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At least 415 records · Page 23Linked to original sources

PubMed2003

The evaluation of a synthetic long bone structure as a substitute for human tissue in gunshot experiments.

Our goal was to compare experimental gunshot wounds in our non-biological bone model with similarly created wounds in swine bones, and evaluate the results. The design of the synthetic (polyurethane) bone was patterned after human bone structure, with a compact outer layer covering a porous inner layer. Ordnance gelatin, as substitute bone marrow, was injected into the bone's hollow core. To simulate the periostium, the bone was covered with a layer of latex. Then the bone was embedded in gelatin used to simulate surrounding soft tissue. For comparison, fresh swine bones were also embedded in gelatin, and fired upon under the same guidelines. All gunshots were high-speed filmed. In our experimental study, gunshot wounds to swine bones, and to our synthetic, non-biological bones were compared. The results (the comparison between the biological swine bones and the non-biological model bones) in regard to the following points are absolutely equal: the loss of velocity and energy after striking bone, bone fragmentation, bullet deformation, and the penetrating wound channel. Continuing studies with our synthetic bone model will bring about an even greater understanding of the mechanisms of "bullet-bone interaction". For this reason, we have extended our variety of bone models to include other skeletal structures such as skull, spine, pelvis and flat bones for further gunshot experiments.

Animals↗

PubMed2000

Diffusion-limited aggregation: A relationship between surface thermodynamics and crystal morphology

We have combined the original diffusion-limited aggregation model introduced by Witten and Sander with the surface thermodynamics of the growing solid aggregate. The theory is based on the consideration of the surface chemical potential as a thermodynamic function of the temperature and nearest-neighbor configuration. The Monte Carlo simulations on a two-dimensional square lattice produce the broad range of shapes such as fractal dendritic structures, densely branching patterns, and compact aggregates. The morphology diagram illustrating the relationship between the model parameters and cluster geometry is presented and discussed.

Journal Article↗

PubMed2006

Noncompact crystalline solids in the square-well potential.

We reexamine the phase diagram of the square-well potential, using both theoretical and computer-simulation techniques, for not too short ranges of the potential. The phase diagram turns out to contain a variety of crystalline structures, both compact and, interestingly, also noncompact. The latter result from a large increase in negative energy when pairs of particles come at distances within the interaction range, which more than compensates the entropy loss associated with reduced packing. Transitions between these crystalline structures give rise to a surprisingly rich phase diagram.

Journal Article↗

PubMed2000

Characterization of collective and anisotropic reorientational protein dynamics.

Intramolecular reorientational dynamics of proteins are described in terms of reorientational quasiharmonic modes. These modes provide important insight into anisotropic and collective axial fluctuations of distinct molecular fragments, and they represent a highly compact description of intramolecular protein motions that are spectroscopically observable via nuclear spin relaxation. The method is applied to a molecular dynamics computer simulation of the protein ubiquitin.

Anisotropy↗

PubMed2004

Cationic DMPC/DMTAP lipid bilayers: molecular dynamics study.

Cationic lipid membranes are known to form compact complexes with DNA and to be effective as gene delivery agents both in vitro and in vivo. Here we employ molecular dynamics simulations for a detailed atomistic study of lipid bilayers consisting of a mixture of cationic dimyristoyltrimethylammonium propane (DMTAP) and zwitterionic dimyristoylphosphatidylcholine (DMPC). Our main objective is to examine how the composition of the DMPC/DMTAP bilayers affects their structural and electrostatic properties in the liquid-crystalline phase. By varying the mole fraction of DMTAP, we have found that the area per lipid has a pronounced nonmonotonic dependence on the DMTAP concentration, with a minimum around the point of equimolar DMPC/DMTAP mixture. We show that this behavior has an electrostatic origin and is driven by the interplay between positively charged TAP headgroups and the zwitterionic phosphatidylcholine (PC) heads. This interplay leads to considerable reorientation of PC headgroups for an increasing DMTAP concentration, and gives rise to major changes in the electrostatic properties of the lipid bilayer, including a significant increase of total dipole potential across the bilayer and prominent changes in the ordering of water in the vicinity of the membrane. Moreover, chloride counterions are bound mostly to PC nitrogens implying stronger screening of PC heads by Cl ions compared to TAP headgroups. The implications of these findings are briefly discussed.

Computer Simulation↗

PubMed1992

Trefoil knotting revealed by molecular dynamics simulations of supercoiled DNA.

Computer simulations of the supercoiling of DNA, largely limited to stochastic search techniques, can offer important information to complement analytical models and experimental data. Through association of an energy function, minimum-energy supercoiled conformations, fluctuations about these states, and interconversions among forms may be sought. In theory, the observation of such large-scale conformational changes is possible, but modeling and numerical considerations limit the picture obtained in practice. A new computational approach is reported that combines an idealized elastic energy model, a compact B-spline representation of circular duplex DNA, and deterministic minimization and molecular dynamics algorithms. A trefoil knotting result, made possible by a large time-step dynamics scheme, is described. The simulated strand passage supports and details a supercoiled-directed knotting mechanism. This process may be associated with collective bending and twisting motions involved in supercoiling propagation and interwound branching. The results also demonstrate the potential effectiveness of the Langevin/implicit-Euler dynamics scheme for studying biomolecular folding and reactions over biologically interesting time scales.

Chemical Phenomena↗

PubMed2001

Use of a Shack-Hartmann aberrometer to assess the optical outcome of corneal transplantation in a keratoconic eye.

We report the optical outcome of corneal transplantation treatment on a keratoconic eye as measured with a Shack-Hartmann aberrometer, and we compare the results with the recovery of visual acuity after surgery. Before surgery, the naked keratoconic eye exhibited extremely large aberrations that could not be measured unless the patient wore a rigid gas-permeable contact lens. With the lens, the computed point-spread function of the eye was large and multimodal, and simulated retinal images confirmed the patient's subjective report of multiple, overlapping images. After full recovery from surgery, aberrations of the corrected eye were much smaller compared with the presurgical eye, which implied a more compact point-spread function and clearer retinal images. These optical changes were mirrored by an improvement in uncorrected visual acuity from 1.3 logarithm of the minimum angle of resolution (logMAR) before surgery to 0 logMAR with spectacle correction after full recovery. We conclude that the Shack-Hartmann aberrometer provides an objective, quantitative assessment of the optical outcome of penetrating keratoplasty that allows the clinician to measure retinal image quality objectively and to accurately simulate the complex visual distortions associated with keratoconus.

Cornea↗

PubMed2003

Effects of confinement in chaperonin assisted protein folding: rate enhancement by decreasing the roughness of the folding energy landscape.

Chaperonins, such as the GroE complex of the bacteria Escherichia coli, assist the folding of proteins under non-permissive folding conditions by providing a cavity in which the newly translated or translocated protein can be encapsulated. Whether the chaperonin cage plays a passive role in protecting the protein from aggregation, or an active role in accelerating folding rates, remains a matter of debate. Here, we investigate the role of confinement in chaperonin mediated folding through molecular dynamics simulations. We designed a substrate protein with an alpha/beta sandwich fold, a common structural motif found in GroE substrate proteins and confined it to a spherical hydrophilic cage which mimicked the interior of the GroEL/ES cavity. The thermodynamics and kinetics of folding were studied over a wide range of temperature and cage radii. Confinement was seen to significantly raise the collapse temperature, T(c), as a result of the associated entropy loss of the unfolded state. The folding temperature, T(f), on the other hand, remained unaffected by encapsulation, a consequence of the folding mechanism of this protein that involves an initial collapse to a compact misfolded state prior to rearranging to the native state. Folding rates were observed to be either accelerated or retarded compared to bulk folding rates, depending on the temperature of the simulation. Rate enhancements due to confinement were observed only at temperatures above the temperature T(m), which corresponds to the temperature at which the protein folds fastest. For this protein, T(m) lies above the folding temperature, T(f), implying that encapsulation alone will not lead to a rate enhancement under conditions where the native state is stable (T<T(f)). For confinement to positively impact folding rates under physiological conditions, it is hence necessary for the protein to exhibit a folding transition above the temperature at which it exhibits its fastest folding rate (T(m)<T(f)). We designed a protein with this property by reducing the energetic frustration in the original alpha/beta sandwich substrate protein. The modified protein exhibited a twofold acceleration in folding rates upon encapsulation. This rate enhancement is due to a mechanistic change in folding involving the elimination, upon encapsulation, of accessible local energy minima corresponding to structures with large radii of gyration. For this protein, confinement hence plays more than the role of a passive cage, but rather adopts an active role, accelerating folding rates by decreasing the roughness of the energy landscape of the protein.

Chaperonin 60↗

PubMed1999

Structure of a beheaded 30 S ribosomal subunit from Thermus thermophilus.

The 22 S ribonucleoproten particles containing the 5' (body) and the central (platform) domains of the Thermus thermophilus 30 S subunit has been studied by sedimentation, neutron scattering and electron microscopy. The RNP particles have been obtained by oligonucleotide-directed cleavage of 16 S RNA with ribonulease H in the region of the 900th nucleotide of the protein-deficient derivatives of the 30 S subunits. It is shown that these RNP particles are very compact, though their form and dimensions differ slightly from those expected from the electron microscopy model of the 30 S subunit beheaded by computer simulation. The particles are subdivided into two structural domains whose mutual arrangement differs from that of the corresponding morphological parts of the native 30 S subunit. Electron microscopy demonstrates that the mutual arrangement of domains in the RNP particles is not strictly fixed suggesting that interaction with the third domain of the 30 S subunit is a requisite for their correct fitting.

Computer Simulation↗

PubMed1991

A self-organizing multiple-view representation of 3D objects.

We explore representation of 3D objects in which several distinct 2D views are stored for each object. We demonstrate the ability of a two-layer network of thresholded summation units to support such representations. Using unsupervised Hebbian relaxation, the network learned to recognize ten objects from different viewpoints. The training process led to the emergence of compact representations of the specific input views. When tested on novel views of the same objects, the network exhibited a substantial generalization capability. In simulated psychophysical experiments, the network's behavior was qualitatively similar to that of human subjects.

Cybernetics↗

PubMed2002

Structure and dynamics of zymogen human blood coagulation factor X.

The solution structure and dynamics of the human coagulation factor X (FX) have been investigated to understand the key structural elements in the zymogenic form that participates in the activation process. The model was constructed based on the 2.3-A-resolution x-ray crystallographic structure of active-site inhibited human FXa (PDB:1XKA). The missing gamma-carboxyglutamic acid (GLA) and part of epidermal growth factor 1 (EGF1) domains of the light chain were modeled based on the template of GLA-EGF1 domains of the tissue factor (TF)-bound FVIIa structure (PDB:1DAN). The activation peptide and other missing segments of FX were introduced using homology modeling. The full calcium-bound model of FX was subjected to 6.2 ns of molecular dynamics simulation in aqueous medium using the AMBER6.0 package. We observed significant reorientation of the serine-protease (SP) domain upon activation leading to a compact multi-domain structure. The solution structure of zymogen appears to be in a well-extended conformation with the distance between the calcium ions in the GLA domain and the catalytic residues estimated to be approximately 95 A in contrast to approximately 83 A in the activated form. The latter is in close agreement with fluorescence studies on FXa. The S1-specificity residues near the catalytic triad show significant differences between the zymogen and activated structures.

1-Carboxyglutamic Acid↗

PubMed2006

Solution structure and functional importance of a conserved RNA hairpin of eel LINE UnaL2.

The eel long interspersed element (LINE) UnaL2 and its partner short interspersed element (SINE) share a conserved 3' tail that is critical for their retrotransposition. The predicted secondary structure of the conserved 3' tail of UnaL2 RNA contains a stem region with a putative internal loop. Deletion of the putative internal loop region abolishes UnaL2 mobilization, indicating that this putative internal loop is required for UnaL2 retrotransposition; the exact role of the putative internal loop in retrotransposition, however, has not been elucidated. To establish a structure-based foundation on which to address the issue of the putative internal loop function in retrotransposition, we used NMR to determine the solution structure of a 36 nt RNA derived from the 3' conserved tail of UnaL2. The region forms a compact structure containing a single bulged cytidine and a U-U mismatch. The bulge and mismatch region have conformational flexibility and molecular dynamics simulation indicate that the entire stem of the 3' conserved tail RNA can anisotropically fluctuate at the bulge and mismatch region. Our structural and mutational analyses suggest that stem flexibility contributes to UnaL2 function and that the bulged cytidine and the U-U mismatch are required for efficient retrotransposition.

Animals↗

PubMed2005

Pulmonary sarcoidosis induced by interferon-alpha therapy.

Recombinant interferon-alpha (IFN-alpha) is being increasingly used in the treatment of chronic hepatitis C. It has been recently recognized that IFN-alpha can induce the development of sarcoidosis, presumably through its ability to stimulate the TH1 immune response. IFN-associated sarcoidosis is histologically similar to de novo sarcoidosis and is characterized by tightly compact epithelioid non-necrotizing granulomas. IFN-induced sarcoidosis may be unsuspected clinically, as the most common side effects of IFN-alpha simulate the symptoms of sarcoidosis. It is therefore important for pathologists to be aware of this association and encourage clinicians to carefully review the medication history in cases of pulmonary non-necrotizing granulomatous inflammation where there is a history of hepatitis C, as discontinuation of IFN-alpha can ameliorate the symptoms of sarcoidosis.

Anti-Inflammatory Agents↗

PubMed2000

Topological effects in ring polymers. II. Influence Of persistence length

The interplay of topological constraints and the persistence length of ring polymers in their own melt is investigated by means of dynamical Monte Carlo simulations of a three-dimensional lattice model. We ask if the results are consistent with an asymptotically regime where the rings behave like (compact) lattice animals in a self-consistent network of topological constraints imposed by neighboring rings. Tuning the persistence length provides an efficient route to increase the ring overlap required for this mean-field picture to hold: The effective Flory exponent for the ring size decreases down to nu less, similar1/3 with increasing persistence length. Evidence is provided for the emergence of one additional characteristic length scale d(t) approximately N0, only weakly dependent on the persistence length and much larger than the excluded volume screening length xi. At distances larger than d(t) the conformational properties of the rings are governed by the topological interactions; at smaller distances rings and their linear chain counterparts become similar. (At distances smaller than xi both architectures are identical.) However, the crossover between both limits is intricate and broad, as a detailed discussion of the local fractal dimension (e.g., obtained from the static structure factor) reveals. This is due to various crossover effects which we are unable to separate even for the largest ring size (N=1024) presented here. The increased topological interactions also influence the dynamical properties. Mean-square displacements and their distributions depend crucially on the ring overlap, and show evidence of the existence of additional size and time scales. The diffusion constant of the rings goes down from effectively D(N) approximately N-1.22 for flexible rings with low overlap to D(N) approximately N-1.68 for strongly overlapping semiflexible rings.

Journal Article↗

PubMed2004

Multistability of discrete-time recurrent neural networks with unsaturating piecewise linear activation functions.

This paper studies the multistability of a class of discrete-time recurrent neural networks with unsaturating piecewise linear activation functions. It addresses the nondivergence, global attractivity, and complete stability of the networks. Using the local inhibition, conditions for nondivergence are derived, which not only guarantee nondivergence, but also allow for the existence of multiequilibrium points. Under these nondivergence conditions, global attractive compact sets are obtained. Complete stability is studied via constructing novel energy functions and using the well-known Cauchy Convergence Principle. Examples and simulation results are used to illustrate the theory.

Linear Models↗

PubMed1981

[A mechanical carrier for the functional load of the mandible (author's transl)].

An apparatus is described in which mandibles can be suspended according to natural conditions. The masticator muscles can be simulated so that static equilibrium is ensured between these muscles, the two joints, and a resting point corresponding to the site of the incisors. As far as this is possible direction and force of the simulated muscles are respected. The total force at site of the incisors is about 24 kg. Holes were perforated at chosen sites in the compact bone. The deformation of these holes produced by tension or compression in the compact bone was measured by a capacitive transducer. In the 8 mandibles measured, tension characterized the pars alveolaris, compression the inferior edge of the corpus mandibulae. The highest values (tensions) were observed at the angular mandibulae (superior edge) and the lowest at the inferior edge of the protuberantia mentalis. Three mandibles were fractured and reconstructed with osteo-synthesis-plates. The load of 24 kg were applied at a rate of 1 to 2 per sec for approx. 15 min. The dislocation of the bony fragments produced by these loads oscillated between 19 and 47 micrometer. Repeated application of the load never produced a systematic increase of the displacement. The sites of measurement did not always show the displacement that might have been expected.

Biomechanical Phenomena↗

PubMed1997

Salt effects on the structure and internal dynamics of superhelical DNAs studied by light scattering and Brownian dynamics.

Using laser light scattering, we have measured the static and dynamic structure factor of two different superhelical DNAs, p1868 (1868 bp) and simian virus 40 (SV40) (5243 bp), in dilute aqueous solution at salt concentrations between 1 mM and 3 M NaCl. For both DNA molecules, Brownian dynamics (BD) simulations were also performed, using a previously described model. A Fourier mode decomposition procedure was used to compute theoretical light scattering autocorrelation functions (ACFs) from the BD trajectories. Both measured and computed autocorrelation functions were then subjected to the same multiexponential decomposition procedure. Simulated and measured relaxation times as a function of scattering angle were in very good agreement. Similarly, computed and measured static structure factors and radii of gyration agreed within experimental error. One main result of this study is that the amplitudes of the fast-relaxing component in the ACF show a peak at 1 M salt concentration. This nonmonotonic behavior might be caused by an initial increase in the amplitudes of internal motions due to diminishing long-range electrostatic repulsions, followed by a decrease at higher salt concentration due to a compaction of the structure.

Biophysical Phenomena↗

PubMed2003

Free-energy landscape of a chameleon sequence in explicit water and its inherent alpha/beta bifacial property.

A sequence in yeast MATalpha2/MCM1/DNA complex that folds into alpha-helix or beta-hairpin depending on the surroundings has been known as "chameleon" sequence. We obtained the free-energy landscape of this sequence by using a generalized-ensemble method, multicanonical molecular dynamics simulation, to sample the conformational space. The system was expressed with an all-atom model in explicit water, and the initial conformation for the simulation was a random one. The free-energy landscape demonstrated that this sequence inherently has an ability to form either alpha or beta structure: The conformational distribution in the landscape consisted of two alpha-helical clusters with different packing patterns of hydrophobic residues, and four beta-hairpin clusters with different strand-strand interaction patterns. Narrow pathways connecting the clusters were found, and analysis on the pathways showed that a compact structure formed at the N-terminal root of the chameleon sequence controls the cluster-cluster transitions. The free-energy landscape indicates that a small conditional change induces alpha-beta transitions. Additional unfolding simulations done with replacing amino acids showed that the chameleon sequence has an advantage to form an alpha-helix. Current study may be useful to understand the mechanism of diseases resulting from abnormal chain folding, such as amyloid disease.

Amino Acid Sequence↗