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PubMed2005

Spectral representation--analyzing single-unit activity in extracellularly recorded neuronal data without spike sorting.

One step in the conventional analysis of extracellularly recorded neuronal data is spike sorting, which separates electrical signal into action potentials from different neurons. Because spike sorting involves human judgment, it can be subjective and time intensive, particularly for large sets of neurons. Here we propose a simple, automated way to construct alternative representations of neuronal activity, called spectral representation (SR). In this approach, neuronal spikes are mapped to a discrete space of spike waveform features and time. Spectral representation enables us to find single-unit stimulus-related changes in neuronal activity without spike sorting. We tested the ability of this method to predict stimuli using both simulated data and experimental data from an auditory mapping study in anesthetized marmoset monkeys. We find that our approach produces more accurate classification of stimuli than spike-sorted data for both simulated and experimental conditions. Furthermore, this method lends itself to automated analysis of extracellularly recorded neuronal ensembles. Additionally, we suggest ways in which these representations can be readily extended to assist in spike sorting and the evaluation of single-neuron peri-stimulus time histograms.

Acoustic Stimulation↗
PubMed2003

BSS-based filtering of physiological and ARFI-induced tissue and blood motion.

Blind source separation (BSS) for adaptive filtering is presented in application to imaging both physiological and acoustic radiation force impulse (ARFI)-induced tissue and blood motion in the common carotid artery. The collected raw radiofrequency (RF) data includes vessel wall motion, blood flow and ARFI-induced motion. In the context of these complex motion patterns, the same BSS adaptive filtering method was employed for three diverse applications: 1. clutter filtering ensembles prior to blood velocity estimation, 2. extracting small axial velocity components from noisy velocity measurements given large flow angles and 3. reducing noise in measured ARFI-induced tissue displacement profiles to enhance differentiation of local tissue structures. The filter separated physiological vessel wall motion from axial blood flow and ARFI-induced motion; successful filter performance is demonstrated in velocity estimates, color flow images and ARFI displacement profiles. The results demonstrate the breadth of applications for BSS adaptive filtering in the clinical imaging environment.

Blood Flow Velocity↗
PubMed2001

Sources of error in maximum velocity estimation using linear phased-array Doppler systems with steady flow.

Using linear-array Doppler ultrasound (US) transducers, the measured maximum velocity may be in error and lead to incorrect clinical diagnosis. This study investigates the existence and cause of maximum velocity estimation errors for steady flow of a blood-mimicking fluid in a tissue-mimicking phantom. A specially designed system was used that enabled fine control of flow rate, transducer positioning and transducer angle relative to the flow phantom. Doppler machine settings (transducer aperture size, focal depth, beam-steering, gain) were varied to investigate a wide range of clinical applications. To estimate the maximum velocity, a new signal-to-noise ratio (SNR) independent method was developed to calculate the maximum frequency from an ensemble averaged Doppler power spectrum. This enabled the impact of each factor on the total Doppler error to be determined. When using the new maximum frequency estimator, it was found that the effect of transducer focal depth, intratransducer, intramachine, intermachine (that was tested) and beam-steering did not significantly contribute to maximum velocity estimation errors. Instead, it was the dependence of the maximum velocity on the Doppler angle that made, by far, the greatest contribution to the estimation error. Because our maximum frequency estimator took into account the effect of intrinsic spectral broadening, the degree of overestimation error was not as great as that previously published. Thus, the effects of Doppler angle and intrinsic spectral broadening are the chief sources of Doppler US error and should be the focus of future efforts to improve the accuracy.

Blood Flow Velocity↗
PubMed2006

Conformational equilibrium of cytochrome P450 BM-3 complexed with N-palmitoylglycine: a replica exchange molecular dynamics study.

UV-vis absorbance measurements and associated studies of cytochrome P450 BM-3 in complex with N-palmitoylglycine (NPG) indicate that a conformational change occurs in the active site of the complex where the terminal atoms of the ligand move from a site distant from the heme iron, as seen in the low temperature crystal structure to a site proximal to the heme iron at biological temperatures. We employ replica exchange molecular dynamics simulations to study this conformational change. The population of the proximal state is found to increase with temperature in agreement with UV-vis absorbance and NMR measurements. In addition to the conformations characterized by X-ray crystallography and computer modeling, this study shows that a new conformational state is significantly populated at room temperature. The observed increase in the population of conformations where the terminal atoms of NPG are proximal to the heme iron with increasing temperature indicates that the proximal state is stabilized by conformational entropy. A proposal for the origin of this entropic stabilization is provided on the basis of the structure of the newly identified state. We use the temperature weighted histogram (T-WHAM) method to characterize the transition state regions of the conformational ensemble and propose a mechanism of interconversion between these low free energy conformational states.

Crystallography, X-Ray↗
PubMed2006

Geometry, energetics, and dynamics of hydrogen bonds in proteins: structural information derived from NMR scalar couplings.

An accurate description of hydrogen bonds is essential to identify the determinants of protein stability and function as well as folding and misfolding behavior. We describe a method of using J couplings through hydrogen bonds as ensemble-averaged restraints in molecular dynamics simulations. Applications to the cases of ubiquitin and protein G show that these scalar couplings provide powerful structural information that, when used through the methodology that we present here, enables the description of the geometry and energetics of hydrogen bonds with an accuracy approaching that of high-resolution X-ray structures.

Computer Simulation↗
PubMed2003

The precision of NMR structure ensembles revisited.

Biomolecular structures provide the basis for many studies in research areas such as structure-based drug design and homology modeling. In order to use molecular coordinates it is important that they are reliable in terms of accurate description of the experimental data and in terms of the overall and local geometry. Besides these primary quality criteria an indication is needed for the uncertainty in the atomic coordinates that may arise from the dynamic behavior of the considered molecules as well as from experimental- and computational procedures. In contrast to the crystallographic B-factor, a good measure for the uncertainty in NMR-derived atomic coordinates is still not available. It has become clear in recent years that the widely used atomic Root Mean Square Deviation (RMSD), which is a measure for the precision of the data, overestimates the accuracy of NMR structure ensembles and therefore is a problematic measure for the uncertainty in the atomic coordinates. In this study we report a method that yields a more realistic estimate of the uncertainty in the atomic coordinates by maximizing the RMSD of an ensemble of structures, while maintaining the accordance with the experimentally derived data. The results indicate that the RMSD of most NMR structure ensembles can be significantly increased compromising neither geometric quality nor NMR data. This maximized RMSD therefore seems a better estimate of the true uncertainty in the atomic coordinates.

Crystallography, X-Ray↗
PubMed2005

Direct determination of phase behavior of square-well fluids.

We have combined Gibbs ensemble Monte Carlo simulations with the aggregation volume-biased method in conjunction with the Gibbs-Duhem method to provide the first direct estimates for the vapor-solid, vapor-liquid, and liquid-solid phase coexistences of square-well fluids with three different ranges of attraction. Our results are consistent with the previous simulations and verify the notion that the vapor-liquid coexistence behavior becomes metastable for cases where the attraction well becomes smaller than 1.25 times the particle diameter. In these cases no triple point is found.

Journal Article↗
PubMed2006

On a new self-consistent-field theory for the canonical ensemble.

A significant amount of many-body problems of quantum or classical equilibrium statistical mechanics are conveniently treated at fixed temperature and system size. In this paper, we present a new functional integral approach for solving canonical ensemble problems over the entire coupling range, relying on the method of Gaussian equivalent representation of Efimov and Ganbold. We demonstrate its suitability and competitiveness for performing approximate calculations of thermodynamic and structural quantities on the example of a repulsive potential model, widely used in soft matter theory.

Journal Article↗
PubMed2005

Vibrational energy relaxation in proteins.

An overview of theories related to vibrational energy relaxation (VER) in proteins is presented. VER of a selected mode in cytochrome c is studied by using two theoretical approaches. One approach is the equilibrium simulation approach with quantum correction factors, and the other is the reduced model approach, which describes the protein as an ensemble of normal modes interacting through nonlinear coupling elements. Both methods result in similar estimates of the VER time (subpicoseconds) for a CD stretching mode in the protein at room temperature. The theoretical predictions are in accord with previous experimental data. A perspective on directions for the detailed study of time scales and mechanisms of VER in proteins is presented.

Adenosine Triphosphate↗
PubMed1998

Cascaded redundancy reduction.

We describe a method for incrementally constructing a hierarchical generative model of an ensemble of binary data vectors. The model is composed of stochastic, binary, logistic units. Hidden units are added to the model one at a time with the goal of minimizing the information required to describe the data vectors using the model. In addition to the top-down generative weights that define the model, there are bottom-up recognition weights that determine the binary states of the hidden units given a data vector. Even though the stochastic generative model can produce each data vector in many ways, the recognition model is forced to pick just one of these ways. The recognition model therefore underestimates the ability of the generative model to predict the data, but this underestimation greatly simplifies the process of searching for the generative and recognition weights of a new hidden unit.

Algorithms↗
PubMed2002

General random matrix approach to account for the effect of static disorder on the spectral properties of light harvesting systems.

We develop a random matrix model approach to study static disorder in pigment-protein complexes in photosynthetic organisms. As a case study, we examine the ring of B850 bacteriochlorophylls in the peripheral light-harvesting complex of Rhodospirillum molischianum, formulated in terms of an effective Hamiltonian describing the collective electronic excitations of the system. We numerically examine and compare various models of disorder and observe that both the density of states and the absorption spectrum of the model show remarkable spectral universality. For the case of unitary disorder, we develop a method to analytically evaluate the density of states of the ensemble using the supersymmetric formulation of random matrix theory. Succinct formulas that can be readily applied in future studies are provided in an appendix.

Models, Molecular↗
PubMed2004

Steady-state representation of the homogeneous cooling state of a granular gas.

The properties of a dilute granular gas in the homogeneous cooling state are mapped to those of a stationary state by means of a change in the time scale that does not involve any internal property of the system. The new representation is closely related with a general property of the granular temperature in the long time limit. The physical and practical implications of the mapping are discussed. In particular, simulation results obtained by the direct simulation Monte Carlo method applied to the scaled dynamics are reported. This includes ensemble averages and also the velocity autocorrelation function, as well as the self-diffusion coefficient obtained from the latter by means of the Green-Kubo representation. In all cases, the obtained results are compared with theoretical predictions.

Journal Article↗
PubMed2004

Bath-assisted cooling of spins.

A suitable sequence of sharp pulses applied to a spin coupled to a bosonic bath can cool its state, i.e., increase its polarization or ground state occupation probability. Starting from an unpolarized state of the spin in equilibrium with the bath, one can reach very low temperatures or sizable polarizations within a time shorter than the decoherence time. Both the bath and external fields are necessary for the effect, which comes from the backreaction of the spin on the bath. This method can be applied to cool at once a disordered ensemble of spins.

Journal Article↗
PubMed2006

Efficient molecular docking of NMR structures: application to HIV-1 protease.

Docking ligands into an ensemble of NMR conformers is essential to structure-based drug discovery if only NMR structures are available for the target. However, sequentially docking ligands into each NMR conformer through standard single-receptor-structure docking, referred to as sequential docking, is computationally expensive for large-scale database screening because of the large number of NMR conformers involved. Recently, we developed an efficient ensemble docking algorithm to consider protein structural variations in ligand binding. The algorithm simultaneously docks ligands into an ensemble of protein structures and achieves comparable performance to sequential docking without significant increase in computational time over single-structure docking. Here, we applied this algorithm to docking with NMR structures. The HIV-1 protease was used for validation in terms of docking accuracy and virtual screening. Ensemble docking of the NMR structures identified 91% of the known inhibitors under the criterion of RMSD < 2.0 A for the best-scored conformation, higher than the average success rate of single docking of individual crystal structures (66%). In the virtual screening test, on average, ensemble docking of the NMR structures obtained higher enrichments than single-structure docking of the crystal structures. In contrast, docking of either the NMR minimized average structure or a single NMR conformer performed less satisfactorily on both binding mode prediction and virtual screening, indicating that a single NMR structure may not be suitable for docking calculations. The success of ensemble docking of the NMR structures suggests an efficient alternative method for standard single docking of crystal structures and for considering protein flexibility.

Algorithms↗
PubMed1991

[The polymerase chain reaction PCR and its use in genetic diagnosis].

In genomic diagnosis the ensemble of techniques has been recently expanded by the powerful method of the polymerase chain reaction (PCR). Using pairs of synthetic oligonucleotides for priming of synthesis and a thermoresistant DNA polymerase a millionfold amplification of target DNA sequences from patients provides DNA fragments for following investigations such as electrophoresis. The paper presents some examples of PCR application for diagnosis in cystic fibrosis and Duchenne muscular dystrophy.

Cystic Fibrosis↗
PubMed2005

Magnetic field tracking with MCNP5.

With the introduction of continuous-energy heavy charged particle transport in MCNP5, the need for tracking charged particles in a magnetic field becomes increasingly important. Two methods for including magnetic field effects on charged particles are included in the proton transport version of the code. The first technique utilises transfer maps produced by the beam dynamics simulation and analysis code COSY INFINITY. This method is fast and accurate; however, its use is limited to void cells only and to ensembles of particles with a fairly small energy spread. The second technique, particle ray tracing, is based on an algorithm adopted from the MARS transport code. This method can be applied to both void and material cells and is valid over a very large range of particle energies. Results from tracking particles in a quadrupole 'identity lens' using the two techniques are compared.

Computer Simulation↗
PubMed2004

Using amino acid patterns to accurately predict translation initiation sites.

The translation initiation site (TIS) prediction problem is about how to correctly identify TIS in mRNA, cDNA, or other types of genomic sequences. High prediction accuracy can be helpful in a better understanding of protein coding from nucleotide sequences. This is an important step in genomic analysis to determine protein coding from nucleotide sequences. In this paper, we present an in silico method to predict translation initiation sites in vertebrate cDNA or mRNA sequences. This method consists of three sequential steps as follows. In the first step, candidate features are generated using k-gram amino acid patterns. In the second step, a small number of top-ranked features are selected by an entropy-based algorithm. In the third step, a classification model is built to recognize true TISs by applying support vector machines or ensembles of decision trees to the selected features. We have tested our method on several independent data sets, including two public ones and our own extracted sequences. The experimental results achieved are better than those reported previously using the same data sets. Our high accuracy not only demonstrates the feasibility of our method, but also indicates that there might be "amino acid" patterns around TIS in cDNA and mRNA sequences.

Algorithms↗
PubMed2004

An application of flexible constraints in Monte Carlo simulations of the isobaric--isothermal ensemble of liquid water and ice Ih with the polarizable and flexible mobile charge densities in harmonic oscillators model.

The method of flexible constraints was implemented in a Monte Carlo code to perform numerical simulations of liquid water and ice Ih in the constant number of molecules, volume, and temperature and constant pressure, instead of volume ensembles, using the polarizable and flexible mobile charge densities in harmonic oscillators (MCDHO) model. The structural and energetic results for the liquid at T=298 K and rho=997 kg m(-3) were in good agreement with those obtained from molecular dynamics. The density obtained at P=1 atm with flexible constraints, rho=1008 kg m(-3), was slightly lower than with the classical sampling of the intramolecular vibrations, rho=1010 kg m(-3). The comparison of the structures and energies found for water hexamers and for ice Ih with six standard empirical models to those obtained with MCDHO, show this latter to perform better in describing water far from ambient conditions: the MCDHO minimum lattice energy, density, and lattice constants were in good agreement with experiment. The average angle HOH of the water molecule in ice was predicted to be slightly larger than in the liquid, yet 1.2% smaller than the experimental value.

Journal Article↗