water access to the protein interior. In bovine Mc cyt b(5), two of these positions, Ser-18 and Arg-47, are occupied by hydrophilic residues. This leads to breaking the hydrophobic cluster and allowing the protein to occupy a more open conformation. A measure of this structural transition is the opening of a cleft on the protein surface, which is 5 A wider in the OM cyt b(5) simulation compared to the Mc form. The OM protein also appears to have a more compact hydrophobic core in its beta-sheet region. These effects may be used to explain observed stability differences between the two proteins.

Amino Acid Sequence↗
PubMed2006

Comparison of the amount of nuclides released from the spent fuel in contact with and without a compacted bentonite block.

A spent LWR fuel specimen between Ca-bentonite blocks was leached in a simulated bentonite-saturated granitic water (SBGW) for 165 days and its results were compared with those of a specimen leached without a bentonite block. The amounts of Cs, Sb, Sr, Eu, Am, U and Pu released from a 4.3 mm thickness of a fuel pellet with a 50,400 MWD/MTU burn-up in the SBGW without a bentonite block were 2.2, 0.25, 0.15, 0.02, 0.01, 0.01 and approximately 5 x 10(-4)% of their inventories, respectively. However, the amounts of nuclides released from the specimen between the 1.4 Mg/m(3) bentonite blocks were decreased by three times at least. Moreover, the concentrations of the nuclides in the leachate were very low because most of them were retained in the bentonite blocks.

Bentonite↗
PubMed1995

Seven-helix bundles: molecular modeling via restrained molecular dynamics.

Simulated annealing via restrained molecular dynamics (SA/MD) has been used to model compact bundles of seven approximately (anti)parallel alpha-helices. Seven such helix bundles occur, e.g., in bacteriorhodopsin, in rhodopsin, and in the channel-forming N-terminal domain of Bacillus thuringiensis delta-endotoxin. Two classes of model are considered: (a) those consisting of seven Ala20 peptide chains; and (b) those containing a single polypeptide chain, made up of seven Ala20 helices linked by GlyN interhelix loops (where N = 5 or 10). Three different starting C alpha templates for SA/MD are used, in which the seven helices are arranged (a) on a left-handed circular template, (b) on a bacteriorhodopsin-like template, or (c) on a zig-zag template. The ensembles of models generated by SA/MD are analyzed in terms of their geometry and energetics, and the most stable structures from each ensemble are examined in greater detail. Structures resembling bacteriorhodopsin and structures resembling delta-endotoxin are both represented among the most stable structures. delta-Endotoxin-like structures arise from both circular and bacteriorhodopsin-like C alpha templates. A third helix-packing mode occurs several times among the stable structures, regardless of the C alpha template and of the presence or absence of interhelix loops. It is characterized by a "4 + 1" core, in which four helices form a distorted left-handed supercoil around a central, buried helix. The remaining two helices pack onto the outside of the core. This packing mode is comparable with that proposed for rhodopsin on the basis of two-dimensional electron crystallographic and sequence analysis studies.

Amino Acid Sequence↗
PubMed1998

Biomechanical behavior of the arterial wall and its numerical characterization.

This paper presents the biomechanical behavior of two types of rat arteries under the passive state of the vascular smooth muscles. The hyperelastic, highly nonlinear, incompressible and orthotropic stress-strain behavior of arteries is described by adopting a classical material model of the exponential type and a 'biphasic' one, recently proposed by the authors. In order to obtain the fundamental relations for a computer simulation the theoretical continuum-mechanical background is briefly reviewed in a compact manner as well. By using the new material model the study shows a significant improvement in approaching the experimental stress-strain data within the entire pressure domain (from 0 up to 200 mm Hg) and for various levels of prestretch encompassing physiological pressures and the individual in vivo axial prestretches.

Animals↗
PubMedDate not supplied

Analytical estimation of scaling behavior for the entanglement complexity of a bond network.

Geometrical entanglements in a polymer network can be characterized in terms of the mean number of projected bond-bond crossings, N. Here, we present an analytical method to study the dependence of N on the number of bonds in the network, n. Our approach shows the occurrence of power-law scaling, N - n(beta). The estimated upper bound to the exponent for maximally compact networks, Beta approximately 1.38, agrees well with the values observed in simulations of transient networks in liquids and in the folding features of native states of globular proteins.

Journal Article↗
PubMed2004

Mobilizing particles in a saturated zone during air sparging.

The mobilization of soil particles changes the porosity of saturated zone during air sparging. Soil porosity is shown to be correlated with soil electrical resistivity. This study performs porosity-resistivity tests to establish the relationship between porosity and resistivity of quartz sand. Experiments, involving a large sandbox to simulate the saturated zone, are then performed to compare the resistivity of compacted sand before air injection with that after air injection. The relevant data enable the mobilization of quartz sand particles to be quantified. Results of the experiments indicate the mobilization of sand particles and an increase in porosity directly proportional to the rate at which air is injected. Besides, a layer of fine-grained particles covered the compacted sand at the upper boundary of sandbox after each air injection experiment. This is direct evidence that finer particles were transported upward during air sparging. Two methods were applied to verify the results of this study. The first verification method indicated that changes in porosity increased directly proportional to the air injection rate, which is consistent with shear theory. The other validation method indicated that the mass of sand in the tank did not change after air sparging, which indicates that the resistivity-porosity method is unbiased.

Air↗
PubMedDate not supplied

Oscillations and irregular emission in networks of linear spiking neurons.

The dynamics of a network of randomly connected inhibitory linear integrate and fire (LIF) neurons (with a floor for the depolarization), in the presence of stochastic external afferent input, is considered in various parameter regimes of the neurons and of the network. Applying a technique recently introduced by Brunel and Hakim, we classify the regimes in which such a network has stable stationary states and in which spike emission rates oscillate. In the vicinity of the bifurcation line, the oscillation frequency and its amplitude are computed and compared with simulations. As for leaky IF neurons, the space of parameters can be compacted into two. Yet despite significant technical differences between the two models, related to both the different dynamics of the depolarization as well as to the different boundary conditions, the qualitative behavior is rather similar. The significance of LIF neurons and of the differences with leaky IF neurons is discussed.

Action Potentials↗
PubMed2005

Replica Ornstein-Zernike theory of adsorption in a templated porous material: interaction site systems.

Molecular templating offers the possibility of porous materials whose selectivity rivals the molecular recognition observed in nature. The design of templated materials requires a molecular understanding of the templating effect on the material structure and performance. We present here a theoretical description of adsorption in a model templated porous material. Our model material is a quenched, equilibrated mixture of template and matrix molecular species where the template component has been subsequently removed. We propose a set of site-site [i.e., reference interaction site model (RISM)] replica Ornstein-Zernike equations relating the correlation functions of template, matrix, and adsorbing fluid molecules. To test this approach, we focus here on systems interacting via hard-sphere site-site potentials and employ a Percus-Yevick closure. We consider chain and cluster species composed of up to five spheres and observe a range of effects associated with template structure, including higher affinity toward, and enhanced templating by, compact cluster molecules. We assess these effects by grand canonical Monte Carlo simulation and discuss their implication to the design of templated molecular recognition materials.

Adsorption↗
PubMed1991

The development of a test system for investigating the performances of personal aerosol samplers under actual workplace conditions.

The performances of new "total" aerosol samplers for use in workplaces are required to match the inhalability criteria as contained in the latest recommendations of the International Standards Organization (ISO) and the American Conference of Governmental Industrial Hygienists (ACGIH). In the past, practical evaluations have been carried out under idealized conditions in wind tunnels, and there is now the need to extend these to more realistic workplace conditions. This paper describes a new test system that was designed and built for this purpose. It consisted of a life-size mannequin mounted on a trolley so that it can be taken to and wheeled around in workplaces. The mannequin itself incorporated a robotic arm so that, under joystick control, it can be made to simulate a range of worker movements, orientations, and attitudes. An electronically controlled, compact breathing machine provided a range of typical breathing parameters for the mannequin. The pump also provided air movement for a number of personal samplers that were mounted on the torso of the mannequin and tested in that position. Sampler performance should be assessed by comparing directly the aerosol collected by the sampler with that inhaled by the mannequin (and collected on filters inside the head).

Aerosols↗