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PubMed2004

Thermodynamics of lattice heteropolymers.

We calculate thermodynamic quantities of hydrophobic-polar (HP) lattice proteins by means of a multicanonical chain-growth algorithm that connects the new variants of the Pruned-Enriched Rosenbluth Method and flat histogram sampling of the entire energy space. Since our method directly simulates the density of states, we obtain results for thermodynamic quantities of the system for all temperatures. In particular, this algorithm enables us to accurately simulate the usually difficult accessible low-temperature region. Therefore, it becomes possible to perform detailed analyses of the low-temperature transition between ground states and compact globules.

Algorithms↗

PubMed2004

Efficient learning algorithms for three-layer regular feedforward fuzzy neural networks.

A key step of using gradient descend methods to develop learning algorithms of a regular feedforward fuzzy neural network (FNN) is to differentiate max--min functions, which contain max and min operations. The paper aims at several objectives. First, investigate further the differentiation of max--min functions. Second, employ general fuzzy numbers, which include triangular and trapezoidal fuzzy numbers as special cases to define a three-layer regular FNN. The general fuzzy numbers related can be approximately determined by their corresponding finite level sets. So, we can approximately represent the input-output (I/O) relationship of the regular FNN as functions of the endpoints of all finite level sets. Third, a fuzzy back-propagation algorithm is presented. And to speed up the convergence of the learning algorithm, a fuzzy conjugate gradient algorithm for fuzzy weights and biases is developed, furthermore, the convergence of the algorithm is analyzed, systematically. Finally, some real simulations demonstrate the efficiency of our learning algorithms. The regular FNN is applied to the approximate realization of fuzzy inference rules and fuzzy functions defined on given compact sets.

Algorithms↗

PubMedDate not supplied

Chemical control of growth and morphological characteristics of anaplastic glioma cells.

Nerve growth factor (NGF) and glia maturation factor (GMF) reverse some of the transformed characteristics of T9 glioma cells (Marushige et al., Cancer Res 47: 4109-4115, 1987). As an attempt to define the mechanisms of such actions, various chemical agents which modulate second messenger systems were examined for their effects on growth and morphological characteristics of these cells. Administration of bromo-cAMP, forskolin and methylisobutylxanthine retarded cell growth and induced formation of long, branching processes which were similar to those induced by GMF. Perturbation of Ca2(+)-mediated processes by a Ca2+ ionophore, ionomycin, and by calmodulin antagonists, chlorpromazine and W-7, on the other hand, arrested cell growth, and caused clustering of cells, spreading of the cytoplasm and development of lamellipodium-like protrusions which were reminiscent of the effects of NGF. Administration of bromo-cAMP in combination with chlorpromazine, W-7 or ionomycin prevented spreading of the cytoplasm and produced compact cell bodies with well-developed processes. The results of this study demonstrate that modulation of specific second messenger systems by chemical agents are capable of simulating selective morphological changes inducible by NGF and GMF.

1-(5-Isoquinolinesulfonyl)-2-Methylpiperazine↗

PubMed1999

Folding protein models with a simple hydrophobic energy function: the fundamental importance of monomer inside/outside segregation.

The present study explores a "hydrophobic" energy function for folding simulations of the protein lattice model. The contribution of each monomer to conformational energy is the product of its "hydrophobicity" and the number of contacts it makes, i.e., E(h,c) = -Sigma N/i=1 c(i)h(i) = -(h.c) is the negative scalar product between two vectors in N-dimensional cartesian space: h = (h1,., hN), which represents monomer hydrophobicities and is sequence-dependent; and c = (c(1),., c(N)), which represents the number of contacts made by each monomer and is conformation-dependent. A simple theoretical analysis shows that restrictions are imposed concomitantly on both sequences and native structures if the stability criterion for protein-like behavior is to be satisfied. Given a conformation with vector c, the best sequence is a vector h on the direction upon which the projection of c - c is maximal, where c is the diagonal vector with components equal to c, the average number of contacts per monomer in the unfolded state. Best native conformations are suggested to be not maximally compact, as assumed in many studies, but the ones with largest variance of contacts among its monomers, i.e., with monomers tending to occupy completely buried or completely exposed positions. This inside/outside segregation is reflected on an apolar/polar distribution on the corresponding sequence. Monte Carlo simulations in two dimensions corroborate this general scheme. Sequences targeted to conformations with large contact variances folded cooperatively with thermodynamics of a two-state transition. Sequences targeted to maximally compact conformations, which have lower contact variance, were either found to have degenerate ground state or to fold with much lower cooperativity.

Models, Chemical↗

PubMed2005

On the salt-induced stabilization of pair and many-body hydrophobic interactions.

Salting-out of hydrophobic solutes in aqueous salt solutions and their relevance to salt effects on biophysical phenomena are now well appreciated. Although salt effects on hydrophobic transfer have been well studied, to our knowledge, no quantitative molecular simulation study of salt-induced strengthening of hydrophobic interactions has yet been reported. Here we present quantitative characterization of salt-induced strengthening of hydrophobic interactions at the molecular and nanoscopic length scales through molecular dynamics simulations. Specifically, we quantify the effect of NaCl on the potential of mean force between molecular hydrophobic solutes (methanes) and on conformational equilibria of a 25-mer hydrophobic polymer that efficiently samples ensembles of compact and extended states in water. In both cases, we observe relative stabilization of compact conformations that is accompanied by a clear depletion of salt density (preferential exclusion) and a slight enhancement of water density (preferential hydration) in the solute vicinity. We show that the structural details of salt exclusion can be related to the salt-induced free energy changes using preferential interaction coefficients. We also test the applicability of surface-area-based models to describe the salt-induced free energy changes. These models provide a useful empirical description that can be used to predict the effects of salt on conformational equilibria of hydrophobic solutes. However, we find that the effective increase in the surface tension of the solute-aqueous solution interface depends on the type and concentration of salt as well as the length-scale (i.e., molecular vs nanoscopic) of the conformational change. These calculations underscore the utility of simulation studies to connect quantitatively structural details at the molecular level (described by preferential hydration/exclusion) to macroscopic solvation thermodynamics. The hydrophobic polymer also provides a useful model for studies of effect of thermodynamic variables (P, T, salt/additives) on many-body hydrophobic interactions at nanometer length scales.

Computer Simulation↗

PubMed1994

Monte Carlo simulations of protein folding. II. Application to protein A, ROP, and crambin.

The hierarchy of lattice Monte Carlo models described in the accompanying paper (Kolinski, A., Skolnick, J. Monte Carlo simulations of protein folding. I. Lattice model and interaction scheme. Proteins 18:338-352, 1994) is applied to the simulation of protein folding and the prediction of 3-dimensional structure. Using sequence information alone, three proteins have been successfully folded: the B domain of staphylococcal protein A, a 120 residue, monomeric version of ROP dimer, and crambin. Starting from a random expanded conformation, the model proteins fold along relatively well-defined folding pathways. These involve a collection of early intermediates, which are followed by the final (and rate-determining) transition from compact intermediates closely resembling the molten globule state to the native-like state. The predicted structures are rather unique, with native-like packing of the side chains. The accuracy of the predicted native conformations is better than those obtained in previous folding simulations. The best (but by no means atypical) folds of protein A have a coordinate rms of 2.25 A from the native C alpha trace, and the best coordinate rms from crambin is 3.18 A. For ROP monomer, the lowest coordinate rms from equivalent C alpha s of ROP dimer is 3.65 A. Thus, for two simple helical proteins and a small alpha/beta protein, the ability to predict protein structure from sequence has been demonstrated.

Amino Acid Sequence↗

PubMed1992

Computer simulation of occupant neck response to airbag deployment in frontal impacts.

A mathematical simulation was performed to study the potential of head and neck injury to an unbelted driver restrained by an airbag. The baseline study represented a 50th percentile male dummy driving in a compact car with the steering wheel perpendicular to the floor. The vehicle was moving at 48 km/hour at the time of impact. Model predictions were compared with sled test results. The data agreed reasonably well. A parametric study was performed to study the effect of changing the steering wheel angle and the size of the airbag. It was found that when the standard 20 degrees angle steering wheel was used, neck joint torques were decreased by 22 percent while the resultant head acceleration increased 41 percent from the base line study. When the vertical dimension of the airbag was reduced by 10 percent, neck joint torques were increased by 14 percent, while head acceleration showed a slight decrease of 9 percent.

Acceleration↗

PubMed2005

[Simulation of lung lobe resection with personal computer].

Various patterns of branching are seen for pulmonary arteries and veins in the lung hilum. However, thoracic surgeons usually cannot expect to discern much anatomical detail preoperatively. If the surgeon can gain an understanding of individual patterns preoperatively, the risks inherent in exposing the pulmonary vessels in the hilum can be avoided, reducing invasiveness. This software will meet the increasing needs of them in video-assisted thoracoscopic surgery (VATS) which prefer lesser dissections of the vessels and bronchus of hilum. We have produced free application software, where we can mark on pulmonary arteries, vein, bronchus and tumor of the successive images of computed tomography (CT). After receiving a compact disk containing 60 images of 2 mm CT slices, from tumor to hilum, in DICOM format, we required only 1 hour to obtain 3-dimensional images for a patient with other free software (Metasequoia LE). Furthermore, with Metasequoia LE, we can simulate cut the vessels and change the figure of them 3-dimensionally. Although the picture image leaves much room for improvement, we believe it is very attractive for residents because they can simulate operations.

Computer Simulation↗

PubMed2005

Aggregation-fragmentation in a model of DNA-mediated colloidal assembly.

We present results from an off-lattice Monte Carlo simulation of DNA-mediated colloidal assembly. In this simulation, the aggregation-fragmentation of a binary mixture of DNA-coated colloidal particles is studied through a simplified model of base-pair hybridization. Bonding between monomers is modeled as a simple temperature-sensitive A/B-type interaction, where type A and B monomers can bond to only the opposite type (no A/A or B/B attachments are allowed). The actual chemistry of base-pair hybridization is not included in the model. The morphological structures of the clusters formed as well as the kinetics of growth are analyzed in our 2D simulations. The fractal dimension and kinetic growth exponents for clusters formed near the DNA "melting" temperature agree with those seen previously for 2D diffusion-limited cluster aggregation (DLCA) models. The clusters appear more compact, exhibiting signs of local order at intermediate temperature values. At higher temperatures, the formation of large clusters is not favorable under the action of temperature-dependent fragmentation, and the system eventually reaches a steady state as a collection of small aggregates. The temperature profile for this dissolution of the colloidal assembly is sharp, indicating that the selective hybridization process provides a highly sensitive measurement tool. At high temperatures, we analyze the steady-state behavior of the average cluster size in terms of an aggregation-fragmentation model.

Algorithms↗

PubMed2003

In situ heavy metal attenuation in landfills under methanogenic conditions.

The purpose of this research was to determine the fate and behavior of heavy metals co-disposed with municipal waste under methanogenic conditions. Two landfill simulating reactors, one with leachate recirculation and the other without, were operated in a constant room temperature at 32 degrees C. These reactors were filled with shredded and compacted municipal solid waste having a typical solid waste composition of Istanbul region. After the onset of the methanogenic conditions, the selected heavy metals including iron, copper, nickel, cadmium and zinc were added according to the amounts suggested for co-disposal under the directives of the Turkish Hazardous Waste Control Regulations. The results of the experiments indicated that about 90% of all heavy metals were precipitated from the reactors within the first 10 days due to the establishment of highly reducing environment and the formation of sulfide from sulfate reduction which provided heavy metal precipitation. No inhibition to the biological stabilization was observed.

Chemical Precipitation↗

PubMed2000

DNase I digestion reveals alternating asymmetrical protection of the nucleosome by the higher order chromatin structure.

DNase I was used to probe the higher order chromatin structure in whole nuclei. The digestion profiles obtained were the result of single-stranded cuts and were independent of pH, type of divalent ion and chromatin repeat length. Furthermore, the protection from digestion of the DNA at the entry/exit points on the nucleosome was found to be caused not by the H1/H5 histone tails, but by the compact structure that these proteins support. In order to resolve symmetry ambiguities, DNase I digestion fragments over several nucleosome repeat lengths were analysed quantitatively and compared with computer simulations using combinations of the experimentally obtained rate constants (some of which were converted to 0 to simulate steric protection from DNase I digestion). A clear picture of precisely defined, alternating, asymmetrically protected nucleosomes emerged. The linker DNA is inside the fibre, while the nucleosomes are positioned above and below a helical path and/or with alternating orientation towards the dyad axis. The dinucleosomal modulation of the digestion patterns comes from alternate protection of cutting sites inside the nucleosome and not from alternating exposure to the enzyme of the linker DNA.

Animals↗

PubMed2006

A novel akermanite bioceramic: preparation and characteristics.

Akermanite (Ca(2)MgSi(2)O(7)) ceramics are prepared by sintering akermanite powder compacts at 1370 C for 6 h. The sintering behavior and mechanical properties of akermanite ceramics are investigated. The bioactivity of akermanite ceramics is evaluated by soaking in simulated body fluid (SBF), and hydroxyapatite (HAp) formation on the surface of akermanite ceramics after soaking is characterized by X-ray diffraction (XRD), energy dispersive spectrometry (EDS), and scanning electron microscopy (SEM). The results show that the bending strength of akermanite ceramics can reach 176 MPa, the fracture toughness is 1.83 MPa m(1/2), and akermanite ceramics can induce HAp formation on their surface when soaked in SBF. Our results indicate that akermanite ceramics are bioactive, and possess improved mechanical properties compared with those of HAp ceramics and may be used as bioactive implant materials.

Biocompatible Materials↗

PubMed2004

Compact scalable diode-pumped Nd:YAG ceramic slab laser.

We describe our preliminary studies of the use of neodymium-doped slab-shaped ceramic YAG media in the construction of compact, rugged, high-power diode-pumped solid-state lasers. A maximum extraction of more than 160 W at a 20% slope efficiency level, with a narrow transverse direction beam-parameter product of the order of 4 mm mrad(-1) is experimentally obtained from an extremely simple and compact (overall dimensions 160 mm x 100 mm x 60 mm) laser head in a quasi-continuous-wave regime. Experimental data together with finite-elements method simulations indicate that power extraction can be scaled up at least to 900 W cw with this laser head geometry.

Journal Article↗

PubMed2004

Micellization behavior of star-block copolymers in a selective solvent: A Brownian dynamics simulation approach.

Micellization behavior of (AB)n type star-block copolymer in a selective solvent for its outer block is investigated by using a Brownian dynamics simulation. Micellar properties are compared in terms of the arm number (n) of star-block copolymer. It is observed that the critical micelle concentration (cmc) shows a minimum when the cmc is plotted against the arm number. The star-block copolymer with longer soluble block shows the cmc minimum at smaller arm number than that with shorter soluble block. Although the star-block copolymer with multiple arms forms more compact core as compared to diblock copolymer, the average aggregation number is inversely proportional to the arm number (approximately 1/n), which implies that the micelle size is invariant with the arm number. Theoretical predictions based on a simple mean field theory agree qualitatively well with the simulation results.

Journal Article↗

PubMed2001

The molecular basis for the inverse temperature transition of elastin.

Elastin undergoes an "inverse temperature transition" such that it becomes more ordered as the temperature increases. To investigate the molecular basis for this behavior, molecular dynamics simulations were conducted above and below the transition temperature. Simulations of a 90-residue elastin peptide, (VPGVG)(18), with explicit water molecules were performed at seven different temperatures between 7 and 42 degrees C, for a total of 80 ns. Beginning from an idealized beta-spiral structure, hydrophobic collapse was observed over a narrow temperature range in the simulations. Moreover, simulations above and below elastin's transition temperature indicate that elastin has more turns and distorted beta-structure at higher temperatures. Water was critical to the inverse temperature transition and elastin-associated water molecules can be divided into three categories: those closely associated with beta II turns; those that form hydrogen bonds with the main-chain groups; and those hydrating the hydrophobic side-chains. Water-swollen, monomeric elastin above the transition temperature is best described as a compact amorphous structure with distorted beta-strands, fluctuating turns, buried hydrophobic residues, and main-chain polar atoms that participate in hydrogen bonds with water. Below the transition temperature, elastin is expanded with approximately 40 % local beta-spiral structure. Overall the simulations are in agreement with experiment and therefore appear to provide an atomic-level description of the conformational properties of elastin monomers and the basis for their elastomeric properties.

Amino Acid Sequence↗

PubMed2002

Toward minimalist models of larger proteins: a ubiquitin-like protein.

Our recently developed off-lattice bead model capable of simulating protein structures with mixed alpha/beta content has been extended to model the folding of a ubiquitin-like protein and provides a means for examining the more complex kinetics involved in the folding of larger proteins. Using trajectories generated from constant-temperature Langevin dynamics simulations and sampling with the multiple multi-histogram method over five-order parameters, we are able to characterize the free energy landscape for folding and find evidence for folding through compact intermediates. Our model reproduces the observation that the C-terminus loop structure in ubiquitin is the last to fold in the folding process and most likely plays a spectator role in the folding kinetics. The possibility of a productive metastable intermediate along the folding pathway consisting of collapsed states with no secondary structure, and of intermediates or transition structures involving secondary structural elements occurring early in the sequence, is also supported by our model. The kinetics of folding remain multi-exponential below the folding temperature, with glass-like kinetics appearing at T/T(f) approximately 0.86. This new physicochemical model, designed to be predictive, helps validate the value of modeling protein folding at this level of detail for genomic-scale studies, and motivates further studies of other protein topologies and the impact of more complex energy functions, such as the addition of solvation forces.

Amino Acid Sequence↗

PubMed2005

Does water play a structural role in the folding of small nucleic acids?

Nucleic acid structure and dynamics are known to be closely coupled to local environmental conditions and, in particular, to the ionic character of the solvent. Here we consider what role the discrete properties of water and ions play in the collapse and folding of small nucleic acids. We study the folding of an experimentally well-characterized RNA hairpin-loop motif (sequence 5'-GGGC[GCAA]GCCU-3') via ensemble molecular dynamics simulation and, with nearly 500 micros of aggregate simulation time using an explicit representation of the ionic solvent, report successful ensemble folding simulations with a predicted folding time of 8.8(+/-2.0) micros, in agreement with experimental measurements of approximately 10 micros. Comparing our results to previous folding simulations using the GB/SA continuum solvent model shows that accounting for water-mediated interactions is necessary to accurately characterize the free energy surface and stochastic nature of folding. The formation of the secondary structure appears to be more rapid than the fastest ionic degrees of freedom, and counterions do not participate discretely in observed folding events. We find that hydrophobic collapse follows a predominantly expulsive mechanism in which a diffusion-search of early structural compaction is followed by the final formation of native structure that occurs in tandem with solvent evacuation.

Amino Acid Motifs↗

PubMed2002

Folding and stability of the three-stranded beta-sheet peptide Betanova: insights from molecular dynamics simulations.

The dynamics of the three-stranded beta-sheet peptide Betanova has been studied at four different temperatures (280, 300, 350, and 450 K by molecular dynamics simulation techniques, in explicit water. Two 20-ns simulations at 280 K indicate that the peptide remains very flexible under "folding" conditions sampling a range of conformations that together satisfy the nuclear magnetic resonance (NMR)-derived experimental constraints. Two simulations at 300 K (above the experimental folding temperature) of 20 ns each show partial formation of "native"-like structure, which also satisfies most of the NOE constraints at 280 K. At higher temperature, the presence of compact states, in which a series of hydrophobic contacts remain present, are observed. This is consistent with experimental observations regarding the role of hydrophobic contacts in determining the peptide's stability and in initiating the formation of turns and loops. A set of different structures is shown to satisfy NMR-derived distance restraints and a possible mechanism for the folding of the peptide into the NMR-determined structure is proposed.

Computer Simulation↗