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PubMed2004

Single-molecule fluorescence spectroscopy and microscopy of biomolecular motors.

The methods of single-molecule fluorescence spectroscopy and microscopy have been recently utilized to explore the mechanism of action of several members of the kinesin and myosin biomolecular motor protein families. Whereas ensemble averaging is removed in single-molecule studies, heterogeneity in the behavior of individual motors can be directly observed, without synchronization. Observation of translocation by individual copies of motor proteins allows analysis of step size, rate, pausing, and other statistical properties of the process. Polarization microscopy as a function of nucleotide state has been particularly useful in revealing new and highly rotationally mobile forms of particular motors. These experiments complement X-ray and biochemical studies and provide a detailed view into the local dynamical behavior of motor proteins.

Fluorescence Polarization↗
PubMed2000

Noise characterization of block-iterative reconstruction algorithms: I. Theory.

Researchers have shown increasing interest in block-iterative image reconstruction algorithms due to the computational and modeling advantages they provide. Although their convergence properties have been well documented, little is known about how they behave in the presence of noise. In this work, we fully characterize the ensemble statistical properties of the rescaled block-iterative expectation-maximization (RBI-EM) reconstruction algorithm and the rescaled block-iterative simultaneous multiplicative algebraic reconstruction technique (RBI-SMART). Also included in the analysis are the special cases of RBI-EM, maximum-likelihood EM (ML-EM) and ordered-subset EM (OS-EM), and the special case of RBI-SMART, SMART. A theoretical formulation strategy similar to that previously outlined for ML-EM is followed for the RBI methods. The theoretical formulations in this paper rely on one approximation, namely, that the noise in the reconstructed image is small compared to the mean image. In a second paper, the approximation will be justified through Monte Carlo simulations covering a range of noise levels, iteration points, and subset orderings. The ensemble statistical parameters could then be used to evaluate objective measures of image quality.

Algorithms↗
PubMed2005

Thermodynamic characterization of fluids confined in heterogeneous pores by monte carlo simulations in the grand canonical and the isobaric-isothermal ensembles.

Materials presenting nanoscale porosity are able to condense gases in their structure. This "capillary condensation" phenomenon has been studied for more than one century. Theoretical models help to understand experimental results but fail in explaining all experimental features. Most of the time, the difficulties in making quantitative or even qualitative predictions are due to the geometric complexity of the porous materials, such as large pore size distribution, chemical heterogeneities, or pore interconnections. Numerical calculations (lattice gas models or molecular simulations) are of considerable interest to calculate the adsorption properties of a fluid confined in a porous model with characteristic sizes up to several tens of nanometers. For instance, the grand canonical Monte Carlo method allows one to compute the average amount of fluid adsorbed in the porous model as a function of the temperature and the chemical potential of the fluid. However, the grand potential, necessary for a complete characterization of the system, is not a direct output of the algorithm. It is shown in this paper that the use of the isobaric-isothermal (NPT) ensemble allows one to circumvent this problem; that is, it is possible to get in one single Monte Carlo run the absolute grand potential for any given thermodynamic state of the fluid. A simplified thermodynamic integration scheme is then used to evaluate the grand potential over the whole isotherm branch passing through this initially given point. Since the usual NPT technique is a priori limited to homogeneous pores, it is proposed, for the first time, to generalize this procedure to a pore presenting a chemical heterogeneity along its axis. The new method gives the same results as the previous for homogeneous pores and allows new predictions for chemically heterogeneous pores. Comparison with the full integration scheme shows that the proposed direct calculation is faster since it avoids multiple Monte Carlo runs and more precise because it avoids the possible cumulative errors of the integration procedure.

Journal Article↗
PubMed2003

Nonlinear synchronization in EEG and whole-head MEG recordings of healthy subjects.

According to Friston, brain dynamics can be modelled as a large ensemble of coupled nonlinear dynamical subsystems with unstable and transient dynamics. In the present study, two predictions from this model (the existence of nonlinear synchronization between macroscopic field potentials and itinerant nonlinear dynamics) were investigated. The dependence of nonlinearity on the method of measuring brain activity (EEG vs. MEG) was also investigated. Dataset I consisted of 10 MEG recordings in 10 healthy subjects. Dataset II consisted of simultaneously recorded MEG (126 channels) and EEG (19 channels) in 5 healthy subjects. Nonlinear coupling was assessed with the synchronization likelihood S and dynamic itinerancy with the synchronization entropy Hs. Significance was assessed with a bootstrap procedure ("surrogate data testing"), comparing S and Hs with their distribution under the null hypothesis of stationary, linear dynamics. Significant nonlinear synchronization was detected in 14 of 15 subjects. The nonlinear dynamics were associated with a high index of itinerant behaviour. Nonlinear interdependence was significantly more apparent in MEG data than EEG. Synchronous oscillations in MEG and EEG recordings contain a significant nonlinear component that exhibits characteristics of unstable and itinerant behaviour. These findings are in line with Friston's proposal that the brain can be conceived as a large ensemble of coupled nonlinear dynamical subsystems with labile and unstable dynamics. The spatial scale and physical properties of MEG acquisition may increase the sensitivity of the data to underlying nonlinear structure.

Adult↗
PubMed2001

Co-operativity between mouse connexin30 gap junction channels.

HeLa cells stably transfected with mouse cDNA coding for connexin30 (Cx30) were used to study the electrical properties of gap junction channels. The experiments involved the measurement of intercellular currents (Ij) from cell pairs using dual whole-cell recording with the patch-clamp method. The aim was to compare Ij from cell pairs whose gap junctions consisted of a single channel and cell pairs whose gap junctions consisted of many channels. We found that both the ensemble average currents gained from single-channel records and the currents obtained from multichannel records inactivated exponentially with time. However, the former inactivated significantly slower than the latter. At ajunctional voltage (Vj) of 50 mV, the time constants of inactivation (tau(i)) were 8.1 s and 1.6 s, respectively. Moreover, the ratio tau(i)(single-channel)/tau(i)(multichannel) turned out to be voltage sensitive, i.e. it decreased with increasing V(j) These observations suggest that the operation of Cx30 gap junction channels in the multichannel configuration involves co-operative interactions.

Animals↗
PubMed2004

Src family tyrosine kinases inhibit single L-type: Ca2+ channel activity in human atrial myocytes.

OBJECTIVE: Tyrosine kinases (TKs) are important regulators of the L-type Ca(2+) channel (LTCC) current in various cell types. However, there are no data addressing the role of TKs in the control of single LTCC activity in human atrial cardiac myocytes, where changes in LTCC gating properties have been described in a number of disease states. METHODS AND RESULTS: Single LTCC activity was recorded in isolated human atrial myocytes. The broad-spectrum TK inhibitor genistein and the Src family-selective TK inhibitor PP1 significantly enhanced single LTCC ensemble average current, availability, and open probability; the latter was due to significant increases of mean open time and mode 2 gating. Conversely, the tyrosine phosphatase inhibitor bisperoxo-phenanthroline-vanadate inhibited single LTCC activity, indicating that LTCC gating properties in human atrial myocytes are controlled by TKs and tyrosine phosphatases in a reciprocal fashion. The effects of genistein on single LTCC activity were not affected by stimulation (8Br-cAMP) or inhibition (Rp-8-CPT-cAMPS) of protein kinase A (PKA) or by inhibition of serine/threonine phosphatases types I and IIa (okadaic acid), indicating that TKs inhibit LTCC gating in human atrial myocytes independent of PKA and phosphatases types I and IIa. However, inhibition of protein kinase C (PKC) by staurosporine or bisindolylmaleimide reversed the stimulatory effects of genistein on single LTCC gating properties, indicating that PKC is required for the inhibitory effect of TKs on single LTCC activity. CONCLUSION: Src family TKs inhibit single LTCC activity in human atrial myocytes via PKC-dependent, but PKA and phosphatase types I and IIa-independent, molecular pathways.

Aged↗
PubMed1994

Studies by pulsed Doppler ultrasonography of velocity fields downstream of graded stenoses on the abdominal aorta in pigs.

PURPOSE: To investigate local hemodynamics downstream of arterial stenoses, a perivascular five-element Doppler ultrasound transducer was used for registration of one-dimensional velocity profiles and estimation of Reynolds (turbulent) normal stresses downstream of smooth, graded stenoses on the abdominal aorta in six 90 kg pigs. METHODS: Blood velocities were registered by a 10 MHz pulsed Doppler velocimeter that used a modified zero-crossing detector with an upper -3 dB cutoff frequency of 200 Hz. Signal analysis included ensemble averaging, turbulence analysis, and dimensional visualization of velocity profiles. RESULTS: Velocity profiles downstream of minor (< or = 40%) and moderate (40% to 65%) stenoses were skewed with the highest systolic velocities toward the anterior vessel wall and diastolic flow reversal occasionally present at the posterior vessel wall. Immediately downstream of severe (> or = 65%) stenoses a prominent poststenotic jet and systolic recirculation zones were present. Further downstream, vortices and eddies dominated the flow field. Reynolds normal stresses were highest at locations in the velocity field with high-velocity gradients corresponding to the parajet zone. CONCLUSIONS: The present study demonstrated that pulsed Doppler ultrasonography can provide detailed and quantitative information of flow phenomena such as jetlike flow, vortices, and recirculation zones in a poststenotic flow field in the abdominal aorta.

Animals↗
PubMed1989

Phase synchronization of an ion ensemble by frequency sweep excitation in Fourier transform ion cyclotron resonance.

The Fourier transform ion cyclotron resonance (FT-ICR) signal is produced by the coherent motion of a population of ions. The ability to produce a well-defined ion packet by excitation of an initially random ion ensemble is a major limiting factor of high mass FT-ICR. Ions must be both resonant and in phase with the applied radio frequency excitation field to be accelerated to radii suitable for detection by FT-ICR. Synchronization of the phase angles of an ensemble of ions occurs by off-resonant acceleration during frequency swept excitation. Results from computer-simulated ion trajectories suggest that phase synchronization of the ion packet prior to resonant excitation results in better spatial definition of the ion ensemble.

Computer Simulation↗
PubMed2006

Calculation of phase coexistence properties and surface tensions of n-alkanes with grand-canonical transition-matrix monte carlo simulation and finite-size scaling.

Grand-canonical transition-matrix Monte Carlo is combined with configurational-bias and expanded ensemble Monte Carlo techniques to obtain saturated densities and vapor pressures of select n-alkanes. Surface tension values for butane, hexane, and octane are also computed via the finite-size scaling method of Binder. The exponential-6 model of Errington and Panagiotopoulos is used to describe the molecular interactions. The effect of the number of configurational-bias trial conformations on the efficiency of phase equilibra calculations is studied. We find that a broad range of trial conformation numbers give reasonable performance, with the optimal value increasing with decreasing temperature for a fixed chain length. Phase coexistence properties are in good agreement with literature values and are obtained with very reasonable computing resources. Similar to other recently developed n-alkane force fields, the exponential-6 model overestimates the surface tension relative to experimental values. Statistical uncertainties for coexistence properties obtained with the current approach are relatively small compared to existing methods.

Alkanes↗
PubMed2004

BAEPs averaging analysis using autoregressive modelling.

OBJECTIVE: The present paper introduces a new perspective on the classical ensemble averaging which can be useful to analyse the Brainstem Auditory Evoked Potentials (BAEPs). The analysis of the dynamics, related to the BAEP, is performed directly after its acquisition from the electroencephalogram (EEG). METHODS: The method primarily consists of dynamically modelling the averaged potential, obtained during the acquisition mode. Each averaging of signal at a given instant is considered as an autoregressive (AR) process. RESULTS: It has been shown that the predicting error power of AR modelling can be useful to provide an efficient tool to analyse the BAEPs. It has also been shown that the method is capable of taking the non-stationarities of both the BAEP and the EEG into account. CONCLUSION: In order to validate our approach, the proposed technique has been implemented for both simulated and real signals. This approach can also be employed in the context of estimating other evoked potentials and shows rich promise for potential clinical applications in future.

Algorithms↗
PubMed2006

Simple estimation of absolute free energies for biomolecules.

One reason that free energy difference calculations are notoriously difficult in molecular systems is due to insufficient conformational overlap, or similarity, between the two states or systems of interest. The degree of overlap is irrelevant, however, if the absolute free energy of each state can be computed. We present a method for calculating the absolute free energy that employs a simple construction of an exactly computable reference system which possesses high overlap with the state of interest. The approach requires only a physical ensemble of conformations generated via simulation and an auxiliary calculation of approximately equal central-processing-unit cost. Moreover, the calculations can converge to the correct free energy value even when the physical ensemble is incomplete or improperly distributed. As a "proof of principle," we use the approach to correctly predict free energies for test systems where the absolute values can be calculated exactly and also to predict the conformational equilibrium for leucine dipeptide in implicit solvent.

Algorithms↗
PubMed2005

Partly melted DNA conformations obtained with a probability peak finding method.

Peaks in the probabilities of loops or bubbles, helical segments, and unzipping ends in melting DNA are found in this article using a peak finding method that maps the hierarchical structure of certain energy landscapes. The peaks indicate the alternative conformations that coexist in equilibrium and the range of their fluctuations. This yields a representation of the conformational ensemble at a given temperature, which is illustrated in a single diagram called a stitch profile. This article describes the methodology and discusses stitch profiles vs the ordinary probability profiles using the phage lambda genome as an example.

Algorithms↗
PubMed2001

Critical geometry of two-dimensional passive scalar turbulence.

Passive scalars advected by a magnetically driven two-dimensional turbulent flow are analyzed using methods of statistical topography. The passive tracer concentration is interpreted as the height of a random surface, and the scaling properties of its contour loops are analyzed. Various exponents that describe the loop ensemble are measured and compared to a scaling theory. This leads to a geometrical criterion for the intermittency of scalar fluctuations.

Journal Article↗
PubMed2001

Adaptation to temporal contrast in primate and salamander retina.

Visual adaptation to temporal contrast (intensity modulation of a spatially uniform, randomly flickering stimulus) was examined in simultaneously recorded ensembles of retinal ganglion cells (RGCs) in tiger salamander and macaque monkey retina. Slow contrast adaptation similar to that recently discovered in salamander and rabbit retina was observed in monkey retina. A novel method was developed to quantify the effect of temporal contrast on steady-state sensitivity and kinetics of light responses, separately from nonlinearities that would otherwise significantly contaminate estimates of sensitivity. Increases in stimulus contrast progressively and reversibly attenuated and sped light responses in both salamander and monkey RGCs, indicating that a portion of the contrast adaptation observed in visual cortex originates in the retina. The effect of adaptation on sensitivity and kinetics differed in simultaneously recorded populations of ON and OFF cells. In salamander, adaptation affected the sensitivity of OFF cells more than ON cells. In monkey, adaptation affected the sensitivity of ON cells more than OFF cells. In both species, adaptation sped the light responses of OFF cells more than ON cells. Functionally defined subclasses of ON and OFF cells also exhibited asymmetric adaptation. These findings indicate that contrast adaptation differs in parallel retinal circuits that convey distinct visual signals to the brain.

Action Potentials↗
PubMed2006

The 3D profile method for identifying fibril-forming segments of proteins.

Based on the crystal structure of the cross-beta spine formed by the peptide NNQQNY, we have developed a computational approach for identifying those segments of amyloidogenic proteins that themselves can form amyloid-like fibrils. The approach builds on experiments showing that hexapeptides are sufficient for forming amyloid-like fibrils. Each six-residue peptide of a protein of interest is mapped onto an ensemble of templates, or 3D profile, generated from the crystal structure of the peptide NNQQNY by small displacements of one of the two intermeshed beta-sheets relative to the other. The energy of each mapping of a sequence to the profile is evaluated by using ROSETTADESIGN, and the lowest energy match for a given peptide to the template library is taken as the putative prediction. If the energy of the putative prediction is lower than a threshold value, a prediction of fibril formation is made. This method can reach an accuracy of approximately 80% with a P value of approximately 10(-12) when a conservative energy threshold is used to separate peptides that form fibrils from those that do not. We see enrichment for positive predictions in a set of fibril-forming segments of amyloid proteins, and we illustrate the method with applications to proteins of interest in amyloid research.

Amino Acid Sequence↗
PubMed2000

Protein fold recognition by total alignment probability.

We present a protein fold-recognition method that uses a comprehensive statistical interpretation of structural Hidden Markov Models (HMMs). The structure/fold recognition is done by summing the probabilities of all sequence-to-structure alignments. The optimal alignment can be defined as the most probable, but suboptimal alignments may have comparable probabilities. These suboptimal alignments can be interpreted as optimal alignments to the "other" structures from the ensemble or optimal alignments under minor fluctuations in the scoring function. Summing probabilities for all alignments gives a complete estimate of sequence-model compatibility. In the case of HMMs that produce a sequence, this reflects the fact that due to our indifference to exactly how the HMM produced the sequence, we should sum over all possibilities. We have built a set of structural HMMs for 188 protein structures and have compared two methods for identifying the structure compatible with a sequence: by the optimal alignment probability and by the total probability. Fold recognition by total probability was 40% more accurate than fold recognition by the optimal alignment probability. Proteins 2000;40:451-462.

Algorithms↗
PubMed2002

Stochastic resonance of ensemble neurons for transient spike trains: wavelet analysis.

By using the wavelet transformation (WT), I have analyzed the response of an ensemble of N (=1, 10, 100, and 500) Hodgkin-Huxley neurons to transient M-pulse spike trains (M=1 to 3) with independent Gaussian noises. The cross correlation between the input and output signals is expressed in terms of the WT expansion coefficients. The signal-to-noise ratio (SNR) is evaluated by using the denoising method within the WT, by which the noise contribution is extracted from the output signals. Although the response of a single (N=1) neuron to subthreshold transient signals with noises is quite unreliable, the transmission fidelity assessed by the cross correlation and SNR is shown to be much improved by increasing the value of N: a population of neurons plays an indispensable role in the stochastic resonance (SR) for transient spike inputs. It is also shown that in a large-scale ensemble, the transmission fidelity for suprathreshold transient spikes is not significantly degraded by a weak noise which is responsible to SR for subthreshold inputs.

Animals↗
PubMed2005

Protein loop structure prediction with flexible stem geometries.

The structure prediction of loops with flexible stem residues is addressed in this article. While the secondary structure of the stem residues is assumed to be known, the geometry of the protein into which the loop must fit is considered to be unknown in our methodology. As a consequence, the compatibility of the loop with the remainder of the protein is not used as a criterion to reject loop decoys. The loop structure prediction with flexible stems is more difficult than fitting loops into a known protein structure in that a larger conformational space has to be covered. The main focus of the study is to assess the precision of loop structure prediction if no information on the protein geometry is available. The proposed approach is based on (1) dihedral angle sampling, (2) structure optimization by energy minimization with a physically based energy function, (3) clustering, and (4) a comparison of strategies for the selection of loops identified in (3). Steps (1) and (2) have similarities to previous approaches to loop structure prediction with fixed stems. Step (3) is based on a new iterative approach to clustering that is tailored for the loop structure prediction problem with flexible stems. In this new approach, clustering is not only used to identify conformers that are likely to be close to the native structure, but clustering is also employed to identify far-from-native decoys. By discarding these decoys iteratively, the overall quality of the ensemble and the loop structure prediction is improved. Step (4) provides a comparative study of criteria for loop selection based on energy, colony energy, cluster density, and a hybrid criterion introduced here. The proposed method is tested on a large set of 3215 loops from proteins in the Pdb-Select25 set and to 179 loops from proteins from the Casp6 experiment.

Cluster Analysis↗