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At least 361 records · Page 20Linked to original sources

PubMed2006

Neuronal ensemble control of prosthetic devices by a human with tetraplegia.

Neuromotor prostheses (NMPs) aim to replace or restore lost motor functions in paralysed humans by routeing movement-related signals from the brain, around damaged parts of the nervous system, to external effectors. To translate preclinical results from intact animals to a clinically useful NMP, movement signals must persist in cortex after spinal cord injury and be engaged by movement intent when sensory inputs and limb movement are long absent. Furthermore, NMPs would require that intention-driven neuronal activity be converted into a control signal that enables useful tasks. Here we show initial results for a tetraplegic human (MN) using a pilot NMP. Neuronal ensemble activity recorded through a 96-microelectrode array implanted in primary motor cortex demonstrated that intended hand motion modulates cortical spiking patterns three years after spinal cord injury. Decoders were created, providing a 'neural cursor' with which MN opened simulated e-mail and operated devices such as a television, even while conversing. Furthermore, MN used neural control to open and close a prosthetic hand, and perform rudimentary actions with a multi-jointed robotic arm. These early results suggest that NMPs based upon intracortical neuronal ensemble spiking activity could provide a valuable new neurotechnology to restore independence for humans with paralysis.

Adult↗

PubMed1993

Searching sequence space to engineer proteins: exponential ensemble mutagenesis.

We describe an efficient method for generating combinatorial libraries with a high percentage of unique and functional mutants. Combinatorial libraries have been successfully used in the past to express ensembles of mutant proteins in which all possible amino acids are encoded at a few positions in the sequence. However, as more positions are mutagenized the proportion of functional mutants is expected to decrease exponentially. Small groups of residues were randomized in parallel to identify, at each altered position, amino acids which lead to functional proteins. By using optimized nucleotide mixtures deduced from the sequences selected from the random libraries, we have simultaneously altered 16 sites in a model pigment binding protein: approximately one percent of the observed mutants were functional. Mathematical formalization and extrapolation of our experimental data suggests that a 10(7)-fold increase in the throughput of functional mutants has been obtained relative to the expected frequency from a random combinatorial library. Exponential ensemble mutagenesis should be advantageous in cases where many residues must be changed simultaneously to achieve a specific engineering goal, as in the combinatorial mutagenesis of phage displayed antibodies. With the enhanced functional mutant frequencies obtained by this method, entire proteins could be mutagenized combinatorially.

Amino Acid Sequence↗

PubMed2004

Large-scale recording of neuronal ensembles.

How does the brain orchestrate perceptions, thoughts and actions from the spiking activity of its neurons? Early single-neuron recording research treated spike pattern variability as noise that needed to be averaged out to reveal the brain's representation of invariant input. Another view is that variability of spikes is centrally coordinated and that this brain-generated ensemble pattern in cortical structures is itself a potential source of cognition. Large-scale recordings from neuronal ensembles now offer the opportunity to test these competing theoretical frameworks. Currently, wire and micro-machined silicon electrode arrays can record from large numbers of neurons and monitor local neural circuits at work. Achieving the full potential of massively parallel neuronal recordings, however, will require further development of the neuron-electrode interface, automated and efficient spike-sorting algorithms for effective isolation and identification of single neurons, and new mathematical insights for the analysis of network properties.

Action Potentials↗

PubMed2001

Targeted proteomics in the kidney using ensembles of antibodies.

Building on extensive physiological characterization of sodium transport mechanisms along the renal tubule over the past 30 years, complementary DNAs for almost all of the major transporters and channels responsible for renal tubular sodium reabsorption have been cloned over the past 10 years. The consequence is the generation of a broad range of cDNA and antibody probes which can be used to investigate physiological mechanisms on a molecular level. An ensemble of such probes can be exploited for comprehensive analysis of integrative physiological processes, approaches which are referred to as 'physiological genomics' or 'physiological proteomics'. In this review, we describe a targeted proteomic approach to comprehensive analysis of sodium transporter and water channel protein abundance along the renal tubule using an ensemble of rabbit polyclonal antibodies directed to the major sodium transporters and water channels expressed in each renal tubule segment. We discuss preparation and characterization of the antibodies, strategies for quantification of transporter protein abundance, and provide examples of the application of antibody-based targeted proteomics analysis of kidney tissue, revealing the effects of elevations of circulating aldosterone levels and circulating vasopressin levels on sodium transporter, sodium channel, and water channel abundance in kidney.

Animals↗

PubMed2003

Using nonisochronicity to control synchronization in ensembles of nonidentical oscillators.

We investigate the transition to synchronization in ensembles of coupled oscillators with quenched disorder. We find that small coupling is able to increase the frequency disorder and to induce a spread of oscillator frequencies. This new effect of anomalous desynchronization is studied with numerical and analytical means in a large class of systems including Rössler, Lotka-Volterra, Landau-Stuart, and Van-der-Pol oscillators. We show that anomalous effects arise due to an interplay between nonisochronicity and natural frequency of each oscillator and can either increase or inhibit synchronization in the ensemble. This provides a novel possibility to control the synchronization transition in nonidentical systems by suitably distributing the disorder among system parameters. We conjecture that our results are of relevance for biological systems.

Biology↗

PubMed2003

Spatiotemporal stochastic forcing effects in an ensemble consisting of arrays of diffusively coupled Lorenz cells.

Spatiotemporal stochastic forcing of an ensemble system consisting of chaotic Lorenz cells diffusively coupled is analyzed. The nontrivial effects of time and length correlations on the ensemble mean error and spread are studied and the implications to new trends in weather forecast methodologies are discussed. A maximum for the forecast scores is observed to occur for specific values of time and length correlations. This maximum is studied in terms of an interplay between the natural scales occurring in the system and the noise parameters.

Forecasting↗

PubMed2004

Generalized-ensemble simulations of the human parathyroid hormone fragment PTH(1-34).

A generalized-ensemble technique, multicanonical sampling, is used to study the folding of a 34-residue human parathyroid hormone fragment. An all-atom model of the peptide is employed and the protein-solvent interactions are approximated by an implicit solvent. Our results demonstrate that generalized-ensemble simulations are well suited to sample low-energy structures of such large polypeptides. Configurations with a root-mean-square deviation to the crystal structure of less than 1 A are found. Finally, we discuss limitations of our implicit solvent model.

Humans↗

PubMed2004

Determination of fluid--solid transitions in model protein solutions using the histogram reweighting method and expanded ensemble simulations.

Protein crystallization conditions are usually identified by empirical screening methods because of the complexity of the process, such as the existence of nonequilibrium phases and the different crystal forms that may result from changes in solution conditions. Here the crystallization of a model protein is studied using computer simulation. The model consists of spheres that have both an isotropic interaction of short range and anisotropic interactions between patch-antipatch pairs. The free energy of a protein crystal is calculated using expanded ensemble simulations of the Einstein crystal, and NpT-Monte Carlo simulations with histogram reweighting are used to determine the fluid-solid coexistence. The histogram reweighting method is also used to trace out the complete coexistence curve, including multiple crystal phases, with varying reduced temperature, which corresponds to changing solution conditions. At a patch-antipatch interaction strength five times that of the isotropic interaction, the protein molecules form a stable simple cubic structure near room temperature, whereas an orientationally disordered face-centered-cubic structure is favored at higher temperatures. The anisotropic attractions also lead to a weak first-order transition between orientationally disordered and ordered face-centered-cubic structures at low temperature, although this transition is metastable. A complete phase diagram, including a fluid phase, three solid phases, and two triple points, is found for the six-patch protein model. A 12-patch protein model, consistent with the face-centered-cubic structure, leads to greater thermodynamic stability of the ordered phase. Metastable liquid-liquid phase equilibria for isotropic models with varying attraction tails are also predicted from Gibbs ensemble simulations.

Crystallization↗

PubMed2004

Dual control cell reaction ensemble molecular dynamics: a method for simulations of reactions and adsorption in porous materials.

We present a simulation tool to study fluid mixtures that are simultaneously chemically reacting and adsorbing in a porous material. The method is a combination of the reaction ensemble Monte Carlo method and the dual control volume grand canonical molecular dynamics technique. The method, termed the dual control cell reaction ensemble molecular dynamics method, allows for the calculation of both equilibrium and nonequilibrium transport properties in porous materials such as diffusion coefficients, permeability, and mass flux. Control cells, which are in direct physical contact with the porous solid, are used to maintain the desired reaction and flow conditions for the system. The simulation setup closely mimics an actual experimental system in which the thermodynamic and flow parameters are precisely controlled. We present an application of the method to the dry reforming of methane reaction within a nanoscale reactor model in the presence of a semipermeable membrane that was modeled as a porous material similar to silicalite. We studied the effects of the membrane structure and porosity on the reaction species permeability by considering three different membrane models. We also studied the effects of an imposed pressure gradient across the membrane on the mass flux of the reaction species. Conversion of syngas (H2/CO) increased significantly in all the nanoscale membrane reactor models considered. A brief discussion of further potential applications is also presented.

Journal Article↗

PubMed2004

Generalized simulated tempering realized on expanded ensembles of non-Boltzmann weights.

A generalized version of the simulated tempering operated in the expanded ensembles of non-Boltzmann weights has been proposed to mitigate a quasiergodicity problem occurring in simulations of rough energy landscapes. In contrast to conventional simulated tempering employing the Boltzmann weight, our method utilizes a parametrized, generalized distribution as a workhorse for stochastic exchanges of configurations and subensembles transitions, which allows a considerable enhancement for the rate of convergence of Monte Carlo and molecular dynamics simulations using delocalized weights. A feature of our method is that the exploration of the parameter space encouraging subensembles transitions is greatly accelerated using the dynamic update scheme for the weight via the average guide specific to the energy distribution. The performance and characteristic feature of our method have been validated in the liquid-solid transition of Lennard-Jones clusters and the conformational sampling of alanine dipeptide by taking two types of Tsallis [C. Tsallis, J. Stat. Phys. 52, 479 (1988)] expanded ensembles associated with different parametrization schemes.

Computer Simulation↗

PubMed2005

Molecular simulation of dendrimers and their mixtures under shear: comparison of isothermal-isobaric (NpT) and isothermal-isochoric (NVT) ensemble systems.

Flow properties of dendrimers are studied with the aid of nonequilibrium molecular dynamics techniques. Simulations are performed in the NpT ensemble using the NpT-SLLOD algorithm [P. J. Davis and D. J. Evans, J. Chem. Phys. 100, 541 (1994)] and are compared to the results from simulations performed in the NVT ensemble reported earlier [J. T. Bosko, B. D. Todd, and R. J. Sadus, Chem. Phys. 121, 12050 (2004)]. Shear thickening observed at high strain rates vanishes in systems kept under constant pressure. Also the exponents in the power-law dependencies of the viscosity and the normal stress coefficients change. The variations are significant only at high strain rates and do not affect largely microscopic properties such as shape, alignment, or rotation of molecules. The NpT-SLLOD algorithm has been applied to study various systems including dendrimers in solution and their blends with linear chain molecules of the same molecular mass, and some results for these systems are presented.

Journal Article↗

PubMed2005

Statistical theory for protein ensembles with designed energy landscapes.

Combinatorial protein libraries provide a promising route to investigate the determinants and features of protein folding and to identify novel folding amino acid sequences. A library of sequences based on a pool of different monomer types are screened for folding molecules, consistent with a particular foldability criterion. The number of sequences grows exponentially with the length of the polymer, making both experimental and computational tabulations of sequences infeasible. Herein a statistical theory is extended to specify the properties of sequences having particular values of global energetic quantities that specify their energy landscape. The theory yields the site-specific monomer probabilities. A foldability criterion is derived that characterizes the properties of sequences by quantifying the energetic separation of the target state from low-energy states in the unfolded ensemble and the fluctuations of the energies in the unfolded state ensemble. For a simple lattice model of proteins, excellent agreement is observed between the theory and the results of exact enumeration. The theory may be used to provide a quantitative framework for the design and interpretation of combinatorial experiments.

Models, Statistical↗

PubMed2005

Molecular dynamics in the isothermal-isobaric ensemble: the requirement of a "shell" molecule. I. Theory and phase-space analysis.

Current constant pressure molecular-dynamics (MD) algorithms are not consistent with the recent reformulation of the isothermal-isobaric (NpT) ensemble. The NpT ensemble partition function requires the use of a "shell" molecule to identify uniquely the volume of the system, thereby avoiding the redundant counting of configurations [e.g., G. J. M. Koper and H. Reiss, J. Phys. Chem. 100, 422 (1996); D. S. Corti, Phys. Rev. E, 64, 016128 (2001)]. So far, only the NpT Monte Carlo method has been updated to allow the system volume to be defined by a shell particle [D. S. Corti, Mol. Phys. 100, 1887 (2002)]. A shell particle has yet to be incorporated into MD simulations. The proper modification of the NpT MD algorithm is therefore the subject of this paper. Unlike Andersen's method [H. C. Andersen, J. Chem. Phys. 72, 2384 (1980)] where a piston of unknown mass serves to control the response time of volume fluctuations, the newly proposed equations of motion impose a constant external pressure via the introduction of a shell particle of known mass. Hence, the system itself sets the time scales for pressure and volume fluctuations. The new algorithm is subject to a number of fundamentally rigorous tests to ensure that the equations of motion sample phase space correctly. We also show that the Hoover NpT algorithm [W. G. Hoover, Phys. Rev. A. 31, 1695 (1985); 34, 2499 (1986)] does sample phase correctly, but only when periodic boundary conditions are employed.

Journal Article↗

PubMed2006

Molecular-dynamics simulation of argon nucleation from supersaturated vapor in the NVE ensemble.

The possibility to conduct simulations of homogeneous nucleation of argon from a supersaturated vapor phase using a microcanonical or NVE ensemble is evaluated (NVE: number of particles N, volume V, and energy E are constant). In order to initiate a phase separation kinetic energy is removed from the system in one step which transfers the system into a supersaturated state. After this temperature jump the simulation is continued in a NVE ensemble. The simulations are performed for different initial-state points and different temperature jumps. The cluster formation and growth over the course of the adiabatic simulations are analyzed. The progression of the temperature being related to the cluster size in NVE systems is traced. Also the influence of the size of the simulation system is investigated. For a certain range of low supersaturation a dynamic coexistence between two states has been found. Furthermore, the obtained nucleation rates are correlated with two simple functions. By applying the nucleation theorems to these functions the size and excess energy of the critical cluster are estimated. The results are consistent with other theoretical data and experimental data available in the literature.

Journal Article↗

PubMed2006

Pressure derivatives in the classical molecular-dynamics ensemble.

The calculation of thermodynamic state variables, particularly derivatives of the pressure with respect to density and temperature, in conventional molecular-dynamics simulations is considered in the frame of the comprehensive treatment of the molecular-dynamics ensemble by Lustig [J. Chem. Phys. 100, 3048 (1994)]. This paper improves the work of Lustig in two aspects. In the first place, a general expression for the basic phase-space functions in the molecular-dynamics ensemble is derived, which takes into account that a mechanical quantity G is, in addition to the number of particles, the volume, the energy, and the total momentum of the system, a constant of motion. G is related to the initial position of the center of mass of the system. Secondly, the correct general expression for volume derivatives of the potential energy is derived. This latter result solves a problem reported by Lustig [J. Chem. Phys. 109, 8816 (1998)] and Meier [Computer Simulation and Interpretation of the Transport Coefficients of the Lennard-Jones Model Fluid (Shaker, Aachen, 2002)] and enables the correct calculation of the isentropic and isothermal compressibilities, the speed of sound, and, in principle, all higher pressure derivatives. The derived equations are verified by calculations of several state variables and pressure derivatives up to second order by molecular-dynamics simulations with 256 particles at two state points of the Lennard-Jones fluid in the gas and liquid regions. It is also found that it is impossible for systems of this size to calculate third- and higher-order pressure derivatives due to the limited accuracy of the algorithm employed to integrate the equations of motion.

Journal Article↗

PubMed2006

Determination of energetics and kinetics from single-particle intermittency and ensemble-averaged fluorescence intensity decay of quantum dots.

Quantification of energetics and kinetics for the band-edge exciton states of quantum dots and the long-lived dark state is important for better understanding of the underlying mechanism for single-particle intermittency and ensemble fluorescence intensity decay. Based on a multistate diffusion-reaction model by extending our previous studies, we analyze experimental data from ensemble measurements and fluorescence intermittency of single quantum dots and determine important molecular-based quantities such as Stokes shift, free energy gap, activation energy, reorganization energy, and other kinetic parameters.

Journal Article↗

PubMed2006

Mesoscale simulation of polymer reaction equilibrium: combining dissipative particle dynamics with reaction ensemble Monte Carlo. I. Polydispersed polymer systems.

We present a mesoscale simulation technique, called the reaction ensemble dissipative particle dynamics (RxDPD) method, for studying reaction equilibrium of polymer systems. The RxDPD method combines elements of dissipative particle dynamics (DPD) and reaction ensemble Monte Carlo (RxMC), allowing for the determination of both static and dynamical properties of a polymer system. The RxDPD method is demonstrated by considering several simple polydispersed homopolymer systems. RxDPD can be used to predict the polydispersity due to various effects, including solvents, additives, temperature, pressure, shear, and confinement. Extensions of the method to other polymer systems are straightforward, including grafted, cross-linked polymers, and block copolymers. To simulate polydispersity, the system contains full polymer chains and a single fractional polymer chain, i.e., a polymer chain with a single fractional DPD particle. The fractional particle is coupled to the system via a coupling parameter that varies between zero (no interaction between the fractional particle and the other particles in the system) and one (full interaction between the fractional particle and the other particles in the system). The time evolution of the system is governed by the DPD equations of motion, accompanied by changes in the coupling parameter. The coupling-parameter changes are either accepted with a probability derived from the grand canonical partition function or governed by an equation of motion derived from the extended Lagrangian. The coupling-parameter changes mimic forward and reverse reaction steps, as in RxMC simulations.

Journal Article↗

PubMed2005

Protein folding by distributed computing and the denatured state ensemble.

The distributed computing (DC) paradigm in conjunction with the folding@home (FH) client server has been used to study the folding kinetics of small peptides and proteins, giving excellent agreement with experimentally measured folding rates, although pathways sampled in these simulations are not always consistent with the folding mechanism. In this study, we use a coarse-grain model of protein L, whose two-state kinetics have been characterized in detail by using long-time equilibrium simulations, to rigorously test a FH protocol using approximately 10,000 short-time, uncoupled folding simulations starting from an extended state of the protein. We show that the FH results give non-Poisson distributions and early folding events that are unphysical, whereas longer folding events experience a correct barrier to folding but are not representative of the equilibrium folding ensemble. Using short-time, uncoupled folding simulations started from an equilibrated denatured state ensemble (DSE), we also do not get agreement with the equilibrium two-state kinetics because of overrepresented folding events arising from higher energy subpopulations in the DSE. The DC approach using uncoupled short trajectories can make contact with traditionally measured experimental rates and folding mechanism when starting from an equilibrated DSE, when the simulation time is long enough to sample the lowest energy states of the unfolded basin and the simulated free-energy surface is correct. However, the DC paradigm, together with faster time-resolved and single-molecule experiments, can also reveal the breakdown in the two-state approximation due to observation of folding events from higher energy subpopulations in the DSE.

Kinetics↗